ABSTRACT Title of Document: NOR-SECO-CUCURBITURILS Wei-Hao Huang, Ph.D, 2008 Directed By: Profesor, Lyle Isacs, Department of Biochemistry and Chemistry With rapid growth in molecular recognition and self-asembly in recent years, ??, ??, and ?-cyclodextrins, as a platform for molecular recognition have been widely applied as molecular containers in water. In particular, cyclodextrins have been extensively used in industrial applications, such as drug delivery, cosmetics, and analytical chemistry (mainly chromatography). We, and others, believe that the cucurbit[n]uril family of molecular containers have the potential to supplant the cyclodextrins as platform of choice for molecular recognition in aqueous solution. Even though the one-pot synthesis of CB[n] under strongly acidic aqueous condition can be easily performed on multi-kilogram scale, the separation of the various CB[n] (n = 5, 6, 7, 8, 10) is chalenging and time consuming. This diseration focuses on the mechanism of CB[n] formation with the expectation that would alow the tailor-made synthesis of specific CB[n] and suggest versatile routes to new CB[n]- type compounds that might display exciting new properties like chirality, chiral recognition, and alostery. Herein, the condensation of glycoluril with les than two equivalents of formaldehyde delivers a reaction mixture that contains glycoluril oligomers (dimer, trimer, tetramer, pentamer and hexamer) and CB[n] compounds that lack one or more methylene bridges known as nor-seco-cucurbit[n]urils (ns-CB[n]). We studied the ability of double cavity host bis-ns-CB[10] to undergo size dependent homotropic alostery, (?)-bis-ns-CB[6] to undergo diastereoselective recognition toward amino acids and amino alcohols in water, and the transformation of ns-CB[6] to a CB[6] derivative which contains the folding of long chain alkanediamonium ions in water. A comprehensive mechanistic scheme is proposed that acounts for the observed formation of dimer ? hexamer and ns-CB[n]. Overal, the experiments establish that a step-growth cyclo-oligomerization proces operates during CB[n] formation. NOR-SECO-CUCURBITURILS By Wei-Hao Huang Disertation submited to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfilment of the requirements for the degre of Doctor of Philosophy 2008 Advisory Commite: Asociate Profesor Lyle Isacs, Chair Profesor Philip DeShong Profesor Jefery Davis Asistant Profesor Andrei Vedernikov Asociate Profesor Srinivasa Raghavan, Dean?s Representative ? Copyright by Wei-Hao Huang 2008 ii Dedication To my parents, my parents-in-law, my wife, Yen-Chuan Liu, my daughter, Angela Huang. iii Acknowledgements I am grateful to thank Profesor Lyle Isacs for his help and guidance throughout my research and disertation. I would like to thank al faculty and staf in Chemistry Department to guide me moving forward. I would like to thank Department of Chemistry and Biochemistry to provide me a great opportunity to pursue my Ph.D. in Maryland. I would like to thank Ann Wylie Disertation Felowship for supporting me to finish my disertation. iv Table of Contents Dedication ???.....................................................................................???ii Acknowledgement................................................................................................iii Table of Contents ................................................................................................iv List of Tables .??????????????????????????vii List of Figures ...................................................................................................vii List of Schemes.................................................................................................... x I. Chapter 1: Cucurbit[n]uril............................................................................ 1 1.1 Introduction ..................................................................................... 1 1.2 Synthesis and Structure of Cucurbit[6]uril and Decamethylcucurbit[5]uril.................................................................. 1 1.3 Molecular Recognition Properties of Cucurbit[6]uril........................... 2 1.4 New Members of the Cucurbit[n]uril Family....................................... 4 1.5 Proposed Mechanism of Cucurbit[n]uril Formation............................. 4 1.6 Synthesis and Structure of Cucurbit[n]uril Homologues (n = 5, 7, 8, 10)....................................................................................6 1.6.1 Reaction Conducted Under Milder Conditions............................. 6 1.6.2 CB[5] Can be Released from CB[10]?CB[5] to Yield Fre Cucurbit[10]uril ........................................................................... 7 1.7 Applications of Members of the Cucurbit[n]uril Family...................... 8 1.7.1 Preparation of olecular Switches................................................ 8 1.7.2 Self-Asembled Dendrimers.........................................................10 1.7.3 Preparation of Molecular Machines.............................................11 1.7.4 Preparation of Complex Self-Sorting Systems............................ 12 1.7.5 Alosteric Control of the Conformation of a Calix[4]arene Inside CB[10]........................................................................................ 14 1.7.6 As a Carier of Anti-Cancer Agents............................................. 16 1.8 Experimental Support for the Proposed Mechanism of CB[n] Formation..........................................................................................17 1.8.1 S-shaped and C-Shaped Methylene Bridged Glycoluril Dimers... 17 1.8.2 Synthesis of Methylene Bridged Glycoluril Dimers..................... 17 1.8.3 S- to C-Shaped Isomerization of Methylene Bridged Glycoluril Dimers........................................................................................ 19 1.8.4 Mechanism of S- to C-Shaped Isomerization................................21 1.8.5 Implications for the Synthesis of Cucurbit[n]uril Analogues and Derivatives...................................................................................22 1.9 Building Block Approach to Cucurbit[n]uril Analogues.....................23 1.10 Building Block Approach to Cucurbit[n]uril Derivatives....................25 1.11 Identification and Isolation of Inverted Cucurbit[n]urils (n = 6, 7.......25 1.12 Direct Functionalization of Cucurbit[n]urils.......................................27 1.12.1 Perhydroxylation and Further Derivatization of CB[5] ? CB[8] ...27 1.13 Multivalent Binding of Sugar Decorated Vesicles to Lectins.............28 v 1.14 Cucurbit[n]uril Based Artificial Ion Channels...................................29 1.15 Experimental Procedures...................................................................30 1.16 Synthesis of Glycolurils....................................................................30 1.17 Synthesis and Separation of Cucurbit[n]urils.....................................31 1.18 Summary and Conclusions................................................................35 II. Chapter 2: Cucurbit[n]uril Formation Proceds by Step-Growth Cyclo- Oligomerization.......................................................................................39 2.1 Introduction.......................................................................................39 2.2 Cyclic Oligomeric CB[n]...................................................................41 2.3 Results and Discussion.......................................................................42 2.3.1 Previous MechanistiStudie...........................................................42 2.3.2 Reaction ixtures Deficient in Formaldehyde Deliver Glycoluril Oligomers I-2 ? I-6 and Nor-seco-CB[n] as Isolable Specie.......44 2.3.3 X-ray Crystal Structures of I-2 ? I-6...........................................46 2.4 Reaction Mixtures Deficient in Formaldehyde Also Deliver Nor-seco- CB[n] as Isolable Species...................................................................49 2.5 Implications of the Isolation of I-2 ? I-6, bis-ns-CB[10], (?)-bis-ns- CB[6], and ns-CB[6] Toward the Mechanism of CB[n] Formation.....51 2.5.1 Oligomer Resubmision Experiments...........................................55 2.5.2 Reactions Conducted Betwen Formaldehyde and I-1 ? I-6.......56 2.5.3 Reactions Conducted Betwen Formaldehyde and Binary Combinations of Building Blocks I-1 ? I-6................................57 2.6 Glycoluril Oligomers I-5 and I-6 Retain the Ability to Binding Amonium Ions................................................................................59 2.7 Conclusions.......................................................................................62 2.8 Experimental Section. General Experimental Details.........................64 2.8.1 Oligoers I-2 ? I6......................................................................65 2.8.2 General Procedures for Product Resubmision Experiments.........67 2.8.3 Synthesis of bis-ns-CB[10] from I-5............................................67 II. Chapter 3: Nor-Seco-Cucurbit[10]uril Exhibits Positive Homotropic Alosterism............................................................................................ 69 3.1 Introduction...................................................................................... 69 3.2 1 H NMR spectra of fre ns-CB[10] ...................................................70 3.3 X-Ray Crystals of ns-CB[10] ...........................................................71 3.4 Molecular Recognition Properties of Nor-Seco-Cucurbit[10]uril........72 3.5 Positive Homotropic Alosterism........................................................73 3.6 Summary...........................................................................................74 3.7 Synthesis of Nor-Seco-Cucurbit[10]uril.............................................75 IV. Chapter 4: Chiral Recognition Inside a Chiral Cucurbituril.........................76 4.1 Introduction.......................................................................................76 4.2 Step-Growth Polymerization..............................................................77 4.3 The Afinity of (?)-bis-ns-CB[6] .......................................................78 4.4 Electrostatic Surface Potential Maps for Both CB[6] and (?)-bis-ns-CB[6]................................................................................80 4.5 Chiral Recognition of (?)-bis-ns-CB[6]..............................................81 4.6 Summary...........................................................................................82 V. Chapter 5: Nor-Seco-Cucurbit[6]uril Functions as an Aldehyde Cucurbituril vi Synthon .................................................................................................84 5.1 Introduction.......................................................................................84 5.2 Isolation and 1 H NMR spectrum of ns-CB[6] ....................................85 5.3 Binding Properties of ns-CB[6]..........................................................86 5.4 Electrostatic Surface Potential (ESP) Map for CB[6] and ns-CB[6] ...88 5.5 Controlling Diastereoselectivity for V-2.............................................90 5.6 Summary...........................................................................................92 Appendices .....................................................................................................93 References ...................................................................................................210 vii List of Tables Chapter 2 Table 1. The molar ratio of glycoluril and formaldehyde units needed to construct CB[n], i-CB[n], ns-CB[n], and oligomers II2 ? II-6. ...............................50 Table 2. The distribution of CB[n] obtained from reaction of II-1 ? II-6 with formaldehyde (2 equivalents) alone and in combination. ..........................58 vii List of Figures Chapter 1 Figure 1. Molecular models of CB[5] ? CB[8] and their calculated cavity volumes. ...................................................................................................6 Figure 2. 1 H NMR spectrum (400 MHz, 20% DCl, RT) of the crude CB[n] reaction mixture. ..................................................................................................33 Chapter 2 Figure 1. 1 H NMR spectra (400 MHz, 35% DCl) for: a) dimer II-2, b) trimer II-3, c) tetramer II-4, d) pentamer II-5, and e) hexamer II-6...................46 Figure 2. Cross-eyed stereoviews of the crystal structures of: a) II-2, b) II-3, c) II-4, d) II-5, and e) II-6. Solvating CF 3 CO 2 H and H 2 O molecules have been removed for clarity. Color code: C, gray; H, white; N, blue; O, red; H-bonds, red-yelow striped. ..................................................................49 Figure 3. 1 H NMR spectra (400 MHz, D 2 O, RT) for: a) II-23, b) II-6?II-23, c) a mixture of II-6?II-23 and exces II-23, d) II-24, and e) II-6?II-24. ......61 Figure 4. Cross-eyed stereoview of the MF minimized geometry of the II-6?II-24 complex. Color code: C, grey; H, white; N, blue; O, red; H- bonds, red-yelow striped...................................................................62 Chapter 3 Figure 1. 1 H NMR spectra for: a) ns-CB[10] (400 MHz, 20% DCl), b) ns-CB[10]?III-2 2 , c) ns-CB[10]?III-11 2 , d) 2:2:2 mixture of ns-CB[10], III-2, and III-11 (b-d: 500 MHz, D 2 O). X = trace EtOH impurity...........71 Figure 2. Cross-eyed stereoview of the crystal structure of ns-CB[10]?III-3 2 . Solvating H 2 O molecules have been removed for clarity. Color code: C, gray; H, gren; N, blue; O, red. ...............................................................72 Figure 3. Thre potential diastereomers of ns-CB[10]?III-7 2 . The arows ilustrate the key CH 2 ??CH 2 non-bonded distance that changes acording to guest size..........................................................................................................73 Chapter 4 Figure 1. Cross-eyed stereoviews of the crystal structures of: a) IV-1, b) (?)-bis-ns- CB[6]?CF 3 CO 2 H, and c) (?)-bis-ns-CB[6]?IV-3 with 30% probability elipsoids. Solvating CF 3 CO 2 H and H 2 O molecules have been removed for clarity. ..............................................................................................78 Figure 2. a) UV/is spectroscopic titration of IV-3 (60 mM) with (?)-bis-ns-CB[6] (50 mM NaO 2 CD 3 buffered D 2 O, pD 4.74), b) plot of absorbance versus [(?)-bis-ns-CB[6]] used to obtain K a . ......................................................79 Figure 3. Electrostatic surface potential maps (red to blue: -90 to +31 kcal mol -1 ) for: a) (?)-bis-ns-CB[6], and b) CB[6]. L, M, H = low, medium, high electrostatic surface potentials. ...............................................................80 Figure 4. 1 H NMR spectra (400 MHz, D 2 O) for: a) (?)-bis-ns-CB[6]?IV-2, b) ix a mixture of (?)-bis-ns-CB[6] and exces (+)-IV-8, c) a mixture of (?)-bis-ns-CB[6] and exces (?)-IV-8.....................................................82 Chapter 5 Figure 1. 1 H NMR spectra (400 MHz, D 2 O, RT) recorded for: a) ns-CB[6] (20% DCl / D 2 O), b) a mixture of ns-CB[6] and exces V-5, c) V-2, and d) a mixture of V-2 and exces V-5, (D 2 O).......................................86 Figure 2. a) Cross-eyed stereoview of 2, and b) ilustration of the packing of 2 in the crystal by C=O??K + ??O=C interactions. Color code: C, grey; H, white; N, blue; O, red; O??K + interactions, red-yelow striped. Solvating CF 3 CO 2 H and H 2 O molecules have been removed for clarity. .................................87 Figure 3. Electrostatic surface potential maps for: a) CB[6] and b) V-2. The red to blue color range spans -85 to +35 kcal mol -1 . c) Ilustration of the two diastereomeric complexes possible with ns-CB[6] and V-2, and d) structures of guests for ns-CB[6].............................................................88 Figure 4. a) Ilustration of thre possible diastereomers for ns-CB[6]?V-3, and 1 H NMR spectra (400 MHz, D 2 O) for a mixture of V-2 and b) V-3g, c) V-3e, d) V-3c. (x = trace eOH). ......................................................90 Figure 5. Cross-eyed stereoview of the structure of V-2?V-3f in the crystal. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped.....................................................................................................91 x List of Schemes Chapter 1 Scheme 1. Synthesis of CB[6] and Me 10 CB[5]. ........................................................2 Scheme 2. Molecular recognition properties of CB[6]..............................................4 Scheme 3. Proposed mechanism of CB[n] formation................................................5 Scheme 4. Sequence used to remove CB[5] from CB[10]?CB[5]. The structures of CB[10]?CB[5] 17 and CB[10]?I-19 2 18 are based on the x-ray crystal. structures whereas those for CB[10]?I-19 and CB[10] are purely schematic representations.........................................................................8 Scheme 5. A pH responsive molecular switch that signals by color and fluorescence changes. ..................................................................................................9 Scheme 6. Electrochemical control of dendrimer asembly.....................................11 Scheme 7. A molecular loop lock that responds to chemical and redox stimuli.......12 Scheme 8. High selectivity binding within CB[n]. .................................................13 Scheme 9. Kinetic versus thermodynamic self-sorting using two-faced guests........14 Scheme 10. Alosteric control of the macromolecular conformation inside CB[10]. .................................................................................................16 Scheme 11. Complexation of oxaliplatin I-29 within CB[7]. 17 Scheme 12. Synthesis of S- and C-shaped methylene bridged glycoluril dimers. R = CO 2 Et. Conditions: a) PTSA, (CH 2 O) n , ClCH 2 CH 2 Cl, reflux; b) PTSA, ClCH 2 CH 2 Cl, reflux...............................................................................19 Scheme 13. Equilibration of I-37C and I-37S. .......................................................20 Scheme 14. Mechanism of diastereoselective intramolecular isomerization of S- to C-shaped compounds.........................................................................22 Scheme 15. Predicted synthesis of CB[n] derivatives..............................................23 Scheme 16. Synthesis of CB[n] analogues. R = CO 2 Et. .........................................24 Scheme 17. Synthesis of Me 4 CB[6]........................................................................25 Scheme 18. Chemical structures, x-ray crystal structures, and electrostatic potential maps for i-CB[6] and i-CB[7]. ...............................................................26 Scheme 19. Direct functionalization of CB[n]. Conditions: a) K 2 S 2 O 8 , H 2 O, 85 ?C; b) NaH, DMSO, alyl bromide; c) CH 3 (CH 2 ) 7 SH, h?; d) PEG-thiol, h?.....................................................................................28 Scheme 20. Decoration of supramolecular vesicles with fluorescent labels.............29 Scheme 21. Preparation of artificial ion-channels with CB[5] and CB[6] derivatives..............................................................................................30 Chapter 2 Scheme 1. Synthesis of CB[6]. ..............................................................................40 Scheme 2. Chemical structures of CB[n], iCB[n], bis-ns-CB[10], and (?)-bis-ns-CB[6]. ..................................................................................41 Scheme 3. Proposed mechanism of CB[n] formation..............................................43 Scheme 4. Synthesis of C-shaped II-2 ? II-6. ........................................................45 Scheme 5. Comprehensive mechanistic scheme for the formation of CB[n]. Color xi coding: chain growth, aqua arows; step growth; red arows (addition of 2), blue arows (addition of 3); gren arows (addition of 4). .................53 Scheme 6. Guests for II-5 and II-6.........................................................................61 Chapter 3 Scheme 1. Structure of ns-CB[10] and guests used in this study.............................70 Chapter 4 Scheme 1. Structure of compounds used in this study..............................................77 Chapter 5 Scheme 1. Structure of compounds used in this study..............................................85 1 I. Chapter 1: Cucurbit[n]uril (Huang, W.-H.; Liu, S.; Isacs, L. Cucurbit[n]urils, Diederich, F.; Stang, P. J.; Tykwinski, R. R. Ed; In Modern Supramolecular Chemistry, Wiley-VCH, 2008, ch. 4, pp. 113-142.) 1.1 Introduction. This chapter focuses on the synthetic and supramolecular chemistry of the cucurbit[n]uril (CB[n]) family of macrocycles. Isacs and co-workers? research in this area which began in 1998 at the University of Maryland has been largely driven by their eforts to understand the mechanism of CB[n] formation. This Chapter is, therefore, organized around that theme sprinkled with subsequently developed applications of the CB[n] family which validate our initial goal of understanding the mechanism of formation of the CB[n] family. 1.2 Synthesis and Structure of Cucurbit[6]uril and Decamethylcucurbit[5]uril. The cucurbituril story begins in 1905 when Behrend published the condensation of glycoluril (I-1a) with 2 equivalents of formaldehyde (Scheme 1) under aqueous acidic conditions (HCl, 100 ?C). 1 The substance formed during this reaction ? refered to as Behrend?s polymer in the literature ? was insoluble in al common solvents but could be recrystalized from hot H 2 SO 4 which yielded a wel defined substance. Although Behrend was not able to structuraly characterize this substance he did demonstrate that it forms complexes with a wide variety of species including KMnO 4 , AgNO 3 , and methylene blue. It was not until 1981 that Mock reported that the product of Behrend?s reaction was the macrocyclic hexameric cucurbit[6]uril comprising 6 equivalents of glycoluril and 12 equivalents of formaldehyde. 2 During the course of this remarkable reaction, six rings and 24 2 bonds are formed with complete control over the disposition of the glycoluril methine C-H groups which point outward from the central cavity. It would be nearly 10 years later that Stoddart reported that the condensation of dimethylglycoluril (I-1b) with formaldehyde (2 equivalents) under similar conditions yielded the first cucurbituril derivative ? macrocyclic pentameric Me 10 CB[5] (Scheme 1). 3 These two early members of the cucurbit[n]uril family provided us, and several other groups, with numerous questions: 4-6 1) What is the scope of glycolurils that can be used in the CB[n] forming reaction?, 2) Why does the CB[n] forming reaction deliver hexameric CB[6] but pentameric Me 10 CB[5]?, 3) What factors are responsible for the remarkably high yield (82%) obtained for CB[6]?, 4) What is the mechanism of CB[n] formation? H 2 CO, reflux, 16% NH O O RR con. Hl O N N O N N O O N N O a) CH 2 O, Cl, heat CB[6] (R =H) b) H 2 SO 4 I-1a R =H I-1b R =MeMe 10 CB[5] (R =Me, n= 0) O N N O N N O O N N O O n Scheme 1. Synthesis of CB[6] and Me 10 CB[5]. 1.3 Molecular Recognition Properties of Cucurbit[6]uril. Throughout the 1980?s Mock published a series of pioneering papers that demonstrated that CB[6] has remarkable abilities as a molecular container in aqueous solution. 2,7-9 For example, Mock showed that pentanediamine (I-2) and hexanediamine (I-3) bind to CB[6] as their amonium salts with values of K a > 10 6 M -1 in 40% aq. HCO 2 H. Even more remarkable was the fact that compounds with shorter or longer spacer 3 groups betwen the amonium centers (e.g. butanediamine I-4 or heptanediamine I- 5) bind significantly more weakly (K a ? 10 4 ? 10 5 M -1 ). This high afinity and selectivity can be ascribed to the juxtaposition of thre distinct binding regions: 1) two symmetry equivalent ureidyl?carbonyl lined portal which have a pronounced negative electrostatic potential which interact with cations (e.g. H + , M + , or RNH 3 + ) by ion-dipole interactions and/or hydrogen bonds, and 2) a central hydrophobic cavity which has a gently negative electrostatic potential which preferentialy interacts with hydrophobic guests (Scheme 2). The high selectivity observed for I-2 and I-3 over I- 4 and I-5 is due to the good match betwen the H 3 N??NH 3 separation on the guest and the C=O??O=C separation on the host. CB[6] is also quite selective based on size and shape. For example, CB[6] binds nicely to p-methylaniline (I-6) but completely rejects the meta-isomer (I-7). Similarly, CB[6] readily encapsulates I-8 which has a volume of 86 ? 3 but rejects the similarly sized I-9 (89 ? 3 ). Lastly, polyamonium species like spermine (I-10) achieve very high afinity in their binding with CB[6] (K a = 1.3 ? 10 7 M -1 ). 8 These high afinity and highly selective binding events were utilized by Mock to achieve a 10 4 -fold rate enhancement of a dipolar cycloaddition within the cavity 10 and in the construction of a molecular shuttle based on changes in pH. 11 These examples convinced us that the supramolecular chemistry of CB[6], its derivatives, and it analogues would be especialy wel suited for the preparation of molecular machines and biomimetic systems. In 1998, therefore, we embarked on a journey to understand the mechanism of CB[6] formation since we were confident that would lead to the preparation of new members of the cucurbituril family with exciting new properties. 4 H 3 N NH 3 O N N O N N O O O N N CB[6]?I-3 H 3 N NH 3 CB[6] n + I-4 (n =1) I2 2 I-3 (n =3) I5 4 NH 2 NH 2 NH 2 NH 2 NH 3 NH 2 H 2 N H 3 N Hydrophbic eft H-bondig Ion-dipole itreactins I-6I-8 I-9I-7 I-10 Scheme 2. Molecular recognition properties of CB[6]. 1.4 New Members of the Cucurbit[n]uril Family. This section describes the preparation of CB[n] homologues (n = 5, 7, 8, 10). We begin the discussion with a mechanistic hypothesis for CB[n] formation advanced by the Day and Isacs groups. 5,12 1.5 Proposed Mechanism of Cucurbit[n]uril Formation. Although the CB[n] forming reaction is remarkably complex, we sketched out a rough mechanism in 1998 and supplemented it along the way as new information became available. 4,5,13,14 Scheme 3 depicts our current understanding of the mechanism of CB[n] formation. Initialy, glycoluril (I-1a) reacts with formaldehyde to yield methylene bridged glycoluril dimers (I-11C and I-11S). These two compounds are diastereomers that difer in the relative orientation of the H-atoms on the convex face of the molecule. In CB[6], however, al of the methine C-H groups project outward from the center of the macrocycle similar to I-11C. Key questions that we wished to addres, therefore, were: 1) Are compounds with I-11S-type stereochemistry formed?, 2) Are I-11S and 5 I-11C in equilibrium with each other?, and 3) What is the mechanism of the I-11S to I-11C interconversion? These methylene bridged glycoluril dimers can then undergo further oligomerization to yield methylene bridged glycoluril oligomers (e.g. trimer ? decamer) as a mixture of S-shaped and C-shaped diastereomers (I-12). This mixture of oligomers has been refered to in the literature as Behrend?s polymer. The mixture of oligomers can then undergo S- to C-shaped isomerization, perhaps under the influence of a templating group to yield the al C-shaped oligomer (I-13). The ends of oligomer I-13 then react with one another to enter the CB[n] manifold as a mixture of CB[n] (n = 5, 6, 7, 8, 10). Through product resubmision experiments, Anthony Day demonstrated that CB[8] undergoes ring contraction to yield CB[5] ? CB[7] whereas the smaler CB[n] homologues (CB[5] ? CB[7]) are stable to the reaction conditions. 12 Mineral cid, CH 2 O, ht NH O O CB [n] ( =5-7 ) NH O O H NH O O N O O H NH O O + NR O O HH N O O H NR O O H n I-12 Behrnd's Polymer HHH O N NH O N N O O N N O O O H n-4 Dimer Foration Dimer Equilbration Template CB [n 8] I-1a ! I-1S I-1C I-13i-CB[n] s-[10] Scheme 3. Proposed mechanism of CB[n] formation. 6 1.6 Synthesis and Structure of Cucurbit[n]uril Homologues (n = 5, 7, 8, 10). The isolation of CB[n] homologues (CB[5], CB[7], and CB[8]) by the groups of Kim and Day around the turn of the milennium represented a major breakthrough in the cucurbituril field. 12,15 Figure 1 shows top views of CB[5] ? CB[8] (drawn to scale) which ilustrate the circular shape of the cavity and the gradual progresion to larger cavity volumes. 15,16 In particular, the larger homologues CB[7] (279 ? 3 ) and CB[8] (479 ? 3 ) with their larger cavities which paralel those of ?- and ?-cyclodextrin promise to greatly expand the range of applications to which CB[n] can be applied. Figure 1. Molecular models of CB[5] ? CB[8] and their calculated cavity volumes. 1.6.1 Reaction Conducted Under Milder Conditions. To aces the unknown cucurbituril homologues, Kim and Day performed the CB[n] forming reactions under milder conditions (100 ?C, conc. HCl; 75 ?C, 9M H 2 SO 4 ). 12,15 Although CB[6] is stil the major component of the reaction mixture, the CB[n] homologues (CB[5], CB[7], and CB[8]) can be readily isolated on the 10 ? 100 g scale by straightforward ? but time consuming ? washing and recrystalization procedures that are detailed in Section 1.17. 7 1.6.2 CB[5] Can be Released from CB[10]?CB[5] to Yield Fre Cucurbit[10]uril. In addition to CB[5] ? CB[8], Day and co-workers were also able to isolate CB[10] as its CB[10]?CB[5] complex (Scheme 4). 12,17 Day and co-workers also demonstrated that added 13 C-labeled CB[5] undergoes chemical exchange with unlabeled CB[5] in the CB[10]?CB[5] complex. This observation suggested that it should be possible to remove CB[5] and isolate fre CB[10] in its uncomplexed form. From our 1 kilogram scale CB[n] forming reaction (Section 1.17) we were lucky enough to isolate a significant quantity of CB[10]?CB[5] and decided to try and remove CB[5]. We discovered that some of the guests commonly used (e.g. I-14 ? I- 18) to complex to the larger CB[n] (n = 7, 8) are capable of partialy displacing CB[5] from the CB[10]?CB[5] complex. Unfortunately, in many cases, al of the components (CB[5], exces guest, and CB[10]?guest) remained in solution which complicated the isolation of the CB[10]?guest complex. Luckily, we discovered that addition of exces guest I-19 to CB[10]?CB[5] results in the formation of the soluble CB[10]?I-19 2 complex and precipitation of the (CB[5]?I-19) n supramolecular polymer (Scheme 4). The pure CB[10]?I-19 2 complex is isolated by filtration and rotary evaporation. Removal of the les strongly bound second equivalent of I-19 occurs readily by washing with MeOH which yields CB[10]?I-19. The final equivalent of I- 19 can be removed by heating with acetic anhydride which transforms the amonium groups into acetamides followed by washing (DMSO, MeOH, H 2 O). Uncomplexed CB[10] has a cavity volume of approximately 870 ? 3 and is poorly soluble in water and mildly acidic solution. Luckily, its complexes have good solubility in D 2 O which alowed us to study its molecular recognition properties (Section 1.7.5). 8 Scheme 4. Sequence used to remove CB[5] from CB[10]?CB[5]. The structures of CB[10]?CB[5] 17 and CB[10]?I-19 2 18 are based on the x-ray crystal structures whereas those for CB[10]?I-19 and CB[10] are purely schematic representations. 1.7 Applications of Members of the Cucurbit[n]uril Family. The early work of Mock on the recognition properties of CB[6] established that this macrocycle was amongst the tightest binding and most selective synthetic hosts in aqueous solution. 2,7- 9 Subsequent work from our group demonstrated that the high afinity and selectivity translates to individual host-guest complexes of CB[7] and CB[8]. Even more impresively, the selectivity of a single guest toward CB[6], CB[7], and CB[8] can be remarkably large (> 10 4 ). 19 These, and related observations, 20,21 suggested to us and others that CB[n] would function as smart components in a variety of applications that are described in this section. 1.7.1 Preparation of Molecular Switches. Compounds that function as molecular switches exist in two stable forms and can be reversibly switched betwen those two 9 forms by application of a given stimulus (e.g. pH change, electrochemistry, photochemistry, or chemical). A particularly interesting molecular switch based on the triaminofluorene compound I-20 was reported by Kim in 2000 (Scheme 5). 22 When CB[6] is added to I-20 in pH 1.0 solution, rotaxane CB[6]?I-20 is formed where the CB[6] bead resides on the longer hexylene spacer in order to maximize both ion-dipole interactions and hydrophobic binding. In this form, the anilinium N- atom is protonated and the fluorene chromophore is highly fluorescent. When the pH is raised (8.0), however, the anilinium N-atom is deprotonated and the CB[6] macrocycle slides over to the butylene spacer to maintain two ion-dipole interactions while sacrificing some hydrophobic driving force. In this new complex (CB[6]?I-21), the aniline N-atom is conjugated to the fluorene ring and the complex has a violet color; the N-atom also quenches the fluorescence output of the system. Upon lowering the pH, the CB[6] bead again switches back to the original location. Thus, CB[6] acts as a pH controlled molecular switch with both UV/is and fluorescent output. Scheme 5. A pH responsive molecular switch that signals by color and fluorescence changes. 10 1.7.2 Self-Asembled Dendrimers. The ability of members of the CB[n] family to bind tightly to their guests has been used by the groups of Kaifer 23,24 and Kim 25 to modify the properties of dendrons containing guests at their focal points and to bring two or more dendrons together to create a self-asembled dendrimer. For example, Kaifer synthesized 1 st , 2 nd , and 3 rd generation Newkome-type dendrons I-22a ? I-22d containing viologen units at the focal point (Scheme 6). 23 UV/is titrations alowed Kaifer to demonstrate that the asociation constant for the formation of the binary complex CB[8]?I-22 decreases as the generation of the dendrimer increases. The electrochemical behavior was even more interesting. Upon a two-electron reduction the viologen is transformed from its dicationic to its monocationic form which subsequently induces dimerization inside CB[8] yielding ternary complex CB[8]?I- 22 2 as evidenced by changes in the UV/is spectrum. The dramatic change in size of the ternary complex was also determined by measurement of its difusion constant by pulsed field gradient NMR techniques. No dimerization is observed in the absence of CB[8]. This lovely example demonstrates proof-of-concept for redox-switchable dendrimer self-asembly. 11 Scheme 6. Electrochemical control of dendrimer asembly. 1.7.3 Preparation of Molecular Machines. The Kim group has capitalized on the ability of CB[8] to simultaneously bind two aromatic rings in the construction of a variety of molecular machines. 26,27 A recent and particularly elegant example is the construction of a molecular loop lock (Scheme 7). 27 They found that the interaction of CB[8] with I-23 3+ leads to the folded conformation of CB[8]?I-23 3+ (Scheme 7) which benefits from intramolecular charge transfer interaction betwen the electron rich naphthalene and electron poor viologen units. The addition of 1 equivalent of methylviologen (I-24 2+ ) does not result in a change in conformation of CB[8]?I-23 3+ presumably because I-24 2+ binds les strongly than the intramolecularly held viologen unit. Very interestingly, however, upon reduction of the solution of the mixture of CB[8]?I-23 3+ and I-24 2+ with Na 2 S 2 O 4 , the equilibrium shifts toward the unfolded ternary complex CB[8]?I-23 2+ ?I-24 + . This ternary complex benefits from the enhanced ?-? interactions as evidenced by the appearance of new bands at 368, 550, and 890 nm in the UV/is spectrum of the viologen radical-cation dimer. The system 12 is fully reversible betwen the CB[8]?I-23 2+ ?I-24 + and CB[8]?I-23 3+ states by exposing the system to molecular oxygen (O 2 ). This system may be regarded as a safeguarded molecular loop lock in that it requires not only the addition of I-24 2+ , but also the application of a redox stimulus (Na 2 S 2 O 4 or O 2 ) to open or close the lock. Scheme 7. A molecular loop lock that responds to chemical and redox stimuli. 1.7.4 Preparation of Complex Self-Sorting Systems. Mock has shown that CB[6] undergoes tight and selective binding with cationic guest molecules in aqueous solution. 8 Our investigations of complex (e.g. 12-component) self-sorting mixtures which utilized CB[6] and CB[8] as components suggested that the binding strengths (K a ) and selectivities might be even higher than previously appreciated. 20 To provide quantitative evidence for this hunch, we measured the binding constants for CB[6], CB[7], and CB[8] toward a variety of guests by 1 H NMR competition experiments. 19 We found that values of K a ranged betwen 10 2 ? 10 12 M -1 and moreover that selectivities could be excedingly large (> 10 3 ) in response to smal structural changes. For example, CB[8] binds I-19 3250-fold tighter than CB[7] and induces a folding proces at the same time (Scheme 8). Similarly, CB[7] binds I-14 5150-fold 13 tighter than CB[8] due to an excelent size, shape, and electrostatic match betwen host and guest. Scheme 8. High selectivity binding within CB[n]. NH(C 2 ) 3 H 3 I-26 NH 2H 2 N I-25 In addition to the high afinity and selectivity, members of the CB[n] family can exhibit unusual dynamics of complex asociation and disociation. 9,21,28 We used the high binding afinities, high selectivities, and unusual dynamics to construct a system that undergoes wel defined transitions from fre components, to one set of aggregates under kinetic control, to a second set of aggregates under thermodynamic control (Scheme 9). For example, when a solution of CB[6] and CB[7] is mixed with a second solution containing guests I-25 and I-26 the components initialy asociate 14 to form CB[6]?I-26 and CB[7]?I-25. In this proces, I-25 undergoes fast kineticaly controlled asociation with CB[7] in preference to CB[6] to form CB[7]?I-25. Subsequently, I-26 ? which we refer to as a two-faced guest since it contains two binding epitopes ? uses its slimer alkylamonium binding epitope to asociate with CB[6]. This kineticaly controled self-sorting state comprising CB[6]?I-26 and CB[7]?I-25 slowly transforms over the course of 56 days into the thermodynamic self-sorting state comprising CB[6]?I-25 and CB[7]?I-26. Scheme 9. Kinetic versus thermodynamic self-sorting using two-faced guests. 1.7.5 Alosteric Control of the Conformation of a Calix[4]arene Inside CB[10]. After we synthesized CB[10] we wanted to investigate its abilities as a host molecule. We found that CB[10] forms host-guest complexes with many of the guests typicaly used with the smaler members of the CB[n] family (e.g. alkyl and arylamines, adamantanes, viologens, and ferocene derivatives like I-14 ? I-19). 15 CO 2 H I-28 CH 2 NMe 2 OH C 2 4 I-27 We discovered that CB[10] was also capable of forming a complex with cationic calix[4]arene I-27 which itself usualy functions as a host molecule in aqueous solution (Scheme 10). 18 Interestingly, when I-27 goes inside CB[10] we observed two sets of resonances that were in slow exchange on the NMR time-scale. The major set of resonances corresponds to the CB[10]?1,3-alt-I-27 conformer whereas the minor set of resonances corresponds to a dynamic equilibrium betwen CB[10]?1,2-alt-I-27, CB[10]?partial cone-I-27, and CB[10]?cone-I-27 conformations. Scheme 10 shows the MF calculated geometry of the CB[10]?1,3- alt-I-27 conformation which shows a good match betwen the circular shape of 1,3- alt-I-27 and the cavity of CB[10]. We wondered whether it would be possible to stabilize one of the other thre conformers of the macromolecular CB[10]?I-27 complex by the addition of a guest molecule. After some experimentation, we found that adamantane carboxylic acid I-28 is capable of shifting the equilibrium toward the CB[10]?cone-I-27?I-28 complex. In this ternary complex, the calixarene I-27 asumes the cone-I-27 conformation in order to maximize non-covalent interactions with I-28. The cone-I-27?I-28 complex in turn binds within CB[10]; in the MF computed conformation of CB[10]?cone-I-27?I-28 we once again se a good match betwen the overal size, shape, and electrostatic complementarity betwen the cone- I-27?I-28 complex and the cavity of CB[10]. To complete the cycle of alosteric control of conformation within CB[10], we added CB[7] which binds tightly to I-28 16 forming CB[7]?I-28 which switches the conformation of calix[4]arene I-27 back to the original mixture of CB[10]?I-27 conformers. This result demonstrates that CB[10] has great potential in controlling the conformation of non-natural macromolecular complexes. Scheme 10. Alosteric control of the macromolecular conformation inside CB[10]. 1.7.6 As a Carrier of Anti-Cancer Agents. One of the potential uses of any molecular container compound is in the formulation of active pharmaceutical agents. Acordingly, the groups of Kim 29 and Day 30 have demonstrated the ability of CB[7] and CB[8] to modify the properties of Pt-based anti-cancer agents (Scheme 11). For example, Kim?s group reported that CB[7] forms a 1:1 complex with oxaliplatin (CB[7]?I-29). They found that encapsulation of the drug within CB[7] results in a dramatic increase in its lifetime (e.g. 6 hours versus > 1 year). Furthermore, CB[7]?I- 29 shows markedly decreased reactivity toward L-methionine as a protein model relative to its reactivity toward guanosine as a DNA model. This result suggests that encapsulation of I-29 within CB[7] may reduce unwanted side efects caused by protein binding of the drug. 17 Scheme 11. Complexation of oxaliplatin I-29 within CB[7]. 1.8 Experimental Suport for the Proposed Mechanism of CB[n] Formation. Although none of the applications of the CB[n] family described in Section 1.7 of this Chapter were known in 1998 when the Isacs? group began their work in the area they provide post-facto support for our asertion that a firm knowledge of the mechanism of CB[n] formation would be important. This section describes our work with S- and C-shaped methylene bridged glycoluril dimers that gave us insights into the early steps in the mechanism of CB[n] formation. 1.8.1 S-shaped and C-Shaped Methylene Bridged Glycoluril Dimers. The high level of complexity of the CB[n] forming reaction lead us to choose to study S-shaped and C-shaped methylene bridged glycoluril dimers (I-11C and I-11S, Scheme 3) initialy. This section details the lesons learned from those model studies. 1.8.2 Synthesis of Methylene Bridged Glycoluril Dimers. Although we wanted to study methylene bridged glycoluril dimers I-11C and I-11S, we were mindful of the fact that the presence of four fre ureidyl NH groups and the absence of solubilizing groups on the convex face of the glycoluril skeleton might lead to poor 18 solubility characteristics. Thus, in acord with the precedent of the Nolte and Rebek groups, we decided to target compounds whose NH-groups were ?protected? by o- xylylene groups and that contain solubilizing substituents on their convex face. 31 Although we have investigated this reaction in detail, the bare esence of the proces is presented in Scheme 12. In brief, we discovered thre pathways to methylene bridged glycoluril dimers that each occur in refluxing dichloroethane containing p- toluenesulfonic acid with azeotropic removal of water. The first method involves the homodimerization of glycoluril NH-compounds (e.g. I-30) with CH 2 O and delivers both I-31C and I-31S. The second involves the homodimerization of glycoluril cyclic ethers (e.g. I-32) that occurs with formal extrusion of formaldehyde and selectively delivers I-33C (I-33S not detected). The third involves heterodimerization of a glycoluril NH-compound (e.g. (?)-I-34) with a glycoluril cyclic ether (e.g. I-35) which delivers a mixture of (?)-I-36C and (?)-I-36S. In this example of heterodimerization, the unsymmetrical substitution on the aromatic ring renders (?)-I-34 and (?)-I-36C and (?)-I-36S chiral and racemic. Al thre reactions occur in good to high yield and generaly deliver the C-shaped diastereomers selectively. Al thre reactions are tolerant of substitution on the convex face of the glycoluril units (e.g. R = Ph, (CH 2 ) 4 , CO 2 Et, CO 2 H, imide) and substitution on the o- xylylene rings (e.g. OMe, CH 3 , Br, NO 2 , and F). Interestingly, the heterodimerization reaction alows the selective preparation of C-shaped methylene bridged glycoluril dimers (e.g. I-34C) containing diferentialy functionalized aromatic rings. These thre methods not only alowed us to prepare a wide variety of methylene bridged glycoluril dimers for studies of self-asembly, they also suggested methods for the 19 tailor-made synthesis of partialy substituted CB[n] from appropriate glycoluril building blocks (Section 1.9). N O O RR N O O R Br Br Br Br NH O O RR Br Br N O O RR N O O R Br Br Br Br I-31C I-31SI-30 a) + 47% 10% N O RR N O R N O RR N O RR N O R I-3C I-3SI-32 b) + 92% n.d O NH O RR N O RR N O R Me NO 2 (?)-I36C (31%) (?)-I34 N O RR I-35 b) + O OMe NO 2 O OMe e N O RR N O R OMe NO 2 OMe e (?)-I36S (4%) Scheme 12. Synthesis of S- and C-shaped methylene bridged glycoluril dimers. R = CO 2 Et. Conditions: a) PTSA, (CH 2 O) n , ClCH 2 CH 2 Cl, reflux; b) PTSA, ClCH 2 CH 2 Cl, reflux. 1.8.3 S- to C-Shaped Isomerization of Methylene Bridged Glycoluril Dimers. In our synthesis of methylene bridged glycoluril dimers (Section 1.8.2) we were somewhat surprised that only very smal amounts of the S-shaped diastereomers were observed in most cases. To determine whether this diastereoselectivity is due to thermodynamic or kinetic preferences we isolated diastereomericaly pure samples of six C-shaped and S-shaped compounds and separately resubmited them to the 20 reaction conditions. Scheme 13 shows the separate isomerization of I-37C and I-37S. We found that both the C-shaped and S-shaped forms deliver an equilibrium mixture of S-and C-shaped forms in which the C-shaped form predominates (? 95:5) for a variety of compounds. This result established that the C-shaped form is thermodynamicaly more stable than the S-shaped form by ? 2 kcal mol -1 which provides a rationale for the high yield observed in the formation of CB[6] which presumably required al C-shaped oligomers. To delve deeper into the origin of this thermodynamic preference we performed the equilibration of I-37C and I-37S in a variety of solvents (e.g. CHCl 3 , Cl 4 , C 6 F 6 , THF, CH 3 CN, ClCH 2 CH 2 Cl, CH 3 NO 2 , MeOCH 2 CH 2 OMe). The C-shaped to S-shaped ratio remains high (> 90:10) across this series which indicates that solvation is not a key factor determining the thermodynamic preference for the C-shaped form. We also ruled out the possibility that PTSA acts as a template by selectively engaging in ?-? interactions with the cavity of the C-shaped form. Currently, we believe that the C-shaped form is more stable due to the conformational preference of the newly formed 8-membered ring for the crown-conformation. 32 N R O N R O N R O N R O I-37C (-shaped)I-37S (-shaped) PTSA, ClH 2 Cl reflux Time % C 0 10 Equilbrim C:S atio =CO 2 Et Br r Br r Br Br Br Br Scheme 13. Equilibration of I-37C and I-37S. 21 1.8.4 Mechanism of S- to C-Shaped Isomerization. The selective heterodimerization of glycoluril NH-compounds and glycoluril cyclic ethers (Section 1.8.2) and the general preference for the C-shaped diastereomers suggested that the mechanism of S-shaped to C-shaped equilibrium might proced by an intramolecular rather than an intermolecular proces under anhydrous acidic conditions (e.g. PTSA, ClCH 2 CH 2 Cl, reflux). To test this hypothesis, we designed a ?double-labeling? experiment that utilized (?)-I-38 and I-39 (Scheme 14). In the equilibration of chiral but racemic (?)-I-38S, for example, one might expect to obtain either (?)-I-38C or I- 39, or potentialy a mixture of both. 5 Similarly, the equilibration of I-39S might deliver either (?)-I-38C or I-39, or both. In the experiment, we observed that (?)-I- 38S cleanly delivered the chiral but racemic (?)-I-38C whereas the achiral meso compound I-39S cleanly delivered the achiral meso compound I-39C. This result indicates that the transformation of S- to C-shaped methylene bridged glycoluril dimers is an intramolecular proces under anhydrous acidic conditions that proceds via retention of configuration of the two glycoluril ?halves?. Scheme 14 also shows a proposed mechanism that tracks the position of the labels (gren dots). Initialy, I-40 undergoes protonation and ring opening to yield iminium ion I-41. Iminium ion I-41 can undergo ring closure by nucleophilic atack of the glycoluril N-atom to yield spirocyclic intermediate I-42 which can fragment in the opposite direction to yield iminium ion I-43. Subsequent ring closure of I-43 followed by deprotonation gives I- 44 which rationalizes the experimental results. 22 N O O RR N O O R OMe NO 2 OMe NO 2 (?)-I38S N O O RR N O O R OMe NO 2 NO 2 OMe (?)-I38C N O RR N O R OMe NO 2 NO 2 OMe N O RR N O R OMe NO 2 OMe NO 2 I-39S N O RR N O R N O RR N O R ? N N O OH R R N O O R ? ? ?? ? N O RR N O H R ?? N O RR N OH R ? ? I-40 + H + PTSA ClH 2 lC 2 PTSA ClH 2 lC 2 I-39C I-41 I-42 I-43 I-4 Scheme 14. Mechanism of diastereoselective intramolecular isomerization of S- to C-shaped compounds. 1.8.5 Implications for the Synthesis of Cucurbit[n]uril Analogues and Derivatives. The results presented in Sections 1.8.2 ? 1.8.4 provide a number of insights into the mechanism of CB[n] formation. For example, the isolation of the S- shaped diastereomers provides strong evidence that both I-11S and I-11C form in the initial stages of the CB[n] forming reaction. The observed strong preference for the C-shaped diastereomers (> 90:10) provides a rationale for the high yield obtained in the synthesis of CB[6]. 33 A simple calculation suggests that in a worst case scenario 53% (0.9 6 ) of the linear glycoluril hexamers would exist as the al C-shaped 23 diastereomer required to form CB[6]. In addition, the intramolecular nature of the S- shaped to C-shaped equilibration suggested that the length of the growing methylene bridged glycoluril oligomer chain (I-13, Scheme 3) determines the size (e.g. n) of the CB[n] formed. When considered together with highly selective heterodimerization reactions the results further suggest that the patern of substituents on the surface of the growing methylene bridged glycoluril oligomer wil be preserved in the CB[n] derivatives formed. As a specific example, we predicted that heating a combination of I-1a and bis(cyclic ether) I-45a under anhydrous acidic conditions (e.g. PTSA or MeSO 3 H) would deliver the hexa-substituted CB[6] derivative I-46a (Scheme 15). 5 Although this reaction did not yield the desired product in practice, the predictions made above were subsequently borne out in the synthesis of CB[n] analogues and derivatives described below (Sections 1.9 and 1.10). R R NHH O O Anh. cid I-1a I-46a (EtO 2 C) 6 B[] Ib Me 6 [] O N N O N N O N N O O N O O RROO+ I-45a R =C 2 Et Ib Me R Scheme 15. Predicted synthesis of CB[n] derivatives. 1.9 Building Block Aproach to Cucurbit[n]uril Analogues. We hypothesized that the reaction depicted in Scheme 16 did not proced smoothly in practice because the CO 2 Et-groups on the convex face of the glycoluril reduce its reactivity (stericaly and electronicaly) relative to the unsubstituted glycoluril I-1a. To circumvent this isue we decided to search for a glycoluril analogue that might participate eficiently 24 in heterodimerization reactions with compounds like I-45 to yield CB[n] analogues. With a litle bit of luck we discovered that phthalhydrazides are superior nucleophiles ? presumably due to the ?-efect ? that undergo selective heterodimerization with glycoluril cyclic ethers under anhydrous acidic conditions. 34-36 Specificaly, bis(phthalhydrazide) I-47 was found to undergo separate macrocyclization with dimeric I-48 and trimeric I-49 to yield CB[n] analogues (I-50 and (?)-I-51) in remarkably high yield which incorporate the UV/is, fluorescent, and electrochemicaly active bis(phthalhydrazide) wals. The carboxylic acid version of I- 50 can be used as a fluorescent sensor in aqueous solution. 36 Compound (?)-I-51 was particularly intriguing to us since the presence of two fre ureidyl NH-groups and the twisted connection betwen the tips of the two glycoluril trimer building blocks I-49 imparts C 2 -symmetry to the macrocycle which renders (?)-I-51 chiral and racemic. Compound (?)-I-51 is the only chiral member of the CB[n] family. N O O RR N O O RO O N O O RR N O O RO N O O RO I-48 I-49 N R O N R N N R O N R O N O OO O O O N R O N R N N H R N R O N R O N NO O OO R NH HN O O O O I-47, MeS 3 H, 80 ?C I-47 I-47, MeS 3 H, 80 ?C I-50 (78%) (?)-I51 (67%) Scheme 16. Synthesis of CB[n] analogues. R = CO 2 Et. 25 1.10 Building Block Aproach to Cucurbit[n]uril Derivatives. Concurrently with the synthesis of the CB[n] analogues, the groups of Day and Tao were also pursuing a building block approach toward CB[n] derivatives. 37,38 For example, Day was able to isolate Me 6 CB[6] (I-46b) from the reaction of I-1a and I-45b using aqueous acidic reaction conditions (Scheme 15). An elegant example of a building block approach toward CB[n] derivatives was realized by reacting the unsubstituted methylene bridged glycoluril dimer I-52 with cyclic ether I-45b which delivered the tetra-substituted CB[6] derivative Me 4 CB[6] in 30% yield (Scheme 17). Quite interestingly, Me 4 CB[6] has an elipsoidal shape which binds aromatic rings with a common orientation of the long axes of both host and guest. 38 H H Me Me O N O N N O O N N H NH O O H NH O O I-52 Me 4 CB[6] N O O MeMeOO I-45b + 10 ?C Hl / 2 O Scheme 17. Synthesis of Me 4 CB[6]. 1.11 Identification and Isolation of Inverted Cucurbit[n]urils (n = 6, 7). The prefered ? but not exclusive ? formation of C-shaped methylene bridged glycoluril dimers provided a rationale for the observed high yields in CB[n] forming reactions. Conversely, those same experiments can also be interpreted as suggesting the possibility of diastereomeric CB[n]. Such diastereomeric CB[n] in which one or more pairs of glycoluril H-atoms point into the central CB[n] cavity are refered to as inverted CB[n] (i-CB[n]). The first members of the i-CB[n] family were discovered 26 by the groups of Isacs and Kim and investigated jointly (Scheme 18). 13 i-CB[6] and i-CB[7] are formed in smal amounts in the CB[n] forming reaction and can be detected in the 1 H NMR spectrum of the mixture by diagnostic resonances for the inverted H-atoms (? 5 ppm, vide infra). Pure i-CB[6] and i-CB[7] could be isolated in low yield (2.0 and 0.4%) by a combination of fractional recrystalization and gel permeation chromatography. Scheme 18 also shows the x-ray crystal structures of i- CB[6] and i-CB[7] and their electrostatic potential energy surfaces. The consequences of the inverted glycoluril ring are reduced cavity volumes, flatened elipsoidal shaped cavities, more positive intra-cavity electrostatic potentials, and more open C=O lined portals. In acord with these considerations, i-CB[6] and i- CB[7] preferentialy bind elipsoidal and electrostaticaly negative aromatic guests like p-xylylene diamine I-53 and ferocene derivative I-54. Overal, the inverted glycoluril modulates the guest binding afinity and rates of disociation in a way that might be useful in the creation of function CB[n] based systems. Scheme 18. Chemical structures, x-ray crystal structures, and electrostatic potential maps for i-CB[6] and i-CB[7]. 27 1.12 Direct Functionalization of Cucurbit[n]urils. One of the major chalenges in CB[n] chemistry is the poor solubility of CB[n] in neutral water and far worse solubility in organic solution. A potential solution to this problem that has been pursued by several groups involves the preparation of CB[n] derivatives or analogues that contain solubility enhancing functional groups on the convex face of the macrocycle. That strategy is easier to propose than to execute in practice, and the sections above detailed some of the chalenges of using glycoluril derivatives in CB[n] forming reactions. Perhaps the most onerous isue to be addresed in such a route is the modification of the separation scheme for each new CB[n] derivative. An alternative approach to the preparation of CB[n] derivatives is the direct functionalization of purified unfunctionalized CB[n]. 1.12.1 Perhydroxylation and Further Derivatization of CB[5] ? CB[8]. Kim and co-workers addresed a major isue in CB[n] chemistry with their discovery of a method for their direct functionalization. 39 They found that heating CB[5], CB[6], CB[7], or CB[8] with K 2 S 2 O 8 in water results in the perhydroxylation of CB[n] (n = 5 ? 8) yielding (HO) 2n CB[n] in modest to low yield (Scheme 19). Furthermore, the (HO) 2n CB[n] have excelent solubility in DMSO and DMF which alows for subsequent functionalization. For example, (HO) 2n CB[n] (n = 5, 6) undergo reaction with NaH and alyl bromide in DMSO to yield (H 2 C=CHCH 2 O) 2n CB[n] in good yields. (H 2 C=CHCH 2 O) 2n CB[n] (n = 5, 6) undergo photochemical addition of thiols (e.g. CH 3 (CH 2 ) 7 SH or CH 3 [O(CH 2 ) 2 ] 3 SH) to yield the highly lipophilic {CH 3 (CH 2 ) 7 S(CH 2 ) 3 } 2n CB[n] and {CH 3 [O(CH 2 ) 2 ] 3 S(CH 2 ) 3 } 2n CB[n]. 28 R RR R O N N O N N O O N N O R n-5 R =OH b) C 2 CH 2 n =6 5, R 2n CB[] R =O( 2 ) 3 S( 2 ) 7 CH 3 n =, 6 (CH 2 ) 3 ( 22 O) 33 c) d) CB[n](HO) 2n CB[] a) (HO) 12 CB[6] (45%) () 4 [7] () () 16 B[8] (4) () 0 [] () Scheme 19. Direct functionalization of CB[n]. Conditions: a) K 2 S 2 O 8 , H 2 O, 85 ?C; b) NaH, DMSO, alyl bromide; c) CH 3 (CH 2 ) 7 SH, h?; d) PEG-thiol, h?. 1.13 Multivalent Binding of Sugar Decorated Vesicles to Lectins. The study of vesicles is an area of wide interest due largely to their potential use in areas as drug and gene delivery, biomimetic systems, and in the preparation of nanostructured materials. Kim?s group discovered that the amphiphilic CB[6] derivative {CH 3 [O(CH 2 ) 2 ] 3 S(CH 2 ) 3 } 2n CB[6] formed vesicles of 170 ? 50 nm diameter as evidenced by transmision electron microscopy (I-55, Scheme 20). 40 When the vesicles were prepared in a solution containing sulforhodamine G and purified by gel permeation chromatography, the vesicles showed bright fluorescence which demonstrates their low permeability. The eficient non-covalent derivatization of the exterior of vesicles I-55 is possible simply by the addition of the spermine-fluorescein conjugate I-56 to yield I-55?I-56 n . Conjugate I-56 is bound strongly to the cavities of the CB[6] derivatives on the surface of the vesicles by the hydrophobic efect and ion-dipole interactions as evidenced by 1 H NMR and confocal microscopy. This vesicle scafold can also be used for the multivalent display of ?-mannose groups tagged with a spermine tail. These ?-mannose derived vesicles are capable of aggregating concanavalin A due to biospecific interactions betwen the sugar and the 29 lectin. The potential for the introduction of multiple tags onto a single vesicle suggests a route toward the targeted delivery of pharmaceutical agents. Scheme 20. Decoration of supramolecular vesicles with fluorescent labels. 1.14 Cucurbit[n]uril Based Artificial Ion Chanels. One of the major isues that faced the development of applications of the CB[n] family ? that has partialy faded with Kim?s direct functionalization route ? is poor solubility in organic solution. To improve the solubility in organic solution and in lipid membranes Kim and co-workers atached long alkyl chains to the outside of CB[5] and CB[6] as described above. 39 Kim and co-workers found that {CH 3 (CH 2 ) 7 S(CH 2 ) 3 } 2n CB[n] (n = 5, 6) could be incorporated into large unilamelar vesicles (LUV?s) comprising egg yolk L-?-phosphatidyl-choline (EYPC), cholesterol, and dicetyl phosphate (Scheme 21). 41 The flux of protons and alkali metal cations across the membrane could be quantified by following the fluorescence intensity (I 460 / I 403 ) of 8-hydroxypyrene- 1,3,6,-trisulfonate (HPTS) which functions as a pH sensitive dye. Interestingly, the order of transport activity across LUVs containing {CH 3 (CH 2 ) 7 S(CH 2 ) 3 } 2n CB[n] was Li + > Cs + ? Rb + > K + > Na + which is opposite to the binding afinity of CB[6] toward 30 alkali metal cations. Somewhat surprisingly, planar bilayer conductance measurements show that the ion transport occurs by a channel rather than a carier mechanism. The ion-channel properties of {CH 3 (CH 2 ) 7 S(CH 2 ) 3 } 12 CB[6] could be switched off by the addition of acetylcholine (Me 3 NCH 2 CH 2 OAc, I-57) which binds in the cavity of the CB[6] derivative. The CB[6] derivative {CH 3 (CH 2 ) 7 S(CH 2 ) 3 } 2n CB[n] permits remarkably fast transport of Cs + across the membrane (? 5 pA; ? 3 ? 10 7 ions s -1 ) which is comparable to that observed for gramicidin. By using synthetic chemistry to tailor the structure and solubility of CB[n] and its derivatives, it is possible to expand the range of applications to which the CB[n] family can be applied! N O O RR CH 2 2 H + , Li, Na + , K, Rb + , Cs + n =5, 6 (H 17 C 8 S 3 H 6 ) 12 CB[] 0 5 Scheme 21. Preparation of artificial ion-channels with CB[5] and CB[6] derivatives. 1.15 Experimental Procedures. This experimental section describes several key procedures encountered during the synthesis of members of the CB[n] family. 1.16 Synthesis of Glycolurils. An excelent review by Petersen describes the preparation of numerous glycolurils. 42 In general, the formation of glycolurils occurs by the condensation betwen urea and its derivatives with 1,2-diketones under acidic 31 conditions. Two specific examples are presented below which use either aqueous or anhydrous acidic conditions. Synthesis of Glycoluril I-1a. A modification of the literature procedure was used. 33 To a solution of urea (600 g, 10 mol) in water (1 L) was added a 40% aq. solution of glyoxal (500 g, 3.445 mol) and conc. HCl (86 mL). The resulting solution was heated at ? 85 ? 90 ?C until a heavy precipitate has formed. The reaction mixture is alowed to cool to room temperature and filtered. The filter cake is washed with copious amounts of water (2 L) followed by acetone to remove residual water. The resulting white solid is dried under high vacuum (397.5 g, 81%). 1 H NMR (DMSO, 400 MHz): 7.11 (s, 4H), 5.20 (s, 2H). Synthesis of Glycoluril I-1b. A modification of the literature procedures was used. 43 A mixture of benzil (21.0 g, 0.10 mol) and urea (12.1 g, 0.20 mol) in benzene (380 mL) was treated with TFA (20 mL) which results in a homogenous mixture. The reaction mixture is then heated at reflux with azeotropic removal of water for overnight. After cooling to room temperature, the white precipitate is isolated by filtration, washed with EtOH, and dried on high vacuum yielding I-1b as a white solid (22.8 g, 78%). 1 H NMR (DMSO, 400 MHz): 7.70 (s, 4H), 7.05 - 6.95 (m, 10H). 1.17 Synthesis and Separation of Cucurbit[n]urils. Although the synthesis and separation procedures given below may appear straightforward there are numerous details which do efect the outcome of the CB[n] forming reaction (e.g. rate 32 of stiring, physical state and degre of physical mixing of the starting materials, homogeneity of the solution, etc.) and the eficiency of the separation procedure (e.g. HCl content in the crude solid). Therefore, each of the major laboratories involved in CB[n] chemistry has developed their own modifications of the basic procedures published by Day and Kim. 12,15 We present here the procedures used by our group at the University of Maryland. Synthesis of CB[n] and i-CB[n]. Powdered glycoluril (795 g, 5.59 mol) and powdered paraformaldehyde (354 g, 11.20 mol) were mixed thoroughly. An ice-cold concentrated HCl solution (1130 mL) was added gradualy while stiring with a large glas rod. After the addition of ? 100 mL, stiring was no longer possible as the reactants were transformed into a brick like material. At this point the reaction becomes highly exothermic. The heterogenous mixture was gradualy heated to 80 ?C over 2.5 h and maintained at that temperature for an additional 2.5 hours at which point al of the solid had disolved. The homogenous red solution was heated to 100 ?C for 14 hours. After cooling to room temperature, the purification proces was begun. Monitoring of the Separation Proces. It is possible to monitor the purification proces by 1 H NMR using 20% DCl as the solvent. In this solvent CB[5] ? CB[8] and CB[10]?CB[5] and i-CB[6] show diagnostic resonances for the high field diastereotopic CH 2 -group (4.5 ? 4.1 ppm). Figure 3 shows a representative 1 H NMR spectrum of the crude CB[n] forming reaction mixture. 33 Figure 2. 1 H NMR spectrum (400 MHz, 20% DCl, RT) of the crude CB[n] reaction mixture. Purification of CB[5], CB[6], CB[7], CB[8], CB[10]?CB[5] and i-CB[6]. The reaction mixture which contains a large amount of solid was evaporated to a minimum volume (? 600 mL). This slurry was poured into water (2.5 L). The solid was collected by filtration (Crop 1 contains CB[6], CB[7], CB[8], some i-CB[6], and some CB[10]?CB[5]). The filtrate was evaporated to about 600 mL and then slowly poured into a mixture of MeOH (3 L) and water (200 mL) with vigorous stiring. After stiring overnight, the precipitate was isolated by filtration (Crop 2 contains mainly CB[7] and CB[5] and smaler amounts of CB[6]). Subsequent purification. The separation of each component (CB[5], CB[6], CB[7], CB[8], CB[10]?CB[5], and i-CB[6]) from Crop 1 and Crop 2 took advantage of their diferential solubility in HCl solutions of diferent concentration. For example, CB[5] and CB[7] have moderate solubility in water but other CB[n] are nearly 34 insoluble in pure water. The crude solids were stired in a beaker with large volumes of water (2 L) repeatedly to isolate a solution consisting of mainly CB[5] and CB[7]. After concentration to 200 mL, the solution is poured into MeOH (1.5 L) and the solid isolated by filtration. Separation of CB[5] from CB[7] is based on its moderate solubility (about 33 mg/mL) in 50% aqueous MeOH solution (v/v). The solubility of CB[7] is les than 4 mg/mL in this solution. Acordingly, the solid mixture of CB[5] and CB[7] was repeatedly stired in a large beaker with 50% aq. MeOH to disolve the CB[5] and leave the CB[7] as a solid. The solution of CB[5] is concentrated (not to drynes) which yields crystaline CB[5] (8% overal yield). Difusion of acetone into an aqueous solution of CB[7] is used to obtain CB[7] as a crystaline solid (25% overal yield). The solid material from which CB[5] and CB[7] has been removed is subsequently procesed to yield CB[6], i-CB[6], CB[8], and CB[10]?CB[5]. In 3 M HCl, CB[6], i-CB[6], and CB[10]?CB[5] have appreciable solubility whereas CB[8] is substantialy les soluble. By stiring the crude mixture of CB[6], CB[8], CB[5]@CB[10], and introverted CB[6], with 3 M HCl in a large beaker it is posible to isolate CB[8] as an insoluble solid. CB[8] can then be recrystalized from warm conc. HCl to yield a crystaline solid (10% overal yield). The solution of CB[6], i- CB[6], and CB[10]?CB[5] in 3 M HCl is concentrated by rotary evaporation resulting in precipitation of CB[6]. The CB[n] remaining in solution are precipitated by pouring the aq. soln. into MeOH. The solid obtained which stil contains CB[6], i- CB[6], and CB[10]?CB[5] can be separated by repeated fractional crystalization from diferent concentration HCl solutions. For example, CB[10]?CB[5] can be obtained by crystalization of the mixture from conc. HCl (2% overal yield). In samples that 35 contain a large amount of i-CB[6], the CB[6] impurity can be removed by disolving the mixture in 20% HCl, adding the calculated amount of hexanediamine and diluting 10-fold with water. i-CB[6] is obtained as an insoluble precipitate (2% overal yield). CB[6] is obtained from multiple fractions and can be recrystalized from concentrated HCl (50% overal yield). The synthesis and purification procedure described above takes approximately 6 weks. 1.18 Sumary and Conclusions. The first synthesis of CB[6] by Behrend in 1905, its structural elucidation by Mock and co-workers in 1981, and subsequent studies by Mock and co-workers throughout the 1980?s demonstrated the high potential of CB[6] in studies of molecular recognition in aqueous acidic solution. The field has taken rapid steps forward since 2000 with the discovery of the CB[n] homologues CB[5], CB[7], CB[8] by the groups of Kim and Day whose cavity volumes span and exced those available with ?-, b-, and ?-cyclodextrin. For example, the smaler CB[5] readily encapsulates gases 44 whereas the larger CB[n] homologues encapsulate species with high biological and chemical potential (e.g. anticancer agents, dyes, peptides, viologens, ferocenes). When Isacs and co-workers began their work in this area in 1998 they decided to tackle the isue of preparing CB[n] derivatives that contained solubilizing groups on the exterior of the macrocycle that would extend the range of applications to which CB[n] could be applied. This Chapter has described the mechanistic approach pursued by the Isacs? group that initialy targeted the preparation of methylene bridged glycoluril dimers as the fundamental building blocks of the CB[n] 36 family. These model studies alowed us to provide evidence for some of the key early steps in the CB[n] formation mechanism, namely: 1) the presence of both S- and C- shaped diastereomers, 2) the presence of a thermodynamic driving force in favor of the C-shaped form (? 2 kcal mol -1 ), and 3) the intramolecular nature of the S- to C- shaped equilibrium under anhydrous acidic conditions. These observations lead us to propose a building block strategy toward the preparation of CB[n] compounds 4,5 which was subsequently demonstrated experimentaly in the synthesis of CB[n] derivatives and analogues. 34,37,38 Kim?s synthetic advance in developing the direct per-hydroxylation of CB[5] ? CB[8] alowed his group to prepare a wide range of per-functionalized CB[5] and CB[6] derivatives and use them in new applications like synthetic ion-channels and supramolecular vesicles. 39-41 More recently, in collaboration with Kim?s group, we isolated inverted cucurbiturils (i-CB[6] and i-CB[7]) which are kinetic intermediates along the pathway toward CB[n] whose transformation into CB[5], CB[6], and CB[7] was demonstrated by product resubmision experiments. 13 These key experiments provided evidence on the fate of some of the final intermediates along the mechanistic pathway toward CB[n] and stimulated us to further probe the later stages of the mechanism of CB[n] formation. Our key realization was that CB[n] forming reaction mixtures containing a deficiency of formaldehyde would be unable to proced to completion and therefore deliver intermediates as final products. Based on this idea, we were able to isolate ns- CB[10] which is formaly derived from CB[10] by the removal of two CH 2 groups with subsequent bond reorganization. ns-CB[10] has displays recognition properties 37 including that are reminiscent of biological systems including the stabilization of ternary complexes and homotropic alostery based on guest size. If the CB[n] family is to supplant the cyclodextrins as the platform of choice for basic and applied studies of molecular recognition then a series further developments must take place many of which involve the development of new synthetic procedures. First, improved methods for the separation of crude CB[n] mixture on laboratory (e.g. up to 1 kg) to industrial (e.g. tons) scale must be developed. Alternatively, synthetic procedures that selectively target a specific CB[n] (e.g. CB[8] or CB[10]) would be tremendously valuable. Second, the development of high yielding methods of functionalizing pre-formed CB[n] ? particularly for CB[7], CB[8], and CB[10] would have a dramatic impact on the field. Third, a deficiency of the CB[n] family relative to the cyclodextrins is that they are inherently achiral which renders chiral recognition inside CB[n] chalenging. Our group and Inoue?s group have recently shown that chiral recognition inside CB[n] can be achieved by ?asembled enantioselection? where a chiral binary complex can be transformed into a diastereomericaly enriched ternary complex by interaction with a chiral but racemic guest. 18,45 Fourth, to date a smal number of studies have targeted the development of CB[n] for electronic applications. 46 Fifth, for applications involving humans (e.g. drug delivery, foodstuff additive, perfume additive, etc.) it wil be necesary to demonstrate that CB[n] are not toxic and that they are properly excreted from the body. Given the high chemical stability of CB[n] it sems unlikely that CB[n] wil be metabolized in vivo. Lastly, it sems likely that CB[n] wil be equal or 38 superior in the numerous application areas that have been demonstrated for the cyclodextrins and much future work wil be directed in this direction. 39 II. Chapter 2: Cucurbit[n]uril Formation Proceds by Step- Growth Cyclo-oligomerization (Huang, W.-H.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2008, submited.) 2.1 Introduction. In 1981 Mock reported that the condensation of glycoluril and formaldehyde delivers the cyclic hexameric macrocycle cucurbit[6]uril (CB[6]). 2,18- 19,47-48 This remarkable reaction (Scheme 1) results in the formation of 24 new C-N bonds and six eight-membered rings al with complete control over the relative orientation of the glycoluril C-H atoms which point out of the cavity. During the 1980?s Mock extensively studied the host-guest recognition behavior of CB[6] and found that CB[6] exhibits remarkably tight (K a up to 10 8 M -1 ) and selective binding toward organic amonium ions in water. 8,1 Subsequent work by Mock showed that these binding characteristics could be used to catalyze a dipolar cycloaddition (click- chemistry) and to create one of the first examples of a molecular shuttle. 10,49 As supramolecular chemists, we were inspired by the outstanding recognition properties of CB[6] and hypothesized that if we could tailor the recognition properties of CB[6] by synthetic chemistry (e.g., the creation of cucurbit[n]uril homologues (CB[n]), 16,49 analogues, derivatives, or congeners) that we might be in the position to create contemporary molecular devices like chemical sensors, supramolecular catalysts, ion and molecular channels, and molecular machines (e.g. molecular shuttles). As physical organic chemists, we decided to target a thorough understanding of the mechanism of CB[n] formation with the expectation that such knowledge would enable the tailor-made synthesis of CB[n]-type receptors with new geometrical features and recognition properties. 40 NHH HNH O O Cl, 2 O, C 2 O N N O N N O O N N O N N O CB[6] Scheme 1. Synthesis of CB[6]. Since I began my work on the mechanism of CB[n] formation upon ariving at the University of Maryland in 2003 there have been a number of developments in the CB[n] area that post facto validate our plan to enhance the range of applications to which the CB[n] family 49,50 can be applied by the creation of new CB[n]-type receptors. For example, the isolation of the cucurbit[n]uril homologues (n = 5, 6, 7, 8) by the groups of Kim and Day provided a series of macrocycles whose sizes (82, 164, 279, 479 ? 3 ) paralel those of ?-, ?-, and ?-cyclodextrins. 12,15 These new macrocycles, therefore, participate in a variety of interesting applications including supramolecular dye lasers, 51 novel drug delivery vehicles 29,30,52 as a mediator of organic reactions, 53 peptide recognition, 54 chemical sensors, 36,5 as components of complex self-sorting systems, 1,19-21 and in the development of molecular machines. 26,27,56 More recently, our group has reported the isolation of fre CB[10] from its CB[10]?CB[5] complex and the ability of its 870 ? 3 cavity to promote folding, forced unfolding, and refolding of non-natural oligomers in water and as a host for metalo-porphyrins. 17,57 Most recently, in collaboration with Kimoom Kim?s group, we have reported the isolation and recognition properties of diastereomeric CB[n] known as inverted-CB[n] (i-CB[n]) in which a single pair of methine C-H 41 groups point into the central cavity. 13,58 The formation of these new CB[n] under milder kineticaly controlled conditions provide an existence proof for intermediates in the mechanism of CB[n] formation and have helped guide our mechanistic studies over the years. 5,6,13,34,35,58,59 H O N N O N N O O N N O O N N O iCB[n] O N N O N N O O N N O N N O CB[n] n-5 n-5 (?)-bis-n-CB[6] C O N N O N N O O O HN N N O N H N O O 2 2 O N N N N O H C N N O OO O N N N N N N O N N O O H 2 N N O O H H 2 bis-n-CB[10] Scheme 2. Chemical structures of CB[n], iCB[n], bis-ns-CB[10], and (?)-bis-ns- CB[6]. 2.2 Cyclic Oligomeric CB[n]. In this chapter we explore the consequences of our realization that the cyclo-oligomerization reaction of glycoluril and formaldehyde ? tetra-functional and di-functional monomers, respectively ? is in many ways related to a clasical polymerization reaction. For example, clasical polymerization reactions betwen two diferent multi-functional monomers only proced to give high molecular weight material when there is a stoichiometric balance betwen the reactive groups of the two monomers. 60 When there is an exces of one of the 42 monomers, it acts as an end-capping group and shorter oligomers are obtained. Realizing that cyclic oligomeric CB[n] can be viewed as infinitely long oligomers raised the question in our mind of what would happen if we starved the CB[n] forming reaction of formaldehyde. Would new mechanistic intermediates in the formation of CB[n] be delivered as kineticaly stable isolable materials? Our previous reports on the isolation, structural characterization, and recognition properties of bis-nor-seco-CB[10] 14 and (?)-bis-nor-seco-CB[6] provide an answer in the afirmative and we describe our complete mechanistic study in detail here. 2.3 Results and Discusion. We begin this results and discussion section with a brief review of the state-of-the-art concerning the mechanism of CB[n] formation that sets the stage for a discussion of the results reported in this paper. 2.3.1 Previous Mechanistic Studies. Scheme 3 shows the fundamental steps of the mechanism of CB[n] formation that were previously presented by the groups of Isacs and Day. 5,12 First, glycoluril II-1 reacts with two equivalents of formaldehyde to potentialy deliver a mixture of diastereomers (II-2 and II-2S) that difer in the relative orientation of the pairs of methine C-H groups. It was further hypothesized that these dimers undergo further oligomerization via II-3 ? II-8 to ultimately yield a substance known as Behrend?s polymer. The length of the polymer chain and diastereomeric orientation of methine C-H groups in Behrend?s polymer is il- defined. At this stage, Behrend?s polymer must undergo an isomerization reaction that converts its S-shaped to C-shaped subunits ? potentialy aided by templating 43 groups 61 ? to create an oligomer (e.g. II-9 or II-10) that is poised to undergo macrocyclization to enter the CB[n] family manifold by either end-to-end cyclization or back-biting mechanisms. Acid, CH 2 O, heat NH O O CB[n] ( =5-7) NR O O HH NR' ' O O H N' ' O O H NR O O H+ NR O O HH N O O H NR O O H n Behrnd's Polymer HHH O N H O N N O O N NN O O O H n-4 R R R O N H O N N O O N NN O O O R R H N O O R NN O O R ' ' Dimer Foration Dimer Equilbration Template n' n-4 I-2S I-2 CB[n !8] I-1 I-A I-B iCB[n] Scheme 3. Proposed mechanism of CB[n] formation. Our group and the group of Anthony Day have been heavily involved in elucidating the mechanistic details of the CB[n] forming reaction. 5,12,35,61 Day?s group has focused on the final steps of the mechanism of CB[n] formation and have examined the influence of numerous potential templating agents on the distribution of CB[n] obtained (e.g. amonium ions and alkali metal ions). 62 Further transformations can occur inside the manifold of CB[n]-type receptors. For example, Day showed that heating CB[8] under the reaction conditions ? where CB[5], CB[6], and CB[7] are stable ? results in a partial ring contraction to deliver the smaler CB[n] homologues. 12 Similarly, we recently reported product resubmision experiments that show that i-CB[6] and i-CB[7] are converted into CB[n] which establishes that these diastereomeric CB[n] are kineticaly controlled intermediates in the mechanism of CB[n] formation. 58 44 Based on our realization that the methylene bridged glycoluril dimer substructure (bold in Chart 1) constituted the fundamental building block of the CB[n] family of macrocycles we initialy studied derivatives of II-2 and II-2S that contained solubilizing CO 2 Et groups on their convex face and capping o-xylylene groups. 5,59 These model studies of the earliest steps of the mechanism of CB[n] formation (e.g. dimer formation and interconversion) alowed us to establish the high thermodynamic preference for the C-shaped forms (??G ? 2 kcal mol -1 ), elucidate the intramolecular nature of the S-shaped to C-shaped interconversion, and to propose and validate the great potential of building block strategies in the formation of CB[n]-type receptors. 5,6,34,35,37,38,59 In combination, the results described above shed significant light on the earliest and latest steps of the mechanism of CB[n] formation. What was lacking was information about what goes on in the middle. 2.3.2 Reaction Mixtures Deficient in Formaldehyde Deliver Glycoluril Oligomers I-2 ? I-6 and Nor-seco-CB[n] as Isolable Species. Based on the connections described above betwen a clasical co-polymerization betwen multifunctional monomers and CB[n] formation we decided to conduct the condensation of glycoluril (II-1) with les than two equivalents of formaldehyde under aqueous acidic conditions (Scheme 4). From these reaction mixtures, we were able to isolate the series of glycoluril oligomers II-2 ? II-6 by a combination of Dowex TM ion-exchange chromatography and recrystalization. We were able to establish the constitution of glycoluril oligomers II-2 ? II-6 by mas spectrometry. Given the large number of potential diastereomers of these oligomers II-2, II-3, II-4, 45 II-5, II-6 structural elucidation by 1 H NMR spectroscopy alone is chalenging (Figure 1). Compounds II-2 ? II-6 with al methine C-H groups on a single side of the molecule are C-shaped and C 2v -symmetric. Symetry consideration dictate that dimer II-2 show two doublets for the methine C-H groups (H a and H b ) and two doublets for the diastereotopic CH 2 -groups (H c and H d ) as is observed experimentaly. The 1 H NMR spectrum for trimer II-3 consists of two doublets and one singlet for the glycoluril methine C-H groups (H a , H b , H c ) in addition to two doublets for the diastereotopic CH 2 -groups. The 1 H NMR spectra for II-4 ? II-6 are complicated in by spectral overlap in the methine CH region ? although the number and relative intensity of the resonances for the diastereotopic CH 2 -groups are in acord with symmetry considerations ? and complete asignment was not possible on the basis of mas spectrometry and 1 H NMR spectroscopy alone. NHH O O HN O O H ba NH O O CH 2 O I-2 I-5 I-3 I-4 I-6 l I-1 N O O HH NH O O HN O H ba N O O H c NH O O HN O O H ba N O O H dc N O O H NH O O HN O O H ba N O H dc N O e N O HH N O H NH O HN O H ba N O O H dc N O fe + + + cd e f h gi k hj l d eg kigjhf Scheme 4. Synthesis of C-shaped II-2 ? II-6. 46 Figure 1. 1 H NMR spectra (400 MHz, 35% DCl) for: a) dimer II-2, b) trimer II-3, c) tetramer II-4, d) pentamer II-5, and e) hexamer II-6. 2.3.3 X-ray Crystal Structures of I-2 ? I-6. Although we were quite confident in our asignment of the structures of the oligomers II-2 ? II-6 based on spectroscopic techniques and previous model studies which indicated a significant thermodynamic preference for the C-shaped diastereomers we wanted to obtain final structural proof in the form of x-ray crystal structures. With some efort we were able to obtain single crystals of II-2, II-3, II-4, II-5, and II-6 (Figure 2). The structures of II-2 ? I-6 are striking for several reasons: 1) the anticipated C-shaped geometries are observed in al cases, 2) the curvature of II-2 ? II-5 is mainly restricted to a single plane (e.g. out of plane twisting is not significant, and 3) the degre of curvature maps wel onto that of CB[6] which is in acord with theoretical calculations which show that CB[6] is the least strained CB[n] on a per glycoluril basis. 50 Beyond the simple 47 connectivity of the molecular structures of II-2 ? II-6 there are intriguing aspects of the solvation and packing of II-2 ? II-6 in the crystal (Supporting Information). For example, compound II-2 crystalizes (Figure 2a) as the CF 3 CO 2 H (TFA) solvate which segregates the molecules of II-2 from one another by forming H-bonds to the ureidyl groups of II-2. Trimer II-3 also crystalizes (Figure 2b) as the TFA solvate by H-bonding interactions with the ureidyl groups of II-3. In this case, however, multiple molecules of II-3 segregate themselves into slabs in the ab-plane that are separated by solvating slabs of TFA molecules along the c-axis. The packing of tetramer II-4 (Figure 2c) in the crystal is facilitated by the interaction of the center two ureidyl C=O groups of two equivalents of II-4 forming a head-to-tail dimeric entity by ion-dipole interactions with Na + . Interestingly, these dimers of II-4 are further organized by NH??O=C H-bonds betwen the tips of II-4 and the C=O rim of another molecule of II-4 to form a complex network motif (Appendices). The packing of pentamer II-5 which begins to look like CB[5] is even more interesting. Each molecule of pentamer II-5 contains one solvating molecule of TFA within its cavity. Furthermore, these molecules of II-5 organize themselves into infinite 1- dimensional tapes along the a-axis by four H-bonds betwen the N-H tips of II-5 with the ureidyl C=O of the adjacent equivalents of II-5 (Appendices). Most interesting and relevant toward the mechanism of CB[n] formation is the packing observed in the crystal structure of II-6. Individual molecules of II-6 are distorted from a symmetric CB[6]-like shape and exhibit a out-of-plane twist toward the tips of the molecule. Both features speak to the inherent flexibility of the growing glycoluril oligomer chains which is les apparent by examination of the macrocyclic CB[n]. Furthermore, 48 two molecules of II-6 dimerize in the crystal driven by NH??O H-bonds. Although glycoluril derived supramolecular structures 65 are wel-known to undergo self- asociation in organic and aqueous solution by H-bonds or ?-? interactions this is the first example that we are aware of that implicates self-asociation of water soluble CB[n] fragments. The implication is that self-asociation of glycoluril oligomers may be considered as a relevant side pathway during the CB[n] forming reaction. 49 Figure 2. Cross-eyed stereoviews of the crystal structures of: a) II-2, b) II-3, c) II-4, d) II-5, and e) II-6. Solvating CF 3 CO 2 H and H 2 O molecules have ben removed for clarity. Color code: C, gray; H, white; N, blue; O, red; H-bonds, red-yelow striped. 2.4 Reaction Mixtures Deficient in Formaldehyde Also Deliver Nor-seco-CB[n] as Isolable Species. From similar reaction mixtures we have previously isolated bis- ns-CB[10], (?)-bis-ns-CB[6], and ns-CB[6]. 14,63,64 Although the quantitation of the 50 amounts of each oligomer and nor-seco-CB[n] in a given reaction mixture has proved chalenging due to extensive peak overlap in the 1 H NMR spectrum and losses that occur during Dowex TM ion exchange we have developed a guiding principle to maximize the yield of a given compound from condensations of glycoluril and formaldehyde that contain a deficiency of formaldehyde. This guideline is based on the theoretical ratio of glycoluril to formaldehyde in a given oligomer or ns-CB[n] (Table 1) and can be considered a consequence of Le Chatelier?s principle. For example, dimer II-2 is composed of two equivalents of glycoluril and two equivalents of formaldehyde and is best targeted with reaction mixtures containing a 1:1 ratio of the two starting materials. Similarly, the recently described ns-CB[n] (ns-CB[6], bis- ns-CB[10], and (?)-bis-ns-CB[6]) can be eficiently isolated from reaction mixtures comprising a 1:1.5 ? 1:1.67 molar ratio of glycoluril:formaldehyde. This ratio is slightly lower than the calculated ratio since entry into the CB[n] manifold is an ireversible proces that reduces overal yield and complicates product isolation. Lastly, the synthesis of CB[n] is known to be most eficient at a stoichiometric ratio of 1:2. 12 Table 1. The molar ratio of glycoluril and formaldehyde units needed to construct CB[n], i-CB[n], ns-CB[n], and oligomers II2 ? II-6. Compound Glycoluril Formaldehyde CB[n] 1 2 i-CB[n] 1 2 ns-CB[6] 1 1.84 51 bis-ns-CB[10] 1 1.80 (?)-bis-ns-CB[6] 1 1.67 II-6 1 1.67 II-5 1 1.60 II-4 1 1.50 II-3 1 1.33 II-2 1 1 2.5 Implications of the Isolation of I-2 ? II-6, bis-ns-CB[10], (?)-bis-ns-CB[6], and ns-CB[6] Toward the Mechanism of CB[n] Formation. The isolation of glycoluril oligomers II-2 ? II-6 and nor-seco-CB[n] alows us to add levels of detail to the mechanism of CB[n] formation that was not previously possible. Scheme 4 ilustrates in detail our current level of understanding of the CB[n] formation proces. The isolation of oligomers II-2 ? II-6 from reaction mixtures comprising glycoluril and a deficiency of formaldehyde provides an existence proof for these structures as kineticaly controlled intermediates in the formation of CB[n]. Acordingly, Scheme 5 shows the stepwise interconversion of glycoluril II-1 into hexamer II-6 by stepwise addition of monomer II-1 (aqua arows). Such a proces where monomer is added stepwise is known in polymer chemistry as chain growth polymerization. 60 Although we have not isolated glycoluril heptamer or octamer (II-7 and II-8) we depict them as highly likely mechanistic intermediates. As the oligomer lengthens from II-1 to II-8 the formation of undesired S-shaped diastereomers is likely. As depicted for II-2S 52 and II-2 ? and studied in detail in model systems by us 5,59 ? an equilibration occurs that dramaticaly favors the C-shaped forms II-3 ? II-8. Once these oligomer chains have grown long enough (II-5 ? II-8) they may undergo direct intramolecular end-to- end cyclization by way of chiral hydroxymethylated intermediate (?)-II-11(n), ns- CB[n], and finaly enter into the CB[n] manifold by addition of the final CH 2 -group. This portion of Scheme 4 is in esence an enhanced version of Scheme 2 which acounts in detail for the presence of oligomers II-3 ? II-6 and also takes into acount the intermediacy of ns-CB[6]. 53 H H N H NHH O O HN O O H NH O OI-2SI-1 + N O O H NH O OI-2 I-3I-4I-5I-6I-7I-8 I-5 ?I-8 O N H O N N O O N N O ns-CB[n] n-5 CB[n] i-CB[n] n !5 n-2 HN O O H N O O H NH O O (?)-I1() H (?)-I14(m,n) (?)-bis-nCB[n+m] C O N N O N O O HN N O N H N O O 2 2 O N H O H N N O O N N O n-5 (C 2 ) n !5 (?)-nsCB[n] I-2 ?I-8 HN O O H N O O H NH O O HN O O H N O O H N O Om-2 n-2 I-13(m,n) Conection betwn eatiopic N-atoms N H O H N O O H NH O O HN O H N O H NH O (CH 2 ) m-2 n-2 (?)-I12(,n) Conection betwn homtpi N-ams H H O N O N N O O N N O N N O O I-15(m,n) bisnCB[+] + O N O N N O O N N O I-17(m,n) bis-nCB[n+m] chiralwhe " ) n-5 H O N O N N O O N N O I-18(m,n) bis-nCB[n+] Calix-type) n-2 O N O N N O O N N O n-2 (C 2 ) (?)-I16(m,n) bis-CB[] n-2 m-2 m-2 m-2 m-2 Ad CH 2 -bridge tolngthe C-shaped oligmer .g I-4 ?I-8 Aditon fa CH 2 - brigemkesn S-shpd diatror of I-4 ?I-8 Scheme 5. Comprehensive mechanistic scheme for the formation of CB[n]. Color coding: chain growth, aqua arows; step growth; red arows (addition of 2), blue arows (addition of 3); gren arows (addition of 4). The isolation of bis-ns-CB[10] and (?)-bis-ns-CB[6] ? comprising two oligomer chains (e.g. II-5 and II-3, respectively) linked by two CH 2 -groups ? alerted us to the potential operation of a second type of mechanistic pathway known as a step-growth proces. In a step-growth proces, the reaction betwen two oligomer chains is also possible. Consider, for example, intermediate (?)-II-11(n) (n ? 4) 54 which is too short to undergo direct intramolecular end-to-end cyclization. Intermediate (?)-II-11(n) is, therefore, forced to undergo intermolecular reaction with an oligomer of identical or diferent length. The sets of colored equilibrium arows in Scheme 4 indicate the step-growth occurring by addition of dimer II-2 (blue arows), trimer II-3 (red arows), and tetramer II-4 (gren arows) and two equivalents of formaldehyde to give longer C-shaped oligomers. Analysis of the intermediate stage of addition of one equivalent of formaldehyde is instructive. Despite the fact that II-1 ? II-8 are achiral, their ureidyl NH groups are prochiral and pairs of NH groups are either homotopic (pairs of red or pairs of gren NH groups in structure of I-2) or enantiotopic (pairs of red and gren NH groups in structure of II-2). Connection of a pair of homotopic groups betwen two oligomers results in intermediate (?)-II- 12(m,n) whereas connection of a pair of enantiotopic NH groups by means of a CH 2 - bridge results in the formation of II-13(m,n). 66 Intermediates II-13(m,n) and (?)-II- 12(m,n) may add a second CH 2 -group in the middle of the molecule to form longer C- shaped oligomers II-4 ? II-8 or diasteromeric oligomers with one S-shaped subunit, respectively. Alternatively, if intermediates (?)-II-12(m,n) and II-13(m,n) are long enough (m + n ? 5) they may make a new N-CH 2 -N bridge betwen the ends of the oligomer chain to deliver macrocyclic compounds In this manner, (?)-II-12(m,n) leads to (?)-II-14(m,n) and II-15(m,n) by connection of homotopic NH groups. The previously isolated (?)-bis-ns-CB[6] and bis-ns-CB[10] serve as examples of these types of macrocycles and provide strong evidence for the depicted mechanistic pathway. To provide even stronger evidence for this mechanistic scheme we performed product resubmision experiments with trimer II-3 and pentamer II-5. 55 When trimer II-3 was treated with 1 equivalent of formaldehyde in HCl we observed the formation of (?)-bis-ns-CB[6] by 1 H NMR at partial conversion. 63,67 When II-5 was treated similarly, we observed and quantified the formation of CB[6] and bis-ns- CB[10] (0.39:1 ratio) by 1 H NMR spectroscopy of the crude reaction mixture. In combination, these results provide strong evidence for the operation of a step-growth cyclo-oligomerization reaction in the mechanism of CB[n] formation. This mechanistic analysis that can be used to rationalize the formation of II-2 ? II-8, ns-CB[6], (?)-bis-ns-CB[6], and bis-ns-CB[10] can also be used to predict the structures of ns-CB[n] that have not yet been isolated. 68 For example, although (?)- II-11(n) may cyclize to yield ns-CB[n] by connection betwen enantiotopic NH groups it may also react to form (?)-ns-CB[n] by connection betwen enantiotopic NH groups. Similarly, either II-13(m,n) or (?)-II-12(m,n) may be transformed into (?)-II-16(m,n) by addition of an appropriate bridging group. Two additional bis-ns- CB[n] can be conceived by addition of a CH 2 -bridge betwen enantiotopic NH groups of II-13(m,n) which delivers II-17(m,n) and II-18(m,n). 66 We are particularly intrigued by the geometrical features of II-18(m,n) which is reminiscent of the calixarenes with bridging at the lower rim and flexibility at the upper rim. We predict that II-18(m,n) wil display quite interesting hybrid recognition and dynamic behavior. 2.5.1 Oligomer Resubmision Experiments. Although we viewed the evidence for the mechanistic scheme presented above as strong given the isolation of II-2 ? II-6, 56 bis-ns-CB[10], (?)-bis-ns-CB[6], and ns-CB[6] and previous mechanistic studies by us 5,6,34,35,37,38,59 and others 12,62,69 we wanted to obtain further evidence that applies directly to CB[n] formation rather than relying on evidence from ns-CB[n] formation. For this purpose we decided to perform product resubmision experiments betwen formaldehyde (2 equiv.) and oligomers II-2 ? II-6 alone and in binary mixtures. We ases the outcome of these reactions by 1 H NMR spectroscopy of the crude reaction mixtures in 20% DCl in which CB[5], CB[6], CB[7], and CB[8] display separate easily integrated resonances (Table 2). 70 2.5.2 Reactions Conducted Betwen Formaldehyde and I-1 ? I-6. Initialy, we conducted the separate reaction betwen formaldehyde (2 equiv.) and II-1 ? II-6 (Table 2). The reaction of monomer alone (Table 2, entry 1) ? which serves as our point of reference for the results described below ? delivers a reaction mixture that contains mainly CB[5] (15%), CB[6] (53%), and CB[7] (30%); CB[8] content is low (2%). In contrast, use of dimer II-2 and trimer II-3 lead to reaction mixtures that contain higher percentages of CB[6] and diminished amounts of CB[5] and CB[7] (Table 2, entries 2 and 3). This result is in acord with the portion of our mechanistic scheme which is based on step-growth polymerization in that II-2 would be expected to give enhanced yields of CB[n] where n is an even number (e.g. a multiple of 2) and II-3 would be expected to give enhanced yields of CB[n] where n is a multiple of 3. As anticipated based on the step-growth cyclo-oligomerization model for CB[n] formation, the reaction of tetramer II-4 was found to give a high yield of CB[8] (40%) and leser amounts of CB[6] and CB[7] (Table 2, entry 4). The reactions of 57 pentamer II-5 and hexamer II-6 ? the first oligomers capable of direct unimolecular macrocyclization ? were particularly interesting (Table 2, entries 5 and 6). Pentamer II-5 delivers mainly CB[5] (84%) and II-6 delivers only CB[6] (100%) which indicates that these oligomers are pre-organized to undergo macrocyclization in preference to further oligomerization. In these reactions conducted under aqueous acidic conditions ? with the use of purified oligomeric building blocks II-2 ? II-6 ? the operation of step-growth proceses is not exclusive as can be sen for example in the reaction of II-3 (Table 2, entry 3) which gives CB[5] and CB[7] as side products. This indicates that under the reaction conditions a given oligomer can undergo fragmentation proceses (e.g. tetramer fragments to two dimers or to a trimer and monomer) to yield shorter oligomers which can then recombine to also give longer oligomers. 10 We have indicated this reversibility explicitly in Scheme 4. 2.5.3 Reactions Conducted Betwen Formaldehyde and Binary Combinations of Building Blocks I-1 ? I-6. Although a complete analysis of the reactions conducted betwen formaldehyde (2 equivalents with respect to total building block concentration) and binary mixtures of building blocks II-1 ? II-6 is not possible given the mixtures that are generaly obtained from CB[n] forming reactions it is possible to tease out some information that we believe is significant (Table 2, entries 7 ? 17). For example, combinations of oligomers II-2 ? II-4 with monomer II-1 increases the proportion of the first oligomer capable of macrocyclization ? CB[5] ? which is consistent with the increased importance of a chain-growth proces when the amount of monomer is significant. 12,71 The results obtained with combinations of building 58 blocks intended to lead to CB[7] (II-1 + II-6, II-2 + II-5, and II-3 + II-4; Table 2, entries 11, 14, 15) are interesting. Of these combinations, II-1 + II-6 delivers mainly CB[6], II-2 + II-5 delivers a significant portion of CB[5] due to competing cyclization of 5 along with CB[7] (35%), and II-3 + II-4 delivers a substantial amount of CB[6] presumably due to competing formation of CB[6] formed from two molecules of II-3 along with CB[7] (42%). In combination, these reactions shed light on the reason why CB[6] is the dominant CB[n] formed under a variety of condition. Although there are a variety of pathways that lead to CB[6] in high relative yield (e.g. II-6, II-1 + II-5, II-2 + II-4, II-3 + II-3) there are fewer pathways that lead to CB[7] (e.g. II-2 + II-5 and II-3 + II-4) or CB[8] (only II-4 + II-4) and those do so only in modest yield due to competing dimerization, cyclization, or fragmentation (e.g. tetramer to trimer and monomer) pathways. In this regard, the quantitative cyclization of II-6 suggests that this cyclization (Table 2, compare entries 5 and 6) may be particularly favorable from a kinetic standpoint. Table 2. The distribution of CB[n] obtained from reaction of II-1 ? II-6 with formaldehyde (2 equivalents) alone and in combination. Entry Reactant(s) CB[5] CB[6] CB[7] CB[8] 1 1 15% 53% 30% 2% 2 2 12% 68% 17% 3% 3 3 8% 75% 17% 0% 4 4 5% 22% 33% 40% 5 5 84% 10% 6% 0% 59 6 6 0% 100% 0% 0% 7 1 + 2 14% 52% 31% 3% 8* 1 + 3 20% 43% 33% 4% 9 1 + 4 35% 44% 18% 3% 10 1 + 5 27% 67% 6% 0% 11 1 + 6 3% 90% 7% 0% 12 2 + 3 26% 41% 30% 3% 13 2 + 4 10% 53% 17% 7% 14 2 + 5 41% 24% 35% 0% 15 3 + 4 11% 42% 42% 5% 16 3 + 5 48% 36% 13% 3% 17 4 + 5 57% 21% 15% 7% * A smal amount (4%) of i-CB[6] was also detected in this reaction mixture. 2.6 Glycoluril Oligomers I-5 and I-6 Retain the Ability to Binding Amonium Ions. Previously, Day?s group has extensively studied the ability of organic and alkali metal cations to act as templates for a specific CB[n] during the CB[n] forming reaction from II-1 and formaldehyde (2 equivalents). 61 The influence of such guests as templates is generaly modest and the point in the mechanism of CB[n] formation that they influence remains unclear although Day hypothesizes that they exert their influence by forming oligomer?guest complexes that either promote or disfavor certain cyclization reactions. Given aces to oligomers II-2 ? II-6 we decided to test their ability to form complexes with representative guests. In acord with the recognized importance of ion-dipole interactions provided by a fully formed the 60 ureidyl C=O portals of CB[n] as an important driving force in the formation of CB[n] guest complexes, 50,63,70 we did not observe any evidence of binding betwen II-2 ? II- 4 and II-19 or II-20 in water. In contrast, we find that pentamer II-5 and hexamer II- 6 begin to exhibit recognition properties characteristic of CB[n]. For example, II-5 forms a complex with II-19 that displays slow exchange on the chemical shift timescale. Evidence of binding betwen II-5 and other guests (II-21 ? II-24) is apparent based on induced upfield shifts in the 1 H NMR spectrum although exchange is faster than the 1 H NMR chemical shift timescale. The recognition behavior of II-6 is equaly interesting (Figure 3). Hexamer II-6 retains the ability to bind with common guests for CB[6] (e.g. II-19 ? II-21 and II-25) and does so with slow exchange on the chemical shift timescale which is noteworthy given the acyclic nature of II-6. Other guests that are rejected by CB[6] (e.g. II-23, II-24, and II-26) are readily complexed by II-6. The ability to bind these guests ? which are good guests for CB[7] (II-23 and II-26) or even CB[8] (II-24) ? indicates that hexamer II- 6 is quite flexible in solution and is able to expand its cavity and wrap itself around larger guests (e.g. II-24) in order to form complexes (Figure 4). One particularly interesting aspect shown in Figure 4 is that the NH tips of II-6 are held apart from one another in a way that would disfavor direct cyclization to CB[6]. Overal, these results show that glycoluril oligomers II-5 and II-6 and by extension II-7 and II-8 are capable of binding guests typical of the CB[n] family. This suggests that the use of suitable templating groups that either promote or disfavor cyclization of a particular oligomer may be useful in directing the CB[n] forming reaction toward an enhanced yield of a single CB[n] compound. 61 Scheme 6. Guests for II-5 and II-6. NH 2 NH 2 NH 2 H 2 N N N H 2 NNH 2 NH 2 H 2 N Fe CH 2 N 2 22 a b c a b c d e f NH 2 NH 2 I-23 I-24 I-19 I-25 I-20 I-2I-1 I-26 Figure 3. 1 H NMR spectra (400 MHz, D 2 O, RT) for: a) II-23, b) II-6?II-23, c) a mixture of II-6?II-23 and exces II-23, d) II-24, and e) II-6?II-24. 62 Figure 4. Cross-eyed stereoview of the MF minimized geometry of the II-6?II- 24 complex. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 2.7 Conclusions. In summary, we have described the synthesis, purification, and solution and solid state characterization of methylene bridged glycoluril oligomers II- 2 ? II-6. As expected based on previous model studies, glycoluril oligomers II-2 ? II-6 posses the energeticaly favored al C-shaped geometry. The curvature of II-2 ? II-5 maps wel onto that exhibited by CB[6] which is calculated to be the least strained member of the CB[n] family. The packing of oligomers II-4 ? II-6 in the crystal is dominated by C=O??Na??O=C and NH??O=C interactions. Most interesting is the dimeric geometry of II-6 in the crystal which demonstrates the inherent flexibility of the methylene bridged glycoluril oligomer chain and suggests that self-asociation should be considered as a side pathway in the mechanism of CB[n] formation. Based on the isolation of II-2 ? II-6 and the previously isolated bis-ns-CB[10], (?)-bis-ns-CB[6], and ns-CB[6] we were able to formulate a detailed picture of the mechanism of CB[n] formation based on a step-growth cyclo- oligomerization proces. To further support the step-growth mechanism we 63 performed product resubmision experiments betwen formaldehyde (2 equivalents) and oligomers II-1 ? II-6 and binary combinations thereof and observed the efect on the ratio of CB[5] ? CB[8] formed. Finaly, we find that pentamer II-5 and hexamer II-6 ? but not II-2 ? II-4 retain the ability to bind organic amonium ions (e.g. I-19 ? II-26) in water. In conclusion, this study has painted a much more detailed picture of the mechanism of CB[n] formation ? based on step-growth cyclo-oligomerization ? than was previously possible. For example, this study alows us to rationalize the prefered formation of CB[6] in CB[n] forming reactions as a consequence of the multiplicity of pathways that leads to CB[6] relative to CB[7] or CB[8] and the pronounced kinetic tendency of II-6 to undergo cyclization to CB[6] rather than oligomerization or fragmentation. The formulation of the mechanism of CB[n] formation as a step growth cyclo-oligomerization patway also alows us to predict the structures of diferent sized relatives of the previously isolated bis-ns-CB[10], (?)- bis-ns-CB[6], and ns-CB[6] and formulate the structures of clases of nor-seco-CB[n] that have not yet been isolated including (?)-ns-CB[6] and II-17(m,n) and II-18(m,n). We predict that II-18(m,n) wil show particularly interesting recognition properties that blend the advantages of the CB[n] family of macrocycles with those of the calixarenes. Of particular interest is the observation that II-5 and II-6 are capable of binding CB[6] sized guests (e.g. II-19 and II-20) and can even expand their cavities 64 to asociate with larger guests (e.g. II-23 and II-24) typicaly bound within CB[7] or CB[8]. This result establishes a high level of flexibility of the growing methylene bridged glycoluril oligomer chain that suggests that the presence of suitable templating guests in the CB[n] forming reaction may be able to direct the reaction toward enhanced yield of a single sized CB[n]. This result also raises the prospect of using suitable guests to template the formation of larger ns-CB[n] (n ? 10), ns-CB[n] containing multiple cavities and lacking more than two CH 2 -groups, 14 and even the enantioselective synthesis of chiral ns-CB[n] (e.g. (?)-II-14(m,n), bis-ns-CB[n+m]). Given the wide range of applications to which CB[n] (e.g. sensing, molecular machines, drug delivery) 6 and its derivatives can be applied (e.g. polymer nanocapsules, afinity chromatography, and artificial ion-channels) 49,50 we expect that the ability to target tailor-made CB[n], CB[n] derivatives, and ns-CB[n] which is enabled by the mechanistic insights described herein wil lead to new application areas that currently benefit from calixarene or cyclodextrin molecular containers. 2.8 Experimental Section. General Experimental Details. The guests used in this study were purchased from commercial suppliers and were used as their HCl salts. Dimer II-2 was reported previously but no experimental details or characterization data are given. 38 The synthesis, characterization, and x-ray crystal structure of II-3 (CDC 647412) were previously reported by us. 63 Melting points were measured on a Meltemp apparatus in open capilary tubes and are uncorrected. IR spectra were recorded on Thermo Nicolet IR200 spectrometer and are reported in cm -1 . NMR spectra were measured on spectrometers operating at 400 and 500 MHz for 1 H and 65 100 or 125 MHz for 13 C. Mas spectrometry was performed using a VG 7070E magnetic sector instrument by fast atom bombardment (FAB) using the indicated matrix or on a JEOL AcuTOF electrospray instrument. Computational results were obtained using Spartan 02 running on a Macintosh personal computer. 2.8.1 Oligomers I-2 ? II-6: A mixture of glycoluril (1.42 g, 9.99 mol), paraformaldehyde (0.300 g, 9.99 mol) and conc. HCl (4 mL) was heated at 50 ?C for 18 hours. The precipitate was isolated by filtration, washed with MeOH and dried overnight at high vacuum to yield a crude white solid (577 mg) containing II-2. The soluble portion of the reaction mixture containing II-2 ? II-6 was precipitated by the addition of MeOH followed by filtration and drying at high vacuum to yield a crude solid (952 mg). The white solid was recrystalized from TFA to yield II-2 as a white solid (480 mg, 16%). Purification of the crude solid containing II-2 ? II-6 was performed by column chromatography on Dowex 50WX2. A 5 cm diameter column was packed with Dowex 50WX2 resin to a height of 34 cm. The crude solid was disolved in 88% HCOH:0.2 M HCl (1:1, v:v) and loaded onto the column. The column was eluted using 88% HCOH:0.2 M HCl (1:1, v:v). The oligomers come off the column in the following order II-2, II-3, II-4, II-5, and then II-6. The column fractions were individualy concentrated by rotary evaporation and dried by high vacuum overnight. Purity was asesed by 1 H NMR and appropriate fractions were combined. The solids thus obtained were washed with MeOH to remove soluble impurities, dried overnight at high vacuum, and then recrystalized from TFA to yield: II-3 (120 mg, 10%), II-4 (30 mg, 3%), II-5 (30 mg, 3%), and II-6 (10 mg, 1%) as white solids. Dimer II-2: Mp: > 300 ?C. IR (KBr, cm -1 ): 3595s, 3205s, 3068s, 66 1696s, 1492s, 1466s, 1329s, 1234s, 1156s, 1109s, 958s, 884s, 801s, 707s, 680s, 640s. 1 H NMR (400 MHz, 35% DCl, RT): 5.73 (d, J = 8.8 Hz, 2H), 5.60 (d, J = 8.8 Hz, 2H), 5.37 (d, J = 16.0 Hz, 2H), 4.48 (d, J = 16.0 Hz, 2H). 13 C NMR (125 MHz, 35% DCl, RT, ext. dioxane reference): 159.4, 74.1, 62.2, 50.5. ES-MS: m/z 309 (100, [M + H] + : ([M + H] + , C 10 H 12 N 8 O 4 , calcd 308.10). X-ray crystal structure (from TFA). Tetramer II-4: Mp: > 300 ?C. IR (KBr, cm -1 ): 3405br, 1726s, 1472s, 1418s, 1379s, 1328s, 1295s, 1243s, 1199s, 1180s, 1127s, 969s, 802s. 1 H NMR (400 MHz, 35% DCl, RT, ext. dioxane reference): 5.74 (d, J = 8.6 Hz, 2H), 5.62 (d, J = 8.6 Hz, 2H), 5.60 (s, 4H), 5.49 (d, J = 14.8 Hz, 2H), 5.46 (d, J = 15.6 Hz, 4H), 4.42 (d, J = 15.6 Hz, 4H), 4.40 (d, J = 14.8 Hz, 2H). 13 C NMR (125 MHz, 35% DCl, RT): 159.3, 156.0, 74.1, 69.9, 69.8, 62.3, 51.1, 50.8. ES-MS: m/z 641 (100, [M + H] + : ([M + H] + , C 22 H 24 N 16 O 8 , calcd 640.2). X-ray crystal structure (from TFA). Pentamer II-5: Mp: > 300 ?C. IR (KBr, cm -1 ): 3399br, 1728s, 1471s, 1418s, 1377s, 1330s, 1295s, 1240s, 1222s, 1197s, 1181s, 968s, 804s. 1 H NMR (400 MHz, 35% DCl, RT, ext. dioxane reference): 5.73 (d, J = 8.6 Hz, 2H), 5.62 (d, J = 8.6 Hz, 2H), 5.58 (s, 6H), 5.46 (d, J = 14.8 Hz, 4H), 5.43 (d, J = 15.4 Hz, 4H), 4.41 (d, J = 15.4 Hz, 4H), 4.37 (d, J = 14.8 Hz, 4 H). 13 C NMR (125 MHz, 35% DCl, RT): 159.2, 155.8, 74.1, 69.8, 69.7, 62.2, 51.0, 50.8. (only 8 of the 10 expected resonances were observed). MS (ES): m/z 472 (100, [M + p-xylenediamine + 2H] 2+ , m/z spacing = 0.5 confirmed for molecular ion). C 28 H 30 N 20 O 10 , X-ray crystal structure (from TFA). Hexamer II-6: Mp: > 300 ?C. IR (KBr, cm -1 ): 1717s, 1469s, 1422s, 1375s, 1325s, 1232s, 1190s, 1090s, 966s, 890s, 804s, 757s. 1 H NMR (400 MHz, 35% DCl, RT): 5.80 (d, J = 8.4 Hz, 2H), 5.69 (d, J = 8.4 Hz, 2H), 5.64 (s, 4H), 5.62 (s, 4H), 5.52 (d, J = 15.4 Hz, 6H), 5.49 (d, J = 15.4 67 Hz, 4H), 4.46 (d, J = 15.6 Hz, 4 H). 4.39 (d = 15.4 Hz, 6H). 13 C NMR (125 MHz, 35% DCl, RT, ext. dioxane reference): 159.4, 155.9, 74.4, 70.1, 70.0, 62.1, 51.4, 51.3, 51.1. (only 9 of the 12 expected resonances were observed). MS (ES): m/z 555 (100, [M + p-xylenediamine + 2H] 2+ , m/z spacing = 0.5 confirmed for molecular ion). C 34 H 36 N 24 O 12 , X-ray crystal structure (from TFA). 2.8.2 General Procedures for Product Resubmision Experiments. Procedure A: A mixture of one glycoluril oligomer (II-1, II-2, II-3, II-4, II-5, or II-6, 5.0 mg) and paraformaldehyde (2.0 equivalents) was disolved in 35% DCl (0.5 mL) and heated at 80 ?C for 18 hours. The resulting solution was precipitated by the addition of MeOH. The precipitate was isolated by centrifugation and dried overnight to yield a crude white solid. The content of CB[5], CB[6], CB[7], and CB[8] in the solid was determined by careful integration of the appropriate resonances in the 1 H NMR spectrum (20% DCl in D 2 O). Procedure B: A equimolar mixture of two diferent glycoluril oligomers (II-1, II-2, II-3, II-4, II-5, or II-6, 7.5 mg total weight) and paraformaldehyde (2.0 equivalents) was disolved in 35% DCl (0.5 mL) and heated at 80 ?C for 18 hours. The resulting solution was precipitated by the addition of MeOH. The precipitate was isolated by centrifugation and dried overnight to yield a crude white solid. The content of CB[5], CB[6], CB[7], and CB[8] in the solid was determined by careful integration of the appropriate resonances in the 1 H NMR spectrum (20% DCl in D 2 O). 2.8.3 Synthesis of bis-ns-CB[10] from I-5. A mixture of II-5 (30.0 mg, 0.037 mol), paraformaldehyde (1.1 mg, 0.037 mol), and conc. HCl (0.5 mL) was heated at 50 ?C overnight. The reaction mixture was pipeted into MeOH. The resulting precipitate was isolated by centrifugation and dried under high vacuum overnight to yield a crude solid (27 mg). The CB[6]:bis-ns-CB[10] ratio in this crude solid was 68 determined by 1 H NMR to be 0.39:1. Final purification was achieved by suspending the sample in an aqueous solution containing the calculated amount of hexanediamonium ion to complex the CB[6] impurity. The heterogenous mixture was then centrifuged and the solid obtained by decanting the supernatant. The solid was washed with several portions of water and dried at high vacuum overnight to yield bis-ns-CB[10] as a white solid (11 mg, 36%). 69 II. Chapter 3: Nor-Seco-Cucurbit[10]uril Exhibits Positive Homotropic Alosterism (Huang, W.-H.; Liu, S.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2006, 128, 14744-14745.) 3.1 Introduction. Cucurbit[6]uril (CB[6]) ? the prototypical member of the CB[n] family (16,49) ? has outstanding recognition properties toward aliphatic and aromatic amines in aqueous solution. 2,73 In recent years, a homologous series of hosts (CB[n]: n = 5, 7, 8, 10) 12,15,17,18 has been isolated and investigated. These new CB[n] ? with their increased cavity volumes ? bind to a wide range of chemicaly and biologicaly important guests and therefore participate in a variety of interesting applications including fluorophore photostabilization, 74 gas binding, 75 chemical sensing, 14,36,76 supramolecular vesicles, 40 supramolecular dendrimers, 23 molecular machines, 26,27 and complex self-sorting systems. 19,20,7 Stimulated by the discovery of inverted CB[n] (n = 6, 7), 13 we postulated that other kineticaly controlled structures might be formed as stable mechanistic intermediates 5 during CB[n] formation. We report the isolation and recognition properties of nor-seco-cucurbit[10]uril (ns- CB[10]) which results from formal extrusion of two CH 2 bridges from CB[10] along with bond reorganization. 70 NH 2 NH 2 X NH 2 NH 2 I-7 R =NH 2 8C 2 I-9 Me 3 I NH 2 NH 2 N N N N I-12 I-4 X =CH 2 I5 S I- R =NH 2 I14 I-3I-6 R NH NH O CH 2 CH 2 NN CH 2 C R MePh I-13 O N N O N N O O H C N N O O O N N N N N O N N O O H 2 N N N O O H 2 ns-CB[10] a bc hi n f g d e l m j k NH 2 NH 2 Fe H 2 N NH 2 I-10I-1 Scheme 1. Structure of ns-CB[10] and guests used in this study. 3.2 1 H NMR spectra of fre ns-CB[10]. We discovered that heating a mixture of glycoluril (I-1a) and paraformaldehyde at 50 ?C in concentrated HCl delivers a reaction mixture that contains CB[n] and ns-CB[10] (Scheme 1). We isolated ns- CB[10] as a white solid in 15% yield by washing and recrystalization. The 1 H NMR spectra of fre ns-CB[10] (Figure 1a) was not informative due to significant signal overlap although the resonance for the inwardly directed CH 2 bridge (H a ) appeared in a distinctive region of the spectrum. In contrast, the NMR spectra of ns-CB[10]?III- 2 2 was relatively wel dispersed which alowed unambiguous asignment of its structure by 2D NMR methods (Supporting Information). Of particular diagnostic utility are the resonances for H a and H n which appear as singlets due to the overal C 2h -symmetry of ns-CB[10]?III-2 2 . 71 Figure 1. 1 H NMR spectra for: a) ns-CB[10] (400 MHz, 20% DCl), b) ns- CB[10]?III-2 2 , c) ns-CB[10]?III-11 2 , d) 2:2:2 mixture of ns-CB[10], III-2, and III-11 (b-d: 500 MHz, D 2 O). X = trace EtOH impurity. 3.3 X-Ray Crystals of ns-CB[10]. Fortunately, we obtained single crystals of ns- CB[10] as its p-phenylenediamine (3) complex (ns-CB[10]?III-3 2 ) which were suitable for x-ray structure determination (Figure 2). Several structural features are intriguing including: 1) the absence of two CH 2 bridges and the internal disposition of the two single CH 2 bridges, 2) two symmetry equivalent cavities and their lack of vertical registration, and 3) infinite guest filed channels defined by the stacking of ns-CB[10]?III-3 2 in the crystal (Supporting Information). Interestingly, the solvating H 2 O molecules in the ureidyl carbonyl region of ns-CB[10]?III-3 2 act as bridges betwen guest NH and host C=O groups. 72 Figure 2. Cross-eyed stereoview of the crystal structure of ns-CB[10]?III-3 2 . Solvating H 2 O molecules have been removed for clarity. Color code: C, gray; H, gren; N, blue; O, red. 3.4 Molecular Recognition Properties of Nor-Seco-Cucurbit[10]uril. After the structure of ns-CB[10] was elucidated, we investigated its recognition properties. The two cavities of ns-CB[10] are caparable in size to those of CB[6] and CB[7] and therefore bind guests commonly used with these hosts. For example, ns-CB[10] forms ternary (1:2) complexes with alkyl, cycloalkyl, aryl, and adamantyl amines (III-2 ? II-10) although some of these complexes display fast exchange on the NMR timescale. ns-CB[10] also binds some more chemicaly and biologicaly interesting species (Supporting Information) like dyes (e.g. coumarins, acridines, nile blue), amino acids (tryptophan, 4-aminophenylalanine, and arginine), and electrochemicaly active substances (ferocenes (e.g. III-11) and viologens). More sizable guests (e.g. II-12 and II-13) which are too large for the individual CB[6] ? CB[7] sized cavities of ns-CB[10] instead form binary (1:1) complexes that fil both cavities simultaneously. Several types of selectivity are observed within ternary complexes of ns-CB[10]. For example, when unsymmetrical guests are bound within ns-CB[10] thre 73 diastereomers are posible (Figure 3: top-top, center-center, and top-center). For some guests a single diastereomer is observed (e.g. ns-CB[10]?III-7 2 ) which we tentatively asign the top-top conformation. In the top-top conformation, the NH 3 + groups bind at the more flexible C=O portals which lack a CH 2 -bridge. For other guests (e.g. III-8) al thre conformations can be observed by 1 H NMR (Supporting Information). 78 A second type of selectivity is possible during the binding of chiral but racemic guests. For example, when a mixture of III-14 and ent-III-14 is offered to ns-CB[10], two homochiral forms (ns-CB[10]?III-14 2 and ns-CB[10]?ent-III-14 2 ) and one heterochiral form (ns-CB[10]?III-14?ent-III-14) are observed as a statistical mixture. Further studies are needed to understand the structural features that alow an eficient transmision of chiral information. NH 3 NH 3 NH 3 H 3 N NH 3 NH 3 top-t centr- top-centr contracts for sml guet expands for lrg uet Figure 3. Thre potential diastereomers of ns-CB[10]?III-7 2 . The arows ilustrate the key CH 2 ??CH 2 non-bonded distance that changes acording to guest size. 3.5 Positive Homotropic Alosterism. Interestingly, during our binding studies we never observed the formation of binary complexes concomitant with ternary complexes, which establishes a sizable positive homotropic alosterism 14 in the system. To demonstrate its potential in alostery, we offered ns-CB[10] guest mixtures containing two (e.g. III-2 and II-11, III-5 and III-7, III-2 and II-5, or III- 74 7 and III-10) diferent guests. When guests of quite diferent sizes are used (II-2 and III-11, Figure 1b?d) alosteric control leads to a mixture of homomeric complexes (e.g. ns-CB[10]?III-2 2 and ns-CB[10]?III-11 2 ). In contrast, mixtures of similarly sized guests (e.g. II-2 and III-5 or II-7 and II-10) result in mixtures of the homomeric and heteromeric ternary complexes. These results show that binding of the first guest to ns-CB[10] preorganizes the second cavity for binding of a similarly sized guest. Computational results suggest that the alosteric control is transmited betwen binding sites in the putative 1:1 complex via the central H 2 C??CH 2 separation which varies systematicaly with the size of the guest (Figure 3 and Supporting Information). 3.6 Sumary. In summary, we have reported the isolation of a new member of the CB[n] family ? ns-CB[10] ? which is both structuraly and functionaly intriguing. For example, ns-CB[10] retains much of the binding profile of CB[n] but also: 1) binds larger guests that are rejected by the corresponding CB[n] due to the les rigid, structuraly more responsive ns-CB[10] cavity, 2) displays unusual top-center isomerism, and 3) displays positive homotropic alostery based on a guest size induced preorganization mechanism. As an intermediate in the formation of CB[n] with reactive NH groups, we believe that ns-CB[10] wil enable straightforward aces to CB[n] derivatives, surface imobilized CB[n], and CB[n] dimers. 38,80 The isolation of ns-CB[10] deepens our understanding of the mechanism of CB[n] formation and presages the formation of CB[n] hosts of even higher complexity. In combination, these results promise to broaden both the structural range of CB[n] that 75 can be acesed and the applications (e.g. biomimetic alosteric systems, supramolecular polymers, and covalent multivalent CB[n] scafolds) to which CB[n] can be applied. 3.7 Synthesis of Nor-Seco-Cucurbit[10]uril. 14 A mixture of glycoluril (1.42 g, 9.99 mol), paraformaldehyde (0.50 g, 16.69 mol), and conc. HCl (4 mL) was heated at 50 ?C for 3 days. The resulting precipitate was separated by centrifugation to yield a crude solid (300 mg). The crude solid was dried on high vacuum for 10 min., washed with HCl:H 2 O (1:1, v/v), washed with MeOH to remove HCl, and dried under high vacuum overnight to yield ns-CB[10] (238 mg, 0.145 mol, 15%) as a white solid. 1 H NMR (400 MHz, 20% DCl): 5.47 (m, 28H), 5.40 (s, 4H), 5.33 (d, J = 4.0, 4H), 4.60 (s, 4H), 4.20 (m, 16H). 76 IV. Chapter 4: Chiral Recognition Inside a Chiral Cucurbituril (Huang, W.-H.; Zavalij, P. Y.; Isacs, L. Angew. Chem. Int. Ed. 2007, 46, 7425- 7427.) 4.1 Introduction. The supramolecular chemistry of the cucurbit[n]uril family (16,49) (CB[n]) of molecular containers has undergone rapid development in recent years including the development of a homologous series of CB[n] hosts (n = 5, 6, 7, 8, 10), (2,12,15,17,18) diastereomeric inverted CB[n], (13) and most recently bis-nor-seco- CB[10]. (14) These new CB[n] compounds have cavity volumes (V = 82 ? 870 ? 3 ) that span and exced those available with ?-, ?-, and ?-cyclodextrin and are therefore capable of interacting with a wide range of chemicaly and biologicaly interesting guest species including gases, chromophores and fluorophores, anti-cancer agents, peptides, and neurotransmiters in water. (28,36,52,74,75,81) The extremely high afinity (K a up to 10 12 M -1 ) and very high selectivity that are characteristic of CB[n] hosts (8,18,82) has been exploited in the creation of molecular machines, supramolecular vesicles, artificial ion channels, self-asembled dendrimers, and complex self-sorting systems. (20,21,23,27,39,30) Chiral recognition ? a property readily achieved inside chiral cyclodextrins ? has been chalenging to reproduce using achiral CB[n]. (18,83) In this paper, we report the isolation of a chiral nor-seco-cucurbituril ? namely (?)-bis-ns- CB[6] ? and demonstrate its ability to undergo enantio- and diastereoselective recognition inside its cavity. 77 4.2 Step-Growth Polymerization. The conversion of glycoluril (1 equiv.) and formaldehyde (2 equiv.) into CB[n] (2,12,15,17,18) is a remarkably complex proces involving the formation of 4n bonds and n rings with complete stereochemical control. Based on the hypothesis that the mechanism of CB[n] formation (5,12,34,60,61) involved step-growth polymerization we decided to starve the NH O O N O O HH NH O O RR IV-3 =NH 3 Cl I4 R 23 l H 2 N NH 2 IV-2 IV-1 H 2 N NH 2 IV-5 (?)-bis-n-CB[6] C O N N O N N O O HN N N O N H N O O 2 2 N N IV-7 i H j k ClH 3 N IV-6 aH bc d,e f,g h Ph NH 2 H 3 C IV-8 R NH 2 PhPh NH 22 H IV-1 R' IV-9 R =CO 2 H, R' =NH 2 10 I- 2 , ' Scheme 1. Structure of compounds used in this study. reaction of one of its monomers ? formaldehyde ? to aces mechanistic intermediates en route to CB[n] that might display exciting recognition properties. From a reaction mixture consisting of glycoluril (1 equiv.) and paraformaldehyde (1.5 equiv.) in conc. HCl at 80 ?C we isolated methylene bridged glycoluril trimer IV-1 and (?)-bis-ns-CB[6] compound (Scheme 1). Fortunately, we were able to obtain x- ray crystal structures of IV-1 and (?)-bis-ns-CB[6] (Figure 1) which conclusively established their structures. (84) A number of features of the structure of (?)-bis-ns- CB[6] deserve comment: 1) the exclusive connection betwen homotopic NH-groups of the two constituent glycoluril trimer fragments, (85) 2) the idealized presence of 78 thre mutualy perpendicular C 2 -axes which leads to overal D 2 -symmetry, and 3) the presence of intramolecular hydrogen bonds betwen the NH-groups and the C=O group on an adjacent glycoluril ring. Figure 1. Cross-eyed stereoviews of the crystal structures of: a) IV-1, b) (?)-bis-ns- CB[6]?CF 3 CO 2 H, and c) (?)-bis-ns-CB[6]?IV-3 with 30% probability elipsoids. Solvating CF 3 CO 2 H and H 2 O molecules have been removed for clarity. 4.3 The Afinity of (?)-bis-ns-CB[6]. After the structure of (?)-bis-ns-CB[6] was elucidated, we decided to study its abilities as a host in aqueous solution. We first sought to experimentaly determine the efective cavity volume of (?)-bis-ns-CB[6] by 1 H NMR complexation experiments. Similar to CB[6] itself, we found that (?)- bis-ns-CB[6] forms inclusion complexes with IV-2 ? IV-5 but not with the larger adamantane amine IV-6 which binds with high afinity to CB[7] (Supporting 79 Information). Unlike CB[6], (?)-bis-ns-CB[6] does form an inclusion complex with methyl viologen (IV-7) which alows us to bracket the cavity volume as follows (CB[6] ? (?)-bis-ns-CB[6] < CB[7]). We next sought to measure the values of K a for (?)-bis-ns-CB[6] toward guests IV-2 ? IV-5 and IV-7. For this purpose, we performed a UV/is spectroscopic titration betwen (?)-bis-ns-CB[6] and IV-3 (K a = 2.5 ? 10 3 M -1 , Figure 2). Taking advantage of the slow chemical exchange displayed by many (?)-bis-ns-CB[6] complexes we performed 1 H NMR competition experiments [6a,b] (Supporting Information) to determine the afinity of (?)-bis-ns- CB[6] toward IV-2 (1.3 ? 10 5 M -1 ), IV-4 (3.6 ? 10 4 M -1 ), IV-5 (320 M -1 ), and IV-7 (9.9 ? 10 3 M -1 ). Figure 2. a) UV/is spectroscopic titration of IV-3 (60 mM) with (?)-bis-ns-CB[6] (50 mM NaO 2 CD 3 buffered D 2 O, pD 4.74), b) plot of absorbance versus [(?)-bis-ns- CB[6]] used to obtain K a . 80 4.4 Electrostatic Surface Potential Maps for Both CB[6] and (?)-bis-ns-CB[6]. To probe the origin of the diferences in binding strength of (?)-bis-ns-CB[6] toward guests IV-2 ? IV-7 relative to CB[6] (8,18) we computed electrostatic surface potential maps for both CB[6] and (?)-bis-ns-CB[6] (Figure 3). The four intramolecular NH??O H-bonds present in fre (?)-bis-ns-CB[6] substantialy narow its carbonyl- lined portals and impart distinct electrostatic surface potentials to the thre chemicaly non-equivalent C=O groups (L, -66; M, -77; H, -98 kcal mol -1 ). For comparison, the electrostatic surface potential on the C=O groups of CB[6] cluster at ? -87 kcal mol -1 . Consequently, the flexibility of (?)-bis-ns-CB[6] and its shape complementarity toward flater guests (e.g. IV-4 and IV-7) results in higher afinity for these guests than can be obtained with CB[6]. Conversely, the afinity of IV-2 toward (?)-bis-ns- CB[6] is 3400-fold lower than CB[6], presumably due to diferences in the strength of ion-dipole interactions, the degre of aqueous solvation of the C=O portals, or both. Figure 3. Electrostatic surface potential maps (red to blue: -90 to +31 kcal mol -1 ) for: a) (?)-bis-ns-CB[6], and b) CB[6]. L, M, H = low, medium, high electrostatic surface potentials. 81 4.5 Chiral Recognition of (?)-bis-ns-CB[6]. Our first hint that (?)-bis-ns-CB[6] would display useful levels of chiral recognition toward racemic guests came in our 1 H NMR studies of the binding of (?)-bis-ns-CB[6] with achiral guest IV-2. Intriguingly, the 1 H NMR spectrum of (?)-bis-ns-CB[6]?IV-2 (Figure 4a) displays a pair of resonances for the diastereotopic CH 2 -group (H i , H i? ) of guest IV-2 which reflects the asymmetric magnetic environment within the chiral host-guest complex. Acordingly, we decided to investigate the ability of (?)-bis-ns-CB[6] to undergo diastereoselective complexation with guests containing one or more stereogenic centers. Although several chiral aliphatic amines bind to (?)-bis-ns-CB[6], they do so with fast exchange on the chemical shift timescale which precludes observation and quantitation of the degre of diastereoselectivity within (?)-bis-ns-CB[6] (Supporting Information). We turned, therefore, to guests IV-8 ? IV-12 which contain aromatic rings that exhibit slower kinetics of exchange. Figure 4b shows the 1 H NMR spectrum recorded for a mixture of (?)-bis-ns-CB[6] and exces (+)-IV-8 which shows resonances for a 50:50 mixture of diastereomers (+)-bis-ns-CB[6]?(+)-IV-8 and (-)-bis-ns-CB[6]?(+)-IV-8. When (?)-bis-ns-CB[6] is combined with exces (?)- IV-8, however, a moderately diastereoselective proces leads to a 72:28 ratio of the diastereomers (Figure 4c). (86) Further studies revealed that (?)-bis-ns-CB[6] displays moderate to very good levels of diastereoselectivity toward amino acids IV-9 (77:23) and IV-10 (88:12) and amino alcohol IV-11 (76:24). Interestingly, (?)-bis-ns-CB[6] is even able to distinguish betwen the enantiotopic groups of meso-compound IV-12 (74:26). (87) 82 Figure 4. 1 H NMR spectra (400 MHz, D 2 O) for: a) (?)-bis-ns-CB[6]?IV-2, b) a mixture of (?)-bis-ns-CB[6] and exces (+)-IV-8, c) a mixture of (?)-bis-ns-CB[6] and exces (?)-IV-8. 4.6 Sumary. In summary, we have reported the isolation of a new member of the CB[n] family ? (?)-bis-ns-CB[6] ? which is formaly prepared by condensation of two equivalents of methylene bridged glycoluril trimer IV-1 with two equivalents of CH 2 O by the exclusive connection betwen homotopic glycoluril NH-groups. (88) The isolation of (?)-bis-ns-CB[6] ? in combination with bis-ns-CB[10] (14) ? deepens our understanding of the mechanism of CB[n] formation (5,12,34,60,61) by establishing the operation of a step-growth polymerization in this reaction. (?)-Bis-ns-CB[6] undergoes moderately diastereoselective complexation (up to 88:12) with chiral amines including amino acids and amino alcohols as wel as meso-diamine IV-12. Larger (?)-bis-ns-CB[n] (n = 7, 8, 10) and N-functionalized derivatives can be readily envisioned and are expected to display even higher enantioselectivity. (89) Aces to (?)-bis-ns-CB[6] and other chiral nor-seco-cucurbit[n]urils promises to dramaticaly 83 broaden the scope of the applications to which the achiral members of the CB[n] family have already ben applied (16,49,83) by enabling the creation of enantioselective molecular devices. 84 V. Chapter 5: Nor-Seco-Cucurbit[6]uril Functions as an Aldehyde Cucurbituril Synthon (Huang, W.-H.; Zavalij, P. Y.; Isacs, L. Angew. Chem. Int. Ed. 2008, submited.) 5.1 Introduction. The supramolecular chemistry of the cucurbit[n]uril family (16,49) (CB[n]) of molecular containers has undergone rapid development in recent years due to availabilty of a homologous series of molecular containers (n = 5, 6, 7, 8, 10) (2,12,15,17,18) with high binding afinity and high selectivity toward cationic species in aqueous solution. These unfunctionalized CB[n] may be employed in a variety of intriguing applications including molecular machines, sensors, drug delivery, and the controlled release of gases. (27,52,75,81,90) In order to tailor the recognition properties toward specific applications ? including supramolecular vesicles, artificial ion channels, sensors, and protein imobilization ? several groups have pursued the preparation of CB[n] derivatives by direct functionalization (39,91-93) and building block strategies. (34,36-38) In this chapter we continue to develop an alternate approach toward novel CB[n]-type compounds based on CB[n] compounds lacking one or more bridging CH 2 -groups known as nor-seco-cucurbiturils. (14,63) In this chapter we report the isolation of ns-CB[6] (V-1), its chemical reactivity toward aldehydes, and the unique recognition properties of the top-bottom desymmetrized ns-CB[6] and V-2 toward guests V-3 ? V-20. 85 NH 2 NH 2 NH 2 NH 2 N N V-6 V-5 V-8 V-3c V-7 O N N H O N N O O N N O ns-CB[6] (V-1) H 2 N NH 2 NH 2 V-4 22 N N O N O N O N O N N O NO H c H c V-2H a d e f g b Scheme 1. Structure of compounds used in this study. 5.2 Isolation and 1 H NMR spectrum of ns-CB[6]. From a reaction mixture comprising glycoluril (1 equiv.) and paraformaldehyde (1.67 equiv.) in conc. HCl at 50 ?C we have now isolated ns-CB[6] (V-1). Although the 1 H NMR spectrum of V-1 was uninformative (Figure 1a), its mas spectrum and the 1 H NMR spectrum of ns- CB[6]?V-5 (Figure 1b) alowed us to conclusively determine its molecular formula and overal C s -symmetry. To provide further proof of structure we alowed ns-CB[6] to react with o-phthalaldehyde under acidic conditions and obtained V-2 in 57% yield after recrystalization. (94) Although the 1 H NMR spectrum of V-2 and its V-2?V-5 complex (Figure 1c-1d) alowed us to elucidate its structure, final proof of structure was obtained in the form of an X-ray crystal structure (Figure 2). (95) Several aspects of the 1 H NMR spectra and X-ray crystal structure are noteworthy: 1) the resonance for H b is significantly upfield shifted due to its proximity to the face of the bridging aromatic ring, 2) the resonance for H c appears at 6.6-6.7 ppm due to the combined deshielding efect of the bridging N-CH-O-CH-N and o-xylylene groups, 3) the presence of the new N-CH-O-CH-N bridge results in distinct upper and lower C=O lined rims of diferent diameter, and 4) the expansion at the upper rim, imposed by 86 the bridging o-xylylene group results in a pinching at the lower rim which promotes its solid state structure via C=O??K + ??O=C interactions (Figure 2b). Figure 1. 1 H NMR spectra (400 MHz, D 2 O, RT) recorded for: a) ns-CB[6] (20% DCl / D 2 O), b) a mixture of ns-CB[6] and exces V-5, c) V-2, and d) a mixture of V-2 and exces V-5, (D 2 O). 5.3 Binding Properties of ns-CB[6]. Once the structures of ns-CB[6] and V-2 had been established we decided to investigate their recognition behavior toward symmetrical diamines of increasing size (V-3c ? V-8) to determine their efective cavity volumes. We found that both ns-CB[6] and V-2 form inclusion complexes with V-3c ? V-7 but not with V-8. These experiments alow us to bracket the cavity volumes of ns-CB[6] and V-2 betwen CB[6] (164 ? 3 ) and CB[7] (279 ? 3 ). Apparently, the expansion of the upper rim of V-2 does not increase the cavity volume of V-2 enough to alow complexation of the best guests for CB[7] (e.g. V-8). 87 Complexation of symmetric guests like V-3c ? V-7 within hosts like ns-CB[6] and V- 2 with diferent upper and lower rims leads to reduction in guest symmetry upon complexation that is readily observed by 1 H NMR (e.g. Figure 1d, H g , H g? ). Figure 2. a) Cross-eyed stereoview of V-2, and b) ilustration of the packing of V-2 in the crystal by C=O??K + ??O=C interactions. Color code: C, grey; H, white; N, blue; O, red; O??K + interactions, red-yelow striped. Solvating CF 3 CO 2 H and H 2 O molecules have been removed for clarity. 88 NH 3 NH 3 Top- ns-CB[6]? guest Botm- ns-C[6]? guest c) d) uper im lower im NH 2 CH 2 N 2 10 R =H Me 1213 O NH 2 NH 2 NH 2 9 R 14 = H 5 Me 18 R= N 2 CH 2 N 2 R 16 R= Me 9 NH 2 CH 2 N 2 17 R= Me 0 NH 2 -86 -86 -86 -86 -85 -85 -97 -91 -87 -71 -87 -94 -96 * ?-108 * R Figure 3. Electrostatic surface potential maps for: a) CB[6] and b) V-2. The red to blue color range spans -85 to +35 kcal mol -1 . c) Ilustration of the two diastereomeric complexes possible with ns-CB[6] and V-2, and d) structures of guests for ns-CB[6]. 5.4 Electrostatic Surface Potential (ESP) Map for CB[6] and ns-CB[6]. Compared to the electrostatic surface potential (ESP) map for CB[6] which has two equivalent ureidyl C=O portals the ESP maps for ns-CB[6] (Supporting Information) and V-2 (Figure 3b) are unsymmetrical. The upper rim of ns-CB[6] and the lower rim of V-2 are significantly more negative. Given the fact that ns-CB[6] and V-2 posses two diferent ureidyl C=O lined portals and that electrostatic potential at CB[n] portals is known to influence binding strength (49,72) we wondered whether the complexation of unsymmetrical amines and diamines (e.g. V-9 ? V-20) would favor one of the two conceivable diastereomers (Figure 3c; e.g. top-ns-CB[6]?guest versus 89 bottom-ns-CB[6]?guest). Initialy we prepared the complexes betwen ns-CB[6] and V-9 and observed a single diastereomer by 1 H NMR (Supporting Information). (96) Encouraged by this result, we decided to investigate the thre series of guests (V-10 ? V-13, V-14 ? V-17, V-18 ? V-20) where Me and NH 3 + groups are moved around the aromatic rings of aniline and benzylamine. For the ns-CB[6]?V-10 (67:33) and ns- CB[6]?V-11 (76:24) complexes we observed two sets of resonances that we asign to a mixture of top- and bottom-diastereomers. Apparently, electrostatic efects alone are insufficient to completely control top-bottom diastereoselectivity. We next investigated the meta-substituted complex ns-CB[6]?V-12, which exists as a single diastereomer. The meta-substitution in V-12 (and V-9) does not alow strong ion- dipole interactions without imposing steric interactions betwen the CH 3 -group and the wal of the ns-CB[6] cavity in one of the diastereomers. (97) Similar trends in top- bottom selectivity are sen for the benzylamine series (V-14 ? V-17). The complexes betwen ortho-substituted compounds V-13, V-17, and V-20 and ns-CB[6] al exhibit fast exchange kinetics which precludes a determination of the ratio of diastereomers in this series. Overal, we find that diastereoselective recognition inside ns-CB[6] can be achieved by combination of electrostatic and steric efects. 90 Figure 4. a) Ilustration of thre possible diastereomers for ns-CB[6]?V-3, and 1 H NMR spectra (400 MHz, D 2 O) for a mixture of V-2 and b) V-3g, c) V-3e, d) V-3c. (x = trace MeOH). 5.5 Controlling Diastereoselectivity for V-2. We discovered an intriguing method of controlling diastereoselectivity for host V-2 during our study of the complexes betwen V-2 and the series of 1,n-alkanediamonium ions (V-3a ? V-3i, n = 4, 5, 6, 7, 8, 9, 10, 11, 12). For example, the 1 H NMR spectra for the V-2?V-3c, V-2?V-3e, and V-2?V-3g complexes (Figure 4) display a single set of resonances that correspond to a single diastereomer. Intriguingly, the symmetry equivalent CH 2 -groups of the 1,n-alkanediamine become non-equivalent in the complex and display n-resonances in their 1 H NMR spectra which reflect the asymmetric magnetic environment in the host-guest complex. Of particular interest are the resonances for the CH 2 -groups adjacent to the + NH 3 groups (1 & 6, 1 & 8, and 1 & 10) that become widely separated 91 (0.4 ? 0.7 ppm) upon binding with one CH 2 downfield and one CH 2 upfield related to the fre diamonium ion. The wel-defined shielding region inside the cavity of CB[n]-type receptors and the deshielding region just outside the ureidyl C=O portals (97,98) alowed us to formulate the back-folding that characterizes the geometry of the longer V-2?alkanediamonium ion (V-3f ? V-3i) complexes (Figure 4a). (99,10) The patern of the magnitude of complexation induced changes in chemical shift for the internal CH 2 -groups are also consistent with the presence of this back-folded conformation. We conclude that the upper rim of V-2 ? in contrast to the lower rim ? is wide enough to simultaneously permit the extension of the alkyl chain and alow ion-dipole interaction of a back-folded NH 3 + group which drives the back-folding proces. We were fortunate to obtain single crystals of V-2?V-3f and solve its x-ray structure (Figure 5). [8] As predicted based on the 1 H NMR studies, V-2?V-3f exhibits a back-folded geometry in the crystal that benefits from the hydrophobic efect and ion-dipole interactions and H-bonds at both ureidyl C=O lined portals. Interestingly, the NH 3 + group at the lower rim forms ion-dipole interactions / H-bonds with the C=O groups below the bridging o-xylylene group which have the highest ESP (Figure 3b). Figure 5. Cross-eyed stereoview of the structure of V-2?V-3f in the crystal. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 92 5.6 Sumary. In summary, we have reported the isolation of ns-CB[6] which is formaly related to CB[6] by the removal of a single CH 2 -group. ns-CB[6] functions as an aldehyde reactive cucurbituril synthon which alowed us to prepare CB[6]- derivative V-2. Both ns-CB[6] and V-2 undergo top-bottom diastereoselective recognition proceses toward amonium and diamonium ions in water. Most intriguing is the ability of V-2 to induce back-folding in the longer diamonium ions (e.g. V-3f ? V-3i). Beyond these recognition properties, the availability of ns-CB[6] ? the first aldehyde reactive CB[n] synthon ? has potentialy widespread impact. For example, ns-CB[6] can undergo reaction with di-, tri-, and oligo-aldehydes to deliver discrete wel defined CB[n] dimers, trimers and oligomers as wel as CB[n] derivatized surfaces, polymers, and separation materials. As such, we expect ns- CB[6] and its CB[n] derivatives to impact a range of application areas [4] including bio-chips, afinity chromatography, and drug delivery. 93 Appendices Chapter 2: Cucurbit[n]uril Formation Proceds by Step-Growth Cyclo- oligomerization ? Supporting Information Wei-Hao Huang, Peter Y. Zavalij, and Lyle Isaacs* Department of Chemistry and Biochemistry, University of Maryland College Park, MD 20742 Table of Contents Pages ????????????????????????????????????????????????????????????????????? ?????? Table of contents ????????. S1 1 H NMR and 13 C NMR spectra of 2 and 4 ? 6 ????????. S2 ? S9 1 H NMR spectra of complexes of 5 with guests ????????. S10 ? S14 1 H NMR spectra of complexes of 6 with guests ????????. S15 ? S22 1 H NMR spectra of the distribution of CB[n] obtained by the reaction of 1 ? 6 with paraformaldehyde ????????. S23 ? S39 Details of the x-ray structure of 2 ????????. S40 ? S42 Details of the x-ray structure of 4 ????????. S43 ? S46 Details of the x-ray structure of 5 S47 ? S50 Details of the x-ray structure of 6 ????????. S51 ? S53 ????????????????????????????????????????????????????????????????????? 94 Figure S1. 1 H NMR spectrum recorded for dimer (400 MHz, 35% DCl, 25 ?C). 95 Figure S2. 13 C NMR spectrum recorded for dimer (125 MHz, 35% DCl, 25 ?C). 96 Figure S3. 1 H NMR spectrum recorded for tetramer (400 MHz, 35% DCl, 25 ?C). 97 Figure S4. 13 C NMR spectrum recorded for tetramer (125 MHz, 35% DCl, 25 ?C). 98 Figure S5. 1 H NMR spectrum recorded for pentamer (400 MHz, 35% DCl, 25 ?C). 99 Figure S6. 13 C NMR spectrum recorded for pentamer (125 MHz, 35% DCl, 25 ?C). 100 Figure S7. 1 H NMR spectrum recorded for hexamer (400 MHz, 35% DCl, 25 ?C). 101 Figure S8. 13 C NMR spectrum recorded for hexamer (125 MHz, 35% DCl, 25 ?C). 102 Figure S9. 1 H NMR spectra recorded for cyclohexanediamine and its complex with 5 (400 MHz, D 2 O, 25 ?C). 103 Figure S9. 1 H NMR spectra recorded for methyl viologen and its complex with 5 (400 MHz, D 2 O, 25 ?C). 104 Figure S9. 1 H NMR spectra recorded for 1,3-Dimethyl-5-aminoadamantane and its complex with 5 (400 MHz, D 2 O, 25 ?C). 105 Figure S9. 1 H NMR spectra recorded for 1-aminoadamantane and its complex with 5 (400 MHz, D 2 O, 25 ?C). 106 Figure S9. 1 H NMR spectra recorded for p-xylenediamineand its complex with 5 (400 MHz, D 2 O, 25 ?C). 107 Figure S9. 1 H NMR spectra recorded for hexanediamine and its complex with 6 (400 MHz, D 2 O, 25 ?C). 108 Figure S10. 1 H NMR spectra recorded for methyl viologen and its complex with 6 (400 MHz, D 2 O, 25 ?C). 109 Figure S11. 1 H NMR spectra recorded for phenylenediamine and its complex with 6 (400 MHz, D 2 O, 25 ?C). 110 Figure S12. 1 H NMR spectra recorded for the p-xylenediamine and its complex with 6 (400 MHz, D 2 O, 25 ?C). 111 Figure S13. 1 H NMR spectra for 1,3-dimethyl-5-aminoadamantane and its mixture with 6 (400 MHz, D 2 O, 25 ?C). 112 Figure S14. 1 H NMR spectra recorded for 1-aminoadamantane and its complex with 6 at 1:1 and 1:2 stoichiometries (400 MHz, D 2 O, 25 ?C). 113 Figure S15. 1 H NMR spectra recorded for the cyclohexanediamine and its complex with 6 (400 MHz, D 2 O, 25 ?C). 114 Figure S16. 1 H NMR spectra recorded for the bis(aminomethyl)ferocene and its complex with 6 (400 Hz, D 2 O, 25 ?C). 115 Figure S17. 1 H NMR spectra recorded for the reaction mixture composed of 1 and paraformaldehyde (2 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 116 Figure S18. 1 H NMR spectra recorded for the reaction mixture composed of 2 and paraformaldehyde (2 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 117 Figure S19. 1 H NMR spectra recorded for the reaction mixture composed of 3 and paraformaldehyde (2 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 118 Figure S20. 1 H NMR spectra recorded for the reaction mixture composed of 4 and paraformaldehyde (2 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 119 Figure S21. 1 H NMR spectra recorded for the reaction mixture composed of 5 and paraformaldehyde (2 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 120 Figure S22. 1 H NMR spectra recorded for the reaction mixture composed of 6 and paraformaldehyde (2 eq. ) upon conversion to CB[6] (400 MHz, 20% DCl / D 2 O, RT). 121 Figure S23. 1 H NMR spectra recorded for the reaction mixture composed of 1, 2, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 122 Figure S24. 1 H NMR spectra recorded for the reaction mixture composed of 1, 3, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], CB[8], znd iCB[6] (400 MHz, 20% DCl / D 2 O, RT). 123 Figure S25. 1 H NMR spectra recorded for the reaction mixture composed of 1, 4, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 124 Figure S26. 1 H NMR spectra recorded for the reaction mixture composed of 1, 5, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 125 Figure S27. 1 H NMR spectra recorded for the reaction mixture composed of 1, 6, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 126 Figure S28. 1 H NMR spectra recorded for the reaction mixture composed of 2, 3, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 127 Figure S29. 1 H NMR spectra recorded for the reaction mixture composed of 2, 4, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 128 Figure S30. 1 H NMR spectra recorded for the reaction mixture composed of 2, 5, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 129 Figure S31. 1 H NMR spectra recorded for the reaction mixture composed of 3, 4, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 130 Figure S32. 1 H NMR spectra recorded for the reaction mixture composed of 3, 5, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 131 Figure S33. 1 H NMR spectra recorded for the reaction mixture composed of 4, 5, and paraformaldehyde (4 eq. ) upon conversion to CB[5], CB[6], CB[7], and CB[8] (400 MHz, 20% DCl / D 2 O, RT). 132 Crystal Structure Information for UM # 1306 Isues by: Peter Y. Zavalij Crystal No. & ID : 1306: Isaacs/Huang - dimer CB2 Compound name : CB2?5CF 3 COH Chemical formula : C 10 H 12 N 8 O 4 ?5(CF 3 COH) Final R 1 [I>2?(I)] : 3.84 % ??????????????? ??????????? ???? Figure S34. A view of CB2?5CF 3 COH showing the numbering scheme employed. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 25% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 133 A colorles prism of C 20 H 17 F 15 N 8 O 14 , aproximate dimensions 0.24 ? 0.35 ? 0.375 m 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 23(2) K on a thre- circle difractometer system equiped with Bruker Smart100 CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?) operated at 50 kV and 40 mA. The detector was placed at a distance of 4.958 cm from the crystal. A total of 1487 frames were colected with a scan width of 0.3? in ? and an exposure time of 13 sec/frame using SMART (Bruker, 199). The total data colection time was 8.32 hours. The frames were integrated with SAINT software package using a narow-frame integration algorithm. The integration of the data using a Orthorhombic unit cel yielded a total of 2474 reflections to a maximum ? angle of 27.50?, of which 7659 were independent (completenes = 9.4%, R int = 1.75%, R sig = 1.6%) and 678 were greater than 2?(I). The final cel dimensions of a = 8.8769(3) ?, b = 12.8191(4) ?, c = 29.5359(9) ?, ?= 90?, ?= 90?, ?= 90?, V = 361.0(19) ? 3 , are based upon the refinement of the XYZ-centroids of 5901 reflections with 2.1 < ? < 28.1? using SAINT. Analysis of the data showed 0.0 % decay during data colection. Data were corected for absorption efects with the Semi-empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.849 and 0.95. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group P2 1 2 1 2 1 with Z = 4 for the formula unit C 20 H 17 F 15 N 8 O 14 . The final anisotropic ful-matrix least-squares refinement on F 2 with 851 variables converged at R 1 = 3.84 % for the observed data and wR 2 = 8.16 % for al data. The godnes-of-fit was 1.00. The largest peak on the final diference map was 0.235?e/? 3 and the largest hole was -0.182?e/? 3 . On the basis of the final model, the calculated density was 1.736 g/cm 3 and F(00), 1760?e. Comments: - Data set quality: very god - Twining: none - Disorder: moderate to heavy disorder of solvent CF3COH (Table 5): #1 - CF3 in 2 orientations #2,3 - CF3 in 3 orientations #4,5 - whole molecule in 2 orientations; in adition one orientation #5 has COH in 3 orientations - H-atoms refinement: constraned, Uiso refined; extensive H-bonding; al posible H-bonds are realized and make sense - Residual density: near disordered groups - Structure quality: very god Check CIF: Platon (al alerts are due to the disorder and are explainable) Publishable! 134 135 Table 1. Crystal data and structure refinement for CB2?5CF 3 COH. ??????????????????????? ?????????????????? X-ray labok No. 1306 Crystal ID Isacs/Huang - dimer CB2 Empirical formula C 20 H 17 F 15 N 8 O 14 Forula weight 878.42 Temperature 23(2) K Wavelength 0.71073 ? Crystal size 0.375 ? 0.35 ? 0.24 m 3 Crystal habit colorles prism Crystal system Orthorhombic Space group P2 1 2 1 2 1 Unit cel dimensions a = 8.8769(3) ? ? = 90? b = 12.8191(4) ? = 90? c = 29.5359(9) ? ? = 90? Volume 361.0(19) ? 3 Z 4 Density, ? calc 1.736 g/cm 3 Absorption coeficient, ? 0.193 m -1 F(00) 1760?e Difractometer Bruker Smart100 CD area detector Radiation source fine-focus sealed tube, MoK? Generator power 50 kV, 40 ma Detector distance 4.958 cm Detector resolution 8.3 pixels/m Total frames 1487 Frame size 512 pixels Frae width 0.3 ? Exposure per frame 13 sec Total measureent time 8.32 hours Data colection method ? scans ? range for data colection 2.68 to 27.50? Index ranges -10 ? h ? 1, -16 ? k ? 15, -38 ? l ? 37 Reflections colected 24774 Independent reflections 7659 Observed reflection, I>2?(I) 6778 Coverage of independent reflections 9.4 % Variation in check reflections 0.0 Absorption corection Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.95 and 0.849 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refineent program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 7659 / 1012 / 851 Godnes-of-fit on F 2 1.00 ?/? max 0.01 Final R indices: R 1 , I>2?(I) 0.0384 wR 2 , al data 0.0816 R int 0.0175 R sig 0.016 Weighting scheme w = 1/[? 2 (F o 2 ) + (0.02P) 2 + 1.53P], P = [max(F o 2 ,0) + 2F o 2 ]/3 Absolute structure parameter 0.0(7) Extinction coeficient 0.035(3) Largest dif. peak and hole 0.235 and -0.182?e/? 3 ??????????????????????? ?????????????????? R 1 = ?||F o |-|F c ||/?|F o |, wR2 = [?w(F o 2 -F c 2 ) 2 /?w(F o 2 ) 2 ] 1/2 136 Crystal Structure Information for UM # 1407 Isued by: Peter Y. Zavalij Crystal No. & ID : 1407: Isaacs tetramer CB4 none-cyclic Compound name : Na*2CB4*H2O*7TFA Chemical formula : [(C 22 H 24 N 16 O 8 ) 2 ?(H 2 O)?Na] + ?6(CF 3 COH)(CF 3 CO) - Final R 1 [I>2?(I)] : 7.79 % ?????????????? ???????????? Figure S35. A view of UM#1407 showing the numbering scheme employed. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 30% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 137 A colorles prism of C 58 H 56 F 21 N 32 NaO 31 , aproximate dimensions 0.09 ? 0.1 ? 0.26 m 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 20(2) K on a thre-circle difractometer system equiped with Bruker Smart100 CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?) operated at 50 kV and 40 mA. The detector was placed at a distance of 4.939 cm from the crystal. A total of 1824 frames were colected with a scan width of 0.5? in ? and an exposure time of 38 sec/frame using SMART (Bruker, 199). The total data colection time was 2.8 hours. The frames were integrated with SAINT software package using a narow-frame integration algorithm. The integration of the data using a Tetragonal unit cel yielded a total of 25719 reflections to a maximum ? angle of 20.0?, of which 2590 were independent (completenes = 9.6%, R int = 6.86%, R sig = 3.89%) and 204 were greater than 2?(I). The final cel dimensions of a = 18.6306(8) ?, b = 18.6306(8) ?, c = 15.2173(12) ?, ?= 90?, ?= 90?, ?= 90?, V = 5281.9(5) ? 3 , are based upon the refinement of the XYZ- centroids of 4859 reflections with 2.4 < ? < 21.7? using SAINT. Analysis of the data showed ? % decay during data colection. Data were corected for absorption efects with the Semi-empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.937 and 0.98. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group P4 2 /m with Z = 2 for the formula unit C 58 H 56 F 21 N 32 NaO 31 . The final anisotropic ful-matrix least-squares refinement on F 2 with 39 variables converged at R 1 = 7.79 % for the observed data and wR 2 = 18.67 % for al data. The godnes-of-fit was 1.01. The largest peak on the final diference map was 0.783?e/? 3 and the largest hole was - 0.297?e/? 3 . On the basis of the final model, the calculated density was 1.33 g/cm 3 and F(00), 2152?e. 138 Comments: - Data set quality: god < 40? 2? - Twining: none - Disorder: substantial solvent removed using SQUEZE (except 1 TFA and 1 water) - H-atoms refinement: constrained - Residual density: near disordered groups - Structure quality: god Publishable! 139 Table 1. Crystal data and structure refinement for UM#1407. ??????????????????????? ?????????????????? X-ray lab bok No. 1407 Crystal ID Isacs tetramer CB4 none-cyclic Empirical formula C 58 H 56 F 21 N 32 NaO 31 Formula weight 219.34 Temperature 20(2) K Wavelength 0.71073 ? Crystal size 0.26 ? 0.1 ? 0.09 m 3 Crystal habit colorles prism Crystal system Tetragonal Space group P4 2 /m Unit cel dimensions a = 18.6306(8) ? ? = 90? b = 18.6306(8) ? ? = 90? c = 15.2173(12) ? ? = 90? Volume 5281.9(5) ? 3 Z 2 Density, ? calc 1.33 g/cm 3 Absorption coeficient, ? 0.134 m -1 F(000) 2152?e Difractometer Bruker Smart100 CD area detector Radiation source fine-focus sealed tube, MoK? Generator power 50 kV, 40 mA Detector distance 4.939 cm Detector resolution 8.3 pixels/m Total frames 1824 Frame size 512 pixels Frame width 0.5 ? Exposure per frame 38 sec Total measurement time 2.8 hours Data colection method ? and ? scans ? range for data colection 1.09 to 20.0? Index ranges -17 ? h ? 17, -17 ? k ? 17, -14 ? l ? 14 Reflections colected 25719 Independent reflections 2590 Observed reflection, I>2?(I) 2044 Coverage of independent reflections 9.6 % Variation in check reflections ? % Absorption corection Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.98 and 0.937 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refinement program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 2590 / 129 / 39 Godnes-of-fit on F 2 1.020 ?/? max 0.00 Final R indices: R 1 , I>2?(I) 0.079 wR 2 , al data 0.1867 R int 0.0686 R sig 0.0389 Weighting scheme w = 1/[? 2 (F o 2 ) + (0.02P) 2 + 29.5P], P = [max(F o 2 ,0) + 2F o 2 ]/3 Largest dif. peak and hole 0.783 and -0.297?e/? 3 ??????????????????????? ?????????????????? R 1 = ?||F o |-|F c ||/?|F o |, wR2 = [?w(F o 2 -F c 2 ) 2 /?w(F o 2 ) 2 ] 1/2 140 Crystal Structure Information for UM # 1426b Isued by: Peter Y. Zavalij Crystal No. & ID : 1426b: Isaacs/Huang Ser from T/H in T xtal-2 - b Compound name : [CB5<0.85TFA]*4.6TFA*4H 2 O Chemical formula : C 28 H 30 N 20 O 10 ?5.45CF 3 COH?4H 2 O Final R 1 [I>2?(I)] : 8.54 % ??????????????? ??????????? ???? Figure S36. A view of UM#1426 showing the numbering scheme employed. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 30% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 141 Figure 1. Packing of UM#1426 along b-axis revealing chains of H-bonded pentamer. 142 A colorles prism of C 28 H 30 N 20 O 10 ?5.45CF 3 COH?4H 2 O, aproximate dimensions 0.14 ? 0.18 ? 0.34 m 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 20(2) K on a thre-circle difractometer system equiped with Bruker Smart100 CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?) operated at 50 kV and 30 mA. The detector was placed at a distance of 4.939 cm from the crystal. A total of 1818 frames were colected with a scan width of 0.3? in ? and an exposure time of 38 sec/frame using SMART (Bruker, 199). The total data colection time was 2.80 hours. The frames were integrated with SAINT software package using a narow-frame integration algorithm. The integration of the data using a Orthorhombic unit cel yielded a total of 28204 reflections to a maximum ? angle of 2.50?, of which 3824 were independent (completenes = 9.4%, R int = 10.58%, R sig = 7.41%) and 2830 were greater than 2?(I). The final cel dimensions of a = 1.62(4) ?, b = 3.042(1) ?, c = 14.952(5) ?, ?= 90?, ?= 90?, ?= 90?, V = 5762(3) ? 3 , are based upon the refinement of the XYZ-centroids of 9031 reflections with 2.2 < ? < 2.3? using SAINT. Analysis of the data showed 0.0 % decay during data colection. Data were corected for absorption efects with the Semi- empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.917 and 0.976. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group Pnma with Z = 4 for the formula unit C 28 H 30 N 20 O 10 ?5.45CF 3 COH?4H 2 O. The final anisotropic ful-matrix least-squares refinement on F 2 with 326 variables converged at R 1 = 8.54 % for the observed data and wR 2 = 17.91 % for al data. The godnes-of-fit was 1.00. The largest peak on the final diference map was 0.325?e/? 3 and the largest hole was -0.294?e/? 3 . On the basis of the final model, the calculated density was 1.723 g/cm 3 and F(00), 3031?e. Comments: - Data set quality: average - Twining: none - Disorder: substantialy disordered solvent ? removed using squeze except guest TFA - H-atoms refinement: constrained - Residual density: near disordered groups - Structure quality: god to average Publishable! 143 144 Table 1. Crystal data and structure refinement for UM#1426. ??????????????????????? ?????????????????? X-ray lab bok No. 1426b Crystal ID Isacs/Huang Ser from T/H in T xtal-2 - b Empirical formula C 28 H 30 N 20 O 10 ?5.45CF 3 COH?4H 2 O Formula weight 1494.74 Temperature 20(2) K Wavelength 0.71073 ? Crystal size 0.34 ? 0.18 ? 0.14 m 3 Crystal habit colorles prism Crystal system Orthorhombic Space group Pnma Unit cel dimensions a = 1.62(4) ? ? = 90? b = 3.042(1) ? ? = 90? c = 14.952(5) ? ? = 90? Volume 5762(3) ? 3 Z 4 Density, ? calc 1.723 g/cm 3 Absorption coeficient, ? 0.175 m -1 F(00) 3031?e Difractometer Bruker Smart100 CD area detector Radiation source fine-focus sealed tube, MoK? Generator power 50 kV, 30 mA Detector distance 4.939 cm Detector resolution 8.3 pixels/m Total frames 1818 Frame size 512 pixels Frame width 0.3 ? Exposure per frame 38 sec Total measurement time 2.80 hours Data colection method ? scans ? range for data colection 2.72 to 2.50? Index ranges -12 ? h ? 12, -35 ? k ? 35, -15 ? l ? 15 Reflections colected 28204 Independent reflections 3824 Observed reflection, I>2?(I) 2830 Coverage of independent reflections 9.4 % Variation in check reflections 0.0 Absorption corection Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.976 and 0.917 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refinement program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 3824 / 84 / 326 Godnes-of-fit on F 2 1.03 ?/? max 0.00 Final R indices: R 1 , I>2?(I) 0.0854 wR 2 , al data 0.1791 R int 0.1058 R sig 0.0741 Weighting scheme w = 1/[? 2 (F o 2 ) + (0.02P) 2 + 18.7P], P = [max(F o 2 ,0) + 2F o 2 ]/3 Largest dif. peak and hole 0.325 and -0.294?e/? 3 ??????????????????????? ?????????????????? R 1 = ?||F o |-|F c ||/?|F o |, wR2 = [?w(F o 2 -F c 2 ) 2 /?w(F o 2 ) 2 ] 1/2 145 Crystal Structure Information for UM # 1513 Isued by: Peter Y. Zavalij Crystal No. & ID : 1513: Isaacs/WHuang CB 6 not-cycle in H 2 O, MeOH Compound name : CB 6 hydrate Chemical formula : (C 34 H 36 N 24 O 12 )?11H 2 O?2HCl Final R 1 [I>2?(I)] : 5.65 % ????????????????????? ??????????????????? Figure S37. A view of UM#1513 showing the numbering scheme employed. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 30% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 146 A colorles bal of (C 34 H 36 N 24 O 12 )?11H 2 O?2HCl, aproximate dimensions 0.08 ? 0.25 ? 0.25 mm 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 20(2) K on a thre-circle difractometer system equiped with Bruker Smart100 CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?) operated at 50 kV and 30 mA. The detector was placed at a distance of 4.950 cm from the crystal. A total of 1381 frames were colected with a scan width of 0.3? in ? and an exposure time of 38 sec/frame using SMART (Bruker, 199). The total data colection time was 17.3 hours. The frames were integrated with SAINT software package using a narow-frame integration algorithm. The integration of the data using a Orthorhombic unit cel yielded a total of 5174 reflections to a maximum ? angle of 2.50?, of which 6402 were independent (completenes = 9.5%, R int = 8.2%, R sig = 6.71%) and 3874 were greater than 2?(I). The final cel dimensions of a = 24.19(2) ?, b = 12.8676(13) ?, c = 31.795(3) ?, ?= 90?, ?= 90?, ?= 90?, V = 9867.6(17) ? 3 , are based upon the refinement of the XYZ-centroids of 6864 reflections with 2.1 < ? < 20.3? using SAINT. Analysis of the data showed 0 % decay during data colection. Data were corected for absorption efects with the Semi-empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.932 and 0.981. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group Pbca with Z = 8 for the formula unit (C 34 H 36 N 24 O 12 )?11H 2 O?2HCl. The final anisotropic ful-matrix least-squares refinement on F 2 with 631 variables converged at R 1 = 5.65 % for the observed data and wR 2 = 12.50 % for al data. The godnes-of-fit was 1.00. The largest peak on the final diference map was 0.297?e/? 3 and the largest hole was -0.269?e/? 3 . On the basis of the final model, the calculated density was 1.675 g/cm 3 and F(00), 520?e. Overall structure quality considerations: 1. Strong data set, no disorder, R 1 4% maximum. Publishable quality. 2. God data set, perhaps some minor disorder, R 1 6% maximum. Publishable quality. 3. Average data set and/or easily modeled disorder or twining. Publishable with care. 4. Weak data and/or major disorder or twining that is not easily modeled. Publishable in some cases. 5. Very weak data and/or unexplained features of data or model. Not of publishable quality. A structure with a quality factor of 4 or 5 should not be used for a regulatory document without prior consultation. Comments: - Data quality: god (barely difract to 45? 2?) - Twining: none - Disorder: solvent ? squezed out using Platon - H-atoms: constrained geometry as riding on atached atom (A) Uiso(H)=1.5*U iso (A) for CH 3 and 1.2*U iso (A) for other groups - Residual density: near heavy atoms & in the midle of the bonds - Structure quality: god to average Publishable Yes 147 148 Table 1. Crystal data and structure refinement for UM#1513. ??????????????????????? ?????????????????? X-ray lab bok No. 1513 Crystal ID Isacs/WHuang CB6 not-cycle in H2O, MeOH Empirical formula (C 34 H 36 N 24 O 12 )?11H 2 O?2HCl Formula weight 1243.96 Temperature 20(2) K Wavelength 0.71073 ? Crystal size 0.25 ? 0.25 ? 0.08 m 3 Crystal habit colorles bal Crystal system Orthorhombic Space group Pbca Unit cel dimensions a = 24.19(2) ? ? = 90? b = 12.8676(13) ? ? = 90? c = 31.795(3) ? ? = 90? Volume 9867.6(17) ? 3 Z 8 Density, ? calc 1.675 g/cm 3 Absorption coeficient, ? 0.243 m -1 F(00) 5200?e Difractometer Bruker Smart100 CD area detector Radiation source fine-focus sealed tube, MoK? Generator power 50 kV, 30 mA Detector distance 4.950 cm Detector resolution 8.3 pixels/m Total frames 1381 Frame size 512 pixels Frame width 0.3 ? Exposure per frame 38 sec Total measurement time 17.3 hours Data colection method ? and ? scans ? range for data colection 2.56 to 2.50? Index ranges -24 ? h ? 25, -13 ? k ? 13, -34 ? l ? 34 Reflections colected 51174 Independent reflections 6402 Observed reflection, I>2?(I) 3874 Coverage of independent reflections 9.5 % Variation in check reflections 0 % Absorption corection Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.981 and 0.932 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refinement program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 6402 / 3 / 631 Godnes-of-fit on F 2 1.00 ?/? max 0.00 Final R indices: R 1 , I>2?(I) 0.0565 wR 2 , al data 0.1250 R int 0.082 R sig 0.0671 Weighting scheme w = 1/[? 2 (F o 2 ) + (0.02P) 2 + 13.15P], P = [max(F o 2 ,0) + 2F o 2 ]/3 Largest dif. peak and hole 0.297 and -0.269?e/? 3 ??????????????????????? ?????????????????? R 1 = ?||F o |-|F c ||/?|F o |, wR2 = [?w(F o 2 -F c 2 ) 2 /?w(F o 2 ) 2 ] 1/2 149 Chapter5: Nor-Seco-Cucurbit[6]uril Functions as an Aldehyde Reactive Cucurbituril Synthon ? Suporting Information Angew. Chem. by Wei-Hao Huang, Peter Y. Zavalij, and Lyle Isaacs* Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742 Table of Contents Pages ????????????????????????????????????????????????????????????????????? Table of contents ????????. S1 Experimental section ????????. S2 ? S3 1 H NMR and 13 C NMR spectra of ns-CB[6] in 35% DCl ???????S4 ? S5 1 H NMR and 13 C NMR spectra of 2 in D 2 O ????????. S6 ? S7 Selected spectra for ns-CB[6]?guest binding ????????. S8 ? S24 Selected spectra for 2?guest binding ????????. S25 ? S42 1 H- 1 H NMR COSY spectra of 2?3g, 2?3e, and 2?3c ????????. S43 ? S45 Details of the x-ray structure of 2 ????????. S46 ? S48 Details of the x-ray structure of 2?3f ????????. S49 ? S51 MF calculated structures for 2?3a ? 2?3i ????????. S52 ? S54 MF minima for top- and bottom-ns-CB[6]?9 ????????. S55 Electrostatic surface potential maps for CB[6], ns-CB[6], and 2 ??.??S56 ? S58 ????????????????????????????????????????????????????????????????????? 150 Experimental Section. General. The guests used in this study were purchased from commercial suppliers and were used as their HCl salts. Melting points were measured on a Meltemp apparatus in open capilary tubes and are uncorrected. IR spectra were recorded on Thermo Nicolet IR200 spectrometer and are reported in cm -1 . NMR spectra were measured on spectrometers operating at 400, 500, or 600 MHz for 1 H and 100 or 125 MHz for 13 C. Mas spectrometry was performed using a VG 7070E magnetic sector instrument by fast atom bombardment (FAB) using the indicated matrix or on a JEOL AcuTOF electrospray instrument. Computational results were obtained using Spartan 02 running on a Macintosh personal computer. Preparation, Purification and Characterization of ns-CB[6]. A mixture of glycoluril (1.42 g, 9.99 mol), paraformaldehyde (0.50 g, 16.69 mol), and conc. HCl (4 mL) was heated at 50 ?C for 3 days. The resulting solution was separated by centrifugation and precipated by pouring into MeOH to yield a crude solid (1300 mg). Purification of the mixture was achieved by chromatography on a Dowex 50WX2 column equilibrated with 1:1 formic acid:water. The sample was loaded onto the column as a solution in the eluent (88% HCOH: (0.2M HCl/H 2 O), 1:1, v:v). The fractions of the column were collected and the solvent was removed by rotary evaporation. The resulting solid was washed with MeOH to remove soluble impurities. The CB[6]:ns-CB[6] ratio in this crude solid can vary depending on column eficiency. It is posible to decrease the amount of CB[6] by recrystalization 151 from TFA. Final purification of samples containing mainly ns-CB[6] can be achieved by suspending in water containing enough hexanediamonium ion to complex the CB[6] impurity. The heterogenous mixture was then centrifuged and the solid obtained by decanting the supernatant. The solid was washed with several portions of water and dried at high vacuum overnight (47 mg, 3%). M.p. > 300 ?C. IR (KBr, cm - 1 ): 3271w, 1726s, 1466s, 1414s, 1375s, 1326s, 1149s, 964s, 667s, 617s, 796s. 1 H NMR (400 MHz, 35% DCl): 5.69 (d, J = 8.8, 2H), 5.64 (d, J = 8.8, 2H), 5.55-5.35 (m, 18H), 5.17 (d, J = 16.0, 1H), 4.44 (d, J = 16.0, 1H), 4.40-4.20 (m, 10H). 13 C NMR (100 MHz, 35% DCl, ext. dioxane reference): 159.3, 159.0, 155.9, 155.8, 155.6, 73.2, 69.9, 69.8, 69.7, 69.6, 67.6, 53.6, 51.3, 51.2, 50.9, 50.7. (only 16 of the 19 expected resonances were observed). MS (ES): m/z 562 (100, [M + p- xylenediamine + 2H] 2+ , m/z spacing = 0.5 confirmed for molecular ion). Compound 2. Compound 1 (100 mg, 0.10 mol) was disolved in HCl (0.2 mL) and o-phthaldialdehyde (13.4 mg, 0.10 mol) was added to the mixture. The reaction mixture was stired at room temperature for two days. The reaction mixture was poured into MeOH (5 mL), the solid isolated by filtration, and dried overnight at high vacuum. The crude solid (80 mg), was recrystalized from TFA (2.6 mL) to yield 2 (64 mg, 57%) as a white solid. IR (neat, cm -1 ): 3474w, 3014s, 2926s, 1726s, 1463s, 1416s, 1376s, 1326s, 1293s, 1225s, 1175s, 962s, 795s, 755s, 671s, 628s. 1 H NMR (400 MHz, D 2 O): 7.35 (br, 2H), 7.29 (br, 2H), 6.70 (s, 2H), 5.65-5.35 (m, 22H), 4.25- 4.00 (d, 10H), 2.34 (d, J = 12.0, 1H). 13 C NMR (125 MHz, D 2 O): 163.4, 160.6, 157.8, 157.0, 135.3, 131.0, 125.4, 118.2, 115.9, 85.0, 71.5, 71.4, 71.2, 71.0, 69.7, 53.1, 52.7, 152 52.2, 51.8. (not al of the 23 expected resonances were observed). ES-MS: m/z 1101 (100, [M + H] + : ([M + H] + , C 43 H 40 N 24 , calcd 1100.32). X-ray crystal structure (from TFA). 153 Figure S1. 1 H NMR spectrum recorded for ns-CB[6] (400 MHz, 35% DCl, 25 ?C). 154 Figure S2. 13 C NMR spectrum recorded for ns-CB[6] (125 MHz, 35% DCl, 25 ?C). 155 Figure S3. 1 H NMR spectrum recorded for 2 (400 MHz, D 2 O, 25 ?C). 156 Figure S4. 13 C NMR spectrum recorded for 2 (125 MHz, D 2 O, 25 ?C). 157 Figure S5. 1 H NMR spectra recorded for cyclohexanediamine and its complex with ns-CB[6] (400 Hz, D 2 O, 25 ?C). 158 Figure S6. 1 H NMR spectra recorded for hexanediamine and its complex with ns- CB[6] (400 MHz, D 2 O, RT, x = trace acetone impurity). 159 Figure S7. 1 H NMR spectra recorded for phenylenediamine and its complex with ns- CB[6] (400 MHz, D 2 O, RT, x = trace acetone impurity). 160 Figure S8. 1 H NMR spectra recorded for methyl viologen and its complex with ns- CB[6] (400 MHz, D 2 O, RT). 161 Figure S9. 1 H NMR spectra recorded for 1-aminoadamantane and its non-binding mixture with ns-CB[6] (400 MHz, D 2 O, RT). 162 Figure S10. 1 H NMR spectra recorded for aminocoumarin and its complex with ns- CB[6] (400 MHz, D 2 O, RT). 163 Figure S11. 1 H NMR spectra recorded for aniline and its complex with ns-CB[6] (400 MHz, D 2 O, RT). The ratio of the two diastereomers is 67:33. 164 Figure S12. 1 H NMR spectra for o-toluidine and its mixture with ns-CB[6] (400 MHz, D 2 O, RT). 165 Figure S13. 1 H NMR spectra recorded for m-toluidine and its complex with ns- CB[6] (400 MHz, D 2 O, RT). 166 Figure S14. 1 H NMR spectra recorded for p-toluidine and its complex with ns-CB[6] (400 MHz, D 2 O, RT). The ratio of the two diastereomers is 76:24. 167 Figure S15. 1 H NMR spectra recorded for benzylamine and its complex with ns- CB[6] (400 MHz, D 2 O, RT). 168 Figure S16. 1 H NMR spectrum recorded for 2-methylbenzylamine and when mixed with ns-CB[6] (400 Hz, D 2 O, RT). 169 Figure S17. 1 H NMR spectra recorded for 3-methylbenzylamine and its complex with ns-CB[6] (400 Hz, D 2 O, RT). 170 Figure S18. 1 H NMR spectra recorded for 4-methylbenzylamine and its complex with ns-CB[6] (400 Hz, D 2 O, RT). The ratio of the two diastereomers is 71:29. 171 Figure S19. 1 H NMR spectrum recorded for 2-aminobenzylamine and its complex with ns-CB[6] (400 Hz, D 2 O, RT). 172 Figure S20. 1 H NMR spectrum recorded for 3-aminobenzylamine and its complex with ns-CB[6] (400 Hz, D 2 O, RT). The ratio of the two diastereomers is 58:42. 173 Figure S21. 1 H NMR spectra recorded for 4-aminobenzylamine and its complex with ns-CB[6] (400 Hz, D 2 O, RT). The ratio of the two diastereomers is 72:28. 174 Figure S22. 1 H NMR spectra recorded for p-xylenediamine and its complex with 2 (400 MHz, D 2 O, RT). 175 Figure S23. 1 H NMR spectra recorded for cyclohexanediamine and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 176 Figure S24. 1 H NMR spectra recorded for methyl viologen and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 177 Figure S25. 1 H NMR spectra recorded for phenylenediamine and its complex with 2 (400 MHz, D 2 O, RT). 178 Figure S26. 1 H NMR spectra recorded for adamantaneamine and as a mixture with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 179 Figure S27. 1 H NMR spectra recorded for 1,4-diaminobutane and its complex with 2 (400 MHz, D 2 O, RT). 180 Figure S28. 1 H NMR spectra recorded for 1,5-diaminopentane and its complex with 2 (400 MHz, D 2 O, RT). 181 Figure S29. 1 H NMR spectra recorded for hexanediamine and its complex with 2 (400 MHz, D 2 O, RT). 182 Figure S30. 1 H NMR spectra recorded for 1,7-diaminoheptane and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 183 Figure S31. 1 H NMR spectra recorded for 1,8-diaminooctane and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 184 Figure S32. 1 H NMR spectra recorded for 1,9-diaminononane and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 185 Figure S33. 1 H NMR spectra recorded 1,10-diaminodecane and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 186 Figure S34. 1 H NMR spectra recorded 1,11-diaminoundecane and its complex with 2 (400 MHz, D 2 O, RT). 187 Figure S35. 1 H NMR spectra recorded for 1,12-diaminododecane and its complex with 2 (400 MHz, D 2 O, RT). 188 Figure S36. 1 H NMR spectra recorded for bis(hexamethylene)triamine and its complex with 2 (400 MHz, D 2 O, RT). 189 Figure S37. 1 H NMR spectra recorded for 1,10-dibenzyl-1,10-diaza-18-crown-6 and its complex with 2 (400 MHz, D 2 O, RT, x = trace MeOH impurity). 190 Figure S38. 1 H NMR spectra recorded for p-toluidine and its complex 2 (400 MHz, D 2 O, RT). 191 Figure S39. 1 H NMR spectra recorded for coumarin and its complex 2 (400 MHz, D 2 O, RT). 192 Figure S40. 1 H- 1 H COSY NMR spectrum recorded for 2?1,10-diaminodecane (600 MHz, D 2 O, RT). 193 Figure S41. 1 H- 1 H COSY NMR spectrum recorded for 2?1,8-diaminooctane (600 MHz, D 2 O, RT). 194 Figure S42. 1 H- 1 H COSY NMR spectrum recorded for 2?1,6-diaminohexane (600 MHz, D 2 O, RT). 195 Crystal Structure Information for UM # 1574 Isued by: Peter Y. Zavalij Crystal No. & ID : 1574: Isaacs/Wei-Hao Huang Compound name : [K(H 2 O) 2 (CB6') 2 ?TFAH](TFA)?~4TFAH?~13H 2 O Chemical formula : KC 100 H 116 F 21 N 48 O 55 Final R 1 [I>2?(I)] : 5.37 % ??????????????????????????????????????? Figure S43. A view of UM#1574 showing the numbering scheme employed. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 30% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 196 A colorles prism of KC 100 H 16 F 21 N 48 O 55 , aproximate dimensions 0.095?0.15?0.40 m 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 150(2) K on a thre-circle difractometer system equiped with Bruker Smart Apex I CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?) . The detector was placed at a distance of 5.8 cm from the crystal. A total of 2491 frames were colected with a scan width of 0.3? an exposure time of 20 sec/frame using Apex2 (Bruker, 205). The total data colection time was 18 hours. The frames were integrated with Apex2 software package using a narow-frame integration algorithm. The integration of the data using a Monoclinic unit cel yielded a total of 6732 reflections to a maximum ? angle of 25.0?, of which 12908 were independent (completenes = 9.9%, R int = 3.86%, R sig = 3.2%) and 9287 were greater than 2?(I). The final cel dimensions of a = 31.0746(1) ?, b = 16.974(6) ?, c = 28.0904(10) ?, ? = 90?, ? = 97.9680(10)?, ? = 90?, V = 14673.9(9) ? 3 , are based upon the refinement of the XYZ- centroids of 16943 reflections with 2.3 < ? < 28.0? using Apex2 software. Analysis of the data showed 0 % decay during data colection. Data were corected for absorption efects with the Semi-empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.917 and 0.984. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group C2/c with Z = 4 for the formula unit KC 100 H 16 F 21 N 48 O 55 5. The final anisotropic ful-matrix least-squares refinement on F 2 with 925 variables converged at R 1 = 5.37 % for the observed data and wR 2 = 10.48 % for al data. The godnes-of-fit was 1.00. The largest peak on the final diference map was 0.618?e/? 3 and the largest hole was -0.697?e/? 3 . On the basis of the final model, the calculated density was 1.498 g/cm 3 and F(00), 680?e. Overall structure quality considerations: 1. Strong data set, no disorder, R 1 4% maximum. Publishable quality. 2. God data set, perhaps some minor disorder, R 1 6% maximum. Publishable quality. 3. Average data set and/or easily modeled disorder or twining. Publishable with care. 4. Weak data and/or major disorder or twining that is not easily modeled. Publishable in some cases. 5. Very weak data and/or unexplained features of data or model. Not of publishable quality. A structure with a quality factor of 4 or 5 should not be used for a regulatory document without prior consultation. Comments: - Data quality: very god - Twining: none - Disorder: solvent TFA and water, removed using Squeze from Platon - H-atoms: constrained geometry as riding on atached atom (A) U iso (H)=1.5U iso (A) for CH 3 and 1.2U iso (A) for other groups - Residual density: near disordered groups - Structure quality: good Publishable Yes 197 198 Table S1. Crystal data and structure refinement for UM#1574. ????????????????????????????????????????? X-ray lab bok No. 1574 Crystal ID Isacs/Wei-Hao Huang Empirical formula KC 100 H 16 F 21 N 48 O 55 Formula weight 308.51 Temperature 150(2) K Wavelength 0.71073 ? Crystal size 0.40?0.15?0.095 m 3 Crystal habit colourles prism Crystal system Monoclinic Space group C2/c Unit cel dimensions a = 31.0746(1) ? ? = 90? b = 16.974(6) ? ? = 97.9680(10)? c = 28.0904(10) ? ? = 90? Volume 14673.9(9) ? 3 Z 4 Density, ? calc 1.498 g/cm 3 Absorption coeficient, ? 0.16 m -1 F(00) 6800?e Difractometer Bruker Smart Apex I CD area detector Radiation source fine-focus sealed tube, MoK? Detector distance 5.8 cm Data colection method ? and scans Total frames 2491 Frame size 1024 pixels Frame width 0.3? Exposure per frame 20 sec Total measurement time 18 hours ? range for data colection 1.32 to 25.0? Index ranges -33 ? h ? 36, -20 ? k ? 20, -33 ? l ? 3 Reflections colected 66732 Independent reflections 12908 Observed reflection, I>2?(I) 9287 Coverage of independent reflections 9.9 % Variation in check reflections 0 % Absorption corection Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.984 and 0.917 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refinement program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 12908 / 256 / 925 Godnes-of-fit on F 2 1.067 ?/? max 0.00 Final R indices: R 1 , I>2?(I) 0.0537 wR 2 , al data 0.1048 R int 0.0386 R sig 0.032 Weighting scheme w = 1/[? 2 (F o 2 )+ (0.02P) 2 + 46.6P], P = [max(F o 2 ,0) + 2F o 2 ]/3 Largest dif. peak and hole 0.618 and -0.697?e/? 3 ????????????????????????????????????????? R 1 = ?||F o |-|F c ||/?|F o |, wR 2 = [?w(F o 2 -F c 2 ) 2 /?w(F o 2 ) 2 ] 1/2 199 Crystal Structure Information for UM # 1597 Isued by: Peter Y. Zavalij Crystal No. & ID : 1597: Isaacs/Wei-Hao Huang 1,9 @150K Compound name : CBPh diamine diodide Chemical formula : [(C 43 H 40 N 24 O 13 )<(C 9 H 24 N 2 )]I 2 ?15H 2 O Final R 1 [I>2?(I)] : 7.23 % _________________________________________ Figure S4. A view of UM#1597. Anisotropic atomic displacement elipsoids for the non-hydrogen atoms are shown at the 30% probability level. Hydrogen atoms are displayed with an arbitrarily smal radius. 200 A yelow prism of [(C 43 H 40 N 24 O 13 )<(C 9 H 24 N 2 )]I 2 ?15H 2 O, aproximate dimensions 0.195? 0.35? 0.39 m 3 , was used for the X-ray crystalographic analysis. The X-ray intensity data were measured at 150(2) K on a thre-circle difractometer system equiped with Bruker Smart Apex I CD area detector using a graphite monochromator and a MoK? fine-focus sealed tube (?= 0.71073 ?). The detector was placed at a distance of 6.0 cm from the crystal. A total of 2035 frames were colected with a scan width of 0.3? in ? and an exposure time of 30 sec/frame using Apex2 (Bruker, 205). The total data colection time was 20.1 hours. The frames were integrated with Apex2 software package using a narow-frame integration algorithm. The integration of the data using a Cubic unit cel yielded a total of 134638 reflections to a maximum ? angle of 2.50?, of which 9175 were independent (completenes = 9.8%, R int = 5.31%, R sig = 2.37%) and 8432 were greater than 2?(I). The final cel dimensions of a = 27.6038(2) ?, b = 27.6038(2) ?, c = 27.6038(2) ?, ?= 90?, ?= 90?, ?= 90?, V = 2103.3(3) ? 3 , are based upon the refinement of the XYZ- centroids of 37157 reflections with 2.2 < ? < 21.0? using Apex2. Analysis of the data showed 0 % decay during data colection. Data were corected for absorption efects with the Semi-empirical from equivalents method using SADABS (Sheldrick, 196). The minimum and maximum transmision coeficients were 0.734 and 0.823. The structure was solved and refined using the SHELXS-97 (Sheldrick, 190) and SHELXL-97 (Sheldrick, 197) software in the space group P2 1 3 with Z = 12 for the formula unit C 52 H 94 I 2 N 26 O 28 . The final anisotropic ful-matrix least-squares refinement on F 2 with 862 variables converged at R 1 =7.23 % for the observed data and wR 2 =18.35 % for al data. The godnes-of-fit was 1.00. The largest peak on the final diference map was 0.576?e/? 3 and the largest hole was -0.852?e/? 3 . On the basis of the final model, the calculated density was 1.691 g/cm 3 and F(00), 1016?e. Overall structure quality considerations: 1. Strong data set, no disorder, R 1 4% maximum. Publishable quality. 2. God data set, perhaps some minor disorder, R 1 6% maximum. Publishable quality. 3. Average data set and/or easily modeled disorder or twining. Publishable with care. 4. Weak data and/or major disorder or twining that is not easily modeled. Publishable in some cases. 5. Very weak data and/or unexplained features of data or model. Not of publishable quality. A structure with a quality factor of 4 or 5 should not be used for a regulatory document without prior consultation. Comments: - Data quality: good - Twining: merohedral, refined using twin/basf to 7:1 ratio - Disorder: substantial disorder of water and iodine ions; acounted for using squeze (se CIF for details); guest molecule disordered in two orientations in about 1:1 ratio - H-atoms: constrained geometry as riding on atached atom (A) Uiso(H)=1.5*U iso (A) for CH 3 and 1.2*U iso (A) for other groups - Residual density: near heavy atoms &near disordered groups - Structure quality: god & average because of strong disorder and significantly elevated thermal motion of guest Publishable Yes with care 201 202 Table S2. Crystal data and structure refinement for UM#1597. _________________________________________ X-ray lab bok No. 1597 Crystal ID Isacs/Wei-Hao Huang 1,9 @150K Empirical formula C 52 H 94 I 2 N 26 O 28 Formula weight 1785.3 Temperature 150(2) K Wavelength 0.71073 ? Crystal size 0.39 ? 0.35 ? 0.195 m 3 Crystal habit yelow prism Crystal system Cubic Space group P2 1 3 Unit cel dimensions a = 27.6038(2) ? ? = 90? b = 27.6038(2) ? ? = 90? c = 27.6038(2) ? ? = 90? Volume 2103.3(3) ? 3 Z 12 Density, ? calc 1.691 g/cm 3 Absorption coefficient, ? 1.00 m -1 F(00) 11016?e Diffractometer Bruker Smart Apex II CCD area detector Radiation source fine-focus sealed tube, MoK? Detector distance 6.0 cm Detector resolution 83.3 pixels/m Total frames 2035 Frame size 512 pixels Frame width 0.3? Exposure per frame 30 sec Total measurement time 20.1 hours Data colection method ? and ? scans range for data colection 1.81 to 2.49? Index ranges -29 ? h ? 29, -29 ? k ? 27, -29 ? l ? 29 Reflections colected 134638 Independent reflections 9175 Observed reflection, I>2 (I) 8432 Coverage of independent reflections 9.8 % Variation in check reflections 0 % Absorption correction Semi-empirical from equivalents SADABS (Sheldrick, 196) Max. and min. transmision 0.823 and 0.734 Structure solution technique direct Structure solution program SHELXS-97 (Sheldrick, 190) Refinement technique Ful-matrix least-squares on F 2 Refinement program SHELXL-97 (Sheldrick, 197) Function minimized ?w(F o 2 - F c 2 ) 2 Data / restraints / parameters 9175 / 189 / 862 Godnes-of-fit on F 2 1.03 / max 0.01 Final R indices: R 1 , I>2 (I) 0.0723 wR 2 , al data 0.1835 R int 0.0531 R sig 0.0237 Weighting scheme w = 1/[? 2 (F o 2 )+(0.09P) 2 +87P], P = [max(F o 2 ,0)+2F o 2 ]/3 Absolute structure parameter 0.13(3) Largest diff. peak and hole 0.576 and -0.852?e /? 3 ________________________________________ R 1 = ?||F o |-|F c ||/?|F o |, wR2 = [?w(F o 2 -F c 2 ) 2 /? w(F o 2 ) 2 ] 1/2 203 Figure S45. Cross-eyed stereoviews of MF minimized geometries of: a) 2?3a, b) 2?3b, c) 2?3c. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 204 Figure S46. Cross-eyed stereoviews of MF minimized geometries of: a) 2?3d, b) 2?3e, c) 2?3f. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 205 Figure S47. Cross-eyed stereoviews of MF minimized geometries of: a) 2?3g, b) 2?3h, c) 2?3i. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 206 Figure S48. Cross-eyed stereoviews of MF minimized geometries and heats of formation for: a) bottom-ns-CB[6]?9, and b) top-ns-CB[6]?9. Color code: C, grey; H, white; N, blue; O, red; H-bonds, red-yelow striped. 207 Figure S49. Stereoscopic representation of the electrostatic surface potential (PM3) plot for CB[6]. The red to blue color range spans ?85 to +35 kcal mol -1 . 208 Figure S50. Stereoscopic representations of the electrostatic surface potential (PM3) plot for the MF minimized geometry of ns-CB[6]: a) top view, and b) bottom view. The red to blue color range spans ?85 to +35 kcal mol -1 . 209 Figure S51. Stereoscopic representation of the electrostatic surface potential (PM3) plot for 2: a) top view, and b) bottom view. The red to blue color range spans ?85 to +35 kcal mol -1 . 210 References (1) Behrend, R.; Meyer, E.; Rusche, F. Liebigs Ann. Chem. 1905, 339, 1-37. (2) Freman, W. A.; Mock, W. L.; Shih, N. Y. J. Am. Chem. Soc. 1981, 103, 7367-7368. (3) Flinn, A.; Hough, G. C.; Stoddart, J. F.; Wiliams, D. J. Angew. Chem., Int. Ed. 1992, 31, 1475-1477. (4) Wu, A.; Chakraborty, A.; Wit, D.; Lagona, J.; Damkaci, F.; Ofori, M. A.; Chiles, J. K.; Fetinger, J. C.; Isacs, L. J. Org. Chem. 2002, 67, 5817-5830. (5) Chakraborty, A.; Wu, A.; Wit, D.; Lagona, J.; Fetinger, J. C.; Isacs, L. J. Am. Chem. Soc. 2002, 124, 8297-8306. (6) Wit, D.; Lagona, J.; Damkaci, F.; Fetinger, J. C.; Isacs, L. Org. Let. 2000, 2, 755-758. (7) Mock, W. L.; Shih, N. Y. J. Org. Chem. 1983, 48, 3618-3619; Mock, W. L.; Shih, N. Y. J. Am. Chem. Soc. 1988, 110, 4706-4710. (8) Mock, W. L.; Shih, N. Y. J. Org. Chem. 1986, 51, 4440-4446. (9) Mock, W. L.; Shih, N. Y. J. Am. Chem. Soc. 1989, 111, 2697-2699. (10) Mock, W. L.; Ira, T. A.; Wepsiec, J. P.; Manimaran, T. L. J. Org. Chem. 1983, 48, 3619-3620; Mock, W. L.; Ira, T. A.; Wepsiec, J. P.; Adhya, M. J. Org. Chem. 1989, 54, 5302-5308. (11) Mock, W. L.; Pierpont, J. J. Chem. Soc., Chem. Commun. 1990, 1509-1511. (12) Day, A. I.; Arnold, A. P.; Blanch, R. J.; Snushal, B. J. Org. Chem. 2001, 66, 8094-8100. 211 (13) Isacs, L.; Park, S.-K.; Liu, S.; Ko, Y. H.; Selvapalam, N.; Kim, K.; Lik, H.; Zavalij, P. Y.; Kim, G.-H.; Le, H.-S.; Kim, K. J. Am. Chem. Soc. 2005, 127, 18000-18001. (14) Huang, W.-H.; Liu, S.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2006, 128, 14744-114745. (15) Kim, J.; Jung, I.-S.; Kim, S.-Y.; Le, E.; Kang, J.-K.; Sakamoto, S.; Yamaguchi, K.; Kim, K. J. Am. Chem. Soc. 2000, 122, 540-541. (16) Le, J. W.; Samal, S.; Selvapalam, N.; Kim, H.-J.; Kim, K. Ac. Chem. Res. 2003, 36, 621-630. (17) Day, A. I.; Blanch, R. J.; Arnold, A. P.; Lorenzo, S.; Lewis, G. R.; Dance, I. Angew. Chem., Int. Ed. 2002, 41, 275-277. (18) Liu, S.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2005, 127, 16798-16799. (19) Liu, S.; Ruspic, C.; Mukhopadhyay, P.; Chakrabarti, S.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2005, 127, 15959-15967. (20) Mukhopadhyay, P.; Wu, A.; Isacs, L. J. Org. Chem. 2004, 69, 6157-6164. (21) Mukhopadhyay, P.; Zavalij, P. Y.; Isacs, L. J. Am. Chem. Soc. 2006, 128, 14093-14102. (22) Jun, S. I.; Le, J. W.; Sakamoto, S.; Yamaguchi, K.; Kim, K. Tetrahedron Let. 2000, 41, 471-475. (23) Moon, K.; Grindstaf, J.; Sobransingh, D.; Kaifer, A. E. Angew. Chem., Int. Ed. 2004, 43, 5496-5499. (24) Ong, W.; Kaifer, A. E. Angew. Chem., Int. Ed. 2003, 42, 2164-2167. 212 (25) Lim, Y.-B.; Kim, T.; Le, J. W.; Kim, S.-M.; Kim, H.-J.; Kim, K.; Park, J.-S. Bioconjugate Chem. 2002, 13, 1181-1185; Le, J. W.; Ko, Y. H.; Park, S.-H.; Yamaguchi, K.; Kim, K. Angew. Chem., Int. Ed. 2001, 40, 746-749. (26) Jeon, W. S.; Ziganshina, A. Y.; Le, J. W.; Ko, Y. H.; Kang, J.-K.; Le, C.; Kim, K. Angew. Chem. Int. Ed. 2003, 42, 4097-4100; Ko, Y. H.; Kim, K.; Kang, J.-K.; Chun, H.; Le, J. W.; Sakamoto, S.; Yamaguchi, K.; Fetinger, J. C.; Kim, K. J. Am. Chem. Soc. 2004, 126, 1932-1933. (27) Jeon, W. S.; Kim, E.; Ko, Y. H.; Hwang, I.; Le, J. W.; Kim, S.-Y.; Kim, H. J.; Kim, K. Angew. Chem. Int. Ed. 2005, 44, 87-91. (28) Marquez, C.; Nau, W. M. Angew. Chem., Int. Ed. 2001, 40, 3155-3160. (29) Jeon, Y. J.; Kim, S.-Y.; Ko, Y. H.; Sakamoto, S.; Yamaguchi, K.; Kim, K. Org. Biomol. Chem. 2005, 3, 2122-2125. (30) Wheate, N. J.; Day, A. I.; Blanch, R.; Arnold, A.; Cullinane, C.; Collins, J. G. Chem. Commun. 2004, 1424-1425; Wheate, N. J.; Buck, D. P.; Day, A. I.; Collins, J. G. Dalton Trans. 2006, 451-458. (31) Rowan, A. E.; Elemans, J. A. A. W.; Nolte, R. J. M. Ac. Chem. Res. 1999, 32, 995-1006; Rebek, J. J. Ac. Chem. Res. 1999, 32, 278-286. (32) Eliel, E. L.; Wilen, S. H. Stereochemistry of Organic Compounds; J. Wiley and Sons: New York, 1994. (33) Buschmann, H.-J.; Fink, H.; Schollmeyer, E. "Preparation of cucurbituril" Ger. Ofen. (Germany): DE 19603377, 1997 [Chem. Abstr. 1997, 127, 205599]. (34) Lagona, J.; Fetinger, J. C.; Isacs, L. Org. Lett. 2003, 5, 3745-3747. 213 (35) Lagona, J.; Fetinger, J. C.; Isacs, L. J. Org. Chem. 2005, 70, 10381-10392. (36) Lagona, J.; Wagner, B. D.; Isacs, L. J. Org. Chem. 2006, 71, 1181-1190. (37) Day, A. I.; Arnold, A. P.; Blanch, R. J. Molecules 2003, 8, 74-84. (38) Zhao, Y.; Xue, S.; Zhu, Q.; Tao, Z.; Zhang, J.; Wei, Z.; L., L.; Hu, M.; Xiao, H.; Day, A. I. Chin. Science Bull. 2004, 49, 1111-1116. (39) Jon, S. Y.; Selvapalam, N.; Oh, D. H.; Kang, J.-K.; Kim, S.-Y.; Jeon, Y. J.; Le, J. W.; Kim, K. J. Am. Chem. Soc. 2003, 125, 10186-10187. (40) Le, H.-K.; Park, K. M.; Jeon, Y. J.; Kim, D.; Oh, D. H.; Kim, H. S.; Park, C. K.; Kim, K. J. Am. Chem. Soc. 2005, 127, 5006-5007. (41) Jeon, Y. J.; Kim, H. J.; Jon, S.; Selvapalam, N.; Oh, D. H.; Seo, I.; Park, C.-S.; Jung, S. R.; Koh, D.-S.; Kim, K. J. Am. Chem. Soc. 2004, 126, 15944-15945. (42) Petersen, H. Synthesis 1973, 243-292. (43) Butler, A. R.; Leitch, E. J. Chem. Soc., Perkin Trans. 2 1980, 103-109. (44) Rudkevich, D. M. Angew. Chem., Int. Ed. 2004, 43, 558-571. (45) Rekharsky, M.; Yamamura, H.; Inoue, C.; Kawai, M.; Osaka, I.; Arakawa, R.; Shiba, K.; Sato, A.; Ko, Y. H.; Selvapalam, N.; Kim, K.; Inoue, Y. J. Am. Chem. Soc. 2006, 128, 14871-14880. (46) Ling, Y.; Kaifer, A. E. Chem. Mater. 2006, 18, 5944-5949. (47) Jeon, W. S.; Moon, K.; Park, S. H.; Chun, H.; Ko, Y. H.; Le, J. Y.; Le, E. S.; Samal, S.; Selvapalam, N.; Rekharsky, M. V.; Sindelar, V.; Sobransingh, D.; Inoue, Y.; Kaifer, A. E.; Kim, K. J. Am. Chem. Soc. 2005, 127, 12984-12989. (48) Rekharsky, M. V.; Mori, T.; Yang, C.; Ko, Y. H.; Selvapalam, N.; Kim, H.; Sobransingh, D.; Kaifer, A. E.; Liu, S.; Isacs, L.; Chen, W.; Moghaddam, S.; 214 Gilson, M. K.; Kim, K.; Inoue, Y. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 20737-20742. (49) Lagona, J.; Mukhopadhyay, P.; Chakrabarti, S.; Isacs, L. Angew. Chem., Int. Ed. 2005, 44, 4844-4870. (50) Kim, K.; Selvapalam, N.; Ko, Y. H.; Park, K. M.; Kim, D.; Kim, J. Chem. Soc. Rev. 2007, 36, 267-279. (51) Mohanty, J.; Pal, H.; Ray, A. K.; Kumar, S.; Nau, W. M. ChemPhysChem 2007, 8, 54-56. (52) Bali, M. S.; Buck, D. P.; Coe, A. J.; Day, A. I.; Collins, J. G. Dalton Trans. 2006, 5337-5344. (53) Jon, S. Y.; Ko, Y. H.; Park, S. H.; Kim, H.-J.; Kim, K. Chem. Commun. 2001, 1938-1939; Choi, S.; Park, S. H.; Ziganshina, A. Y.; Ko, Y. H.; Le, J. W.; Kim, K. Chem. Commun. 2003, 2176-2177; Patabiraman, M.; Natarajan, A.; Kaliappan, R.; Mague, J. T.; Ramamurthy, V. Chem. Commun. 2005, 4542- 4544; Wang, R.; Yuan, L.; Macartney, D. H. J. Org. Chem. 2006, 71, 1237- 1239. (54) Bush, M. E.; Bouley, N. D.; Urbach, A. R. J. Am. Chem. Soc. 2005, 127, 14511-14517; Heitmann, L. M.; Taylor, A. B.; Hart, P. J.; Urbach, A. R. J. Am. Chem. Soc. 2006, 128, 12574-12581; Rekharsky, M. V.; Yamamura, H.; Ko, Y. H.; Kim, K.; Inoue, Y. Peptide Sci. 2006, 43, 393-394. (55) Sindelar, V.; Cejas, M. A.; Raymo, F. M.; Chen, W.; Parker, S. E.; Kaifer, A. E. Chem. Eur. J. 2005, 11, 7054-7059; Ling, Y.; Wang, W.; Kaifer, A. E. Chem. Commun. 2007, 610-612. 215 (56) Ooya, T.; Inoue, D.; Choi, H. S.; Kobayashi, Y.; Loethen, S.; Thompson, D. H.; Ko, Y. H.; Kim, K.; Yui, N. Org. Let. 2006, 8, 3159-3162; Sobransingh, D.; Kaifer, A. E. Org. Let. 2006, 8, 3247-3250; Sindelar, V.; Silvi, S.; Kaifer, A. E. Chem. Commun. 2006, 2185-2187; Liu, Y.; Li, X.-Y.; Zhang, H.-Y.; Li, C.-J.; Ding, F. J. Org. Chem. 2007, 72, 3640-3645; Tuncel, D.; ?zsar, ?.; Tiftik, H. B.; Salih, B. Chem. Commun. 2007, 1369-1371; Ko, Y. H.; Kim, E.; Hwang, I.; Kim, K. Chem. Commun. 2007, 1305-1315. (57) Liu, S.; Zavalij, P. Y.; Lam, Y.-F.; Isacs, L. J. Am. Chem. Soc. 2007, 129, 11232-11241; Liu, S.; Shukla, A. D.; Gadde, S.; Wagner, B. D.; Kaifer, A. E.; Isacs, L. Angew. Chem., Int. Ed. 2008, 47, ASAP. (58) Liu, S.; Kim, K.; Isacs, L. J. Org. Chem. 2007, 72, 6840-6847. (59) Wu, A.; Chakraborty, A.; Wit, D.; Lagona, J.; Damkaci, F.; Ofori, M. A.; Chiles, J. K.; Fetinger, J. C.; Isacs, L. J. Org. Chem. 2002, 67, 5817-5830. (60) So, Y.-H. Ac. Chem. Res. 2001, 34, 753-758; Flory, P. J. Chem. Rev. 1946, 39, 137-197. (61) Day, A. I.; Blanch, R. J.; Coe, A.; Arnold, A. P. J. Inclusion Phenom. Macrocyclic Chem. 2002, 43, 247-250. (62) The influence of glycoluril concentration, acid identity and concentration and temperature have also been studied by Day and co-workers. The point in the mechanistic pathway where these variable exert their influence remains unclear. (63) Huang, W.-H.; Zavalij, P. Y.; Isacs, L. Angew. Chem., Int. Ed. 2007, 46, 7425-7427. 216 (64) Huang, W.-H.; Zavalij, P. Y.; Isacs, L. Angew. Chem., Int. Ed. 2008, 48, submited. (65) Rebek, J. J. Ac. Chem. Res. 1999, 32, 278-286; Rowan, A. E.; Elemans, J. A. A. W.; Nolte, R. J. M. Ac. Chem. Res. 1999, 32, 995-1006; Wu, A.; Chakraborty, A.; Fetinger, J. C.; Flowers, R. A., I; Isacs, L. Angew. Chem., Int. Ed. 2002, 41, 4028-4031; Isacs, L.; Wit, D. Angew. Chem., Int. Ed. 2002, 41, 1905-1907. (66) Compounds 13(m,n) and 17(m,n) are chiral when m ? n. (67) If the reaction is run to completion we observe a more complex mixture whose analysis by 1 H NMR spectroscopy is chalenging. (68) This analysis is theoreticaly based and ignores the potential influence of strain and intramolecular NH??O H-bonds that are known to impact the stability and geometry of CB[n] and (?)-bis-ns-CB[6]. (69) Blanch, R. J.; Sleman, A. J.; White, T. J.; Arnold, A. P.; Day, A. I. Nano Let. 2002, 2, 147-149. (70) In none of these reactions did we observe the formation of CB[10]?CB[5] which suggests that the formation of this aggregate is probably more complex than the reaction of two molecules of 5 to give CB[10] followed by stabilization with CB[5]. (71) Day has previously shown that CB[n] forming reactions when conducted at high dilution lead mainly to CB[5]. At high dilution intermolecular reactions are slowed and chain-growth rather than step-growth proceses tend to dominate. 217 (72) Ong, W.; Kaifer, A. E. Organometallics 2003, 22, 4181-4183. (73) Mock, W. L. Top. Curr. Chem. 1995, 175, 1-24. (74) Mohanty, J.; Nau, W. M. Angew. Chem., Int. Ed. 2005, 44, 3750-3754. (75) a) Miyahara, Y.; Abe, K.; Inazu, T. Angew. Chem. Int. Ed. 2002, 41, 3020- 3023. (b) Kelersberger, K. A.; Anderson, J. D.; Ward, S. M.; Krakowiak, K. E.; Dearden, D. V. J. Am. Chem. Soc. 2001, 123, 11316-11317. (76) Zhao, J.; Kim, H.-J.; Oh, J.; Kim, S.-Y.; Kim, J. W.; Sakamoto, S.; Yamaguchi, K.; Kim, K. Angew. Chem., Int. Ed. 2001, 40, 4233-4235. (77) Wu, A.; Isacs, L. J. Am. Chem. Soc. 2003, 125, 4831-4835. (78) Timerman, P.; Verboom, W.; van Veggel, F. C. J. M.; van Duynhoven, J. P. M.; Reinhoudt, D. N. Angew. Chem., Int. Ed. Engl. 1994, 33, 2345-2348. (79) Shinkai, S.; Ikeda, M.; Sugasaki, A.; Takeuchi, M. Ac. Chem. Res. 2001, 6, 494-503. (80) Nagarajan, E. R.; Oh, D. H.; Selvapalam, N.; Ko, Y. H.; Park, K. M.; Kim, K. Tetrahedron Let. 2006, 47, 2073-2075. (81) Kelersberger, K. A.; Anderson, J. D.; Ward, S. M.; Krakowiak, K. E.; Dearden, D. V. J. Am. Chem. Soc. 2001, 123, 11316-11317. (82) Le, J. Y.; Le, E. S.; Samal, S.; Selvapalam, N.; Rekharsky, M. V.; Sindelar, V.; Sobransingh, D.; Inoue, Y.; Kaifer, A. E.; Kim, K. J. Am. Chem. Soc. 2005, 127, 12984-12989. (83) Rekharsky, M. V.; Yamamura, H.; Inoue, C.; Kawai, M.; Osaka, I.; Arakawa, R.; Shiba, K.; Sato, A.; Ko, Y. H.; Selvapalam, N.; Kim, K.; Inoue, Y. J. Am. Chem. Soc. 2006, 128, 14871-14880. 218 (84) CDC-647412 (1), CDC-647413 (?)-bis-ns-CB[6]?3), and CDC-647414 (?)-bis-ns-CB[6]?TFA) contains the supplementary crystalographic data for this paper. These data can be obtained fre of charge via ww.cdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystalographic Data Centre, 12, Union Road, Cambridge CB21EZ, UK; fax: (+44) 1223-336-033; or deposit@ccdc.cam.ac.uk). (85) The ROESY spectrum of the mixture of diastereomers did not provide information that would alow us to asign the major and minor resonances to a specific diastereomer. To resolve this isue wil require the resolution of (?)-bis-ns- CB[6]. (85) (?)-Bis-ns-CB[6] features connections betwen two pairs of homotopic NH groups of identical topicity whereas bis-ns-CB[10] previously isolated has connections betwen two pairs of homotopic NH groups of opposite topicity. (86) The ROESY spectrum of the mixture of diastereomers did not provide information that would alow us to asign the major and minor resonances to a specific diastereomer. We are in the proces of resolving this isue by separating the enantiomers of (?)-bis-ns-CB[6] by chromatography on a chiral stationary phase. (87) Compound 12 and (?)-bis-ns-CB[6] form a 1:1 inclusion complex rather than a supramolecular polymeric exclusion complex. (88) Product resubmision experiments confirm that trimer 1 is converted to (?)-bis- ns-CB[6] by condensation with CH 2 O under acidic conditions. 219 (89) Several constitutional isomers of (?)-bis-ns-CB[n] are possible depending on the length of the glycoluril oligomer fragments that condense (e.g. (?)-bis-ns- CB[7] can be formed from tetramer and trimer fragments or from dimer and pentamer fragments). (90) A. Henning, H. Bakirci, W. M. Nau, Nature Methods 2007, 4, 629-632. (91) K. Kim, N. Selvapalam, Y. H. Ko, K. M. Park, D. Kim, J. Kim, Chem. Soc. Rev. 2007, 36, 267-279. (92) J. Kim, Y. Ahn, K. M. Park, Y. Kim, Y. H. Ko, D. H. Oh, and K. Kim Angew. Chem. Int. Ed. 2007, 46, 7393 ?7395. (93) I. Hwang, K. Baek, M. Jung, Y. Kim, K. M. Park, D.-W. Le, N. Selvapalam, K. Kim, J. Am. Chem. Soc. 2007, 129, 4170-4171. (94) The reaction betwen ns-CB[6] and (substituted) benzaldehydes was also conducted. These reactions as les clean than betwen ns-CB[6] and o- phthalaldehyde which we atribute to the potential for two diastereomeric orientations of the pendant Ar group. (95) CDC-676703 (2) and CDC-676704 (V-2?V-3f) contains the supplementary crystalographic data for this paper. These data can be obtained fre of charge via ww.cdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystalographic Data Centre, 12 Union Road, Cambridge CB21EZ, UK; fax: (+44) 1223-336-033; or deposit@ccdc.cam.ac.uk). (96) We did not observe intra-complex ROESY cross-peaks that would alow us to asign these complexes as a specific diastereomer. MF calculations 220 (Supporting Information) suggest that the complex betwen ns-CB[6] and V-9 is best formulated as bottom-ns-CB[6]?V-9. (97) Mock previously showed that CB[6] binds to V-11 but rejects isomeric V-12 and V-13 because only the geometry of V-11 alows both substituents to pas through the C=O lined portals. Se: Mock, W. L.; Shih, N. Y. J. Org. Chem. 1986, 51, 4440-4446. Interestingly, meta-substituted V-19 forms a mixture of top- and bottom-diastereomers with ns-CB[6] because both portals are satisfied by ion-dipole interactions. (98) H.-J. Buschmann, A. Wego, A. Zielesny, E. Scholmeyer, J. Incl. Phenom. Macrocyclic Chem. 2006, 54, 241-246. (99) A related phenomenon has ben observed by Kim and co-workers for the complex of CB[8] with long chain alkyltrimethylamonium ions. K. Kim, personal communication. (100) Rebek and co-workers have shown that n-alkanes exhibit helical conformations inside self-asembled capsules to maximize non-covalent interactions betwen host and guest. For a review, se: J. Rebek, Jr. Chem. Commun. 2007, 2777- 2789.