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Chapter 1 Hydrogen Bonding Durham E-Theses Inuences on crystal structure due to hydrogen bonding and other eects Broder, Charlotte K. How to cite: Broder, Charlotte K. (1998) Inuences on crystal structure due to hydrogen bonding and other eects, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/5023/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk Imfimemem #if Cvfstml Stmetmre Other Effmt& Charlotte K, Broder Thesis Submitted for degree of Master of Science Chemistry Durham University Trevelyan College October 1998 The copyright of this thesis rests with the author. No quotation from it should be published without the written consent of the author an information derived from it should be acknowledged. 1 1 MAY 1999 Acknowledgements Thanks to Dr M. Davidson and his lab; Phil, Sarah, Richard and Marina. Dr T.Gunnlangsson Central Drug Research Institute (India) For the crystals and explanations To Dr Andres Goeta Dr A. S. Batsanov Andrew Hamilton For help with data collection To Xenova Discovery Ltd For Financial Support Professor Judith Howard And every one down the lab... Beclaration The work described in this thesis was carried out in the Department of Chemistry at the University of Durham between October 1997 and September 1998. This work has not been submitted, either complete, or in part, for a degree in this or any other University. All the work is my own unless stated to the contrary. The copyright of this thesis rests with the author. No quotation from it should be published without her prior written consent and information derived from it should be acknowledged. II Contents Chapter: Page: Contents III Contents Diagrams V Diagrams Graphs VII Graphs Tables VII Tables Introduction 1 Introduction. Chapter I 3 Hydrogen bonding. 3 What is a hydrogen bond? 5 Hydrogen bonding between amino and phenyl groups. 6 Cambridge Structural Database Search: Method. 8 Results. 14 Conclusions. 17 References. Chapter 2 18 X-ray Crystallography. 18 The technique. 18 Diffraction patterns. 20 The equipment: The Diffractometers. 21 The Cryostream unit. 21 Setting up. 23 References. Chapter 3 24 Crystal growth. 24 Slow evaporation of solvent 25 Super cooling of a supersaturated solution 25 Growth from a fluid phase 26 Gel methods 26 The use of co-crystallisation agents 27 The experunent 28 References. Chapter 4 29 Hydrogen bonding in methane-diphenol-3,5,3',5'-tetra'butyl co-crystal. 30 Crystal data. 31 Crystal structure and packing. 36 References. Chapter 5 37 /7-fe/-f-butylcalix[4]arene with triphenyl phosphonium species. 38 Crystal data. 39 Crystal structure and packing. 41 The crystal structure and packing of ;7-<er/-butylcalix[4]arene with triphenylaminophosphonium or triphenyhnethylphosphonium. Ill 45 The crystal structure and packing of p-?er?-butylcalix[4]arene with triphenylethylphosphonium. 49 Conclusions. 50 References. Chapter 6 51 Effect of the metal on the structure of various metal phosphonium complexes. 52 Experimental details: Series 1, Crystal data. 53 Experimental details: Series 2, Crystal data. 54 Crystal structure and packing. 55 Crystal structure and packing in Series 1. 59 Crystal structure and packing in Series 2. 64 Conclusions. 65 References. Chapter 7 66 Crystal studied: Miscellaneous Organics. '66 [5,6'(5',8'-dihydroxy-l ',4'-naphthoquinone)]-2-methylpent-2-ene phenyl acrylate. 66 Crystaldata. 67 Data solution and refinement. 68 Crystal structure and packing. 71 (2-methyl(diethanoic acid)amine)phenoxyethanoic acid 71 Crystaldata. 72 Crystal structure and packing. 77 Salicyldoxime and benoxazolin-2-one. 77 Crystal data. 78 Crystal structure and packing. 81 Conclusions. 82 References. Chapter 8 83 Crystal Studied: Miscellaneous Organometallics 83 Sodium (hexamethyldisilylamide)(triphenylethylphosphonium). 83 Crystal data 84 Crystal structure and packmg. 87 5-ferrocenyl-4-nitrile-7-acetonitrile-2-(4'-bromophenyl)indole. 87 Crystal data. 88 Data solution and refinement. 89 Crystal structure and packing. 93 Carbazol and triphenylethylphosphonium. 93 Crystal data. 94 Crystal structure and packing. 98 Conclusions. 99 References. IV Biagrams Number Page 1.1 6 The search fragment. 1.2 14 Peptide fragment with torsion angle TORCCC= 180° 4.1 29 The molecular species in the co-crystals. 4.2 31 Classical hydrogen bonded cham A)DMI co-crystal, B)DBI co-crystal. 4.3 32 Double chains A)DMI co-crystal, B)DBI co-crystal. 4.4 32 Aromatic face-face interactions holding the double chains together, A)DMI co-crystal, B)DBI co-crystal. 4.5 33 Stacking of the sheets, each sheet is running vertically perpendicular to plane of page (aromatic face-face interactions are not shown, but link two vertically adjacent double chains). A)DMI co-crystal, B)DBI co-crystal. 4.6 34 Numbering scheme used. 5.1 37 The molecular species in the co-crystal. 5.2 39 Acetonifrile trapped in the calixarene cage. 5.3 41 Packing of the calixarene molecules, packing within a sheet viewed down the a axis. A)methyl species, B)amino species. 5.4 42 Packing of the calixarene molecules, packing within a sheet viewed down the a axis. A)methyl species, B)amino species. 5.5 42 Two triphenyl phosphonium sheets, viewed end on down b axis, acetonitriles give the position of the calixarene molecules. A)methyl species, B)amino species. 5.6 43 a) the full crystal structure, methyl species, b) the full crystal structure, amino species. 5.7 45 Packing of the calixarene molecules. 5.8 46 Packing of the molecules about a triphenylethylphosphonium stack, viewed dovm stack. 5.9 46 Packing of the molecules about a friphenylethylphosphonium stack, viewed along stack. 5.10 47 Packmg of the stacks (viewed down stacks), in the actual crystal. 5.11 48 Packing of the common motif, A)methyl species, B)amino species, C)ethyl species. 6.1 55 Segment of the hydrogen bonded chain. 6.2 56 Hydrogen bonds joining chains (each chain nms from bottom left to top right in diagram. 6.3 57 Comparison of comparative structure of calcium and sfrontium compounds for series 1, calcium species = red, sfrontium species = blue. 6.4 57 Numbering system used in calcium/strontium bis(2,6-di'butyl-4- methylphenoxy)bis(friphenylaminophosphonium) 6.5 59 Comparison of comparative structure of calcium and sfrontium compounds for series 2, calcium species = red, sfrontium species = blue. 6.6 60 Hydrogen bonding patterns, A)calcium species, B)sfrontium species. 6.7 60 Agostic bonds in bis(hexamethyldisilylamide) bis(friphenylmethylphosphonium)-metal compounds A) calcium/sfrontium species, B) barium species. 7.1 68 [5,6'(5',8'-dihydroxy-r,4'-naphthoquinone)]-2-methylpent-2-ene phenyl acrylate. 7.2 68 Why the alcohol groups on the 5,8-dihydroxy-l,4-naphthoquinone forms intra not intermolecular bonds. 7.3 69 The chains formed by a hydrogen bond between 0(1) and H(25) 7.4 69 The sheets formed by a hydrogen bond between 0(28) and H(10) on separate chains. 7.5 70 The packiiig of the sheets. 7.6 72 (2-methyl(diethanoic acid)amine)phenoxyethanoic acid 7.7 72 Schematic of the packing of the benzene rings in the crystal, viewed down the a axis (phenyl rings in cross-section). 7.8 73 Carboxylicacid dimer 7.9 73 Hydrogen bonding between two molecules about an inversion centre. 7.10 74 Possible hydrogen bondmg to give a dimer linked by four hydrogen bonds. Not exhibited by the crystal. 7.11 74 Dimer. 7.12 75 Extended chain. 7.13 76 Full structure. 7.14 78 Salicylaldoxime and benoxazolin-2-one. 7.15 78 The benoxazolin-2-one forms a dimer. 7.16 79 Benoxazolin-2-one dimer surrounded by four salicylaldoxime molecules. 7.17 79 A salcylaldoxime molecule hydrogen bonded to two benoxazolin-2-one dimers. 7.18 80 Full structure. 8.1 84 A) sodium (hexamethyldisilylamide)(triphenylethylphosphonium). B) dimer of sodium (hexamethyldisilylamide)(triphenylethylphosphonium) 8.2 85 Packing ofdimers viewed down the a axis. 8.3 86 Agostic bonds in sodium (hexamethyldisilylamide) (triphenylethylphosphonium). 8.4 89 5-ferroceny l-4-nitrile-7-acetonitrile-2-(4' -bromopheny l)indole 8.5 90 The hydrogen bonded dimer. 8.6 90 A chain of dimers 8.7 91 The hydrogen bond that holds the chain together to give sheets. 8.8 92 The packing of sheets in the crystal. 8.9 94 Carbazol and triphenylethylphosphonium. 8.10 95 Alignment of the carbazol molecules. 8.11 95 Packing within the crystal. 8.12 96 The hydrogen bonding interactions between the carbazol (1) and triphenylethylphosphonium molecules. 8.13 97 The hydrogen bpnding interactions between triphenylethylphosphonium stacks, viewed along the stacks. VI Graphs Number Page 1 8 Distance between centre of ring on residue i, and N of N-H on residue i+1 2 9 Distance between centre of ring on residue i, and H of N-H on residue i+1 3 10 Distance between centre of ring on residue i, and H of N-H on residue i+1 4 11 Distance between CI on residue i, and N of N-H on residue i+1 5 11 Distance between CI on residue i, and H of N-H on residue i+1 6 12 Distance between CI on residue i, and H of N-H on residue i+1 7 13 TORNCC vs TORCCC distribution of data by torsion angle 8 16 Results fi-om Cache computer-modelling calculations Tables Number Page 1.1 15 Results from Cache computer-modelling calculations.
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