198 Topics in Current Chemistry Editorial Board: A. de Meijere KN ...

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Directional Aspects of Intermolecular Interactions Jenny P. Glusker The Institute for Cancer Research, The Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA. E-mail: jp_glusker@fccc.edu Directional intermolecular interactions can be found by statistical analyses of the surroundings of functional groups in all crystal structures containing them. The most notable such interaction is the hydrogen bond, which, if strong as between OH or NH groups and oxygen or nitrogen acceptors, is approximately linear. This provides an important means of aligning molecules together.Analogous but weaker interactions described here are C-H◊◊◊O, F◊◊◊H and H◊◊◊p , and also those between C-S-C groups and electrophiles or nucleophiles. Some directionality can also be identified in aromatic-aromatic interactions. Metal ion coordination can, in certain instances, also have a directional component, particularly if the coordination geometry is inflexible, as for the octahedral binding of divalent magnesium. The geometries of interactions of metal ions with various functional groups in proteins are described, and in many cases they are more rigid than the analogous interaction involving a hydrogen bond. The emerging use of crystal surfaces as probes of molecular recognition is then discussed. Finally some examples of molecular recognition in biological macromolecules are given; these stress the importance of pattern recognition in hydrogen bonding, together with the significance of weaker interactions. Keywords: Recognition, Molecular, metal ion coordination, Hydrogen bonding, Intermolecular interactions, Directionality, Crystal surface recognition. 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2 Methods of Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.1 Sources ofCrystallographic Data . . . . . . . . . . . . . . . . . . . . 6 2.2 Spectroscopic Methods of Studying Intermolecular Interactions . . . 7 3 Types of Intermolecular Forces . . . . . . . . . . . . . . . . . . . . . 7 4 Directed Organic Interactions . . . . . . . . . . . . . . . . . . . . . . 8 4.1 Intermolecular Interactions in Hydrocarbons . . . . . . . . . . . . . 8 4.2 Nucleophile and Electrophile Interactions with Sulfur and Halogen Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 4.3 Hydrogen Bonding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4.4 C-H◊◊◊O Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 4.5 F◊◊◊H Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 4.6 H◊◊◊p Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Topics in Current Chemistry, Vol. 198 © Springer Verlag Berlin Heidelberg 1998
2 J.P. Glusker 5 Interactions of Planar Functional Groups in Proteins . . . . . . . . . 26 5.1 Surroundings ofCarboxylate Groups . . . . . . . . . . . . . . . . . . 26 5.2 Surroundings of Imidazole and Histidine Groups . . . . . . . . . . . 29 5.3 Surroundings of Arginine Side Chains in Proteins . . . . . . . . . . . 30 5.4 Surroundings of a-Hydroxycarboxylate Groups . . . . . . . . . . . . 31 6 Metal Ion-Based Directional Interactions . . . . . . . . . . . . . . . 31 6.1 Metal Ion Coordination . . . . . . . . . . . . . . . . . . . . . . . . . . 33 6.2 Magnesium Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 6.3 Zinc Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 6.4 Calcium Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 6.5 Ionophores and Other Metal-Binding Molecules . . . . . . . . . . . . 37 6.6 Metal-Binding Sites in Proteins . . . . . . . . . . . . . . . . . . . . . 38 7 Networks of Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 39 7.1 Descriptions of Hydrogen Bonding Networks . . . . . . . . . . . . . 40 8 Crystal Surface Recognition and Chirality . . . . . . . . . . . . . . . 40 9 Applications to Macromolecular Structures . . . . . . . . . . . . . . 42 9.1 Binding of Drugs to Dihydrofolate Reductase . . . . . . . . . . . . . 42 9.2 Binding of Drugs to Nucleic Acids . . . . . . . . . . . . . . . . . . . . 44 9.3 Protein-Nucleic Acid Interactions . . . . . . . . . . . . . . . . . . . . 50 10 Incipient Chemical Reaction Pathways . . . . . . . . . . . . . . . . . 52 11 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 12 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 List of Abbreviations and Symbols A adenine A ◊ T, G ◊ C base pairs C cytosine CSD Cambridge Structural Database DNA deoxyribonucleic acid G guanine ICSD Inorganic Crystal Structure Database NADPH nicotinamide adenine dinucleotide phosphate PAH polycyclic aromatic hydrocarbon PDB Protein Data Bank T thymine
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Page 3 and 4: Design of Organic Solids Volume Edi
Page 5 and 6: Volume Editors Prof. Dr. Edwin Webe
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Springer and the environment At Spr
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