Computational Approaches in Supramolecular Chemistry: (426 NATO Science Series C)

This text provides a broad presentation of computer and molecular modelling approaches in supramolecular chemistry. Since it has evolved from a NATO meeting which brought together half computer scientists and half experimentalists, experimental results are also presented. Computations mostly involve molecular mechanics, molecular dynamics, Monte Carlo, free energy simulations and computer graphics. Applications extend from synthetic or biological receptor-substrate or host-guest complexes to molecular assemblies, such as layers, membranes, channels and mesomorphic phases. Gas phase clusters, crystals and liquids, adsorption in chromatography, and drug design are also presented. The book is aimed at the many scientists interested in the atomic level understanding and modelling of the structural and thermodynamical features involved in the processes of molecular recognition and supramolecular organization in chemistry, physics, and biology, involving noncovalent binding interactions.

Table of Contents:
1 Water structure from computational chemistry.- 2 Ionic hydrogen bond assemblies in clusters: resources and opportunities for modeling.- 3 Non-covalent interactions in organic crystals, and the calibration of empirical force fields.- 4 Hydrogen-bond descriptors for solute molecules.- 5 Molecular recognition of dinucleotides and amino acids by artificial receptors containing a bicyclic guanidinium subunit.- 6 Intra- and intermolecular hydrogen bonding control of supramolecular structure.- 7 New supramolecular architecture based on hydrogen bonding..- 8 Studies toward computer liquid phase simulations of the solvent-dependency of apolar association strength: conformational analysis of a cyclophane-pyrene complex by pseudo Monte Carlo and Molecular Dynamics methods.- 9 Rational approaches towards protease inhibition: predicting the binding of thrombin inhibitors.- 10 Receptor-ligand interactions in pharmacology and drug design.- 11 Modeling interactions with benzene: aryl-aryl, cation-?, and chaotrope-?.- 12 The nature of molecular recognition: examples from host/guest chemistry.- 13 Computational aspects in supramolecular chemistry: chiral discrimination in chromatography.- 14 Determination of conformationally dependent point charges for potential of mean force simulations.- 15 Structural and dynamic features of molecular clips derived from diphenylglycoluril.- 16 Solvation and complexation: from cation complexation to excited-state stabilisation.- 17 Metallocycles and -clefts.- 18 Experimental approaches to interaction energies and structures in supramolecular complexes.- 19 Complexation of ions and neutral molecules by functionalized calixarenes.- 20 Experimental and computational studies of cation-? interactions in natural and synthetic receptors. Benzene as apseudoanion.- 21 Architecture of new concave host molecules.- 22 MD Simulations on synthetic ionophores and their cation complexes: Comparison of aqueous/non-aqueous solvents.- 23 The role of energy calculations in the design, synthesis and study of biologically active Iron(III carriers.- 24 A simple approach to modelling supramolecular complexes and mechanically-interlocked molecules.- 25 Molecular motions in catenands and catenates studied by 13C NMR relaxation times.- 26 Simulation of self-assembled monolayers: Microscopic structure of amino alkylthiols.- 27 Langmuir films of amphiphilic alcohols and surfaces of polar crystals as templates for ice nucleation.- 28 Molecular dynamics study of a sequence specific protein-DNA interaction.- 29 Molecular dynamics simulation of a DNA binding protein free and in complex with DNA.- 30 Supramolecular interactions and atomic dynamics in proteins and peptide crystals. Jumps, lattice waves, and liquide-like diffusion.- 31 Molecular recognition: an example from ligand binding to proteins.- 32 HIV-1 proteinase inhibitor binding. The effect of active site conformational restraints on calculated free energies of ligand binding.- 33 Free energy and binding selectivity.- 34 Structure and dynamics of the sidechains of the gramicidin channel in a DMPC bilayer.