Computational Approaches in Supramofeeular Chemistry NATO ASI Series Advanced Science Institutes Series A Series presenting the results of activities sponsored by the NATO Science Committee, which aims at the dissemination of advanced scientific and technological knowledge, with a view to strengthening links between scientific communities. The Series is published by an international board of publishers in conjunction with the NATO Scientific Affairs Division A Life Sciences Plenum Publishing Corporation B Physics London and New York C Mathematical Kluwer Academic Publishers and Physical Sciences Dordrecht, Boston and London D Behavioural and Social Sciences E Applied Sciences F Computer and Systems Sciences Springer-Verlag G Ecological Sciences Berlin, Heidelberg, New York, London, H Cell Biology Paris and Tokyo 1 Global Environmental Change NATO-PCO-DATA BASE The electronic index to the NATO ASI Series provides full bibliographical references (with keywords and/or abstracts) to more than 30000 contributions from international scientists published in all sections of the NATO ASI Series. Access to the NATO-PCO-DATA BASE is possible in two ways: - via online FILE 128 (NATO-PCO-DATA BASE) hosted by ESRIN, Via Galileo Galilei, I-00044 Frascati, Italy. - via CD-ROM "NATO-PCO-DATA BASE" with user-friendly retrieval software in English, French and German (© WTV GmbH and DATAWARE Technologies Inc. 1989). The CD-ROM can be ordered through any member o f the Board of Publishers or through NATO-PCO, Overijse, Belgium. Series C: Mathematical and Physical Sciences - Vol. 426 Computational Approaches in Supramolecular Chemistry edited by Georges Wipff University Louis Pasteur, Laboratory of Molecular Modeling and Simulations, URA-CNRS, Strasbourg, France Springer-Science+Business Media, B.V. Proceedings of the NATO Advanced Research Workshop on Computational Approaches in Supramolecular Chemistry "The Bischenberg" (near Strasbourg), France September 1-5,1993 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN 978-94-010-4460-8 ISBN 978-94-011-1058-7 (eBook) DOI 10.1007/978-94-011-1058-7 Printed on acid-free paper All Rights Reserved ©1994 Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 1994 Softcover reprint of the hardcover 1st edition 1994 No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photo¬ copying, recording or by any information storage and retrieval system, without written permission from the copyright owner. This book contains the proceedings of a NATO Advanced Research Workshop held within the programme of activities of the NATO Special Programme on Supramolecular Chemistry as part of the activities of the NATO Science Com mittee. T ABLE OF CONTENTS Page Preface: G. WIPFF xi - xv 1 - 29 1) Water structure from computational chemistry. G. CORONGIU and E.CLEMENTI 31 - 49 2) Ionic hydrogen bond assemblies in clusters: resources and opportunities for modeling. M. MEOT-NER (MAUTNER) 51 - 62 3) Non-covalent interactions in organic crystals, and the calibration of empirical force fields. A. GAVEZZOTTI, and G. FILIPPINI 63 - 78 4) Hydrogen-bond descriptors for solute molecules. M. H. ABRAHAM 79 - 99 5) Molecular recogOltlOn of dinucleotides and amino acids by artificial receptors containing a bicyclic guanidinium subunit. J. de MENDOZA, and F. GAGO 101 - 108 6) Intra- and intermolecular hydrogen bonding control of supramolecular structure. A. D. HAMILTON, Y. HAMURO, J. YANG, S. J. GEIB, and E. FAN 109 - 115 7) New supramolecular architecture based on hydrogen bonding. S. C. ZIMMERMAN, and T. J. MURRAY 117 - 136 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. T. MORDASINI DENTI, W. van GUNSTEREN, and F. DIEDERICH viii 137 - 149 9) Rational approaches towards protease inhibition: predicting the binding of thrombin inhibitors. P. D. J. GROOTENHUIS, and S. P. van HEIDEN 151 - 159 10) Receptor-ligand interactions in pharmacology and drug design. M. F. HIBERT, S. TRUMPP -KALLMEYER, and J. HOFLACK 161 - 173 11) Modeling interactions with benzene : aryl-aryl, cation-1t, and chaotrope-1t. W. L. JORGENSEN, D. L. SEVERANCE, and E. M. DUFFY 175 - 181 12) The nature of molecular recogmtIOn: examples from host I guest chemistry. P. A. KOLLMAN 183 - 198 13) Computational aspects in supramolecular chemistry chiral discrimination in chromatography. K. B. LIPKOWITZ, and A. G. ANDERSON 199 - 204 14) Determination of conformationally dependent point charges for potential of mean force simulations. T. J. MARRONE, D. S. HARTSOUGH, and K. M. MERZ Jr 205 - 219 15) Structural and dynamic features of molecular clips derived from diphenylglycoluril. J. N. H. REEK, R. P. SIJBESMA, and R. J. M. NOLlE 221 - 235 16) Solvation and complexation : from cation complexation to excited-state stabilisation. D. PARKER 237 - 264 17) Metallocycles and -clefts. F. C. J. M. van VEGGEL, W. P. van HOORN, and D. N. REINHOUDT 265 - 276 18) Experimental approaches to interaction energies and structures in supramolecular complexes. H.-J. SCHNEIDER, V. RUDIGER, and M. WANG ix 277 - 300 19) Complexation of ions and neutral molecules by functionalized calixarenes. R. UNGARO, A. ARDUINI, A. CASNA TI, O. ORI, A. POCHINI, and F. UGOZZOLI 301 -309 20) Experimental and computational studies of cation-TC interactions in natural and synthetic receptors. Benzene as a pseudoanion. D. A. DOUGHERTY, P.e. KEARNEY, L. S. MIZOUE, R. A. KUMPF, J. E. FORMAN, and A. McCURDY 311 - 317 21) Architecture of new concave host molecules. F. VOGTLE, C. SEEL, R. BERSCHEID, J. GROB, and P.-M. WINDSCHEIF 319 - 348 22) MD Simulations on synthetic ionophores and their cation complexes: Comparison of aqueous / non-aqueous solvents. G. WIPFF, L. TROXLER 349 - 376 23) The role of energy calculations in the design, synthesis and study of biologically active Iron(lII) carriers. S. LIFSON, C. E. FELDER, J. LIBMAN, and A. SHANZER 377 - 390 24) A simple approach to modelling supramolecular complexes and mechanically-interlocked molecules. H. G. RICKETTS, J. F. STODDART, and M. M. HANN 391 - 398 25) Molecular motions in catenands and catenates studied by 13C NMR relaxation times. J-P. KINTZINGER, H. BOURGEOIS, A. EDEL, R. GRAFF, J.-C. CHAMBRON, e. O. DIETRICH - BUCHECKER, and J.-P. SAUVAGE 399 - 409 26) Simulation of self-assembled monolayers: Microscopic structure of amino alkylthiols. U. ROTHLISBERGER, M. L. KLEIN, and M. SPRIK 411 - 418 27) Langmuir films of amphiphilic alcohols and surfaces of polar crystals as templates for ice nucleation. R. POPOVITZ-BIRO, J. MAJEWSKI,1. L. WANG, K. KJAER, J. ALS-NIELSEN, M. LAHAV, and L. LEISEROWITZ x 419 - 439 28) Molecular dynamics study of a sequence specific protein-DNA interaction. T. BISHOP, and K. SCHULTEN 441 - 456 29) Molecular dynamics simulation of a DNA binding protein free and in complex with DNA. M. ERIKSSON, T. HARD, and L. NILSSON 457 - 475 30) Supramolecular interactions and atomic dynamics in proteins and peptide crystals. Jumps, lattice waves, and liquide-like diffusion. J. C. SMITH, D. DURAND, M. FIELD, S. FUROIS-CORBIN, G. R. KNELLER, M. NINA, and B. ROUX 477 - 494 31) Molecular recogmtIOn: an example from ligand binding to proteins. M. KARPLUS, and F. T. K. LAU 495 - 513 32) HIV -1 proteinase inhibitor binding. The effect of active site conformational restraints on calculated free energies of ligand binding. T. P. STRAATSMA 515 - 517 33) Free energy and binding selectivity. J. A. McCAMMON 519 - 531 34) Structure and dynamics of the sidechains of the gramicidin channel in a DMPC bilayer. T. B. WOOLF, J. DESHARNAIS, and B. ROUX PREFACE Supramolecular chemistry has been defined by J.-M. Lehn as "a highly interdisciplinary field of science covering the chemical, physical, and biological features of chemical species of higher complexity, that are held together and organized by means of intermolecular (noncovalent) binding interactions" (Science, 1993). Recognition, reactivity, and transport represent three basic functional features, in essence dynami~s, which may be translated into structural features. The purpose of the NATO workshop which took place september 1-5, 1993 at the Bischenberg (near Strasbourg) was to present computations which may contribute to the atomic level understanding of the structural and thermodynamical features involved in the processes of molecular recognition and supramolecular organization. The main focus was therefore, on the many facets of "supra-molecular modeling". Other applications of computers in chemistry, such as automation, simulation of processes, procedures for fitting kinetic or thermodynamic data, computer assisted synthetic strategies, use of data bases for structure elucidation or for bibliographic searches, have an obvious impact in supramolecular chemistry as well, but were not presented at the workshop. As reflected in the book, the participants consisted of approximately half "experimentalists" and half "theoreticians" who presented lectures which covered two main areas of supramolecular chemistry: (i) supermolecules, well defined oligomeric species of a few components with a given stoichiometry (for instance, "Receptor-Substrate" or "Host Guest" complexes), and (ii) molecular assemblies, resulting from a undefined number of components in a specific phase having a more or less well defined microscopic organization (layers, membranes, vesicles, micelles, mesomorphic phases, etc). Although supramolecular chemistry deals basically with chemically synthesized systems, biological systems involved in molecular recognition, or molecular assembling processes are, in essence of supramolecular nature and were considered. Molecular modeling in pharmacology and drug design also contributes to the field. Common features of all of these systems are non-covalent interactions such as hydrogen bonding, electrostatic, van der Waals, and donor-acceptor interactions, which provide the "glue" linking molecules, leading to "structure-specific interactions of high selectivity" (Nobel prize of Pedersen, Lehn, Cram; 1987). Supramolecular chemistry is an excellent field to test and develop simulation and computer modeling tools. The synthetic systems are generally chemically well defined. They are characterized in terms of their structures in the solid state and in solution, and thermodynamic and kinetic data are available. They are therefore particularly suitable for computational approaches. Supramolecular chemistry also offers rich and challenging xi