Computational Approaches in Supramolecular Chemistry

528 Pages·1994·36.786 MB·English

by  G. Corongiu, E. Clementi (auth.), Georges Wipff (eds.)

Computational Approaches in
Supramofeeular Chemistry
NATO ASI Series
Advanced Science Institutes Series
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1 Global Environmental Change
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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