Catalysis in Chemistry and Biochemistry Theory and Experiment: Proceedings of the Twelfth Jerusalem Symposium on Quantum Chemistry and Biochemistry held in Jerusalem, Israel, April 2–4, 1979

389 Pages·1979·14.25 MB·English

by  Bernard Pullman (auth.)

CATALYSIS IN CHEMISTRY AND BIOCHEMISTRY
THEORY AND EXPERIMENT
THE JERUSALEM SYMPOSIA ON
QUANTUM CHEMISTRY AND BIOCHEMISTRY
Published by the Israel Academy of Sciences and Humanities,
distributed by Academic Press (N. Y.)
1st JERUSALEM SYMPOSIUM: The Physicochemical Aspects of Carcinogenesis
(October 1968)
2nd JERUSALEM SYMPOSIUM: Quantum Aspects ofH eterocyclic Compounds in
Chemistry and Biochemistry (April 1969)
3rd JERUSALEM SYMPOSIUM: Aromaticity, Pseudo-Aromaticity, Antiaromaticity
(April 1970)
4th JERUSALEM SYMPOSIUM: ThePurines: Theory and Experiment
(April 1971)
5th JERUSALEM SYMPOSIUM: The Conformation of Biological Molecules and
Polymers (April 1972)
Published by the Israel Academy ofS ciences and Humanities,
distributed by D. Reidel Publishing Company (Dordrecht, Boston and London)
6th JERUSALEM SYMPOSIUM: Chemical and Biochemical Reactivity
(April 1973)
Published and distributed by D. Reidel Publishing Company
(Dordrecht, Boston and London)
7th JERUSALEM SYMPOSIUM: Moleculatand Quantum Pharmacology
(March/April 1974)
8th JER U SALEM SYMPO SlUM: Environmental Effects on Molecular Structure and
Properties (April 1975)
9th JERUSALEM SYMPO SlUM: Metal-Ligand Interactions in Organic Chemistry
and Biochemistry (April 1976)
10th JERUSALEM SYMPOSIUM: Excited States in Organic Chemistry and
Biochemistry (March 1977)
VOLUME 12
CATALYSIS IN CHEMISTRY
AND BIOCHEMISTRY
THEORY AND EXPERIMENT
PROCEEDINGS OF THE TWELFTH JERUSALEM SYMPOSIUM ON
QUANTUM CHEMISTRY AND BIOCHEMISTRY HELD IN
JERUSALEM, ISRAEL, APRIL 2-4, 1979
Edited by
BERNARD PULLMAN
'universite Pie"e et Marie Curie (PARIS VI)
Institut de Biologie Physico-Chimique
(Fondotion Edmond de Rothschild), Paris, France
D. REIDEL PUBLISHING COMPANY
DORDRECHT : HOLLAND I BOSTON: U.S.A.
LONDON:ENGLAND
Library of Congress Cataloging in Publication Data ~
~
Jerusalem Symposium on Quantum Chemistry and Biochemistry, 12th, 1979.
Catalysis in chemistry and biochemistry.
(The Jerusalem symposia on quantum chemistry and biochemistry; v. 12)
Includes indexes.
1. Catalysis-Congresses. I. Pullman, Bernard, 1919- II. Title.
III. Series: Jerusalem symposia on quantum chemistry and biochemistry; v. 12.
QD505.H47 1979 541'.395 79-19397
ISBN-13: 978-94-009-9515-4 e-ISBN-13: 978-94-009-9513-0
001: I 0.1 007/978-94-009-9513-0
Published by D. Reidel Publishing Company,
P.O. Box 17, Dordrecht, Holland
Sold and distributed in the U.S.A., Canada, and Mexico
by D. Reidel Publishing Company, Inc.
Lincoln Building, 160 Old Derby Street, Hingham
Mass. 02043, U.S.A.
All Rights Reserved
Copyright © 1979 by D. Reidel Publishing Company, Dordrecht, Holland
Softcover reprint of the hardcover 1s t edition 1979
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 photocopying, recording or by any information storage and
retrieval system, without written permission from the copyright owner
TABLE OF CONTENTS
PREFACE ix
BERNARD PULLMAN / The Macromolecular Electrostatic Effect
in Biochemical Reactivity of the Nucleic Acids
JILL E. GREADY / Dynamic and Statistical Aspects of Enzyme
11
Action
ANTHONY J. KIRBY / Efficiency and Mechanism in Intramolecular
Catalysis 25
CLAUDE BALNY, GASTON HUI BON HOA, and PIERRE DOUZOU / Cryo
enzymology in Reverse Micelles 37
D. DEMOULIN and A. PULLMAN / Theoretical Studies on Models
of the Active Site of Carbonic Anhydrase 51
BO JoNSSON / The Mechanism of Carbonic Anhydrase - A Solvation
Problem? 67
DAVID M. HAYES and PETER A. KOLLMAN / A Comparison of the
Energetics of Proton Transfer in the Serine and
Cysteine 'Charge Relay' Systems and the Role of the
Protein Electrostatic Potential on the Proton Transfer
Energetics 77
FARIZA B. HASAN and SAUL G. COHEN / Hydrolysis by Acetyl
cholinesterase. Trimethyl and Methyl Subsites 91
YAIR DEGANI and CHEMDA DEGANI / Creatine Kinase: An Asymmetric
Dimer operating by a 'One-at-a-Time' Mechanism 99
HENRY Z. SABLE and DEBRA J. MESCHKE / Studies on the Mechanism
of Catalysis by Thiamin: Progress and Problems 113
GAVRIELLA GABOR / The Conformation of Cocarboxylase (Thiamine
Pyrophosphate) 125
FRANK JORDAN, BIJAN FARZAMI, and OLUFEMI B. AKINYOSOYE / Probing
the Mechanism of Binding of the Thiamin Pyrophosphate
Co-Enzyme on Yeast Pyruvate Decarboxylase 131
vi TABLE OF CONTENTS
MICHAEL H. PALMER and ROELOF J. PLATENKAMP / Ab Initio Orbital
Studies of the Flavins 147
H.J. GRANDE, F. MuLLER, C. VAN SCHAGEN, W.H. SCOUTEN, C. VEEGER
and A.J.W.G. VISSER / Flavin Catalysis, the Experimental
Approach 171
R.C. BAETZOLD / Molecular Orbital Calculations of Metal
M.icrocluster Properties 191
ROBERT L. BURWELL Jr. / Structure Sensitivity and Supported
Platinum Catalysts 207
F. CYROT-LACKMANN / Relation Between Catalytic and Electronic
Properties of Transition Metals 217
J.
P. HEIMBACH, KLUTH, and H. SCHENKLUHN / Basic Parameters in
Metal-Catalysed Processes: Method of Inverse Titration 227
ANGELO CAVEZZOTTI and MASSIMO SIHOI-iETTA / The Chemisorption
of Acetylene on the Pt(III) Surface. Extended
Huckel Results 241
HENRI BRUNNER / Asymmetric Homogeneous Hydrogenation of Pro
chiral Olefins and Control of the Metal Configuration
in Labile Optically Active Organotransition Metal
Complexes 255
JOCHANAN BLUM, ILAN PRI-BAR, and OURI BUCHMAN / Homogeneous
and Heterogeneous Hydrogen Transfer in Carbinols by
Group VIII Metal Catalysts 265
H. LEHMKUHL. K. MEHLER, A. RUFINSKA, and D. SEKUTOWSKI / The
Cooperate Effect of Organomagnesium and Nickel Com-
Pounds in the Catalytic Oligomerization of 1,3-Dienes 273
H.-F. KLEIN, R. HAMMER, J. WENNINGER, and J. GROSS / Trimethyl
phosphine Cobaltates containing Monoolefin and Dinitrogen
Ligands - Model Compounds for Homogeneous Catalysis 285
.JONATHAN B. COHEN and NORMAN D. BOYD / Conformational Transitions
of the Membrane-Bound Cholinergic Receptor 293
PETER POLITZER and VERNON M. ESTES / The Catalytic Effect of
Hydrogen Bonding upon Epoxide Ring-Opening 305
E. BAYER / A Comparison of Dioxygen Activation by Biochemical
and Synthetic Polymeric Chemical Systems 323
O. FROMM and J. KOUTECKY / Surface and End Effects in the
Electronic Structure of Crystals and Polymers 335
PIERO PINO, ANNIBALE STEFANI, and GIAMBATTISTA CONSIGLIO /
Some Aspects of Asymmetric Induction in Addition
Reactions to Olefins 347
TABLE OF CONTENTS vii
HANS-DIETER SCHARF and ROBERT ~~ITZ / The Catalytic Function
of Anthraquinones in the Photooxidation of Chloride
to Chlorine 355
JOOST MANASSEN / Tetraphenylporphyrin Complexes as Chemical,
Photo- and Electro-Catalysts 367
INDEX OF SUBJECTS
377
INDEX OF NAMES
PREFACE
The 12th JerusaLem'Symposium was devoted to the exciting sub
ject of CataLysis in Chemistry and Biochemistry. As usuaL in these Sym
posia Theory and Experiment have been considered simuLtaneousLy in dis
cussions> invoLving renowned experts from many countries.
We wish to thank aLL those who made this meeting possibLe and
contributed to its success: the Baron de RothschiLd whose continuous
generosity is at the source of these gatherings, the IsraeL Academy of
Sciences and Humanities which offers us the cordiaL hospitaLity of its
impressive and beautifuL buiLding and gardens and the Hebrew University
of JerusaLem, faithfuL cosponsor of the Symposia.
THE MACROMOLECULAR ELECTROSTATIC EFFECT IN BIOCHEMICAL OF
~EACTIVITY
THE NUCLEIC ACIDS.
BERNARD PULUIAN
Institut de BioLogie Physico-Chimique, Laboratoire de
Biochimie Theorique, aSSOCle au C.N.R.S., 13, rue P. et M.
Curie, Paris 75005, France.
1. INTRODUCTION
The roLe of the macromoLecuLe and of its overaLL structure upon the
reactivity of its reaction site(s) represents one of the fundamentaL
probLems in the theory of cataLysis. The most impressive and most fre
quentLy considered exampLes occur in the fieLd of proteins where the
probLem generaLLy consists of accounting for the enhancement of the
reaction rate at the active site or at the coenzyme with respect to
modeL systems, devoid of the macromoLecuLar superstructure. Different
effects have been considered as possibLy responsibLe for the infLuence
of the macromoLecuLe on such LocaLized-site reactions. I do not have
the time to summarize or discuss them here. I wouLd Like, however, to
underLine the accent put recentLy in a number of studies, on the possi
bLy primordial role in this respect of the electrostatic effect of the
protein on its specific reactivities. Examples of such considerations
may be found in the work of Hayes and Kollman on carboxypeptidase A
[1][2], in the work of Warshel on lysozyme [3][4], in the work of Van
Duijnen on the role of the a-helix dipole on the reactional properties
of proteins, in particular papain [5][6] etc. (For generaL comments
see also [7]). The different authors differ in the details of their
approach, but have in common to Limit their consideration to proteins.
It is, however, evident that similar effects may be conside
red aLso for other types of biopolymers in particular for nucLeic acids
in which it appears legitimate to ask what is the infLuence of the
overall macromoLecular structure of, say DNA, upon the properties of
the different reaction sites of, say, its purine and pyrimidine bases.
It is this problem that we wish to treat here. I would like
to state immediately that we shalL limit ourselves to consider only
the eLectrostatic aspect of this influence and shalL neglect, for the
while being, other possible aspects. This restriction introduces a se
vere limitation if we wish to compare the resuLts of computations with
experimental findings (vide infra). However, in as much as it may be
estimated that the electrostatic effect is an important one, the study
is obviously of interest if onLy as a step towards a more complete ex-
B. Pullman (Ed.); Catalysis in Chemistry and Biochemistry. Theory and Experiment. 1-10.
Copyright © 1979 by D. Reidel Publishing Company.
2 BERNARD PULLMAN
pLoration.
II. THE ELECTROSTATIC MOLECULAR POTENTIAL
For the sake of expLoring the eLectrostatic effect of the macromoLecu
Lar structure of DNA upon the properties of its purine and pyrimidine
bases we shaLL use the notion of the eLectrostatic moLecuLar potentiaL,
about which Madame PuLLman has Lectured aLready here at a previous
m.
JerusaLem Symposium [ May I remind that under this denomination we
consider the eLectrostatic potentiaL created in the neighbouring space
by the nucLear charges and the electronic distribution of the system.
For a given wave function with the corresponding first order density
function p(i) the average vaLue of such a potentiaL V(P) at a given
point P in space is given by [9]
V(P) = 1: ~ _ p(;) de.
a raP rpi 1
where Z is the nucLear charge of nucLeus a. This quantity has the ad
vantageaof being directLy obtainabLe from the wave function and thus
does not suffer from the drawbacks inherent in the cLassicaL popuLa
tion anaLysis. Moreover its very definition makes it an interesting
index for the study of chemicaL reactivity at Least in the earLy stage
of approach of an ionic reagent. Thus the interaction energy between
the moLecuLar eLectronic distribution (considered unperturbed) and an
externaL point charge q pLaced at point P is qV(P), which is rigou
rousLy the first order perturbation energy of the moLecuLe in the
fieLd of charge q. Taking q as a unit positive charge the interaction
potentiaL can be used directLy for the study of proton affinities. (See
e.g. [10-12] for such a study of the nucLeic acid bases). Its utiLiza
tion for the investigation of the interaction of the Ligands with more
compLex cations such as metaL or aLkyL cations is subject to caution
because of the increased importance in such cases of the compLementary
components of the binding energy (besides the pureLy couLombic one)
nameLy the delocaLization (poLarization + charge transfer) and the ex
change components. The probLem has been investigated expLicitLy in our
Laboratory in reLation with the interaction of the nucLeic acid bases
with Na+ [13], Mg++ [14] and aLso with aLkyL cations [15] •
With this (important) restriction in mind we wouLd Like to
investigate, as the first stage of the expLoration of the effect of
the macromoLecuLar superstructure, the modifications in the moLecuLar
potentiaLs of the individuaL bases brought about by their pairing
through hydrogen bonding in the Watson-Crick compLementary scheme of
DNA : adenine-thymine and guanine-cytosine. The usuaL way of represen~
ting these potentiaLs is, as is weLL known, through the utilization of
the eLectrostatic isopotentiaL maps. Here we shaLL center our atten
tion essentiaLLy on the regions surrounding the minima of the poten
tiaLs in the most attractive regions, which are situated in the isoLa
ted bases in the moLecuLar pLane in the neighbourhood of N1, N3 and
N7 of adenine, N7, 06, N3 of guanine, N1, 02 of cytosine and 04' 02
of thymi ne (i n the order i ndi cated for eacti base).