Supramolecular NATO ASI Series Advanced Science Institutes Series

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Series C: Mathematical and Physical Sciences - Vol. 473 Supramolecular Stereochemistry

edited by Jay S. Siegel Department of Chemistry, University of California, San Diego, California, U.S.A.

SPRINGER-SCIENCE+BUSINESS MEDIA, B.V. Proceedings of the NATO Advanced Research Workshop on Supramolecular Stereochemistry Hveragerdi, Iceland September 14-19,1994

A C.I.P. Catalogue record for this book is available from the Library of Congress.

ISBN 978-94-010-4157-7 ISBN 978-94-011-0353-4 (eBook) DOI 10.1007/978-94-011-0353-4

Printed on acid-free paper

All Rights Reserved © 1995 Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 1995 Softcover reprint of the hardcover 1st edition 1995 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 Committee.

Other books previously published as a result of the activities of the Special Programme are:

WIPFF, G. (Ed.), Computational Approaches in Supramolecular Chemistry. (ASIC 426) 1994. ISBN 0-7923-2767-5 FLEISCHAKER, G.R., COLONNA, S. and LUISI, P.L. (Eds.), Self-Production of Supramolecular Structures. From Synthetic Structures to Models of Minimal Living Systems. (ASIC 446) 1994. ISBN 0-7923-3163-X FABBRIZZI, L., POGGI, A. (Eds.), Transition Metals in Supramolecular Chemistry. (ASIC 448) 1994. ISBN 0-7923-3196-6 BECHER, J., SCHAUMBURG, K. (Eds.), Molecular Engineering for Advanced Materials. (ASIC 456) 1995. ISBN 0-7923-3347-0 LA MAR, G.N. (Ed.), Nuclear Magnetic Resonance ofParamagnetic Macromolecules. (ASIC 457) 1995. ISBN 0-7923-3348-9 to my mother in memory ofmyfather Table of Contents

Preface Xlll

Introduction xv

SECTION I: PLENARY CONTRIBUTIONS

Macromolecular Stereochemistry: The Differing Roles of a Helix Reversal in Dilute Solution, in a Liquid Crystal, and in a Polymer Blend Mark M. Green*

From Molecular to Supramolecular J.H. Van Esch, N.A.J.M. Sommerdijk, R.J.H. Hajkamp, M.e. Feiters, and R.J.M. Nolte* 3

Template Induced Control of Stereochemistry for the Synthesis of Polymers G. Wulff* 13

Dendrimers - Nanoscopic Supermolecules According to Dendritic Rules and Principles Donald A. Tomalia* 21

Construction of DNA Polyhedra and Knots Through Symmetry Minimization Nadrian e. Seeman*, Yuwen Zhang, Shou Ming Du, and Junghuei Chen 27

Molecular Recognition by Catenated Structures David B. Amabilino*, and J. Fraser Stoddart* 33

Novel Protein Topologies Kurt Mislow*, and Chengzhi Liang 41

A New Molecular Encoding System Steven A. Benner*, Jennifer Horlacher, Johannes Vogel, and Ulrike von Krosigk 47

Recognition of B vs. Z-Form DNA using Nickel and Cobalt Complexes Cynthia J. Burrows*, James G. Muller, Hui-Cheng Shih, and Steven E. Rokita 57

Principles of Antibody Catalysis Donald Hilvert* 63

Mechanistic Studies on the Formation of BZIP·DNA Interfaces. A Simple Example of Supramolecular Stereochemistry David N. Paolella, e. Rodgers Palmer, Steven J. Metallo, and Alanna Schepartz* 83 x

Chiral Discrimination in Crystalline Systems: Facts, Interpretations, and Speculations A. Collet*, L. Ziminski, C. Garcia, and F. Vigne-Maeder 91

A Carbohydrate-Carbohydrate Interaction in Water using a Synthetic Model System S. Penades* III

Design of Host Molecules Capable of Forming Extremely Stable Host-Guest Complexes Barbara J. Whitlock, and Howard W. Whitlock* 117

Structural Control over the Formation of Calcium Carbonate Mineral Phases in Biomineralization L. Addadi*, J. Aizenberg, S. Albeck, G. Falini, and S. Weiner 127

Hydrogen Bonding Control of Molecular Self-Assembly Ji Yang, Jean-Luc Marendez, Abdullah ZaJar, Steven J. Geib, and Andrew D. Hamilton* 141

Supramolecular Stereochemistry of Supercharged Polycyclic Aromatic Hydrocarbons Lawrence T. Scott* 147

Enhancement of Electrostatic Binding Through Cooperative Interactions: EnthalpylEntropy Compensation and Peptide-Peptide Recognition Mark S. Searle, Martin S. Westwell, Patrick Groves, Gary J. Sharman, and Dudley H. Williams* 151

Toward Columns and Channels from Torands and Molecular Coils Thomas W. Bell*, Aaron M. Heiss, Helene Jousselin, and Richard T. Ludwig 161

SECTION II: POSTER CONTRIBUTIONS

QMView: As a Supramolecular Visualization Tool Kim K. Baldridge*, and Jerry P. Greenberg 169

Cis-trans-trans-l,2,3,4-Tetracyclohexylcyclohexane: A Monocyclic Unconstrained Cyclohexane Existing in a Twist-Boat Conformation [shay Columbus, Shmuel Cohen, and Silvio E. Biali* 179

The Conformation of Coumarin-Crown Ethers with Spin-Spin and Site Exchange Simulations (:akl1 Erk* 185 Xl

Clathration Properties of Propeller-Shaped Molecules Paolo Finocchiaro* 191

Control of Self-Assembly by Acid-Based Chemistry: Reversible Encapsulation of Xenon by Two Indentical Half-Shells R.M. Grotifeld*, N.R. Branda, C. Valdes, and J. Rebek, Jr. 195

Structural Diversity in a Family of Synthetic Oligoamides Adrian P. Bisson, Fiona J. Carver, Christopher A. Hunter*, Graham S. Lynch, N.J. Osborn, Duncan H. Purvis, Richard J. Shannon, and Kathryn Tse 199

Diastereospecific Recognition of Dyes by Salt Crystals: A Case of Plundered Stereochemistry in Postwar Europe Bart Kahr*, and Michael P. Kelley 203

Selectivity Enhancement by Concave Reagents U. Luning*, and W. Schyja 223

From p-tert-Butyl-Calix[6]arene to p-tert-Butyl-[1 6]metacyclophane. Isolation and Crystal Structure of a Mono Bridged Penta-Phosphoester J.-B. Regnoufde Vains*, R. Lamartine, S. Pellet-Rostaing, M. Perrin, A. Thozet, and S. Lecocq 227

Two Shells About a Nut: Carceplexes, Hemicarceplexes, and Highly Stable Ternary Complexes J.e. Sherman* 233

Cyclodextrin-Metallocene Inclusion Complexes V.I. Sokolov* 239

Dendritic Polyphosphates: Globular Polyelectrolytes? Yitzhak Tor* 247

Author Index 255

Subject Index 257

Preface

Organizing this meeting on Supramolecular Stereochemistry has been a fulfilling and eye• opening adventure. Good fortune reigned through out the process, from the encouragement I received at the outset, to the generous support from NATO and the US National Science Foundation, to the wonderfully positive response that came from the invitees, to the spectacular facilities and surroundings of the conference site in Iceland to the superior proceedings which led to the creation of this book.

Supramolecular Stereochemistry is a topic with enormous breadth, such that participants from widely diverse backgrounds could be invited. The conference brought together experts in polymer chemistry, bioorganic chemistry, crystallography, material science, dendrimer science, nanochemistry, conformational analysis, molecular recognition chemistry, and topological stereochemistry.

The conference was intensive with 29 lectures and 2 poster sessions in 4 days, but was accented by the beautiful Icelandic environment. The town of Hveragerdi, which hosted the meeting was located in an area 50 KIn east of Reykjavik, and provided an excellent isolated spot with a complete supportive infrastructure which allowed us to be about or work without extraneous worries.

It is a special opportunity to be able to document this event with this volume of the NATO-ARW Series. Thanks are due to the publisher for their abundant cooperation in this endeavor.

Jay S. Siegel La Jolla, California, 1995

xiii Acknowledgments

This workshop would not have been possible without the generous financial support of the NATO Supramolecular Chemistry Program (ARW-931583) and the US National Science Foundation. Publicity materials, programs, and conference flyers were provided by the San Diego Supercomputer Center; design and production by Gail Bamber and Kim Baldridge. Conference organization and reservations were handled by Luana Kaar. Many thanks to all.

xiv Introduction

Jay S. Siegel Department of Chemistry, University of California, San Diego, La Jolla, California 92093-0358.

The successful connection between molecular structure and energy accounts for the enormous development of chemistry in the 20th century. The concepts of chemical structure and energy were rigidly held apart by those 19th century chemists who believed that seeing molecular structure (if there was such a thing) was a fantasy never to be realized; however, the allure ofa tangible model for molecular structure proved irresistible to another group of chemists. These chemists perpetrated the fantasy of molecular structure as a connection between the visual three-dimensional mechanical world and the microscopic world of atoms and molecules, and ultimately founded the field of stereochemistry; the use of physical molecular models as representations of molecules (molecular ensembles) thus became the earmark of this field. One area of modern chemistry that has profited enormously from visual tradition of stereochemical models is supramolecular chemistry. Indeed, a century after the founding of stereochemistry, the scale and complexity of the chemical problems have expanded and the principles of stereochemistry have matured such that any supramolecular process can be well served by a parallel understanding of its stereochemistry.

Fundamentally, the tenets of supramolecular chemistry were first set down by the "grandfather of stereochemistry," Louis Pasteur. The main concepts associated with supramolecular phenomena (e.g. molecular recognition, inclusion, self-assembly, lock-n• key selectivity, extended-range order, and molecular transport) are contained in his address to the French Academy on the principles of enantiomer resolutions and characterizations. Without any specific structural theory, Pasteur realized that symmetry arguments and the then novel physical property of optical activity would allow him to follow a variety of recognition processes and aggregate phenomena. He realized the essential difference between organized systems which were reinforced only by the long range order of the medium (e.g., the chiral nature of quartz) and those with properties inherent to their molecular structure (e.g., the tartaric acids). His discussion of conglomerate vs. racemate formation (e.g., in tartaric acids) presaged the concepts of self-assembly and molecular recognition. He also demonstrated the ability of one molecule to recognize another through the formation of diastereomeric salts and compounds. Even the lock-n-key character of nature did not escape his purview, as he demonstrated the ability of yeast to recognize and selectively degrade only one chiral form of a , leading to the first . As stereochemistry developed post Pasteur, the connection with what is now supramolecular chemistry continued.

Supramolecular chemistry has been described as the chemistry of the non-covalent bond and this description has motivated much discussion of just what the noncovalent bond is, as well as when should we speak of supramolecules vs. molecules. A similar problem of bonding definitions has arisen in the discussion of vs. constitutional isomers and in the area of conformational analysis. The description of the molecule as a complete molecular graph with weighted edges, and the application of fuzzy logic has

xv xvi greatly aided these problems. The definitions of when two things are bonded vs. held together by non-covalent interactions has meaning only within a certain time scale• distance resolution-energy boundary; the same holds for molecular shape or symmetry. These ideas are inherent in Pauling's original definition "that there is a bond between two atoms or groups of atoms in the case that the forces acting between them are such as to lead to the formation of an aggregate with sufficient stability to make it convenient for the chemist to consider it as an independent molecular species." Thus, supramolecular chemistry is not so much a new branch of science as a new orientation within the time scale-distance resolution-energy coordinate system that defines every structural chemistry problem.

Reflecting on this analysis, one might ask whether supramolecular chemistry is simply "old tartrates in new vials." On the contrary, the coincidence between supramolecular chemistry and stereochemistry serves to amplify the synergy between them. For example, the realization that conformational analysis is dominated by intramolecular molecular recognition highlights the inalienable nature of stereochemistry in any discussion of "supramolecularity." Stereochemistry greatly simplifies supramolecular chemistry by dispelling the mystique ofsupramolecular jargon and sound-bites. Thus, the field becomes open to the development of investigations directed toward specific scientific questions rather than diffuse technical demonstrations. Along with this opening of research avenues emerges what we might call a experimental "uniqueness criterion," the fulfillment of which insures that every experiment is more than a derivative technical display.

The mechanical aspects of stereochemical models motivate chemists to design new structural motifs and mechanical analogies for supramolecular systems. Polymers of novel configuration and complexity, macrocycles and cyclophanes of novel topology, self-assembling monolayers and membranes, natural and unnatural biomolecular superstructures, catalytic antibodies and molecular receptors, and macroscopic and microscopic crystal habits represent a sampling of the targets now graspable to the modern chemist. With the advent of each new form of matter comes the challenge of providing an insightful chemical analysis of its structure and function. Beyond the mainstays of NMR and atomic resolution X-ray diffraction crystallography, modern techniques include scanning tunneling and atomic force microscopy, electron microscopy, laser ultrafast spectroscopy, and low angle X-ray scattering spectroscopy. Each of these structures manifests chemistry in space on the nanometer scale, and thus, we can speak of a "supramolecular stereochemistry" which employs the atomic resolution of molecular models to explain the nanometer/kilodalton metrics of suprachemical structures.

A successful conference on supramolecular stereochemistry should cover a broad range of structural chemical research, but at a deep philosophical level, with the goal of accenting what we can learn from selected labors rather than flaunting the unfiltered mass of labors lost. The conferees should provide a general enough base such that chemists from all fields can take home thought provoking lessons. Indeed, the following contributions were submitted with these goals in mind. The preceding comments are a few of the thoughts I have taken home after exposure to this caucus. The reader is warned that in order to capture the candid nature of the meeting, there has been little editing of these manuscripts. On the whole, this is a significant and provocative anthology of articles, each with its own special fulfillment of the uniqueness criterion as applied to research in supramolecular stereochemistry.