Fiber Diffraction Methods PDF
Preview Fiber Diffraction Methods
Fiber Diffraction Methods Alfred D. French, EDITOR Southern Regional Research Center KennCorwin H. Gardner, EDITOR E. I. Du Pont de Nemours & Company Based on a symposium sponsored by the Cellulose, Paper and Textile Division at the 178th Meeting of the American Chemical Society, Washington, D.C., September 10-14, 1979. 141 ACS SYMPOSIUM SERIES AMERICAN CHEMICAL SOCIETY WASHINGTON, D. C. 1980 In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. Library of Congress CIP Dat Fiber diffraction methods. (ACS symposium series; 141 ISSN 0097-6156) Includes bibliographies and index. 1. Polymers and polymerization—Analysis—Con gresses. 2. Textile fibers, Synthetic—Analysis—Con gresses. 3. X-rays—Diffraction—Congresses. I. French, Alfred D., 1943- . II. Gardner, KennCorwin H., 1947- . III. American Chemical Society. Cellulose, Paper and Textile Division. IV. Series: American Chemical Society. ACS symposium series; 141. QD380.F5 547.8'4046 80-21566 ISBN 0-8412-0589-2 ASCMC 8 141 1-518 1980 Copyright © 1980 American Chemical Society All Rights Reserved. The appearance of the code at the bottom of the first page of each article in this volume indicates the copyright owner's consent that reprographic copies of the article may be made for personal or internal use or for the personal or internal use of specific clients. This consent is given on the condition, however, that the copier pay the stated per copy fee through the Copyright Clearance Center, Inc. for copying beyond that permitted by Sections 107 or 108 of the U.S. Copyright Law. This consent does not extend to copying or transmission by any means—graphic or electronic—for any other purpose, such as for general distribution, for advertising or promotional purposes, for creating new collective works, for resale, or for information storage and retrieval systems. The citation of trade names and/or names of manufacturers in this publication is not to be construed as an endorsement or as approval by ACS of the commercial products or services referenced herein; nor should the mere reference herein to any drawing, specification, chemical process, or other data be regarded as a license or as a conveyance of any right or permission, to the holder, reader, or any other person or corporation, to manufacture, repro duce, use, or sell any patented invention or copyrighted work that may in any way be related thereto. PRINTED IN THE UNITED STATES OF AMERICA In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. ACS Symposium Series M. Joa Advisory Board David L. Allara W. Jeffrey Howe Kenneth B. Bischoff James D. Idol, Jr. Donald G. Crosby James P. Lodge Donald D. Dollberg Leon Petrakis Robert E. Feeney F. Sherwood Rowland Jack Halpern Alan C. Sartorelli Brian M. Harney Raymond B. Seymour Robert A. Hofstader Gunter Zweig In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. FOREWORD The ACS SYMPOSIUM SERIES founded i 1974 t provid a medium for publishin format of the Series parallels that of the continuing ADVANCES IN CHEMISTRY SERIES except that in order to save time the papers are not typeset but are reproduced as they are sub mitted by the authors in camera-ready form. Papers are re viewed under the supervision of the Editors with the assistance of the Series Advisory Board and are selected to maintain the integrity of the symposia; however, verbatim reproductions of previously published papers are not accepted. Both reviews and reports of research are acceptable since symposia may embrace both types of presentation. In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. PREFACE T his collection of papers was part of a unique symposium held during the 178th Meeting of the American Chemical Society. The symposium, Diffraction Methods for Structural Determination of Fibrous Polymers, had a pronounced international character, with scientists from 12 different countries. The speakers represented both the synthetic polymer and bio- polymer fields, with contributions in each of the three classes of natural polymers: nucleic acids, the symposium centered o polymers, methods that are usually taken for granted despite their inadequacies. In this volume, along with "method" papers, are contributions describ ing new structures that illustrate the methods and assumptions needed to determine the structure of a new polymer. Also included are reviews of classes of polymers for which investigation and methods development have coincided. The participants generally view fiber diffraction as the most useful method for determining the molecular arrangement of a polymer in the solid state, if the polymer is in the form of crystallites randomly ordered about a single axis. Other methods, such as IR spectroscopy, can provide information for evaluating a proposed structure. However, they are not usually as definitive as determining diffraction intensities, constructing a computer model of the polymer, and fitting the computer model to the diffraction data. Electron diffraction patterns often can supplement fiber diffraction patterns by providing information such as accurate cell dimensions and a confirmation of the space group. The sophistication of fiber diffraction has grown along with the devel opment of digital computers. These techniques started with the calculation of diffraction intensities for a few proposed models for comparison with the diffraction pattern. At present, parameters of the models can be varied to produce the minimal variance for the observed and calculated diffraction intensities and simultaneously the minimal stereochemical or packing energy. vii In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. Progress continues to depend on applying computers to several out standing problems. Several chapters deal with automated data collection and reduction. Better computer models and more efficient computer pro grams are being developed to determine the ranges of stereochemically feasible models to be considered. Another application reverses the usual procedures of structure determination. Instead of essentially correcting the observed data for disorder and amorphous scattering, a pattern that in cludes effects of these conditions is calculated. In this way, the conditions become parameters of the structure determination. Although not usually considered as "structural" information, the kind of disorder and its magni tude often have physical consequences. One stumbling block is the limitation of our techniques. For example, are Hamilton's tests appropriat applicable, these tests allo ence between R factors for two competing models. The tests are derived from analysis of variance, and the usual cautions for those analyses apply. But there are often large differences when different laboratories obtain data for the same substance. R factors between data sets range from 20 to 50% even though structures were refined for each set, giving R values (between observed data from one source and the model fitted to those data) of approximately 20%. Two factors, the standardization and distri bution of refinement programs and the continuing effort to develop inter active graphics techniques to obtain and correct diffraction data, should soon bring added confidence to the fiber diffraction field. Also, what is the best means of reporting final results when the posi tions of all the nonhydrogen atoms can be determined directly? Is there a legitimate role for modeling methods if individual atomic positions can be determined? Surely we know bond lengths and valence angles from model compounds more accurately than we could calculate them from the atomic positions derived in a fiber study. To the end of accurately knowing such intramolecular features, it would be an unusual situation indeed that would justify reporting those parameters derived from fiber data. To understand intermolecular interactions, however, the derived atomic positions, with their standard deviations, might be more useful. Calculation of intermolecular effects based on a modeling technique might introduce cumulative errors. Future work should emphasize resolution of the above questions and continue the current strong emphasis on data collection and reduction. viii In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. The editors wish to thank the authors who participated in the sympo sium. In particular, we are grateful to Struther Arnott for his thorough treatment of fiber diffraction given in the first chapter. Southern Regional Research Center ALFRED D. FRENCH USDA P.O. Box 19687 New Orleans, LA 70179 Central Research & Development KENNCORWIN H. GARDNER Department Experimental Station Ε. I. Du Pont de Nemours & Company Wilmington, DE 19898 May 21, 1980 ix In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. 1 Twenty Years Hard Labor as a Fiber Diffractionist STRUTHER ARNOTT Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 X-ray diffraction can be used to help determine the molecular geometry of polymer rather than more complexly folded structures. It is usually possible to prepare specimens in which such helical molecules are aligned with their long axes parallel. Often further lateral organization occurs, but rarely to the degree of a three-dimensionally ordered single crystal. Potentially this is an advantage, since there is more information (about the Fourier transform (1, 2, 3) of a molecular structure) in the continuous intensity distribution in the diffraction pattern from a less well-ordered system than there is the "sampled" distribution characteristic of a single crystal. But, since "sampling" also implies local amplification of the molecular transform (at reciprocal lattice points), its absence results in much weaker diffraction signals and the theoretical advantage of knowing the continuous intensity variation is offset by the experimental difficulty of recording it accurately. A further complication is that there are a great many kinds of partially-ordered systems of helical molecules, each giving rise to different types of diffraction pattern in which both continuous intensity and Bragg maxima occur. If we wish quantitatively to analyze a diffraction pattern we, of course, have to succeed in modelling not only the molecular structure but also the molecular packing. This is true 0-8412-0589-2/80/47-141-001$07.50/0 © 1980 American Chemical Society In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. 2 FIBER DIFFRACTION METHODS for any diffraction pattern, but for fiber diffraction patterns there is additional complexity because the modes of packing are more varied and complex than in single crystals. Fibrous biopolymers are afflicted also by the problem of phase determination common to a l l X-ray analyses of structure, and by the same limitations of resolution that affect diffraction analyses of most macromolecules even when (like globular enzymes) they are organized in single crystals. The ways in which these problems have been overcome for fibrous systems are quite commonplace, although the emphasis may be unfamiliar. These biopolymers do not usuall enough for facile phas high symmetry and tendency to disorder, is i t easy to obtain isomorphous heavy-atorn derivatives without multiple site occupancy. Therefore, many of the well-trodden paths that lead from sets of diffraction intensities to a unique solution of molecular structure are not available. More usually one builds a stereochemically plausible model of a residue that fits into a helix which has the dimensions and symmetry characteristics determined from the layer-line spacings and from the systematic absences and general intensity distribution in the diffraction pattern. Thereafter the problem is one of refinement. If fundamentally different initial models are conceived of, there is then the additional task of refining each possibility and adjudicating among optimized models of each kind by appropriate tests (4J . As I see i t , structural biochemists and polymer scientists using fiber diffraction data should strive to mimic classical crystallographic studies so as to arrive at similarly credible solutions of structures by similarly noncontroversial methods of procedure that are similarly reproducible in other laboratories. We are obviously on the threshold of greatly improving the accuracy of intensity measurement but I will leave discussion of In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980. 1. ARNOTT A Fiber Diffractionist 3 this to others and discuss in turn the different kinds of packing arrangements available to fibrous molecules, a general scheme for determining their structures and packings, and examples of arbitration among competing models. Types of Disorder and Consequent Diffraction Effects Although somewhat idealized, the following general model will serve to indicate the variety of packing modes that may be encountered. The model has parallel arrays of helical molecules with their lon to them at points formin present discussion we will ignore the fact that these nets are not infinite, although finite net area has the important consequence of broadening diffraction signals, thereby aggravating problems of intensity measurement. It should also be recognized that fibers typically consist of many small domains like our model and that these are parallel i n respect of the helix axes' direction but no other. This means (for example) that when the domains are fully crystalline the diffraction from the fiber is like that from a rotated single crystal, with the penalty of overlapping diffraction signals for reciprocal lattice points with the same reciprocal space cylindrical polar radius (R i n Fig. 1). However, for the moment we will discuss only the consequences of different types of disordering of molecular packing within each small domain. An isolated helical molecule i s i n essence a "one-dimensional crystal" because of its axial periodicity. Its Fourier transform (]L, 2> 3) i s therefore confined to layer lines and on each layer line i t i s a continous function proportional to Twhere In Fiber Diffraction Methods; French, A., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 1980.
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