X-Ray Diffraction by Macromolecules PDF
Preview X-Ray Diffraction by Macromolecules
Springer Series in CHEMICAL PHYSICS 80 Springer Series in CHEMICAL PHYSICS Series Editors: A. W. Castleman, Jr. J. P. Toennies W. Zinth The purpose of this series is to provide comprehensive up-to-date monographs in both well established disciplines and emerging research areas within the broad fields of chemical physics and physical chemistry. The books deal with both fun damental science and applications, and may have either a theoretical or an experi mental emphasis. They are aimed primarily at researchers and graduate students in chemical physics and related fields. 65 Fluorescence Correlation 73 Organometallic Conjugation Spectroscopy Structures, Reactions Theory and Applications and Functions of d-d Editors: R. Rigler and E.S. Elson and d-TT Conjugated Systems 66 Ultrafast Phenomena XII Editors: A. Nakamura, N. Ueyama, Editors: T. Elsaesser, S. Mukamel, and K. Yamaguchi M.M. Murnane, and N.E Scherer 74 Surface and Interface Analysis 6y Single Molecule Spectroscopy An Electrochmists Toolbox Nobel Conference Lectures By R. Holze Editors: R. Rigler, M. Orrit, 75 Basic Principles T. Basche in Applied Catalysis 68 Nonequilibrium Nondissipative By M. Baerns Thermo dynamics 76 The Chemical Bond With Application to Low-Pressure A Fundamental Diamond Synthesis Quantum-Mechanical Picture ByJ.-T.Wang By T. Shida 69 Selective Spectroscopy yy Heterogeneous Kinetics of Single Molecules Theory of Ziegler-Natta-Kaminsky By I.S. Osad'ko Polymerization 70 Chemistry By T. Keii of Nanomolecular Systems 78 Nuclear Fusion Research Towards the Realization Understanding Plasma-Surface of Molecular Devices Interactions Editors: T. Nakamura, Editors: R.E.H. Clark and D.H. T. Matsumoto, H. Tada, Reiter K.-I. Sugiura 79 Ultrafast Phenomena XIV 71 Ultrafast Phenomena XIII Editors: T. Kobayashi, Editors: D. Miller, M.M. Murnane, T. Okada, T. Kobayashi, N.R. Scherer, and A.M. Weiner K.A. Nelson, S. De Silvestri 72 Physical Chemistry 80 X-Ray Diffraction of Polymer Rheology by Macromolecules By J. Furukawa By N. Kasai and M. Kakudo N. Kasai M. Kakudo X-Ray Diffraction by Macromolecules With 351 Figures and 56 Tables te\ Kodansha ^ Springer Nobutami Kasai Masao Kakudo Professor Emeritus Professor Emeritus Osaka University Osaka University and and Kobe Women's University Former President Himeji Institute of Technology Series Editors: Professor A. W. Castleman, Jr. Department of Chemistry, The Pennsylvania State University 152 Davey Laboratory, University Park, PA 16802, USA Professor J.P. Toennies Max-Planck-Institut fiir Stromungsforschung Bunsenstr. 10,37073 Gottingen, Germany Professor W. Zinth Universitat Miinchen, Institut fiir Medizinische Optik Ottingerstr. 67, 80538 Munchen, Germany ISSN 0172-6218 ISBN 4-06-207405-2 Kodansha Ltd., Tokyo ISBN-io 3-540-25317-3 Springer Berlin Heidelberg New York ISBN-13 978-3-540-25317-4 Springer Berlin Heidelberg New York Library of Congress Control Number: 2005923756 All rights are reserved. No part of this book may be reproduced in any form, by photostat, microfilm, retrieval system, or any other means, without the written permission of Kodansha Ltd. (except in the case of brief quotation for criticism or review). This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9,1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. Springer is a part of Science + Business Media. springeronline.com © Kodansha Ltd. and Springer-Verlag Berlin Heidelberg 2005 Printed in Japan The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover concept: eStudio Calamar Steinen Cover production: design & production GmbH, Heidelberg Printed on acid-free paper SPIN: 11406860 57/3141/di - 5 4 3 21 0 Preface More than thirty years have past since the publication of X-Ray Diffraction by Polymers by the authors (original edition in Japanese published by Maruzen, Tokyo, 1968, and English edition by Kodansha-Elsevier, Tokyo-Amsterdam, 1972). Since then, accelerated by the very rapid and the remarkable development of electronic computers, both hard- and software as well as new experimental techniques, marvelous de velopments have been achieved on X-ray sources. X-ray detectors. X-ray apparata in exper imental technique and methods of identification of crystalline materials, methods of struc ture solution and structure analysis of small and macromolecular crystals X-ray diffraction data, presentation of the results obtained, i.e. crystal and molecular structures, and the crys- tallographic databases related to them. Today, we can see the words, "'mail-in' crystallography" in scientific journals, refer ring to sending sample(s) with appropriate information to an institution by mail, making it possible to obtain the structure of a complex biological molecule by mail within days ('mail-in' service). However, the authors believe that there are many scientists who are not satisfied with the results obtained by conventional analysis and wish to try to find a way to obtain more detailed structural information on macromolecules or high polymers by them selves based on the fundamentals of X-ray diffraction. The present volume is divided into three parts as in earlier editions: fundamental, ex perimental and analytical. In the fundamental part. X-ray small-angle scattering is more precisely described in Chapter 6. In the experimental part, recently developed devices and the latest version of X-ray instruments equipped with these detectors are described. On the other hand, for the basic understanding of X-ray diffraction, descriptions and usages of rather old X-ray instruments are also given. In the analytical section, in addition to the structure analysis of high polymers, a new introduction has been added on the crystalliza tion and structure determination of biological macromolecules in Chapter 13. In this way, it is hoped that whichever section the reader turns to, depending on the re search field, knowledge and experience, a contribution will be made. That is to say, the volume is intended as an intermediate textbook bridging the gap between beginners and specialist workers. Explanatory daigrams have been planned as far as possible to provide an intuitive understanding, and in the description of the equipment and methods it is shown how these are adapted to suit the aims of the analysis. The procedure adopted in the analyt ical part is to advance from the simple to the complex, starting with analyses of crystalline diffraction spots, amorphous haloes, broadening of diffraction spots, and overall back ground scattering, then concentrating of X-ray diffraction pattern, and proceeding eventual ly to composite analytical methods constructed from these individual analyses. Also, many pages have been allotted to examples from original works in order to facilitate the practical application of the analysis for the less experienced. It is hoped that these examples will serve as a further step beyond the level of most primers, but without obscuring the forest for the trees. VI Preface Most of the revised manuscripts were finished at the end of 1994. However, the homes of both authors were severely damaged by the heavy earthquake which hit Kobe and nearby areas in Japan on 17 January, 1995, causing delay in the publication of the monograph. Last year minimum revisions were again made on the manuscripts and pictures of the latest instruments were included in the experimental part of the work. The painstaking work of the staff of Kodansha Ltd. in preparing the text is gratefully acknowledged. One of the authors (N.K.) deeply thanks the late Mrs. Maria Hiroko KA- SAI for her assistance in the initial stages. Kobe February 2005 Nobutami KASAI Masao KAKUDO Contents Preface v Part I Fundamental 1. Essential Properties of X-Rays 3 1.1 X-Rays as Electromagnetic Waves 3 1.2 Generation of X-Rays 3 1.2.1 X-ray tube 3 1.2.2 Synchrotron radiation 6 1.3 Properties and Effects of X-Rays 8 1.3.1 Absorption of X-rays 8 1.3.2 X-ray scattering 10 1.3.3 X-ray refraction 11 1.3.4 Effects used for the detection of X-rays 11 1.3.5 Other effects 12 References 13 2. X-Ray Scattering, Interference and Diffraction 15 2.1 Scattering by a Single Electron 16 2.2 Interference and Diffraction of Scattered X-Rays 18 2.2.1 The phenomena of interference and diffraction 18 2.2.2 Basis for calculating the amplitudes of, and phase differences between, diffracted waves 21 2.2.3 The relationship between real and reciprocal space 23 2.3 Scattering of X-Rays by a Single Atom 25 2.3.1 Atomic scattering factor 25 2.3.2 Anomalous dispersion 27 2.3.3 Compton scattering intensity 27 2.4 Scattering of X-Rays by a Single Polyatomic Molecule 28 2.5 X-Ray Scattering from a Dense, Disordered Assemblage of Identical Atoms (a Monatomic Liquid) 31 VIII Contents 2.6 A Dense, Disordered Assemblage of Dissimilar Atoms 33 2.7 A Dense, Disordered Assemblage of Polyatomic Molecules (a Molecular Liquid) 34 2.8 Scattering of X-Rays by Amorphous Solids 35 2.9 Scattering of X-Rays by Crystals 37 2.9.1 Amplitude and intensity of the scattered rays 37 2.9.2 Form of the X-ray diffraction pattern 41 2.10 Summary 43 References 43 3. Crystal Structure 45 3.1 Crystal Systems and the Unit Cell 45 3.2 Crystal Planes and Their Indices 47 3.2.1 Crystal planes 47 3.2.2 Lattice plane indices 48 3.2.3 The spacing of lattice planes and the relationship between plane indices and Laue indices 49 3.2.4 Coordinates of atoms, lattice points, and reciprocal lattice points and indices of crystal planes and zone axes 51 3.3 Crystal Symmetry 52 3.3.1 Point groups and their symmetries 52 3.3.2 Space groups 55 3.3.3 Relationship between the atoms present in the unit cell and the equivalent points of the space group 59 References 60 4. Detailed Interpretation of the Diffraction of X-Rays by Crystals 61 4.1 The Bragg Diffraction Condition 61 4.2 Lattice Structure Factors 63 4.3 Reciprocal Space and Reciprocal Lattice 63 4.4 Wider Applications of the Reciprocal Lattice 68 4.4.1 Interpretation of rotating-crystal and oscillating-crystal photographs .. 68 4.4.2 Interpretation of Weissenberg photographs 75 4.4.3 Interpretation of diffraction from crystalline powders or polycrystalline specimens 78 4.4.4 Fibrous polycrystalline specimens 79 Reference 82 Contents IX 5. Diffraction of X-Rays by Imperfect Crystals and Paracrystals 83 5.1 Ideal Crystals and Imperfect Crystals 83 5.1.1 Lattice distortions of the first kind 85 5.1.2 Lattice distortions of the second kind 88 5.2 Fourier Transform Theory of X-Ray Diffraction 89 5.2.1 Fourier transform theorem 89 5.2.2 Shape factor for the scattering body 92 5.2.3 Scattering factor of atoms undergoing thermal vibrations in a crystal... 94 5.2.4 Optical experiments on Fourier transforms 95 5.3 Diffraction of X-Rays by Paracrystals 96 5.3.1 Statistical representation of paracrystalline lattice points and the derivation of their function Q(r) 97 5.3.2 Lattice factor and diffraction intensity for a paracrystal 98 5.4 Summary of the Relationship between Structure and X-Ray Diffraction Intensity 104 References 108 6. Scattering of X-Rays by Very Small Bodies 109 6.1 Small-angle Diffuse Scattering 109 6.2 Small-angle Scattering Theory 110 6.2.1 X-ray scattering by a substance of any structure 110 6.2.2 Small-angle scattering from systems of dilutely dispersed particles (orvoids) Ill 6.2.3 Correlation function and distance distribution function 121 6.2.4 Poly dispersed system of particles with uniform shape 127 6.2.5 Small-angle scattering from systems of densely packed particles 128 6.2.6 Small-angle scattering from a non-particulate system 130 References 133 7. Structure of High Polymeric Substances 135 7.1 Structure of High Polymer Chains in the Liquid State and in Solution 136 7.1.1 Configuration and conformation 136 7.1.2 Classification of chain molecules 142 7.2 Molecular Aggregations in Solid High Polymers 146 7.2.1 Globular proteins 146 7.2.2 Synthetic and some natural high polymers 146 Contents 7.3 Structure of the Amorphous State and of Amorphous Regions in Sohd High Polymers 150 7.3.1 Random-coil model 150 7.3.2 Folded-chain-fringed-micellar-grain model 151 7.4 Fine Texture in Solid High Polymers 151 References 155 Part II Experimental Experimental Methods 159 8.1 Preliminary Considerations 159 8.2 X-Ray Equipment 159 8.2.1 X-ray generators 159 8.2.2 X-ray detectors 163 8.2.3 X-ray cameras 169 8.2.4 X-ray diffractometers 175 8.2.5 X-ray small-angle scattering cameras 183 8.3 Selection of the X-Ray Parameters 192 8.3.1 X-ray wavelength 192 8.3.2 Production of monochromatic X-rays 193 8.3.3 Elimination of unwanted scattered X-rays 196 8.4 The Specimen 197 8.4.1 Preparation of the specimen 197 8.4.2 Determination of the specimen density 200 8.5 Diffraction Studies for Identification Purposes 201 8.5.1 Qualitative identification using polycrystal diffraction data (unoriented X-ray diagrams) 201 8.5.2 Treatment of the results 201 8.6 Diffraction Studies for Crystal Structure Analysis 202 8.6.1 General remarks 202 8.6.2 Weissenberg photographs 203 8.6.3 Precession photographs 214 8.7 Diffraction Studies for Analysis of Fine Textures 219 8.7.1 Measurement of crystallinity 219 8.7.2 Analysis of crystallite orientation 220 8.7.3 Measurement of the size and shape of and/or lattice distortion in crystallites 220 8.7.4 Measurement of diffuse halos due to amorphous solids and liquids 222 8.7.5 Analysis of distorted crystalline diffraction 222
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