X-Ray Diffraction by Macromolecules

511 Pages·2005·49.525 MB·English

by  Nobutami Kasai, Masao Kakudo (auth.)

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