RECENT ADVANCES IN CRYSTALLOGRAPHY Edited by Jason B. Benedict Recent Advances in Crystallography http://dx.doi.org/10.5772/ 2711 Edited by Jason B. Benedict Contributors Bart Kahr, Alexander G. Shtukenberg, Legrand Vincent, Kouhei Okitsu, Yasuhiko Imai, Yoshitaka Yoda, Nickolay Y. Chirgadze, Gera Kisselman, Wei Qiu, Vladimir Romanov, Christine M. Thompson, Robert Lam, Kevin P. Battaile, Emil F. Pai, Henrich H. Paradies, Peter Quitschau, Hendrik Reichelt, Chester A. Faunce, Kurt Zimmermann, Dinesh G. (Dan) Patel, Jason B. Benedict, Xin Ding, Matti Tuikka, Matti Haukka, Rakesh Gudavarthy, Elizabeth A. Kulp, Nader Noroozi Pesyan, Kazimierz Stróż, Kiyoaki Tanaka, Yasuyuki Takenaka, Jiapu Zhang Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Marina Jozipovic Typesetting InTech Prepress, Novi Sad Cover InTech Design Team First published September, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Recent Advances in Crystallography, Edited by Jason B. Benedict p. cm. ISBN 978-953-51-0754-5 Contents Preface IX Section 1 History of Crystallography 1 Chapter 1 Histories of Crystallography by Shafranovskii and Schuh 3 Bart Kahr and Alexander G. Shtukenberg Section 2 Experimental Techniques 37 Chapter 2 Crystallography Under Extreme Conditions: State of the Art and Perspectives 39 Legrand Vincent Chapter 3 X-Ray N-Beam Takagi-Taupin Dynamical Theory and N-Beam Pinhole Topographs Experimentally Obtained and Computer-Simulated 67 Kouhei Okitsu, Yasuhiko Imai and Yoshitaka Yoda Chapter 4 X-CHIP: An Integrated Platform for High-Throughput Protein Crystallography 87 Nickolay Y. Chirgadze, Gera Kisselman, Wei Qiu, Vladimir Romanov, Christine M. Thompson, Robert Lam, Kevin P. Battaile and Emil F. Pai Chapter 5 Mineralization of Lipid A-Phosphates in Three- and Two-Dimensional Colloidal Dispersions 97 Henrich H. Paradies, Peter Quitschau, Hendrik Reichelt, Chester A. Faunce and Kurt Zimmermann Section 3 Crystal Engineering 123 Chapter 6 Crystals in Materials Science 125 Dinesh G. (Dan) Patel and Jason B. Benedict Chapter 7 Halogen Bonding in Crystal Engineering 143 Xin Ding, Matti Tuikka and Matti Haukka VI Contents Chapter 8 Epitaxial Electrodeposition of Chiral Films Using Chiral Precursors 169 Rakesh Gudavarthy and Elizabeth A. Kulp Chapter 9 Crystal Structures of Organic Compounds 191 Nader Noroozi Pesyan Section 4 Computational Modeling 243 Chapter 10 Unique and Effective Characterization of Space Groups in Computer Applications 245 Kazimierz Stróż Chapter 11 XAO Analysis – AO's and Their Populations in Crystal Fields 275 Kiyoaki Tanaka and Yasuyuki Takenaka Chapter 12 Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures 297 Jiapu Zhang Preface The advent of X-ray diffraction in the early twentieth century transformed crystallography from an area of scientific inquiry largely limited to physics, mineralogy, and mathematics, to a highly interdisciplinary field which now includes nearly all life and physical sciences as well as materials science and engineering. The atomic resolution structural information which is now routinely afforded by the combination of X-ray diffraction and crystallography is indispensable for the characterization of many modern materials, the interpretation of their function, and when applicable the rational improvement of their properties. Brighter X-ray sources and improved computing resources drive the evolution of new techniques for the characterization of increasingly exotic materials. This book is a collection of works showcasing some of the most recent developments in the field of crystallography. The history of a scientific field seldom accompanies a field’s most recent technical advances between the same two covers. This collection, however, commences with a search for the elusive single narrative of the history of crystallography. Kahr and Shtukenberg introduce the reader to the numerous works which have attempted to describe the evolution of the study of crystals. Ultimately, the authors conclude that the independent narratives of Ilarion Ilarionovich Shafronovskii and Curtis Schuh provide the most comprehensive accounts of the history of crystallography to date and are ‘unlikely to be surpassed for a very long time.’ The second chapter deals primarily with recent advances in experimental techniques in the study of crystals. Synchrotrons and free electron lasers are now capable of producing X-ray beams many orders of magnitude brighter that those produced by conventional sealed tube and rotating anode sources. The extreme brightness of these sources has enabled experiments which explore matter under extreme conditions. The contribution by Legrand surveys a variety of new experimental apparatuses which allow researchers to use these bright X-ray sources to explore the effects of high and low temperature, strong magnetic fields, and high pressure on a wide variety of materials. Also described in this chapter are the details of the X-CHIP an impressive new tool which enables researchers to grow crystals, examine crystals and collect X- ray diffraction data on a single substrate. Okitsu and coworkers detail remarkable instrumentation for generating multi-beam pinhole X-ray topographs of single crystals which might be used to solve the phase problem in protein crystallography. The final X Preface contribution of this section authored by Paradies and coworkers employs a wide variety of experimental techniques including X-ray scattering and diffraction as well as electron microscopy and diffraction on nanocrystals and crystalline colloids of Lipid A-diphosphate to unravel the structure of this biologically important molecule. Crystals as functional materials drives the field of crystal engineering which seeks to create solid-state structures with targeted physical and chemical properties. The third chapter highlights recent developments in crystal engineering and begins with a survey by Patel and Benedict that explores the latest research in two exciting areas of applied single crystal materials science: photochromic materials and molecular semiconductors. Improving these materials through rational design requires a nuanced understanding of the molecular interactions which determine their structures. Haukka and coworkers examine halogen bonding in a variety of organic and inorganic single crystals and illustrate that this particular non-covalent interaction is a useful synthon in the design and synthesis of advanced functional materials. The submission by Gudavarthy and Kulp describes a method for creating chiral CuO films using chiral precursors and additives which may serve as enantiospecfic catalysts for the synthesis of chiral drugs or other important enantiomerically pure compounds. The chapter concludes with an extensive survey of crystal structures of organic compounds in which Pesyan describes structural helicity, hydrogen bonding, and additional noteworthy observations. The book concludes with works exploring computations related to the field of crystallography. The submission by Stroz describes a precise yet highly compact computational algorithm for the description and determination of the crystallographic space groups. The inability to directly calculate atomic orbitals and their populations from multipole refinements, except for high symmetry cases, places limitations on the analysis of electron density distributions in crystals. Tanaka and Takenaka describe the method of ‘X-ray atomic orbital analysis’ that yields the aforementioned physical quantities through structure refinements based upon quantum mechanical atomic orbitals. Determining the three-dimensional structure of a biologically important molecule can be costly and time consuming. The final chapter by Zhang presents a practical and useful computational approach to produce the three-dimensional structure of Prion Amyloid fibrils. I am grateful to all of the authors for their excellent contributions. I hope you enjoy this book and that it provides inspiration for exciting future experiments in crystallography. Jason B. Benedict Department of Chemistry University at Buffalo State University of New York, Buffalo, NY 14260-3000, USA . Section 3 Crystal Engineering 123 Chapter 6 Crystals in Materials Science 125 Dinesh G. (Dan) Patel and Jason B. Benedict Chapter 7 Halogen Bonding in Crystal Engineering 143 Xin Ding, Matti Tuikka. ideas contained in the book. Publishing Process Manager Marina Jozipovic Typesetting InTech Prepress, Novi Sad Cover InTech Design Team First published September, 2012 Printed in Croatia. the Leningrad Mining Institute. He had a long-standing interest in the history of crystallography (For a biographical sketch, see next section) and earlier published The History of Crystallography