CURRENT TRENDS IN X-RAY CRYSTALLOGRAPHY Edited by Annamalai Chandrasekaran Current Trends in X-Ray Crystallography Edited by Annamalai Chandrasekaran Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 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. 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Depositphotos First published December, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Current Trends in X-Ray Crystallography, Edited by Annamalai Chandrasekaran p. cm. ISBN 978-953-307-754-3 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Part 1 Small Molecules 1 Chapter 1 Polycyclic Aromatic Ketones – A Crystallographic and Theoretical Study of Acetyl Anthracenes 3 Sergey Pogodin, Shmuel Cohen, Tahani Mala’bi and Israel Agranat Chapter 2 Calix[8]arenes Solid-State Structures: Derivatization and Crystallization Strategies 45 David J. Hernández and Ivan Castillo Chapter 3 Novel Challenges in Crystal Engineering: Polymorphs and New Crystal Forms of Active Pharmaceutical Ingredients 69 Vânia André and M. Teresa Duarte Chapter 4 Intramolecular NH···X (X = F, Cl, Br, I, and S) Hydrogen Bonding in Aromatic Amide Derivatives - The X-Ray Crystallographic Investigation 95 Dan-Wei Zhang and Zhan-Ting Li Chapter 5 Supramolecular Arrangements in Organotellurium Compounds via Te···Halogen Contacts 113 Angel Alvarez-Larena, Joan Farran and Joan F. Piniella Chapter 6 -Bonded p-Dioxolene Transition Metal Complexes 137 Anastasios D. Keramidas, Chryssoula Drouza and Marios Stylianou Chapter 7 Structural Diversity on Copper(I) Schiff Base Complexes 161 Aliakbar Dehno Khalaji Chapter 8 Features of Structure, Geometrical, and Spectral Characteristics of the (HL) [CuX ] 2 4 and (HL) [Cu X ] (X = Cl, Br) Complexes 191 2 2 6 Olga V. Kovalchukova VI Contents Chapter 9 Role of X-Ray Crystallography in Structural Studies of Pyridyl-Ruthenium Complexes 219 Dai Oyama Chapter 10 Ruthenium(II)-Pyridylamine Complexes Having Functional Groups via Amide Linkages 239 Soushi Miyazaki and Takahiko Kojima Chapter 11 X-Ray Structural Characterization of Cyclometalated Luminescent Pt(II) Complexes 255 Viorel Cîrcu and Marin Micutz Part 2 Macromolecules 283 Chapter 12 Protein-Noble Gas Interactions Investigated by Crystallography on Three Enzymes - Implication on Anesthesia and Neuroprotection Mechanisms 285 Nathalie Colloc’h, Guillaume Marassio and Thierry Prangé Chapter 13 Crystallization, Structure and Functional Robustness of Isocitrate Dehydrogenases 309 Noriyuki Ishii Chapter 14 Crystallographic Studies on Autophagy-Related Proteins 333 Nobuo N. Noda, Yoshinori Ohsumi and Fuyuhiko Inagaki Chapter 15 Knowledge Based Membrane Protein Structure Prediction: From X-Ray Crystallography to Bioinformatics and Back to Molecular Biology 349 Alejandro Giorgetti and Stefano Piccoli Part 3 Complimentary Methods 365 Chapter 16 Investigating Macromolecular Complexes in Solution by Small Angle X-Ray Scattering 367 Cristiano Luis Pinto Oliveira Chapter 17 Monitoring Preparation of Derivative Protein Crystals via Raman Microscopy 393 Antonello Merlino, Filomena Sica and Alessandro Vergara Chapter 18 Complementary Use of NMR to X-Ray Crystallography for the Analysis of Protein Morphological Change in Solution 409 Shin-ichi Tate, Aiko Imada and Noriaki Hiroguchi Preface Single crystal X-ray crystallography is the most common and easily accessible way to determine the molecular structure of any crystalline material. This method provides two kinds of information which are needed for understanding both single molecule properties and bulk material properties: 1. Molecular Structure - Single Molecules: Unambiguous and three-dimensional information about the structure of the molecular entities. The data useful here are the bond lengths, bond angles, and torsion angles. These details make this method not only useful for structural determination, confirmation, and analysis of three-dimensional geometry of the molecular entities, but also useful for the Structure-Activity Relationship studies, where the structural details are the basis for understanding the chemical reactivity and stability. These data are also useful for understanding most of the spectroscopic data of materials. 2. Intermolecular Interactions (Packing) - Bulk Material: All the individual molecules have to come together to form the bulk crystal. How the molecules interact with each other in the crystal provides additional useful information. Various possible intermolecular interactions present in the crystalline bulk can be obtained from the X-ray studies, which are useful for the study of bulk properties as well. These can help explain the observed bulk properties and thereby enable us to make predictions of bulk properties based on structures. These interactions include H-bonding, pi-pi stacking, CH-pi interactions, halogen-halogen interactions, and other donor-acceptor interactions. If there is any phase separation in bipolar molecules, they can also be seen clearly. In addition to providing the details of the molecular arrangement in the bulk, we can also obtain the structure of the empty spaces (void spaces, channels or pores etc). These data are useful in widely varied fields, such as the design of pharmaceuticals, crystal engineering, zeolites for gas separation or catalysis, guest-host materials, sensors, organic magnets, and charge transport. Single crystal X-ray crystallography has moved a long way from the days I started my research career about a quarter of a century ago. In those days, it took about half a year to complete a structure, due to slow computers and serial data collection by the state- X Preface of-the-art automated diffractometers of that time. The recent advances of using the CCD area detectors have reduced the time needed for data collection from days to hours, and also enabled the use of smaller crystals, which were impossible to study before. Also, the presence of supercomputers in everybody's desk/lab and the improved structure processing programs have made the structure determination a very quick task. These advances have made it possible that, with minimal expertise, one can obtain a structure in hours or in one day. When good crystals are available, an experienced crystallographer can determine the structure in as little as an hour. Thus, the current status of instruments, computers, and programs make it possible to obtain the structural details of many more molecules, with smaller crystals, with less expertise, and in much shorter time. Though these advances create a large volume of data, too much to handle easily by researchers, there are great programs to help the researchers analyze such voluminous data without getting overloaded. The Cambridge Structural Database, which contains over 500,000 structures, has automated programs to search efficiently and its free Mercury program is great for analyzing individual molecules and their packing so effortlessly. The Inorganic Crystal Structure Database (ICSD), which contains over 130,000 structures, is specifically for inorganic structures. The Protein Data Bank (PDB) is the depository for protein structures with over 76,000 structures. It is also important to point out that there are a few drawbacks to this method, just like for any other method. The major problem is that one needs to get a good quality single crystal. The minor problems are that the hydrogens are not located accurately, and the structural details are accurate only to the solid state and may possibly deviate in solution or liquid state. As explained below, these are not of any serious concern. As the technology and instrumentation advance, we are able to deal with smaller and smaller crystals, with only human handling ability making the limit. Since we bought the new instrument a decade ago, the recent advances make it possible to use just one- tenth the size of the crystal we need in our 'old' instrument. Though synchrotron radiation sources can provide great data with even smaller crystals, those sources are rare and costly, and not necessary for the most part. Though the hydrogens can be located more accurately using neutron diffraction, those facilities are fairly rare due to the need for nuclear radiation. However, the lost accuracy is not at all a concern in the vast majority of situations. The structure of the molecules may deviate to some extent in solution, but the crystal structure shows some of the energetically favored form for the molecules. The structure determined in the crystal will be present in solution, if not 100%, to a significant extent. We have had multiple isomers present in solution and only one isomer in solid, with the crystalline structure being the major isomer in solution, though in one case the solution isomer and crystal isomer were totally different. The intermolecular interactions will provide a statistically significant part of all the possibilities for non-crystalline states as