Chandrasekaran A. (ed.) Current Trends in X-Ray Crystallography

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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

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First published December, 2011

Printed in Croatia

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Current Trends in X-Ray Crystallography, Edited by Annamalai Chandrasekaran

p. cm.

ISBN 978-953-307-754-3

free online editions of InTech

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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

]

and (HL)

[Cu

] (X = Cl, Br) Complexes 191

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