Mark Ladd

Examination of Single Crystals: Optical and X-Ray Diffraction Practice

The preliminary optical examination of crystalline specimens is interesting and useful in its own right and is a major tool still employed by mineralogists and geologists. However, in structure determinations with modern equipment, it is not uncommon nowadays to by-pass this step and proceed immediately with X-ray studies. This is because in most cases, the X-ray technique is straightforward and test data can be quickly scanned with a single-crystal X-ray diffractometer, Sects. 5.5 and 5.6, or with area detector (see Sect. 5.7), and the suitability and quality of the crystal assessed. There are other situations, however, where complications may arise, for example, because of an unusual crystal habit, Sect. 5.3.5, pseudosymmetry, Sects. 7.2.2, 7.5.4, and Sect. 8.5.3, or twinning, Sect. 5.10. In such cases, it might be possible to extract useful information from an optical examination of a crystal before the more detailed, costly and time-consuming X-ray methods are tried.

Lattices and Space-Group Theory

In this chapter, we continue our study of crystals by investigating the internal arrangements of crystalline materials. Crystals are characterized by periodicities in three dimensions. An atomic grouping, or pattern motif, which, itself, may or may not be symmetrical, is repeated over and over again by a certain symmetry mechanism that corresponds to the space group of the crystal. Altogether, there are 230 space groups, and each crystalline substance will belong to one or other of them. In its simplest form, a space group may be derived from repeating the pattern motif by the translations of a lattice, as discussed below. It can be developed further by incorporating additional symmetry elements, as demonstrated through Problem 2.1. We now enlarge on these ideas, starting with an examination of lattices.

X-ray structures of two forms of the antibiotic oligomycin A: an inhibitor of ATP synthase.

BACKGROUND Corrections to the chemical and x-ray structures of two forms of the antibiotic oligomycin A are presented: the original and best known, form (E), from Streptomyces diastatochromogenes, and a new form (C) from Streptomyces diastaticus. METHOD The crystal structures are isomorphous, crystallizing in space group P212121, with Z = 4[C45H73O11.CH3OH] per unit cell. Oligomycin A(E) refined with R1 = 0.0734, using Cu Kα x-radiation; and for Oligomycin A(C) R1 = 0.0651 using Mo Kα x-radiation. CONCLUSION Serious corrections to the previously published structure of oligomycin A(C) are discussed and implemented. As a supplementary study geometry optimization of side group R4 of oligomycin A(E) was undertaken and achieved by energy minimization. These additional results clearly confirm the delocalization in this region observed in both x-ray structures. This result is contrary to the generally accepted formulation. Knowledge of the correct structures is important to those involved in the study and applications of the pharmacological and biological properties of these materials.

The Ni(II) Complex of 2-Hydroxy-Pyridine- N-Oxide 2-Isothionate: Synthesis, Characterization, Biological Studies, and X-ray Crystal Structures using (1) Cu Kα Data and (2) Synchrotron Data

C 12 H 20 N 6 NiO 6 S 2 or NiL 2 (SCN) 2 ](NH 4 ) 2 .2H 2 O, where L is 2-hydroxy-pyridine-N-oxide, has been prepared and characterized using elemental analyses, IR, UV and visible spectrometry, magnetic moment measurements, thermal analyses and single crystal X-ray analyis. The results indicate that the complex reacts as a bidentate ligand and is bound to the metal ion via the two oxygen atoms of the ligand (HL). The activation energies, ∆ E*, entropies ∆S*, enthalpies ∆H* and order of reactions have been derived from differential thermogravimetric (DTA) curves. Based on inhibition zone diameter measurements, the complex exhibited significant antibacterial activity against both Staphylococcus aureus and Escherichia coli. It also exhibited significant antifungal activity against Candida albicans, but no activity was found against Aspergillus flavus . The crystal structure of the Ni(II) complex [C 12 H 20 N 6 Ni O 6 S 2 ], Mr = 467.17, was determined from Cu Kα X-ray diffraction data, λ = 1.54178 A, at 100 K using direct methods. The crystals are monoclinic, space group P2 1 /n with Z = 4 and a = 8.9893(2) A, b = 17.6680(5) A, c = 12.5665(3) A, β = 108.609(1)°. In parallel with this study corresponding results were derived for the crystal structure determined independently from synchrotron X-ray diffraction data, λ = 0.61990 A, at 100 K. The unit cell parameters derived in this experiment are a = 9.000(2) A, b = 17.700(4) A, c = 12.590(3) A, β = 108.61(3)°. Both studies show 4 O and 2 N atoms coordinating Ni in a distorted octahedral arrangement. Each of the Ni 2-hydroxy-pyridinium-N-oxide moieties is highly planar and the S=C=N-Ni ligands are approximately linear. The crystal structure is characterised by a number of strong hydrogen bonds.

X-Rays and X-Ray Diffraction

X-rays are an electromagnetic radiation of short wavelength, and can be produced by the sudden deceleration of rapidly moving electrons at a target material. If an electron falls through a potential difference of V volt, it acquires an energy eV electron-volt (eV), where e is the charge on an electron. This energy may be expressed as quanta of X-rays of wavelength λ, where each quantum is given by

Fourier Techniques in X-Ray Structure Determination

\lambda = hc/(eV)

Proteins and Macromolecular X-Ray Analysis

h being the Planck constant and c the speed of light in vacuum. Substitution of numerical values into (3.1) leads to