X ray crystallography

X-ray crystallographic methods, which reflect differences in crystal structure, in most cases can be definitive in the identification and characterization of polymorphs, and whenever possible should be included in the analytical methods utilized to define a polymorphic system. 

Recent and continuing developments in the field of electron diffraction of very small single crystals may also serve to bridge the gap between classical powder and single crystal diffraction techniques (Voigt-Martin et al. 1995 Dorset 1996 Dorset etal. 1998 Yueffll. 2000ft). 

There are some reported cases of two genuinely polymorphic structures exhibiting very similar powder diffraction patterns. One of these cases, the two polymorphs 

Herbstein (2001). The cell constants forthe reduced cell are based on those reported by Colapietroet aZ. (1984) and DomenicanocZaZ. (1990) (for Form 1) and by Fischer et al. (1986) (by neutron diffraction) for Form II. Since they follow the convention for reporting reduced cells (International Tables 1987) they appear in a different order from the original also by convention the cell angles are defined as acute. 

Some other examples of very similar X-ray powder diffraction patterns have been noted. One of these is D,L-leucine (Mnyukh et al. 1975) for which the spectral data are clearly distinguishable. Another is caffeine (Fig. 4.27) (Suzuki et al. 1985 Griesser 2000), which is discussed in the next section. Karfunkel et al. (1999) also quoted the surprisingly similar powder patterns of some diketopyrrolopyrrole derivatives and have attempted to develop a model to describe the structural basis for similar powder patterns. 

X-ray crystallography is a technique used to determine the arrangement of atoms within a crystal. With this technique, the structure of any material that can form a crystal can be determined. Dorothy Crowfoot Hodgkin was a pioneer of X-ray crystallography, using it to determine the structures of cholesterol (1937), penicillin (1945), vitamin Bi2 (1954), and insulin (1969). (The stmctures of these compounds can be found in Sections 3.15,16.15, 24.6, and 22.8, respectively.) In 1953, Rosalind Franklin s X-ray images allowed James Watson and Francis Crick to accurately describe the structure of DNA (Section 26.1). 

A crystal is a solid composed of atoms and molecules in a regular three-dimensional array, called a unit cell, that is repeated indefinitely throughout the crystal. Often the most difficult aspect of X-ray crystallography is obtaining the crystal, which should be at least 0.5 mm long in all three dimensions in order to provide good structural data. Fortimately, 

A ctystal of lysozyme from hen egg white (Section 5.12). It appears blue because it was photographed under polarized light. 

There are a variety of databases that provide structural information to chemists. Two important examples are the Chemical Abstracts Services Database (CAS) and the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). 

CAS (http //www.cas.org/) is a subscription-based service with over 100 million organic, inorganic, protein, and nucleic acid structures. It can be accessed through SciFinder, which allows searches via a structural drawing program as well as searches by subject, author, or structure name. 

The X-ray crystal structure of 3,4-dichoro-l//-pyrrole-2,5-dicarboxylic acid bis-phenylamide tetrabutylammonium salt reveals the formation of an unusual dimer in the solid state via amide NFI- -N pyrrole hydrogen bonds 

1 X-Ray Crystallography. - No listing of published crystallographic analyses has been prepared this year. Readers are referred to electronic searching methods. 

The crystal structures of four mannose-derivatives which might exist as either open-chain Schiffs bases or as glycosylamines showed that the hydroxylamine derivative is the oxime 34, whereas the semicarbazide, aniline- and p-chloroani-line-derivatives are the p-glycosylamines 35.  

X-Ray diffraction has been used to determine the molecular and crystal structure of l-0-(a-D-galactopyranosyl)-myo-inositol dihydrate,and to con- 

Supramolecular assemblies are, by definition, complex affairs and often generate spectral data that are hard to interpret. If the system can resolve into regular single crystals then the possibility of determining the solid-state structure evolves. From experience, supramolecular systems tend to fall into one of two classes in the crystalline state. They may produce wonderfully rigid one-, two- or three-dimensional 

A Practical Guide to Supramolecular Chemistry Peter J. Cragg 2005 John Wiley Sons, Ltd ISBN 0-470-86653-5 

Conversely, the sheer complexity of the supramolecular system may, if it crystallizes at all, lead to a very poorly defined structure. The first problem is then in growing a suitable crystal. If volatile solvents are in any way involved in the crystal lattice the chances are that they will evaporate before or during the data-gathering phase of the crystallographic experiment. Failing this the molecular 

Once mounted in the diffractometer, the crystal is irradiated with X rays, usually so-called CuKa radiation with a wavelength of 0.154 nm. When the X rays strike the enzyme crystal, they interact with electrons in the 

The structure of human muscle fructose-i,6-bisphosphate aldolase, as determined by X-ray crystallography and downloaded from the Protein Data Bank. 

28 Show the steps in preparing each of the following substances, using either a malonic ester synthesis or an acetoacetic ester synthesis  

CHAPTER 17 CARBONYL ALPHA-SUBSTITUTION AND CONDENSATION REACTIONS 

29 For a given a hydrogen atom to he acidic, the C-H bond must be parallel to the p orbitals of the C=0 bond, that is, perpendicular to the plane of the adjacent carbonyl group. Identify the most acidic hydrogen atom in the following structure. Is it axial or equatorial  

The most recent methods use desorption ionization of high molecular weight samples, up to 100 000 dalton, by UV laser irradiation of a matrix surface. 

One or more stable conformations can also be assumed for cyclic peptides which can adopt more or less rigid structures stabilized by hydrogen or other bridges or, strongly, by complexing various metal ions. As an example of many published structures [41], there is the Li-complex of the antitoxic mushroom peptide antamanide (see p. 215), a structure which was determined in 1973 by Isabella L. Karle [42] using the direct method of Jerome Karle (Nobel Prize 1987, shared with J.A. Hauptmann). 

Sanger, A.R. Coulson, The use of thin acrylamide gels for DNA sequencing FEES Lett. 87 107-110 (1978) 

Rittenberg, G.L. Foster, A new procedure for quantitative analysis by isotope dilution with application to the determination of aminoacids and fatty acids. J. Biol. Chem. 133 737-744 (1940) 

Martin, R.L.M. Synge, Analytical chemistry of the proteins, Advan. Prot. Chem. 2 1-83 (1945) 

In this chapter some of the more important methods of studying coordination compounds have been reviewed. The detailed interpretation of the experimental results is often rather difficult, and, for the phenomena of optical activity and NQR, for example, the theory of the method has only been worked out incompletely. Discussion has therefore been confined to the qualitative level, it being considered important that the student should have a pictorial idea of the phenomena considered. In this way he or she should both have been made aware of which technique is likely to be of use in tackling a particular problem and also of some of the difficulties associated with its application. Inevitably, it has been necessary to be selective and this has been done on the basis either of techniques which the student may well meet in the laboratory or of techniques which are of particular importance. Finally, Chapter 16 will provide examples of the application of some of the techniques described in the present chapter, as well as a few more which have proved to be of particular value in the study of bioinorganic molecules. 

Two books which cover the majority of the methods described in this Chapter are Structural Methods in Inorganic Chemistry by E. A. V. Ebsworth, D. W. H. Rankin and S. Cradock, Blackwell, Oxford, 1987 and NMR, NQR, EPR and Mossbauer Spectroscopy in Inorganic Chemistry, R. V. Parish. Ellis Hor-wood, Hemel Hempstead, 1990. An older book, but one that covers a wider subject area, with some good chapters is Physical Methods in Advanced Inorganic Chemistry H. A. O. Hill and P. Day, eds.. Interscience, London, 1968. Readable insights into a limited number of particular areas can be found in Spectroscopy of Inorganic-Based Materials (Advances in Spectroscopy Vol 14). R. J. H. Clark and R. E. Hester, eds. John Wiley, Chichester, 1987. 

There are two key books on the applications of vibrational spectroscopy Metal-Ligand and Related Vibrations by D. M. Adams, Edward Arnold, London, 1984 and Infrared and Raman Spectra of Inorganic and Coordination Compounds, by K. Nakamoto, J. Wiley, New York, 1986. 

A useful source is Volume 1 of Comprehensive Coordination Chemistry G. Wilkinson, R. D. Gillard and J. A. McCleverty (eds.), Pergamon Press, Oxford, 1987, Chapter 8.1 Electrochemistry and Coordination Chemistry by C. J. Pickett. 

2 Based on a study of Fig. 12.3 and using a group theoretical approach, suggest, qualitatively, what band patterns might be observed in the infrared spectra of crystalline K4[Fe(CN)6] and Na4[Fe(CN)6]. 

Such was Powell s reputation relative to that of Crowfoot in 1944 that he defeated her and other strong contenders in a contested election for the readership in chemical crystallography. In 1947 she turned the tables being elected FRS three years before he was. Flis FRS did not lure any college into electing him as a fellow that happened later when he was 57 years old when Hertford responded to his elevation to the chair of chemical crystallography in 1964.  

The success of modern biochemistry in explaining such processes as DNA replication, protein biosynthesis, and enzyme catalysis is a direct result of developments in preparatory, instrumental, and computational procedures that have led to the determination of large numbers of structures of biological macromolecules by techniques based on X-ray diffraction. 

Because much of our knowledge of the three-dimensional structures of biological macromolecules comes from studies of crystals of proteins and nucleic acids, we need to study the arrangements adopted by molecules when they stack together to form a crystalline solid. One of the most important techniques for the determination of the structures of crystals is X-ray diffraction. In its most sophisticated version, known as X-ray crystallography. X-ray diffraction provides detailed information about the location of all the atoms in molecules as complicated as biological macromolecules. 

X-ray diffraction is applied to crystalline arrays of molecules, so we need to know how to describe the arrangement of molecules in a crystal. The pattern that atoms, ions, or molecules adopt in a crystal is expressed in terms of an array of points making up the lattice that identify the locations of the individual species (Fig. 11.8). A unit cell of a crystal is the small three-dimensional figure obtained by joining typically eight of these points, which may be used to construct the entire crystal lattice by purely translational displacements, much as a wall may be constructed from bricks (Fig. 11.9). An infinite number of different unit cells can describe the same structure, but it is conventional to choose the cell with sides that have the shortest lengths and are most nearly perpendicular to one another. 

Unit cells are classified into one of seven crystal systems according to the symmetry they possess under rotations about different axes. The cubic system, for example, has four threefold axes (Fig. 11.10). A threefold axis is an axis of 

Cubic Four threefold axes in a tetrahedral arrangement 

The most powerful method, in the sense that it will give the complete structure and stereochemistry and conformation of a compound. The major constraint is that suitable crystals are needed. In the case of unknown compounds the other spectral data still have to be recorded to be able to identify the compound in future isolations. X-ray crystallography will thus only be applied after all other spectral data have been recorded, probably 

The crystal structure of dehydro-L-ascorbic acid and the structure of its dimer in solution have been reviewed (in Japanese). 

Specific crystal structures have been reported as follows  

Free Sugars and Simple Derivatives Thereof.- D-Glucose 6-(sodlum hydrogen phosphate), dipotassiura glucose 1-phosphate, trisodium 

Dlsaccharldes and Derivatives Thereof.- a,a-Trehalose anhydrous, a-lactose monohydrate (a redetermination),2-acetamldo-l,3,6-tri- 

Anhydro-sugars.- Methyl 2,3-anhydro-4-deoxy-a-DL-rlbo- and -a-DL- 

---

Single-crystal surfaces are characterized by a set of Miller indices that indicate tlie particular crystallographic orientation of the surface plane relative to the bulk lattice [5]. Thus, surfaces are labelled in the same way that atomic planes are labelled in bulk x-ray crystallography. For example, a Ni (111) surface has a surface plane... 

Physical, chemical, and biological properties are related to the 3D structure of a molecule. In essence, the experimental sources of 3D structure information are X-ray crystallography, electron diffraction, or NMR spectroscopy. For compounds without experimental data on their 3D structure, automatic methods for the conversion of the connectivity information into a 3D model are required (see Section 2.9 of this Textbook and Part 2, Chapter 7.1 of the Handbook) [16]. 

The input to a minimisation program consists of a set of initial coordinates for the system. The initial coordinates may come from a variety of sources. They may be obtained from an experimental technique, such as X-ray crystallography or NMR. In other cases a theoretical method is employed, such as a conformational search algorithm. A combination of experimenfal and theoretical approaches may also be used. For example, to study the behaviour of a protein in water one may take an X-ray structure of the protein and immerse it in a solvent bath, where the coordinates of the solvent molecules have been obtained from a Monte Carlo or molecular dynamics simulation. 

PDB, NRL3D Protein Data Bank - protein structures (mostly fror X-ray crystallography). NRL3D is a derived sequence database in PIR format... 

Solid covalent dinitrogen pentoxide can be prepared by freezing the vapour with liquid helium. Normally, solid dinitrogen pentoxide exists as (NO2+) (NOj ), showing absorption bands in its Raman spectrum only at 1050 and 1400 cm the structure of this form has been determined by X-ray crystallography. ... 

In spite of their easy interconversion in solution a and p forms of carbohydrates are capable of independent existence and many have been isolated m pure form as crys talline solids When crystallized from ethanol d glucose yields a d glucopyranose mp 146°C [a]o +112 2° Crystallization from a water-ethanol mixture produces p d glucopyranose mp 148-155°C [aj +18 7° In the solid state the two forms do not mterconvert and are stable indefinitely Their structures have been unambiguously con firmed by X ray crystallography... 

FIGURE 27 6 Structural features of the dipeptide l alanylglycine as determined by X ray crystallography... 

Section 27 20 The folding of a peptide chain is its tertiary structure The tertiary struc ture has a tremendous influence on the properties of the peptide and the biological role it plays The tertiary structure is normally determined by X ray crystallography... 

---