Crystallographic Structural Studies

The structures of vitamin Bo (1 see Fig. 1) and of coenzyme Bo (2) were established through the pioneering x-ray crystallographic studies of Hodgkin et al. [7-9], which discovered the composition of the corrin core of 1 and the nature of the organometallic ligand of 2. Since these landmark analyses, work in this field has turned away from the initial constitutional and stereochemical questions concerning Bo-molecules. Studies towards more accurate structural data of Bo-derivatives, have become of interest, as presented in recent reviews [27,28]. 

Vitamin Bo (1, CNCbl), and other Bo-derivatives, where the cyanide ligand of 1 is replaced by a different upper /3-ligand are 5, 6 -dimethylbenzi-midazolyl-cobamides and are the most commonly discussed Bo-derivatives. Only base-on cobalamins, where the nucleotide functionality coordinates in an intramolecular mode, have been analyzed by x-ray crystallography [27, 28]. In this present chapter a systematic atomic numbering is used for vitamin 

B12-derivatives [29], which builds on the convention that atom numbers of the heavy atoms of a substituent reflect the number of the points of attachment to the corrin ligand and are indexed consecutively [30]. 

Due to the discovery of the replacement of the cobalt coordinated 5,6-dimethylimidazole (DMB) base by a protein-derived imidazole in several Bi2-dependent enzymes (see later), the analysis of Co -cyano-imidazolylcob-amide (8) [31] was of particular interest. The less bulky and more nucleophilic imidazole base of 8 caused a number of structural differences. The corrin ring fold angle of 8 decreased to 11.3° and the axial Co-N bond shortened (from 2.011 A in 1 to 1.968 A in 8). In addition, the base tilt of 8 (i.e., half the difference between the two Co - N - C angles to the coordinating base) decreased to practically zero, within experimental error. In all crystal structures of 5, 6 -dimethylbenzimidazoyl-cobamides a tilt of about 5° is found [36], which appears to be an inherent property of the cobalt-coordinated DMB. 

Crystal structures of a cobalamin complex with a central Co - CN - Re feature have been formed where the cyanide ligand in vitamin B12 acts as 

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Huber, R., et al. Crystallographic structure studies of an IgG molecule and an Fc fragment. Nature 264 ... 

Watenpaugh, K. D., Sieker, L. C., Jensen, L. H. A crystallographic structural study of the oxidation states of Desulfovibrio vulgaris flavodoxin. In Flavins and flavoproteins (Singer, T. P. ed.) pp. 405-410. Amsterdam, Elsevier 1976... 

Compound 37a and its derivatives adopt a boat conformation in the solid state as revealed by X-ray crystallographic structure studies [98-100]. However, the 1,4-dithiin ring in 38 is planar in its complex with acridine [101]. This facilitates 7T-7T stacking of 38 and acridine although their interaction is weak. Furthermore, calculations suggest that there is little energy difference between planar and boat conformers [102]. Thus conformational analysis of 1,4-dithiin is similar to that of thianthrene. 

The neutral and anionic carbonyls and carbonyl hydrides of rhodium that have been prepared and subjected to crystallographic structural study include a greater... 

As an alternative approach to solution-state NMR methods, which are ineffective with lipid bilayer samples, solid-state NMR methods have been refined sufficiently to permit structural details to be obtained for membrane-embedded peptides and proteins. This usually requires isotopic enrichment, either through chemical synthesis or biosynthetic incorporation in expressed peptides and proteins. In the absence of routine X-ray crystallographic structural studies for these molecules, solid-state NMR spectroscopy has the potential to be a powerful and unique approach to determining the structures and describing the dynamics and functions of membranes and membrane-bound proteins. In addition, solid-state NMR spectroscopy has been widely used to describe lipid structure, dynamics and phase properties. Thus, solid-state NMR experiments can be... 

A more recent international journal. Journal of Carbohydrate Chemistry, was introduced in 1982. It requires camera-ready copy and is devoted primarily to the organic and physical chemistry of carbohydrates, such as novel synthetic methods mechanisms involved in carbohydrate reactions uses of carbohydrates in the synthesis of natural products, drugs, and antibiotics use of carbohydrates as synthetic reagents separation methods as applied to carbohydrate reactions and synthesis spectroscopic and crystallographic structure studies of carbohydrates molecular modeling studies and the chemistry of carbohydrate polymers, oligosaccharides, polysaccharides, and glycoconjugates. 

The role of IR spectroscopy in the early penicillin structure studies has been described (B-49MI51103) and the results of more recent work have been summarized (B-72MI51101). The most noteworthy aspect of a penicillin IR spectrum is the stretching frequency of the /3-lactam carbonyl, which comes at approximately 1780 cm" This is in contrast to a linear tertiary amide which absorbs at approximately 1650 cm and a /3-lactam which is not fused to another ring (e.g. benzyldethiopenicillin), which absorbs at approximately 1740 cm (the exact absorption frequency will, of course, depend upon the specific compound and technique of spectrum determination). The /3-lactam carbonyl absorptions of penicillin sulfoxides and sulfones occur at approximately 1805 and 1810 cm respectively. The high absorption frequency of the penicillin /3-lactam carbonyl is interpreted in terms of the increased double bond character of that bond as a consequence of decreased amide resonance, as discussed in the X-ray crystallographic section. Other aspects of the penicillin IR spectrum, e.g. the side chain amide absorptions at approximately 1680 and 1510 cm and the carboxylate absorption at approximately 1610 cm are as expected. 

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

Almost all that is known about the crystal face specificity of double-layer parameters has been obtained from studies with metal single-crystal faces in aqueous solutions. Studies in nonaqueous solvents would be welcome to obtain a better understanding of the influence of the crystallographic structure of metal surfaces on the orientation of solvent molecules at the interface in relation to their molecular properties. 

An interesting mass spectral study of 17 mono- and dflialogenoquinoxahnes, some bearing methyl groups, has been reported the X-ray crystallographic structure of hexachloroquinoxaline has been measured. ... 

The analysis of XRPD patterns is an important tool studying the crystallographic structure and composition of powder compounds including the possibility to study deviation from ideal crystallinity, i.e. defects. Looking at an X-ray powder diffractogram the peak position reflects the crystallographic symmetry (unit cell size and shape) while the peak intensity is related to the unit cell composition (atomic positions). The shape of diffraction lines is related to defects , i.e. deviation from the ideal crystallinity finite crystallite size and strain lead to broadening of the XRPD lines so that the analysis of diffraction line shape may supply information about sample microstructure and defects distribution at the atomic level. 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

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