Methods X-ray crystallography

X-Ray Crystallography method used to determine structure of crystal by examining diffraction pattern produced by x-rays directed at crystal... 

In the literature Raman spectroscopy has been used to characterize protein secondary structure using reference intensity profile method (Alix et al. 1985). A set of 17 proteins was studied with this method and results of characterization of secondary structures were compared to the results obtained by x-ray crystallography methods. Deconvolution of the Raman Amide I band, 1630-1700 cm-1, was made to quantitatively analyze structures of proteins. This method was used on a reference set of 17 proteins, and the results show fairly good correlations between the two methods (Alix et al. 1985). 

Davies DR, Begley DW, Hartley RCetal (2011) Predicting the success of fragment screening by X-ray crystallography. Methods Enzymol 493 91-114... 

There are many other spectroscopic techniques, but let me mention just one more, the X-ray crystallography method, which yield complete 3D information on a molecule (Scheme 9.9b). The technique is based on the phenomenon that when X-rays hit a crystal, which is an ordered solid form made of many molecules, the material diffracts the X-rays in patterns that reflect the distances between the atoms in the molecule. As such, the X-ray diffraction pattern can be analyzed and can provide us with the bond distances and the angles in a molecule. The rather complex statistical mathematical analysis was developed by Herbert Aaron Hauptman and Jerome Karle, who were awarded the Nobel Prize for their work in 1985.In this manner, chemists, called X-ray crystallographers, are able today to determine the structure of any molecule that can be crystallized as an ordered solid (or half-ordered, as in the case of Dan Shechtman, who won the Nobel Prize in 2011 using X-ray crystallography and a related technique called transmission electron microscopy). This powerful method resulted in close to 30 Nobel Prizes. 

The N-F bond length (0.11 nm) in l-fluoro-2,4,6-trichloro-.y-triazine hexafluoro-arsenate is shorter than its calculated value of 0.0214 nm [2]. Also perfluorinated hexahydro-l,3,5-triazin-2,6-dione has been studied by X-ray crystallography method (Fig. 8) [6]. 

Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B., 8c Schulten, K. (2009). Molecular dynamics flexible fitting A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods, 49,174. 

X-ray crystallography Method for determining the molecular structure of crystalline compounds which provides information on the positions of the individual atoms of a molecule, their interatomic distances, bond angles, and other features of molecular geometry. 

Another advantage of MaNP acid 3 is that many MaNP esters could be obtained as single crystals suited for X-ray crystallography, and hence, the ACs of the alcohols were determined by the X-ray internal method using the AC of MaNP acid moiety. Thus, the AC determined by H NMR anisotropy was confirmed by X-ray crystallography in many cases. To date, there is no exception between MaNP acid H NMR anisotropy and X-ray crystallography methods, which causes the empirical H NMR anisotropy method to be more reliable. 

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. 

In superacidic media, the carbocationic iatermediates, which were long postulated to exist duting Friedel-Crafts type reactions (9—11) can be observed, and even isolated as salts. The stmctures of these carbocations have been studied ia high acidity—low nucleophilicity solvent systems usiag spectroscopic methods such as nmr, ir, Raman, esr, and x-ray crystallography. 

X-Ray Crystallography. Structural data exists on more than one thousand steroids. Comparisons of the conformations obtained by x-ray crystallography have been made to the conformations obtained by other methods (161). Several studies use x-ray crystal stmctures in the study of progestins. 

The field of steroid analysis includes identification of steroids in biological samples, analysis of pharmaceutical formulations, and elucidation of steroid stmctures. Many different analytical methods, such as ultraviolet (uv) spectroscopy, infrared (ir) spectroscopy, nuclear magnetic resonance (nmr) spectroscopy, x-ray crystallography, and mass spectroscopy, are used for steroid analysis. The constant development of these analytical techniques has stimulated the advancement of steroid analysis. 

A definitive method for stmctural deterrnination is x-ray crystallography. Extensive x-ray crystal stmcture deterrninations have been done on a wide variety of steroids and these have been collected and Hsted (270). In addition, other analytical methods for steroid quantification or stmcture determination include, mass spectrometry (271), polarography, fluorimetry, radioimmunoassay (264), and various chromatographic techniques (272). 

In general, the advantages of using an automated method may be comparable to those of SA refinement in X-ray crystallography [68], where many of the operations necessary to refine a structure can be done automatically and the remaining manual interventions are easier because the SA refinement usually results in a more easily interpreted electron density map. Automated methods are usually used in combination with manual assignment. However, fully automated assignment of the NOEs is possible (see Eig. 7) [69]. 

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