E X-ray crystallography

The atropoisomerism of N -phenylazoles, i.e. an isomerism of the type shown by biphenyl derivatives, has been studied by several authors. Some torsional angles, measured by X-ray crystallography (Section 4.04.1.3.1) are shown in Table 26. 

A molecular dynamics force field is a convenient compilation of these data (see Chapter 2). The data may be used in a much simplified fonn (e.g., in the case of metric matrix distance geometry, all data are converted into lower and upper bounds on interatomic distances, which all have the same weight). Similar to the use of energy parameters in X-ray crystallography, the parameters need not reflect the dynamic behavior of the molecule. The force constants are chosen to avoid distortions of the molecule when experimental restraints are applied. Thus, the force constants on bond angle and planarity are a factor of 10-100 higher than in standard molecular dynamics force fields. Likewise, a detailed description of electrostatic and van der Waals interactions is not necessary and may not even be beneficial in calculating NMR strucmres. 

Although the structure of [SsN] has not been established by X-ray crystallography, the vibrational spectra of 30% N-enriched [SsN] suggest an unbranched [SNSS] (5.22) arrangement of atoms in contrast to the branched structure (Dsh) of the isoelectronic [CSs] and the isovalent [NOs] ion (Section 1.2). Mass spectrometric experiments also support the SNSS connectivity in the gas phase.Many metal complexes are known in which the [SsN] ion is chelated to the metal by two sulfur atoms (Section 7.3.3). Indeed the first such complex, Ni(S3N)2, was reported more than twenty years before the discovery of the anion. It was isolated as a very minor product from the reaction of NiCl2 and S4N4 in methanol. However, some of these complexes, e.g., Cu and Ag complexes, may be obtained by metathetical reactions between the [S3N] ion and metal halides. 

If chromatin is swelled suddenly in water and prepared for viewing in the electron microscope, the nucleosomes are evident as beads on a string, dsDNA being the string (Figure 12.28). The structure of the histone octamer core has been determined by X-ray crystallography without DNA by E. N. Moudrianakis s laboratory (Figure 12.29) and wrapped with DNA by T. J. 

During the past 20 y numerous other highly coloured halogen cations have been characterized by Raman spectroscopy. X-ray crystallography, and other techniques, as summarized in Table 17.18. Typical preparative routes involve direct oxidation of the halogen (a) in the absence of solvent, (b) in a solvent which is itself the oxidant (e.g. AsFs) or (c) in a non-reactive solvent (e.g. SO2). Some examples are listed below ... 

Fig. 3.3 H NMR and X-ray crystallography study of the bis-ether complex 28. [Denmark, S.E. Edwards, ).P. Wilson, S.R.J. Am. Chem. Soc. 1992, 114, 2592. Reprinted with permission from The American Chemical Society]...

Generation of the anion of 5,7-diphenyl-5//-dibenz[c,e]azepine (6) under phase-transfer conditions in the presence of air results in oxidation and formation of the dibenz[c,c]azepinol 7 whose structure was confirmed by X-ray crystallography.85... 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

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