Molecular dynamics stability analysis

NMR is an incredibly versatile tool that can be used for a wide array of applications, including determination of molecular structure, monitoring of molecular dynamics, chemical analysis, and imaging. NMR has found broad application in the food science and food processing areas (Belton et al., 1993, 1995, 1999 Colquhoun and Goodfellow, 1994 Eads, 1999 Gil et al., 1996 Hills, 1998 O Brien, 1992 Schmidt et al., 1996 Webb et al., 1995, 2001). The ability of NMR to quantify food properties and their spatiotemporal variation in a nondestructive, noninvasive manner is especially useful. In turn, these properties can then be related to the safety, stability, and quality of a food (Eads, 1999). Because food materials are transparent to the radio frequency electromagnetic radiation required in an NMR experiment, NMR can be used to probe virtually any type of food sample, from liquids, such as beverages, oils, and broth, to semisolids, such as cheese, mayonnaise, and bread, to solids, such as flour, powdered drink mixes, and potato chips. 

If all nuclei are assigned and the spectral parameters for the conformational analysis are extracted, a conformation is calculated - usually by distance geometry (DG) or restrained molecular dynamics calculations (rMD). A test for the quality of the conformation, obtained using the experimental restraints, is its stability in a free MD run, i.e. an MD without experimental restraints. In this case, explicit solvents have to be used in the MD calculation. An indication of more than one conformation in fast equilibrium can be found if only parts of the final structure are in agreement with experimental data [3]. Relaxation data and heteronuclear NOEs can also be used to elucidate internal dynamics, but this is beyond the scope of this article. 

For the first time, the primary nitrone (formaldonitrone) generation and the comparative quantum chemical analysis of its relative stability by comparison with isomers (formaldoxime, nitrosomethane and oxaziridine) has been described (357). Both, experimental and theoretical data clearly show that the formal-donitrones, formed in the course of collision by electronic transfer, can hardly be molecularly isomerized into other [C,H3,N,0] molecules. Methods of quantum chemistry and molecular dynamics have made it possible to study the reactions of nitrone rearrangement into amides through the formation of oxaziridines (358). 

Tinte et al.54 have carried out molecular dynamic simulations of first-principles based effective Hamiltonian for PSN under pressure and of PMN at ambient pressure that clearly exhibit a relaxor state in the paraelectric phase. Analysis of the short-to-medium range polar order allows them to locate Burns temperature Tb. Burns temperature is identified as the temperature below which dynamic nanoscale polar clusters form. Below TB, the relaxor state characterized by enhanced short-to-medium range polar order (PNR) pinned to nanoscale chemically ordered regions. The calculated temperature-pressure phase diagram of PSN demonstrates that the stability of the relaxor state depends on a delicate balance between the energetics that stabilize normal ferroelectricity and the average strength of quenched "random" local fields. 

Transition metal coordination of Cu(II) carboxylate groups and pyridine groups was employed as a means of coupling a telechelic butadiene-base polymer with a randomly functionalized styrenic polymer. Dynamic mechanical analysis (DMA) and differential scanning calorimetry (DSC) indicated partial miscibility of the two polymers and Fourier transform infrared (FTIR) spectroscopy demonstrated that interactions occurred on a molecular level. When compared with blends of PSVP and the free acid derivative of CTB, the compositions based on the transition metal complex had improved dimensional stability at elevated temperatures, though there remains some question as to the stability of the copper salt to hydrolysis. Electron spin resonance (ESR) spectroscopy showed that only the... 

N. Yamaotsu, I. Moriguchi, P. A. Kollman, and S. Hirono, Biochim. Biophys. Acta, 1163, 81 (1993). Molecular Dynamic Study of the Stability of Staphylococcal Nuclease Mutants Component Analysis of the Free Energy Difference of Denatuiation. 

As such, we return now to the harmonic oscillator, which as well as being the simplest molecular model is also one of the most relevant for molecular dynamics applications, as many issues of stability and timestep in molecular dynamics simulations arise due to harmonic potentials used to model covalent bonds (such as in crystalline solids and biomolecules). The canonical distributions of position and momentum are also of a simple form (Gaussians), making such oscillators particularly amenable to analysis. 

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