Dynamic case studies

Z. R. Wasserman and C. N. Hodge. Fitting an inhibitor into the active site of thermolysin A molecular dynamics case study. PROTEINS Structure, Function and Genetics, 24 227-237, 1996. 

The field of gas phase reaction dynamics has been extensively reviewed elsewhere [1, 2 and 3] in considerably greater detail than is appropriate for this chapter. Here, we begin by simnnarizing the key theoretical concepts and experimental teclmiques used in reaction dynamics, followed by a case study , the reaction F + H2 HF + H, which serves as an illustrative example of these ideas. 

The above discussion represents a necessarily brief simnnary of the aspects of chemical reaction dynamics. The theoretical focus of tliis field is concerned with the development of accurate potential energy surfaces and the calculation of scattering dynamics on these surfaces. Experimentally, much effort has been devoted to developing complementary asymptotic techniques for product characterization and frequency- and time-resolved teclmiques to study transition-state spectroscopy and dynamics. It is instructive to see what can be accomplished with all of these capabilities. Of all the benclunark reactions mentioned in section A3.7.2. the reaction F + H2 —> HE + H represents the best example of how theory and experiment can converge to yield a fairly complete picture of the dynamics of a chemical reaction. Thus, the remainder of this chapter focuses on this reaction as a case study in reaction dynamics. 

A comprehensive and up-to-date introduction to the ideas of molecular dynamics and Monte Carlo, with statistical mechanical background, advanced teclmiques and case studies, supported by a Web page for software download. 

It must be emphasized that all time-dependent chemical phenomena, such as tautomerism, are sensitive to temperature changes. In this section, we treat classic DNMR (dynamic NMR) studies and cases of changes in the NMR spectra with temperature together. In Table XI we have classified these studies according to the physical state of the sample and to the nuclei... 

Predicated on the dynamics of CA, the case studies of artificial life (and, in the coming years, the many provocative examples that are sure to come from artificial... 

Classical dynamics is studied as a special case by analyzing the Ehrenfest theorem, coherent states (16) and systems with quasi classical dynamics like the rigid rotor for molecules (17) and the oscillator (18) for various particle systems and for EM field in a laser. 

Clay hllers were surface modihed with TMPTA or triethoxyvinyl silane (TEVS) followed by EB irradiation by Ray and Bhowmick [394]. Both the untreated and treated fillers were incorporated in an ethylene-octene copolymer. Mechanical, dynamic mechanical, and rheological properties of the EB-cured unfilled and filled composites were studied and a significant improvement in tensile strength, elongation at break, modulus, and tear strength was observed in the case of surface-treated clay-filled vulcanizates. Dynamic mechanical studies conducted on these systems support the above findings. 

As shown, the data patterns 1 and 2 are classified as Normal with high certainty, as they lie within the boundaries of the normal class. However, 3 and 4 are classified as normal with medium certainty, as they lie outside the normal region, but their similarities are closest to the normal cluster. Similarly, the data pattern represented by 5 is classified as fault2 with medium certainty and the data patterns represented by 6, 7, and 8 are classified as fault2, and so on. If the data are collected every 20 seconds as in the case study, the dynamic interpretation is tabulated as shown in Table V, with the labels in italics representing the correct class and appropriate certainty. An x means there was not an interpretation with this certainty. 

Saxena AM, Udgaonkar JB, Krishnamoorthy G (2005) Protein dynamics control proton transfer from bulk solvent to protein interior a case study with a green fluorescent protein. Protein Sci 14 1787-1799... 

The following case study contains examples of several topics discussed in previous sections, including some aspects of laser technology, laser spectroscopy and laser chemistry. A variety of lasers and laser techniques are applied in a straightforward manner to the problem of ascertaining structural and dynamical information on an excited electronic state of wide chemical interest. This information is obtained rather simply, illustrating the potential of laser techniques in the resolution of problems in solution chemistry. 

Tardy Y, Bustillo V, Boeglin JL (2004) Geochemistry applied to the watershed survey hydrograph separation, erosion and soil dynamics. A case study the basin of the Niger River, Africa. Appl Geochem 19 469-518... 

Gilmour, C.C. and N.S. Bloom. 1995. A case study of mercury and methylmercury dynamics in a Hg-contaminated municipal wastewater treatment plant. Water Air Soil Pollut. 80 799-803. 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

In this section, we give the highlights of a few case studies of the dynamics of chemical reactions. We begin with a brief survey of heavy particle charge transfer reactions, followed by a few words about electron transfer reactions and proton transfer reactions. 

In chapter 1, Profs. Cramer and Truhlar provide an overview of the current status of continuum models of solvation. They examine available continuum models and computational techniques implementing such models for both electrostatic and non-electrostatic components of the free energy of solvation. They then consider a number of case studies with particular focus on the prediction of heterocyclic tautomeric equilibria. In the discussion of the latter they focus attention on the subtleties of actual chemical systems and some of the danger in applying continuum models uncritically. They hope the reader will emerge with a balanced appreciation of the power and limitations of these methods. In the last section they offer a brief overview of methods to extend continuum solvation modeling to account for dynamic effects in spectroscopy and kinetics. Their conclusion is that there has been tremendous progress in the development and practical implementation of useful continuum models in the last five years. These techniques are now poised to allow quantum chemistry to have the same revolutionary impact on condensed-phase chemistry as the last 25 years have witnessed for gas-phase chemistry. 

In the following, the screening power and the scientific potential applying HIE Stage n technologies in gas-phase oxidation are demonstrated for two illustrative case studies (1) the epoxidation of 1,3-butadiene with Ag-based catalysts and (2) dynamic experiments for automotive applications (DcNOJ. 

The Structure and Dynamics of Membrane-Associated Peptides - A Case Study of Neuropeptide Y (NPY)... 

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