Computer modeling studies

North, A.C.T., Steinert, RM., Parry, D.A.D. Coiled-coil stutter and link segments in keratin and other intermediate filament molecules a computer modeling study. Proteins 20 174-184, 1994. 

Alkyl enamides, such as N-(1 -tert-bulyl-viriyl)-acelamide 88 and N-(l-adaman-tyl-vinyl)-acetamide 89, can also be hydrogenated in high enantioselectivity (>99% ee) and activity (TON 5000 TOF >625 h ) with Rh-Me-DuPhos [19]. Remarkably, these bulky alkyl enamides are reduced with the opposite sense of induction, a phenomenon also observed when the bisphospholane Di Square P 63 was applied [87 b]. A computational modeling study by Landis and Feldgus suggested that the reduction of a-alkyl and a-arylenamides involves different coordination pathways [93, 158]. 

The most stable structure of the [CcP, Cc] complex deduced from computer modelling studies by Poulos and coworkers [19] looks much like that of the [oci, P2] ET complex of the Hb hybrids, with roughly parallel heme planes... 

Significant progress has recently been made in several areas which will have a profound effect on the ability of molecular dynamics to handle more complex problems. In this section we speculate on several areas which appear to hold promise for advancing computer modeling studies. In section 4.1, recent progress in both analytic potential energy expressions and first principles calculations are briefly mentioned. Recent advances in computational techniques are discussed in section 4.2. These include the use of constraints within the classical equations of motion to model thermostats in the surface region, and the incorporation of Monte Carlo techniques into molecular dynamics simulations. 

This section covers some of the more important chemical reactions that occur in the polluted atmosphere and attempts to show how these reactions result in photochemical-oxidant formation. For a more thorough understanding of the chemistry involved, the reader should consult recent reviewsand computer modeling studies by Demeijian, Kerr, and Calvert and by Calvert and MoQuigg. Unless otherwise noted, the mechanisms and rate constants of these modeling studies are used in this discussion. 

The apparent partition coefficient (log P) and the calculated molar re-fractivity (CMR) are physicochemical parameters that correlate with the ability of a compound to be involved in MDR, and nonobvious structural homologies between compounds as dissimilar as verapamil (148) and vinblastine (1) exist as revealed by computer modeling studies (115). A far... 

Carter, W. P. L and R. Atkinson, Computer Modeling Study of Incremental Hydrocarbon Reactivity, Enciron. Sci. Technoi, 23, 864-880 (1989). 

Hough, A. M., and R. G. Derwent, Computer Modeling Studies of the Distribution of Photochemical Ozone Production between Different Hydrocarbons, Atmos. Environ., 21, 2015-2033 (1987). 

The above data, along with other data from Meister s group (102, 103), provided the basis for computer modeling studies (104) of the active site conformations of substrates and intermediates in the glutamine synthetase reaction. The conclusions are that both structures II and III are in the reaction mechanism. 

Another interesting point explored in detail by Wedler and Horn 87) is that the apparent binding constant of methionine sulfoximine for the irreversible inhibition is 100 jxM compared to 1.5 fiM for direct binding to the enzyme. This leads to speculation that perhaps methionine sulfoximine can bind to the enzyme in two conformations one for competitive binding that does not lead to irreversible inhibition, while another conformer binds in a different manner, producing the irreversible inhibition. The proposal from computer modeling studies of Gass and Meister 104) is that one conformation is responsible for both, but recent data open the door for further study and speculation. 

The stronger excitonic interaction in EB assemblies than that of ACR or AMAC is apparently due to a greater hydrophobic surface area of the former, as estimated from computer modeling studies (MacSpartan). Such increased hydrophobic surface is not expected from their structures (three six-membered ring systems) it also results in an enhanced entropic contribution to the binding energy when the probe is transferred from the aqueous phase to the interior of BAZrP, where there is little or no water. Therefore, the formation of these supramolecular assemblies may indeed involve a large entropic component, but this needs to be demonstrated experimentally. 

R. J. Waltman, G. W. Tyndall, and J. Pacansky, Computer-modeling study of the interactions of Zdol with amorphous carbon surfaces, Langmuir 15, 6470-6483 (1999). 

Based on the accumulated crystallographic and adsorption data of PCPs, computational modeling studies of small-molecule adsorption have been performed (an... 

In their computer-modeling study, Morini and coauthors used the three-dimensional structure of the sweet receptor and a molecular dynamics modeling program called GRAMM to predict the AG° of binding of sweet molecules to the sweet receptor. First, they trained their model—that is, they refined the parameters so that the AG° values predicted by the model matched the known AG° values for one set of sweet molecules (the training set ). They then tested the model by asking it to predict the AG° values for a new set of molecules (the test set ). 

One technique for reducing this proximity effect is to replace the single layer of resist with a multilevel resist (MLR) system. In this case, a thin radiation sensitive resist is separated from the substrate by a thick layer of organic material (1). The utility of this approach has been demonstrated experimentally in several laboratories and also investigated by various computer modeling studies. 

Computational methods have had a major impact on almost all areas of science in recent years. The range of applications is now very broad, encompassing molecular biology, materials and surface science, mineralogy, and small molecule chemistry. This article focuses on the application of atomistic computer modeling techniques to materials science. We present a brief survey of the aims and scope of the field and short introduction to the main methodologies. We illustrate the current state of the art of computer modeling studies of materials by recent applications to bulk and surface properties of topical systems. 

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