SUBJECTS molecular mechanics

Alcohol abuse is a major clinical problem in many countries and has been the subject of investigation for many years by those interested in determining the molecular basis of ethanol-induced liver dam e (see Lieber, 1990). These intensive and extended efforts have revealed much about the metabolism of ethanol in the liver and about the toxicity of its primary oxidative product, acetaldehyde. They have not, however, folly elucidated the molecular mechanisms that lead to the typical features of alcoholic liver injury steatosis, necrosis and eventually cirrhosis. 

The calculations described here have been called strain calculations, molecular mechanics, or force field calculations. We prefer the latter term. For a discussion of historical developments and a literature survey of earlier work, which are not given here, the reader is referred to a number of other reviews (1-3). The present paper deals with the description of force field types, techniques of energy minimisation, and procedures for the determination of force field parameters, and with some applications, preferentially taken from our own field of interest. In accordance with the experiences of the author, the work of Lifson and coworkers is given special attention other authors are nevertheless well represented in the context of critical comparisons. We hope that this selection, although inevitably biased, will help to improve the consistency of the presentation of the subject. 

In addition to the [4+2] cycloaddition, intramolecular [2+2] photocycloaddition was also successfully used as a main procedure in the synthesis of (i)-ginkgolide B <00JA8453>. The studies on the model reactions and molecular mechanics calculation show that the stereochemistry of the substituents at C6 and C8 should influence severely the reaction diastereoselectivity. When syn-diastereomer 41 is subjected to irradiation the reaction gives a single diastereomer 42 in a quantitative yield since two substituents at C6 and C8 would be in pseudo-equatorial orientation in the chair-like transition state. 

Over 300 peptides isolated in our laboratory were studied in one or more tumor or normal cell cultures [39-44]. Part of the results obtained is summarized in Table 2.3. Over 75% of the peptides showed pronounced proliferative or antiproliferative activity in at least one cell type (Fig. 2.3). As a rule, tumor cells are more sensitive to peptide action. Besides the cell type, experimental conditions such as cell density or composition of the culture medium also affected the overall effect. In several cases (13%, Fig. 2.3) even the sign of the effect was peptide concentration dependent. Generally, experiments with cell cultures conform with the view that the main physiological function of cell and tissue peptidomes is control of long term processes and the homeostatic balance (i.e. cell differentiation, proliferation and elimination). The overall effect of peptide pools is achieved by concerted action of total sets of peptides rather than by single components. The molecular mechanisms of peptide action in cells requires concrete study in each individual case and are the subject of current research. 

Aerobic bacteria which often use H2 as an alternative energy source express hydrogenase genes, with a few exceptions, when the substrate is provided (Table 3.1). How do these organisms recognize the presence of H2, the smallest molecule on Earth The underlying molecular mechanisms are subject of current research and will be discussed in Sections 3.2 and 3.3. 

The N,N -diphenylguanidinium (dpg+) has been foimd to adopt different conformations both in aqueous solutions [9] and in several salts that are being reviewed in this paper. The conformation of dpg+ is very sensitive to the counter-ion, and this effect has been the subject of ab-initio quantum mechanical and molecular mechanics calculations [10]. Stabilization of a particular conformation depends critically on intermolecular interactions with the solvent, since the energetic cost of rotation of the phenyl rings is much lower than typical solvation energies. 

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