Search results for "COMPUTATION"
showing 10 items of 7362 documents
Applications of “Forced Rayleigh Scattering” and “Photon Correlation Spectroscopy” for the examination of transport properties in polymer melts
2007
The importance of optical techniques for the characterization of the dynamics in polymers has increased in the last 10 years. This was caused by the rapid development in optics and microelectronics which has made these techniques easily available and extremely precise. However, in case of the examination of transport properties in bulk polymers, new difficulties arise due to the comparably slow dynamics underlying these phenomena. The topic of this paper is a small survey of two optical techniques which can be applied to solve the arising problems and a presentation of some results of our working group concerning slow translational transport processes in polymers. In a first part, the techn…
Self-diffusion in polymer solutions using the bond-fluctuation MC-algorithm
1991
Abstract A lattice Monte Carlo study of the self-diffusion of polymer chains in an athermal solution of equal chains is presented. The examined chain lengths, N (= 20–200), and volume fractions, φ (= 0.025-0.5), cover the range from dilute solution to concentrated solution, respectively. The dynamics show a gradual crossover from Rouse to reptation-like behaviour. Analysing the data according to a scaling theory and taking into account the density dependence of the microscopic length and time-scales, an almost perfect scaling of the self-diffusion coefficient is achieved. The high statistical accuracy of the data (103–104 chains per parameter combination) was obtainable by using a transpute…
An ab initio softness metric to measure the similarity between all pairs of amino acids
2010
Abstract The search for quantitative index of similarity between molecular moeties is important for its applications in pharmacology. Similarity is also an important concept in computational biology to measure the exchangeability of an amino acid by another in a protein sequence. In the present work, a distance between two molecules based on local and global softnesses of their fragments is defined. The method proposed is general and could be applied to any molecular library. It is first applied to compute the distance between the 190 pairs of different amino acids in their neutral states. Two amino acids belonging to the one of the biochemical class (aliphatic, sulfur-containing, acidic, ……
Synthesis, crystal structures, and solid state quadratic nonlinear optical properties of a series of stilbazolium cations combined with gold cyanide …
2011
Three salts built up from (E)-4′-(dimethylamino)-stilbazolium (DMAS)H+, (E)-4′-(diethylamino)-stilbazolium (DEAS)H+, (E)-4′-{2-(methoxymethyl) pyrrolidinyl}-stilbazolium (MPS)H+, and gold cyanide as a counter-ion, are reported. The crystal structures have been solved for (DEAS)H+ Au(CN)2− (Cc space group), and for (MPS)H+ Au(CN)2− (P1 space group). The semi-empirical (ZINDO) calculated static hyperpolarizability (β0) of (MPS)H+ is equal to 147 × 10−30 cm5esu−1, in solid state, which is 25% higher than that of the cation of the well known (E)-4′-(dimethylamino)-methylstilbazolium tosylate (DAST). (MPS)H+ Au(CN)2− exhibits a unique crystal structure in which the cations are perfectly aligned.…
ChemInform Abstract: Toward an Understanding of the Mechanisms of the Intramolecular [5 + 2] Cycloaddition Reaction of γ-Pyrones Bearing Tethered Alk…
2000
The molecular mechanism for the intramolecular [5 + 2] cycloaddition reaction of β-silyloxy-γ-pyrones bearing tethered alkenes has been characterized using ab initio methods. A comparative study for this sort of cycloaddition carried out at different computational levels points out that the B3LYP/6-31G* calculations give similar barriers to those obtained with the MP3/6-31G* level. Analysis of the energetic results shows that the reaction takes place along a stepwise process: first, the migration of the neighboring silyl group to the carbonyl group of the γ-pyrone takes place to give a weak oxidopyrylium ylide intermediate, which by a subsequent concerted intramolecular [5 + 2] cycloadditi…
Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway
2012
The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect distinctive kinetic characteristics, as well as sequence-dependent properties of the employed enzymes. This study aims to examine possible linkages between kinetic constants and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolytic pathway. The values of Michaelis-Menten constant (K M), turnover number (k cat), and specificity constant (k sp = k cat/K M) were taken from BRENDA (15, 17, and 16 values, respectively) and protein sequences of nine…
Classification of Complex Molecules
2009
Algorithms for classification and taxonomy based on criteria, e.g., information entropy and its production are proposed. In molecular classification, the feasibility of replacing a given molecule (e.g, anaesthetic) by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using characteristic chemical properties of different portions of their molecules. In taxonomy, the detailed comparison of the sequences (primary structures) of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree for some species, e.g. the 1918 influenza virus. The method is applied to the classifications of: (1) …
Density functional theory study of the 5-pyrrolidin-2-yltetrazole-catalyzed aldol reaction
2005
Abstract The replacement of the carboxylic acid functionality with a tetrazolic acid in the proline-catalyzed asymmetric aldol reaction between acetone and trimethylacetaldehyde has been studied using DFT methods at the B3LYP/6-31G** computational level. For the C–C bond-formation step, four reactive channels corresponding to the syn and anti arrangement of the enamine and the re and si attack modes have been analyzed. The B3LYP/6-31G** results allowed us to explain the stereoselectivity and the increase in reactivity relative to the proline-catalyzed process in DMSO.
Internal rotation of 1,2-dichloroethane in haloalkane dehalogenase. A test case for analyzing electrostatic effects in enzymes
2003
1,2-Dichoroethane (DCE) is a prototypical molecule for studying electrostatic solvent effects on molecular conformation as far as rotation around the carbon−carbon bond notably changes the electric...
Mukaiyama–Michael Reactions with trans-2,5-Diarylpyrrolidine Catalysts: Enantioselectivity Arises from Attractive Noncovalent Interactions, Not from …
2013
The scope of the enantioselective Mukaiyama-Michael reactions catalyzed by trans-2,5-diphenylpyrrolidine has been expanded to include both α- and β-substituted enals. However, the rationalization of the observed enantioselectivity is far from obvious since the catalyst is not very sterically hindered. DFT calculations were carried out to rationalize the observed stereoselectivities. Transition states of the C-C bond formation between iminium intermediates and silyloxyfurans were located and their relative energies were used to estimate the stereoselectivity data. We find excellent agreement between the predicted and observed stereoselectivities. The analysis of intermolecular forces reveals…