Search results for "Molecular model"
showing 10 items of 274 documents
How far the substituent effects in disubstituted cyclohexa-1,3-diene derivatives differ from those in bicyclo[2.2.2]octane and benzene?
2018
Substituents effects in cyclic diene derivatives are studied using quantum chemical modeling and compared to the corresponding effects in aromatic (benzene) and fully saturated (bicyclo[2.2.2]octane) compounds. In particular, electronic properties of the fixed group Y in a series of 3- and 4-X-substituted cyclohexa-1,3-diene-Y derivatives (where Y = NO2, COOH, COO− OH, O−, NH2, and X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) are examined using the B3LYP/6-311++G(d,p) method. For this purpose, quantum chemistry models of the substituent effect: cSAR (charge of the substituent active region) and SESE (substituent effect stabilization energy) as well as trad…
Divalent Cations Reduce the pH Sensitivity of OmpF Channel Inducing the PKA Shift of Key Acidic Residues
2011
In contrast to the highly-selective channels of neurophysiology employing mostly the exclusion mechanism, different factors account for the selectivity of large channels. Elucidation of these factors is essential for understanding the permeation mechanisms in ion channels and their regulation in vivo. The interaction between divalent cations and a protein channel, the bacterial porin OmpF, has been investigated paying attention to the channel selectivity and its dependence on the solution pH. Unlike the experiments performed in salts of monovalent cations, the channel is now practically insensitive to pH, being anion selective all over the pH range considered. Electrostatic calculations bas…
In silico prediction of central nervous system activity of compounds. Identification of potential pharmacophores by the TOPS–MODE approach
2004
The central nervous system (CNS) activity has been investigated by using a topological substructural molecular approach (TOPS-MODE). A discriminant analysis to classify CNS and non-CNS drugs was developed on a data set (302 compounds) of great structural variability where more than 81% (247/302) were well classified. Randic's orthogonalization procedures was carried out to allow the interpretation of the model and to avoid the collinearity among descriptors. The discriminant model was assessed by a leave-n-out (when n varies from 2 to 20) cross-validation procedure (79.94% of correct classification), an external prediction set composed by 78 CNS/non-CNS drugs (80.77% of correct classificati…
Semiempirical calculations on the interaction between dimethyltin(IV) and DNA model system
1999
Abstract The interaction between a dinucleotide triphosphate duplex (DD), mimicking the DNA molecule, and the dimethyltin(IV) cation is studied by the semiempirical PM3 method. The results show that the interaction can occur involving the tin atom and the electron-donor centres of DD, requiring in some cases the presence of water molecules. In particular, the binding of the dimethyltin(IV) moiety with two adjacent phosphate oxygen atoms is allowed by the presence of water molecules coordinating to the tin atom. In this case the tin environment shows a geometry in agreement with 119 Sn Mossbauer and X-ray data.
Molecular structures of chlorophyll a aggregates: spectroscopic and molecular modeling study
1993
Molecular structures of chlorophyll a aggregates have been studied. Spectroscopic properties of these aggregates have been studied by absorption and fluorescence spectroscopy in hydrocarbon solution at various temperatures. Observed spectroscopic shifts were interpreted in terms of simple exciton theory. Exciton splittings were estimated from computer optimized models of previously suggested Chl a aggregate structures.
Molecular topology and chromatographic retention parameters for benzodiazepines
1992
Abstract The relationship between gas-liquid chromatographic (GLC) retention properties and R F values in thin-layer chromatography (TLC) with molecular connectivity indices, m X t , was investigated for a series of benzodiazepines using multiple correlation coefficients, standard errors of estimate, F -Snedecor function values and Student's t -test as the criteria for best equation selection. Regression analyses show that the molecular connectivity model predicts the retention properties in GLC with the polar stationary phase OV-17 at 280°C and the R F values in TLC with the stationary phase silica gel. However, zero- or second-order connectivity indices alone are not sufficient; higher-or…
CLUSTER MONTE CARLO ALGORITHMS IN STATISTICAL MECHANICS
1992
The cluster Monte Carlo method, where variables are updated in groups, is very efficient at second order phase transitions. Much better results can be obtained with less computer time. This article reviews the method of Swendsen and Wang and some of its applications.
Group Metropolis Sampling
2017
Monte Carlo (MC) methods are widely used for Bayesian inference and optimization in statistics, signal processing and machine learning. Two well-known class of MC methods are the Importance Sampling (IS) techniques and the Markov Chain Monte Carlo (MCMC) algorithms. In this work, we introduce the Group Importance Sampling (GIS) framework where different sets of weighted samples are properly summarized with one summary particle and one summary weight. GIS facilitates the design of novel efficient MC techniques. For instance, we present the Group Metropolis Sampling (GMS) algorithm which produces a Markov chain of sets of weighted samples. GMS in general outperforms other multiple try schemes…
Theoretical Foundations of the Monte Carlo Method and Its Applications in Statistical Physics
2002
In this chapter we first introduce the basic concepts of Monte Carlo sampling, give some details on how Monte Carlo programs need to be organized, and then proceed to the interpretation and analysis of Monte Carlo results.
The application of Jäntti's method for the fast calculation of equilibrium in case of multilayer adsorption
2002
On the basis of a molecular model for sorption kinetics Jäntti introduced a method to calculate equilibria shortly after a change of the pressure of the sorptive gas. In the present paper we apply that method for the description of multilayer adsorption.