Search results for "molecular modeling"
showing 10 items of 136 documents
Quantum Monte Carlo Simulations of Models Related to High-Tc Superconductivity on a Transputer Network
1991
Much of the insight into the low temperature behaviour of two-dimensional quantum antiferromagnets has been recently obtained by extensive Monte Carlo. These models are relevant in the study of the magnetic behaviour of high Tc compounds containing copper-oxide layers. While of little technical importance, the physical properties of these models are certainly important for the understanding of the new type of behaviour that leads to superconductivity under certain conditions.
Kramers potential study of the Rouse-like dynamics of short alkane chains.
1999
In this work we present a Kramers potential study of the orientational dynamics and shear viscosity of short chain alkanes. In this approach the determination of the orientational relaxation time is reduced to the calculation of static moments of single chain conformations. We study a chemically realistic alkane model that asymptotically produces Gaussian chain conformations by means of a Monte Carlo simulation. Our results are applicable to single chain descriptions of polymer melt dynamics and to the intrinsic viscosity of molecules in a Theta solvent. When we map the unknown time unit of our relaxation time result for one particular chain length and temperature to the value obtained for …
The human OR1G1 olfactory receptor is differentially activated by various sandalwood odorants. A joint approach combining in silico and in vitro expe…
2013
International audience; Sandalwood is a highly valuable component in perfumery. The action mode of sandalwood odorant molecules remains to be addressed. In fact, olfactory receptors involved in their perception have not yet been identified. The interaction of a human olfactory receptor, hOR1G1, with sandalwood odorants has been investigated. By means of cellular biology and functional tests experiments, we provide an additional insight to our atomic model of OR1G1 and our olfactophore approach performed on various odorants. The studied odorants cover a wide range of structures and sandalwood intensities. We experimentally show that beta-santalol is a strong agonist of hOR1G1, contrarily to …
Categorization of chlordecone potential transformation products to predict their environmental fate
2016
EABIOmE; Chlordecone (C10Cl10O; CAS number 143-50-0) has been used extensively as an organochlorine insecticide but is nowadays banned and listed on annex A in The Stockholm Convention on Persistent Organic Pollutants (POPs). Although experimental evidences of biodegradation of this compound are scarce, several dechlorination products have been proposed by Dolfing et al. (2012) using Gibbs free energy calculations to explore different potential transformation routes. We here present the results of an in silico classification (TyPol similar to Typology of Pollutants) of chlordecone transformation products (TPs) based on statistical analyses combining several environmental endpoints and struc…
Phosphonic Acid Analogues of Phenylglycine as Inhibitors of Aminopeptidases: Comparison of Porcine Aminopeptidase N, Bovine Leucine Aminopeptidase, T…
2019
The inhibitory activity of 14 racemic phosphonic acid analogs of phenylglycine, substituted in aromatic rings, towards porcine aminopeptidase N (pAPN) and barley seed aminopeptidase was determined experimentally. The obtained patterns of the inhibitory activity against the two enzymes were similar. The obtained data served as a basis for studying the binding modes of these inhibitors by pAPN using molecular modeling. It was found that their aminophosphonate fragments were bound in a highly uniform manner and that the difference in their affinities most likely resulted from the mode of substitution of their phenyl rings. The obtained binding modes towards pAPN were compared, with these predi…
Inside c-kit tyrosine kinase: molecular modeling and QSAR in the search of new inhibitors
2010
La chemiometria ed il molecular modeling in ausilio alla scoperta ed all’ottimizzazione di lead compounds
2008
On the relations between aromaticity and substituent effect
2019
Aromaticity/aromatic and substituent/substituent effects belong to the most commonly used terms in organic chemistry and related fields. The quantitative description of aromaticity is based on energetic, geometric (e.g., HOMA), magnetic (e.g., NICS) and reactivity criteria, as well as the properties of the electronic structure (e.g., FLU). The substituent effect can be described using either traditional Hammett-type substituent constants or characteristics based on quantum-chemistry. For this purpose, the energies of properly designed homodesmotic reactions and electron density distribution are used. In the first case, a descriptor named SESE (energy stabilizing the substituent effect) is o…
Synthesis of dehydrodipeptide esters and their evaluation as inhibitors of cathepsin C
2015
The procedures for the synthesis of esters of dehydropeptides containing C-terminal (Z)-dehydrophenylalanine and dehydroalanine have been elaborated. These esters appeared to be moderate or weak inhibitors of cathepsin C, with some of them exhibiting slow-binding behavior. As shown by molecular modeling, they are rather bound at the surface of the enzyme and are not submersed in its binding cavities. Electronic supplementary material The online version of this article (doi:10.1007/s00044-015-1366-0) contains supplementary material, which is available to authorized users.
Substituent effects of nitro group in cyclic compounds
2020
AbstractNumerous studies on nitro group properties are associated with its high electron-withdrawing ability, by means of both resonance and inductive effect. The substituent effect of the nitro group may be well described using either traditional substituent constants or characteristics based on quantum chemistry, i.e., cSAR, SESE, and pEDA/sEDA models. Interestingly, the cSAR descriptor allows to describe the electron-attracting properties of the nitro group regardless of the position and the type of system. Analysis of classical and reverse substituent effects of the nitro group in various systems indicates strong pi-electron interactions with electron-donating substituents due to the re…