Search results for "COMPUTATION"

The nature of the chemical bond in (CH3)3N-BCl3 and (CH3)3N-AlCl3

1994

1,2-Dipolar addition model for the cytoprotective activity of selected α,β-unsaturated compounds with CO functionality: an ab initio study

2001

Abstract The mechanism of the addition of a nucleophile (an alkylthiol group) to a double bond of α,β-unsaturated systems in the gas phase was explored. In this study, intermediates of the reaction were also investigated using ab initio calculations (RHF/6-31G ∗ and MP2/6-31+G ∗ ). Our results indicate that direct dipolar attack of the S–H group of an alkylthiol on the CC double bond is a reasonable reaction path. The present results represent, therefore, additional support for our hypothesis. This suggests that the mechanism of cytoprotection might be mediated, at least in part, by a reaction between the olefinic acceptor and the sulfhydryl-containing groups of the mucosa.

The transformation of aromatic molecules into the subspace of their double bonds

1975

A model of new submolecules is presented. As an application some absorptions of aromatic radicals are interpreted in UV and visible spectra. Extension of the model to biological systems is prejudged.

A theoretical study of neutral and reduced tetracyano-p-quinodimethane (TCNQ)

2004

Abstract The molecular structure of neutral, anionic, and dianionic tetracyano- p -quinodimethane (TCNQ), as well as the electron affinity of TCNQ, have been studied with HF, MP2, and different density functional theory (DFT) procedures. The optimized geometries compare well with the available experimental data, although the C N bond distance is not correctly described at the MP2 level. The calculated parameters are rather insensitive to the basis set employed, and the addition of diffuse functions does not yield significant changes. When the extra electrons are added, the central ring of TCNQ progressively becomes more aromatic. Compared with the CCSD(T) estimate, the value of the adiabati…

Can Experimental Electron-Density Studies be Used as a Tool to Predict Biologically Relevant Properties of Low-Molecular Weight Enzyme Ligands?

2013

The case of protease inhibitor model compounds incorporating an aziridine or epoxide ring is used to exemplify how application of experimental electron-density techniques can be used to explain the biological properties of low-molecular weight enzyme ligands. This is furthermore seen in the light of a comparison of crystal and enzyme environments employing QM/MM computations to elucidate to which extent the properties in the crystal can be used to predict behavior in the biological surrounding.

Binding and isomerization energies for the Cu/CN and Cu(I)CN interactions

1993

Abstract Binding and isomerization energies of the CuCN, CuNC, CuCN+, and CuNC+ systems were investigated by means of a multireference CI perturbatively selected, MRCI-PS approach. The inclusion of the main dynamical correlation effects are evaluated. The binding energies for CuCN and CuNC are 4.37 and 4.03 eV, respectively, and those for CuCN+ and CuNC+ are 0.08 and 1.61 eV. Calculated isomerization energies are 7.86 and 35.98 kcal/mol for CuCN and Cu(I)CN isomerizations, respectively.

Dissociation energies within selected configuration interaction and perturbation theory

1993

Abstract Selected configuration interaction (CI) calculations and second-order perturbational theory are used to truncate systematically multireference single and double excitation CI (MRCI) expansions in the calculation of the bond dissociation energies of several systems like the single-bonded LiF molecule or the multiple-bonded N2, NO and O2 diatomic systems. The method is extended to compute the CH bond dissociation energy ofethene C2H4. It is shown how the proposed scheme (perturbation-selected MRCI (MRCI-PS)) is able to reproduce the accuracy of complete MRCI expansions with only a small number of configurations variationally evaluated.

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…

Investigation of Polyol Adsorption on Ru, Pd, and Re Using vdW Density Functionals

2015

Biomass-based feedstocks are often oxygenated compounds characterized by large amounts of hydroxyls. As an example, polyols and sugar alcohols are largely employed as reactants for different chemical catalytic transformations such as oxidation, dehydration, and hydrodeoxigenation, which usually occur in aqueous medium. With the goal of gaining new insights into processes that could be industrially relevant, the adsorption of the OH groups on metal surfaces and in the presence of water has to be correctly reproduced and described, within a chosen theoretical framework. Toward this goal, several tests were performed on the catalytically relevant metal Ru, Pd, and Re, benchmarking their bulk a…

Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome- coronavirus-2 and the receptor of human angiotensin…

2020

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RB…