Search results for "computational"
showing 10 items of 5884 documents
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…
The Catalytic Mechanism of Carboxylesterases: A Computational Study
2014
The catalytic mechanism of carboxylesterases (CEs, EC 3.1.1.1) is explored by computational means. CEs hydrolyze ester, amide, and carbamate bonds found in xenobiotics and endobiotics. They can also perform transesterification, a reaction important, for instance, in cholesterol homeostasis. The catalytic mechanisms with three different substrates (ester, thioester, and amide) have been established at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory. It was found that the reactions proceed through a mechanism involving four steps instead of two as is generally proposed: (i) nucleophilic attack of serine to the substrate, forming the first tetrahedral intermediate, (ii) formation of the ac…
Restricted and complete-active-space multiconfiguration linear response calculations of the polarizability of formamide and urea
1991
Abstract Using the polarized basis sets of Sadlej, we have carried out multiconfiguration linear response (MCLR) calculations of static and dynamic polarizabilities of water, carbon dioxide, formamide and urea. It is found that the polarized basis sets give a good description of the polarizabilities. The uncorrelates (self-consistent field) polarizabilities are in general 10% or more lower than the experimental values. The correlation as introduced in the complete-active-space (CAS) and restricted-active-space (RAS) MCLR calculations recovers the major part of this deviation.
DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes
2017
In this work, we present scaled variants of the DLPNO-CCSD(T) method, dubbed as (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T), to obtain accurate interaction energies in supramolecular complexes governed by noncovalent interactions. The novel scaled schemes are based on the linear combination of the DLPNO-CCSD(T) correlation energies calculated with the standard (LoosePNO and NormalPNO) and modified (Loose2PNO and Normal2PNO) DLPNO-CCSD(T) accuracy levels. The scaled DLPNO-CCSD(T) variants provide nearly TightPNO accuracy, which is essential for the quantification of weak noncovalent interactions, with a noticeable saving in computational cost. Importantly, the accuracy of the proposed schemes is…
DFT study of the interaction free energy of p–p complexes of fullerenes with buckybowls and viologen dimers
2011
We present a theoretical investigation, by means of DFT protocols, of the complexation thermodynamics of (i) complexes of C70 and C60 fullerenes with bowl-shaped hexabenzocoronene derivatives and (ii) complexes of C60 with viologen dimers. The recent functionals of the M06 family, accounting for p-p interactions to a good level of approximation, have been used to calculate the interaction free energies. For the former complexes, the good agreement between the calculated results and the experimental data confirms the reliability of the protocol used. On these grounds, we then checked the stability of a series of complexes of C60 with some viologen dimers, 1BPnBP1 (n = 6-9), where two N-methy…
Detection of RNA modifications
2010
RNA nucleotide modifications are typically of low abundance and frequently go unnoticed by standard detection methods of molecular biology and cell biology. With a burst of knowledge intruding from such diverse areas as genomics, structural biology, regulation of gene expression and immunology, it becomes increasingly clear that many exciting functions of nucleotide modifications remain to be explored. It follows in turn that the biology of nucleotide modification and editing is a field poised to rapidly gain importance in a variety of fields. The detection and analysis of nucleotide modifications present a clear limitation in this respect. Here, various methods for detection of nucleotide …
Unexpected Structural Diversity in Alkali Metal Azide-Crown Ether Complexes: Syntheses, X-ray Structures, and Quantum-Chemical Calculations
2005
A series of alkali metal azide-crown ether complexes, [Li([12]crown-4)(N-3)], [Na([15]crown-5)(N-3)], [Na([15]crown-5)(H2O)(2)]N-3, [K([18]crown-6)(N-3)(H2O)], [Rb([18]crown-6)(N-3)(H2O)], [Cs([18]crown-6)(N-3)](2), and [Cs([18]crown-6)(N-3)(H2O)(MeOH)], has been synthesised. In most cases, single crystals were obtained, which allowed X-ray crystal structures to be derived. The structures obtained have been compared with molecular structures computed by density functional theory (DFT) calculations. This has allowed the effects of the crystal lattice on the structures to be investigated. Also, a study of the M-N-terminal metalazide bond length and charge densities on the metal (M) and termin…