Search results for "DFT Calculations"
showing 10 items of 65 documents
Reactivity of antitumor coinage metal-based N-heterocyclic carbene complexes with cysteine and selenocysteine protein sites
2021
Abstract The reaction of the antitumor M(I)-bis-N-heterocyclic carbene (M(I)-NHC) complexes, M = Cu, Ag, and Au, with their potential protein binding sites, i.e. cysteine and selenocysteine, was investigated by means of density functional theory approaches. Capped cysteine and selenocysteine were employed to better model the corresponding residues environment within peptide structures. By assuming the neutral or deprotonated form of the side chains of these amino acids and by considering the possible assistance of an external proton donor such as an adjacent acidic residue or the acidic component of the surrounding buffer environment, we devised five possible routes leading to the binding o…
The influence of solvent on conformational properties of peptides with Aib residue—a DFT study
2017
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results,…
Azoxybenzene rearrangement catalyzed by solid acids
2008
Abstract For the first time, the potential of acidic cation-exchange resin (sulfonated polystyrene) to catalyze the Wallach rearrangement of azoxybenzene into 4-hydroxyazobenzene has been proved. This finding reveals an alternative reaction path possible in a heterogeneous process using solid acids and may help to clear some doubts concerning the rearrangement mechanism postulated so far. The resin-induced reaction was found to proceed exclusively in a non-polar medium. Reasonable yield was obtained particularly in isooctane due to favorable distribution of azoxybenzene throughout the resin's matrix. On the contrary, the HY type zeolite did not activate the rearrangement, most probably beca…
Can Green Dimethyl Carbonate Synthesis be More Effective? A Catalyst Recycling Study Benefiting from Experimental Kinetics and DFT Modeling
2014
Dibutyldimethoxystannanes are known to catalyze the reaction between carbon dioxide and methanol leading to dimethyl carbonate. Despite similarities between din-butyl- and ditert-butyldimethoxystannane, the recycled complexes have different structural features. In the din-butyl series, a decatin(IV) complex has been characterized and is less active than the stannane precursor. Kinetic experiments likely indicate that all the tin centers are not active, which is confirmed in comparing with the related dinuclear 1,3-dimethoxytetran-butyldistannoxane complex. In the ditert-butyl series, the tritin(IV) complex isolated upon recycling features the steric effect of bulky tBu ancillary ligands. In…
Synthesis, spectroscopic characterization and in vitro antimicrobial activity of diorganotin(IV) dichloride adducts with [1,2,4]triazolo-[1,5-a]pyrim…
2006
Abstract The heterocyclic ligands [1,2,4]triazolo-[1,5-a]pyrimidine (tp) and 5,7-dimethyl-[1,2,4]triazolo-[1,5-a]pyrimidine (dmtp), react with diorganotin dichlorides giving the addition compounds Me2SnCl2(tp)2, Et2SnCl2(tp)2, Me2SnCl2(dmtp)2, Et2SnCl2(dmtp)2, Bu2SnCl2(dmtp), Ph2SnCl2(dmtp). The organotin:ligand stoichiometry goes from 1:2 to 1:1 by increasing the steric hindrance of the organic groups bound to tin. The compounds have been characterized by means of infrared, 119Sn Mossbauer and 1H AND 13C NMR spectroscopy. The ligands presumably coordinate to tin classically through the nitrogen atom at the position 3. The 1:1 complexes adopt trigonal bipyramidal structures, with the organi…
Substituent effects in trans-p,p'-disubstituted azobenzenes: X-ray structures at 100 K and DFT-calculated structures.
2014
The crystal and molecular structures of twopara-substituted azobenzenes with π-electron-donating –NEt2and π-electron-withdrawing –COOEt groups are reported, along with the effects of the substituents on the aromaticity of the benzene ring. The deformation of the aromatic ring around the –NEt2group inN,N,N′,N′-tetraethyl-4,4′-(diazenediyl)dianiline, C20H28N4, (I), may be caused by steric hindrance and the π-electron-donating effects of the amine group. In this structure, one of the amine N atoms demonstrates clearsp2-hybridization and the other is slightly shifted from the plane of the surrounding atoms. The molecule of the second azobenzene, diethyl 4,4′-(diazenediyl)dibenzoate, C18H18N2O4,…
Oxadiazolyl-pyridines and perfluoroalkyl-carboxylic acids as building blocks for protic ionic liquids: crossing the thin line between ionic and hydro…
2012
A series of 18 samples has been prepared in order to obtain fluorinated materials as Protic Ionic Liquids (PILs). These were synthesized by appropriately mixing 1,2,4-oxadiazoles derivatised with two pyridines, or one pyridine and a fluorinated chain, and perfluoroalkyl-carboxylic acids, either mono- or dicarboxylic, leading to symmetric and non-symmetric materials. Many of them showed low melting points. However, the possibility of classifying the synthesized materials as PILs is discussed in terms of effective ionicity of the systems by the combination of Density Functional Theory (DFT) calculation and IR spectroscopy. The important outcome of our investigation is that the complete proton…
Simulations on the mechanism of CNT bundle growth upon smooth and nanostructured Ni as well as θ-Al2O3 catalysts
2011
Abstract In the current study, we have performed ab initio DFT calculations on the gradually growing 2D periodic models of capped single-wall carbon nanotubes (SW CNTs) upon their perpendicular junctions with the Ni(111) substrate, in order to understand the peculiarities of the initial stage of their growth on either smooth or nanostructured catalytic particles. Appearance of the adsorbed carbon atoms upon the substrate follows from the dissociation of CVD hydrocarbon molecules, e.g., CH4: (CH4)ads → (CH)ads+3Hads and (CH)ads → Cads+Hads. (Since the effective growth of CNTs upon Ni nanoparticles occur inside the nanopores of amorphous alumina, we have also simulated analogous surface react…
An experimental and theoretical study of a heptacoordinated tungsten(VI) complex of a noninnocent phenylenediamine bis(phenolate) ligand
2018
[W(N2O2)(HN2O2)] (H4N2O2 = N,N′-bis(3,5-di-tert-butyl-2-hydroxyphenyl)-1,2-phenylenediamine) with a noninnocent ligand was formed by reaction of the alkoxide precursor [W(eg)3] (eg = the 1,2-ethanediolate dianion) with two equivalents of ligand. The phenol groups on one of the ligands are completely deprotonated and the ligand coordinates in a tetradentate fashion, whereas the other ligand is tridentate with one phenol having an intact OH group. The molecular structure, magnetic measurements, EPR spectroscopy, and density functional theory calculations indicate that the complex is a stable radical with the odd electron situated on the tridentate amidophenoxide ligand. The formal oxidation s…
Effects of the net charge on abundance and stability of supramolecular surfactant aggregates in gas phase
2011
Self-assembling of amphiphilic molecules under electrospray ionization (ESI) conditions is characterized by quite unexpected phenomenology. The noticeable differences with respect to the condensed phase are attributable to the absence of the surfactant-solvent interactions, the presence of net charge in the aggregates, and the strong deviation from equilibrium conditions. Aiming to investigate the effects of the net charge on abundance and stability of supramolecular surfactant aggregates, positively and negatively charged aggregates of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) and sodium methane sulfonate (MetS), butane sulfonate (ButS) and octane sulfonate (OctS) have been studied by E…