Search results for "COMPUTATION"
showing 10 items of 7362 documents
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 …
Counterion influence on the N–I–N halogen bond
2015
A detailed investigation of the influence of counterions on the [N–I–N]+ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N–I–N]+ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in …
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…
The Synergetic Interplay of Weak Interactions in the Ion-Pair Recognition of Quaternary and Diquaternary Ammonium Salts by Halogenated Resorcinarenes
2013
The influence of halogens on the noncovalent interactions of different upper-rim-substituted hexylresorcinarenes with quaternary and diquaternary ammonium iodide salts was investigated in the gas phase by electrospray ionization Fourier-transform ion-cyclotron-resonance (ESI-FTICR) mass spectrometry and in solution by 1H NMR titration studies. The electronic nature of the substituents on the upper rim of the resorcinarene was directly reflected in the order of binding strengths of the hosts towards quaternary and diquaternary ammonium cations in the gas phase. In solution, the opposite trend was observed, with generally higher binding constants for the diquaternary over the quaternary salts…
Understanding the domino reactions of alkyne-tethered N-tosylhydrazones yielding fused polycyclic pyrazoles. An MEDT study
2019
Abstract The domino reactions of alkyne-tethered N-mesylhydrazones yielding fused polycyclic pyrazoles have been studied within the Molecular Electron Density Theory (MEDT). Analysis of the Gibbs free energies indicates that the more favourable reactive path is the one in which the elimination of mesylate anion takes place before the intramolecular [3 + 2] cycloaddition (IM32CA) reaction, which corresponds with the rate-determining step of these domino processes. ELF topological analysis of the bond formation along the IM32CA reaction indicates that in spite of the high activation energy associated to this intramolecular reaction, it shows a pmr-type mechanism characterised by the presence …
Competing salt effects on phase behavior of protein solutions: tailoring of protein interaction by the binding of multivalent ions and charge screeni…
2014
The phase behavior of protein solutions is affected by additives such as crowder molecules or salts. In particular, upon addition of multivalent counterions, a reentrant condensation can occur; i.e., protein solutions are stable for low and high multivalent ion concentrations but aggregating at intermediate salt concentrations. The addition of monovalent ions shifts the phase boundaries to higher multivalent ion concentrations. This effect is found to be reflected in the protein interactions, as accessed via small-angle X-ray scattering. Two simulation schemes (a Monte Carlo sampling of the counterion binding configurations using the detailed protein structure and an analytical coarse-grain…