1,721,045 research outputs found
Torsion angle relationship of the (17)O NMR chemical shift in alpha,beta-unsaturated carbonyl compounds
No full texttorsion angle effect on the isotropic shielding of (17)O nucleus in alpha,beta-unsaturated carbonyl groups is studied by means of density functional theory (DFT) calculations using a polarizable continuum model (PCM) for the solvent, employing the PBEO functional together with the 6-311 G(cl,p) basis set for geometry optimization, and the 6-311+G(2d,p) basis set for calculating the NMR shielding with the gauge-including atomic orbitals (GIAO) method. This study adds new information on the sensitivity of the (17)O nucleus to conformational changes, revealing a strong dependence of the (17)O NMR chemical shift on the dihedral angle between the carbonyl and the vinyl moiety in all studied compounds; remarkable differences are observed with the data reported for alpha-diketones. Copyright (C) 2009 John Wiley & Sons, Ltd
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”
No full textNucleic acids are highly charged polyelectrolytes. Their interactions with counterions are of great importance for their structural stability, conformational behaviour and biological functions. Molecular modelling and simulation techniques, particularly molecular dynamics, have been highly useful for studies of interactions between DNA, water and ions at the molecular level, allowing us to explain many experimental observations, or to obtain information not accessible experimentally. In this review we focus on both atomistic and coarse-grained molecular simulation studies concerning the interactions of DNA with different types of counterions, with emphasis on recent studies, still open questions, limits of the method and possible further developments
Molecular Dynamics Simulations of A * T-Rich Oligomers: Sequence- Specific Binding of Na+ in the Minor Groove of B-DNA
No full textMolecular dynamics simulations have been employed to probe the sequence-specific binding of sodium ions to the minor groove of B-DNA of three A . T-rich oligomers having identical compositions but different orders of the base pairs: C(AT)(4)G, CA(4)T(4)G, and CT(4)A(4)G. Recent experimental investigations, either in crystals or in solution, have shown that monovalent cations bind to DNA in a sequence-specific mode, preferentially in the narrow minor groove regions of uninterrupted sequences of four or more adenines (A-tracts), replacing a water molecule of the ordered hydration structure, the hydration spine. Following this evidence, it has been hypothesized that in A-tracts these events may be responsible for structural peculiarities such as a narrow minor groove and a curvature of the helix axis. The present simulations confirm a sequence specificity of the binding of sodium ions: Na+ intrusions in the first layer of hydration of the minor groove, with long residence times, up to similar to3 ns, are observed only in the minor groove of A-tracts but not in the alternating sequence. The effects of these intrusions on the structure of DNA depend on the ion coordination: when the ion replaces a water molecule of the spine, the minor groove becomes narrower. Ion intrusions may also disrupt the hydration spine modifying the oligomer structure to a large extent. However, in no case intrusions were observed to locally bend the axis toward the minor groove. The simulations also show that ions may reside for long time periods in the second layer of hydration, particularly in the wider regions of the groove, often leading to an opening of the groove. (C) 2003 Wiley Periodicals, Inc
Theoretical study on the stability of zwitterionic and neutral form of glycine in water and methanol
No full textMultiscale simulations of human telomeric G-quadruplex DNA
No full textWe present a coarse-grain (CG) model of human telomeric G-quadruplex, obtained using the inverse Monte Carlo (IMC) and iterative Boltzmann inversion (IBI) techniques implemented within the software package called MagiC. As a starting point, the 2HY9 human telomeric [3 + 1] hybrid, a 26-nucleobase sequence, was modeled performing a 1 μs long atomistic molecular dynamics (MD) simulation. The chosen quadruplex includes two kinds of loops and all possible combinations of relative orientations of guanine strands that can be found in quadruplexes. The effective CG potential for a one bead per nucleotide model has been developed from the radial distribution functions of this reference system. The obtained potentials take into account explicitly the interaction with counterions, while the effect of the solvent is included implicitly. The structural properties of the obtained CG model of the quadruplex provided a perfect match to those resulting from the reference atomistic MD simulation. The same set of interaction potentials was then used to simulate at the CG level another quadruplex topology (PDB id 1KF1 ) that can be formed by the human telomeric DNA sequence. This quadruplex differs from 2HY9 in the loop topology and G-strand relative orientation. The results of the CG MD simulations of 1KF1 are very encouraging and suggest that the CG model based on 2HY9 can be used to simulate quadruplexes with different topologies. The CG model was further applied to a higher order human telomeric quadruplex formed by the repetition, 20 times, of the 1KF1 quadruplex structure. In all cases, the developed model, which to the best of our knowledge is the first model of quadruplexes at the CG level presented in the literature, reproduces the main structural features remarkably well
Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations
No full textGlucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification
Molecular Dynamics Investigation of 23Na NMR Relaxation in Oligomeric DNA Aqueous Solution
No full textAn 8 ns molecular dynamics (MD) simulation has been carried out on an oligomeric DNA duplex in a minimal salt sodium aqueous solution in order to study the magnetic relaxation process of Na-23. The explicit modeling of the solvent and the time length of the simulation allow study of the fast and, to some extent, the slow components of the relaxation. In agreement with experimental studies of the quadrupolar relaxation of monatomic cations in oligomeric DNA solution, the relaxation displays a multiexponential decay. According to the simulation, the slow components originate from ions directly bound to the DNA surface. The effects of the binding of the cations to DNA on the static and dynamical relaxation parameters have been studied in different binding sites either in the grooves or in the backbone. This study reveals that the quadrupolar coupling constant and the spectral densities vary largely from site to site, the fastest relaxation occurring for the ion directly bound to the minor groove. The combination of MD results with quadrupolar relaxation experimental data suggests that the occupancy of the binding sites in the minor groove of uninterrupted adenine sequences is relatively low
Novel homogeneous selective electrocatalysts for CO2 reduction: an electrochemical and computational study of cyclopentadienyl-phenylendiamino-cobalt complexes
Full text linkFour cyclopentadienyl-phenylendiamino-cobalt complexes [CoCp(bqdi)] with different substituents (R) at the phenylene moiety (bqdi, I; o-perfluoro-bqdi, II; p-NO2-bqdi, III; p-COOH-bqdi, IV) have been studied with an aim to investigate their capability as catalysts for the CO2 reduction. These compounds were characterized by cyclic voltammetry measurements both under nitrogen and CO2 atmospheres, showing an increase in the cathodic current ranging from 3.36 (III) to 5.59 times (II) that of the measurement under nitrogen. Moreover, with the addition of water, the current enhancement in the presence of CO2 reaches 31.07 times that of the case of complex II. Interestingly, these complexes exhibit very good selectivity toward CO2 reduction irrespective of hydrogen even in the presence of water. The relative turnover frequencies were also estimated, given the values ranging from 3.23 (III) to 187.21 s−1 (II) in the presence of water. In addition, these results were analysed by means of density functional theory (DFT) calculations and Fukui functions analysis. In particular, DFT results clearly show effects of different substituents on the electrochemical properties of these compounds. Whereas, the Fukui functions analysis indicates that the most favourable positions for an electrophilic attack on the reduced complex are the nitrogen and cobalt atoms
Ionic liquids for CO2 electrochemical reduction
No full textElectrochemical reduction of CO2 is a novel research field towards a CO2-neutral global economy and combating fast accelerating and disastrous climate changes while finding new solutions to store renewable energy in value-added chemicals and fuels. Ionic liquids (ILs), as medium and catalysts (or supporting part of catalysts) have been given wide attention in the electrochemical CO2 reduction reaction (CO2RR) due to their unique advantages in lowering overpotential and improving the product selectivity, as well as their designable and tunable properties. In this review, we have summarized the recent progress of CO2 electro-reduction in IL-based electrolytes to produce higher-value chemicals. We then have highlighted the unique enhancing effect of ILs on CO2RR as templates, precursors, and surface functional moieties of electrocatalytic materials. Finally, computational chemistry tools utilized to understand how the ILs facilitate the CO2RR or to propose the reaction mechanisms, generated intermediates and products have been discussed. (C) 2020 The Chemical Industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights reserved
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