Search results for "Computation"

Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

2017

Oxidation of nucleic acids is ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases; however, the specific role of the biological environment remains relatively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations. It is shown…

ChemInform Abstract: Chirality in Calixarenes and Calixarene Assemblies

2001

Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.

2010

A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD + ), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme…

Single chain magnet behaviour in an enantiopure chiral cobalt(II)–copper(II) one-dimensional compound

2010

The self-assembly of an enantiomerically pure, chiral dianionic oxamatocopper(II) complex with cobalt(II) ions leads to neutral oxamato-bridged heterobimetallic chains that combine chirality and slow magnetic relaxation, providing thus the first example of ‘‘chiral single chain magnets (CSCMs). Ruiz Garcia, Rafael, Rafael.Ruiz@uv.es ; Lloret Pastor, Francisco, Francisco.Lloret@uv.es

Determination of equilibrium constants and computational interaction energies for adducts of [Rh2(RCO2)(4-n)(PC)n] (n = 0-2) with Lewis bases.

2007

Properties of dirhodium catalysts with cyclometalated aryl phosphine ligands have been studied. We report here the study of the acid−base reaction of Rh2(RCO2)2(PC)2(H2O)2 catalysts (PC = cyclometalated aryl phosphine) with different Lewis bases. The determination of the equilibrium constants of these reactions can be used to study to which extent the properties of the axial coordination site of the catalyst, considered the active site, are affected by modification of the metalated phosphines, the carboxylate ligands, or the incoming axial ligand. The trends in the computational density functional theory interaction energies show good agreement with the major trends in the equilibrium const…

13C NMR of carbonyl compounds. 3. Structure and dynamics of protonated enones and dienones

1984

Abstract The unsaturated ketones 1 1 – 10 10 were protonated at low temperatures and studied by dynamic 13C NMR spectroscopy. Four interconverting stereoisomers were detected which differ in their conformation with respect to the CO and CC (enone) single bond.

Terphenyl Derivatives from Allantophomopsis lycopodina.

2016

Three secondary fungal metabolites 1–3 with a benzo[b]naphtho[2,1-d]furan skeleton were isolated from submerged cultures of the ascomycete Allantophomopsis lycopodina. The NMR-based structure elucidation was challenging due to a low H/C ratio of only 0.64 and 0.68, respectively. NMR measurements in two different solvents and the use of NMR experiments such as HSQC-TOCSY and LR-HSQMBC proved to be helpful in this respect. The proposed structures obtained from the comprehensive analysis of the NMR data were verified by comparison of recorded and computed NMR chemical shifts from quantum chemical calculations of several constitutional isomers and were further analyzed with the aid of the DP4 a…

Electronic structure and energy decomposition analyses as a tool to interpret the redox potential ranking of naphtho-, biphenyl- and biphenylenequino…

2016

By calling on modelling approaches we have performed a comparative study on the redox properties of various naphtho-, biphenyl- and biphenylene-quinone isomers. These different compounds exhibit as a whole a redox potential range between 2.09 and 2.90 V vs. Li+/Li. A specific methodology was used to decrypt the interplay among isomerism, aromaticity and antiaromaticity modifications and the stabilization/destabilization effects due to other molecular components on this key electrochemical feature for electrode materials of batteries. In particular, energy decomposition analysis, within the Quantum Theory of Atoms in Molecules, along with the electron and electron spin population changes upo…

Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms

2012

A theoretical study on the alkaline hydrolysis of paraoxon, one of the most popular organophosphorus pesticides, in aqueous solution and in the active site of Pseudomonas diminuta phosphotriesterase (PTE) is presented. Simulations by means of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials show that the hydrolysis of paraoxon takes place through an A(N)D(N) or associative mechanism both in solution and in the active site of PTE. The results correctly reproduce the magnitude of the activation free energies and can be used to rationalize the observed kinetic isotope effects (KIEs) for the hydrolysis of paraoxon in both media. Enzymatic hydrolysis of O,O-diethyl p-chlorophenyl …

Understanding the molecular mechanism of the [3 + 2] cycloaddition reaction of benzonitrile oxide toward electron-richN-vinylpyrrole: a DFT study

2016

The [3 + 2] cycloaddition (32CA) reaction of benzonitrile oxide, BNO 2, with an electron-rich N-vinylpyrrole derivative, NVP 3a, in the presence of dichloromethane, has been theoretically studied using density functional theory (DFT) methods at the B3LYP/6-31G(d) level. This 32CA reaction presents a relatively high activation Gibbs free energy as a result of the low polar character of this zwitterionic-type (zw-type) reaction. Analyses of the calculated relative Gibbs free energies and transition state geometries indicate that the studied 32CA reaction, in excellent agreement with experimental outcomes, takes place in a complete regioselective manner as a consequence of the steric repulsion…