Search results for "Quantum theory"
showing 10 items of 234 documents
Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods
2015
The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylamino acids, with N-succinyl-R-phenylglycine being the best substrate. We investigated the molecular mechanisms for both reactions exploring the potential energy surface. Then, molecular dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues wi…
The hyperfine structure in the rotational spectra of D2(17)O and HD(17)O: Confirmation of the absolute nuclear magnetic shielding scale for oxygen
2015
Guided by theoretical predictions, the hyperfine structures of the rotational spectra of mono- and bideuterated-water containing (17)O have been experimentally investigated. To reach sub-Doppler resolution, required to resolve the hyperfine structure due to deuterium quadrupole coupling as well as to spin-rotation (SR) and dipolar spin-spin couplings, the Lamb-dip technique has been employed. The experimental investigation and in particular, the spectral analysis have been supported by high-level quantum-chemical computations employing coupled-cluster techniques and, for the first time, a complete experimental determination of the hyperfine parameters involved was possible. The experimental…
Rhenium(I) and platinum(II) complexes with diimine ligands bearing acidic phenol substituents: hydrogen-bonding, acid-base chemistry and optical prop…
2010
Tricarbonylchloro-rhenium(i) (1-4) and catecholato-platinum(ii) complexes (6, 7) of diimine ligands bearing phenol and O-protected phenol substituents have been prepared and fully characterised including single crystal structure analyses of 1, 4 and 7. The redox behaviour of the catecholato platinum(ii) complexes 6 and 7 has been probed by cyclic voltammetry, preparative oxidation and EPR spectroscopy (6˙(+), 7˙(+)). Reversible deprotonation of the hydroxy substituted complexes 1, 3 and 6 to 1(-), 3(-) and 6(-) resulted in significant changes in their electronic spectra. The luminescence properties of the diamagnetic complexes have been investigated using emission spectroscopy. DFT and TD-D…
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…
Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.
2014
The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine different inhibitors of HIV-1 RT, one of the three key proteins responsible for the virus replication, have been selected to develop and test a computational protocol that allows getting a deep insight into the inhibitors’ binding mechanism. The interaction between the inhibitors and the protein have been quantified by computing binding free energies through FEP calculations, while a more detailed characterization of the kind of inhibitor–protein interactions is based on …
Joziknipholones A and B: The First Dimeric Phenylanthraquinones, from the Roots ofBulbine frutescens
2007
From the roots of the African plant Bulbine frutescens (Asphodelaceae), two unprecedented novel dimeric phenylanthraquinones, named joziknipholones A and B, possessing axial and centrochirality, were isolated, together with six known compounds. Structural elucidation of the new metabolites was achieved by spectroscopic and chiroptical methods, by reductive cleavage of the central bond between the monomeric phenylanthraquinone and -anthrone portions with sodium dithionite, and by quantum chemical CD calculations. Based on the recently revised absolute axial configuration of the parent phenylanthraquinones, knipholone and knipholone anthrone, the new dimers were attributed to possess the P-co…
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…
Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.
2015
Highlights • The possible role of enzymatic reaction dynamical effects is examined. • Solution reactions usefully inform the issue of dynamical effects in enzymes. • Division into regions containing and away from the transition state is important. • Motions in passage to/from the transition state need not lead to dynamical effects. • Transition State Theory is usually a reasonable description of enzyme kinetics.
Activation of the Cyano Group at Imidazole via Copper Stimulated Alcoholysis
2019
Reactions of 4,5-dicyano-1-methylimidazole with CuX2 (X = Cl, Br) in alcohol solvents (ethanol and methanol) resulted in the formation of Cu(II) carboximidate complexes [CuCl2(5- cyano-4-C(OEt)N-1-methylimidazole)(EtOH)] (1), [Cu2(µ
Dispersion Forces and Counterintuitive Steric Effects in Main Group Molecules: Heavier Group 14 (Si-Pb) Dichalcogenolate Carbene Analogues with Sub-9…
2013
The synthesis and spectroscopic and structural characterization of an extensive series of acyclic, monomeric tetrylene dichalcogenolates of formula M(ChAr)2 (M = Si, Ge, Sn, Pb; Ch = O, S, or Se; Ar = bulky m-terphenyl ligand, including two new acyclic silylenes) are described. They were found to possess several unusual features-the most notable of which is their strong tendency to display acute interligand, Ch-M-Ch, bond angles that are often well below 90°. Furthermore, and contrary to normal steric expectations, the interligand angles were found to become narrower as the size of the ligand was increased. Experimental and structural data in conjunction with high-level DFT calculations, in…