Search results for "quantum theory"
showing 10 items of 234 documents
Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase
2009
4-Oxalocrotonate tautomerase enzyme (4-OT) catalyzes the isomerization of 2-oxo-4-hexenedioate to 2-oxo-3-hexenedioate. The chemical process involves two proton transfers, one from a carbon of the substrate to the nitrogen of Pro1 and another from this nitrogen atom to a different carbon of the substrate. In this paper the isomerization has been studied using the combined quantum mechanical and molecular mechanical (QM/MM) method with a dual-level treatment of the quantum subsystem employing the MPW1BK density functional as the higher level. Exploration of the potential energy surface shows that the process is stepwise, with a stable intermediate state corresponding to the deprotonated subs…
Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase.
2013
The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the …
Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions
2012
Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, assuming equilibrium solvation, while reaction trajectories allowed us to incorporate nonequilibrium effects due to the solvent degrees of freedom as well as to evaluate the rate of the diffusion process in competition with the backward reaction. Our calculations that reproduce the experimental rate constant show that decarboxylation takes place with a non-negligible free energy barrier for the backward reaction and that diffusion of carbon dioxide is very fast compared…
Phosphatase-like Activity of Tetranuclear Iron(III) and Zinc(II) Complexes
2018
Three new tetranuclear iron(III) and zinc(II) complexes, [Fe4(cpdp)2(phth)2(OH)2]·8H2O (1), [Fe4(cpdp)2(terephth)2(OH)2] (2), and [Zn4(Hcpdp)2(suc)]Br2·12H2O (3), have been synthesized as models for the active site of phosphoester hydrolases by utilizing a polydentate ligand, N, N'-bis[2-carboxybenzomethyl]- N, N'-bis[2-pyridylmethyl]-1,3-diaminopropan-2-ol (H3cpdp) in combination with exogeneous phthalate (phth), terephthalate (terephth), and succinate (suc). Single crystal X-ray analyses reveal that the metallic core of complex 1 consists of four distorted octahedral iron(III) ions with average intraligand Fe---Fe separation of 3.656(2) A, while the structure 3 represents a tetranuclear m…
A Molecular Electron Density Theory Study of the Competitiveness of Polar Diels–Alder and Polar Alder-ene Reactions
2018
Indexación: Scopus. Funding: Ministry of Economy and Competitiveness (MINECO) of the Spanish Government, project CTQ2016-78669-P (AEI/FEDER, UE) and Fondecyt (Chile) grant 1180348. Acknowledgments: This research was supported by the Ministry of Economy and Competitiveness (MINECO) of the Spanish Government, project CTQ2016-78669-P (AEI/FEDER, UE) and Fondecyt (Chile) grant 1180348. L.R.D. thanks Fondecyt for continuous support through Cooperación Internacional. M.R.-G. also thanks MINECO for a post-doctoral contract cofinanced by the European Social Fund (BES-2014-068258). The competitiveness of the BF3 Lewis acid (LA) catalyzed polar Diels–Alder (P-DA) and polar Alder-ene (P-AE) reactions …
DFT studies on the structural and vibrational properties of polyenes
2015
Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C = C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae. BLYP/6-311++G** calculated ν(C = C) and ν(C–C) frequencies for all-trans and all-cis polyenes containing up to 14 carbon–carbon double bonds were used to estimate these values for very lo…
Photoinduced Formation Mechanism of the Thymine−Thymine (6−4) Adduct
2013
The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just …
Relaxed but highly compact diansa metallacyclophanes.
2011
A series of monoansa [μ-1,1′-PR-3,3′-Co(1,2-C2B9H10)2]− and diansa [8,8′-μ-(1″,2″-benzene)-μ-1,1′-PR-3,3′-Co(1,2-C2B9H9)2]− (R = Ph, tBu) cobaltabisdicarbollidephanes have been synthesized, characterized and studied by NMR, MALDI-TOF-MS, UV-visible spectroscopy, cyclic voltammetry, and DFT calculations. Single crystal X-ray diffraction revealed a highly relaxed structure characterized by the title angle α of 3.8° ([7]−), this being the smallest angle α for a metallacyclophane. In such compounds, the metal-to-phosphorus distance is less than the sum of their van der Waals radii. The availability of a phosphorus lone pair causes an electron delocalization through the metal, as shown by the ab…
A computationally feasible quantum chemical model for 13C NMR chemical shifts of PCB-derived carboxylic acids.
2004
Two quantum chemical models have been derived for the prediction of 13C NMR chemical shifts of novel PCB acids obtained from PCBs by catalytic carbonylation. 13C isotropic shielding constants were calculated employing the GIAO (gauge-independent atomic orbital) method with density functional theory (DFT). The best results were obtained by cluster calculations, which took the solvent effects into account properly. In this approach, a solvent molecule (acetone) was attached by a hydrogen bond to every hydrogen atom present in a PCB acid, and the geometry of the molecular cluster was optimized employing the AM1 method. For 158 chemical shifts, the cross-validated standard error was 2.8 ppm and…
Structural and magnetic characterization of a 1D chain of [Co(II)2(mu-aqua)(mu-carboxylate)2] strung cores.
2009
A novel 1D chain built up from stringing of [Co2(μ-OH 2)(μ-O2CC(CH3)3)2] units with the bridging 2,2′-bipyrimidine ligand has been synthesized and structurally characterized. The chains are well isolated from each other by the bulky tert-butyl groups of the carboxlyates and show an alternating zigzag configuration for the Co(II) metallic centres. DC magnetic measurements show anti-ferromagnetic coupling, Jca.-3 cm-1 between adjacent Co(II) ions along the chain. Noticeably, good data fitting was obtained by means of simple models that neglect any kind of first order orbital contribution to the spin ground state, which is normally observed in Co(II) complexes. These results were further confi…