Biomedical subjects

Victor S Batista

Publications and source records attributed to Victor S Batista.

16 recordsLinked to original sources

PubMed2006

Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine.

A simple approach for numerically exact simulations of nonadiabatic quantum dynamics in multidimensional systems is introduced and applied to the description of the photoabsorption spectroscopy of pyrazine. The propagation scheme generalizes the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] to simulations of nonadiabatic quantum dynamics. The time-evolution operator is applied, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state expansions. These representations are obtained by combining the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting computational approach are demonstrated in calculations of time-dependent survival amplitudes and photoabsorption cross sections, using a model Hamiltonian that allows for direct comparisons with benchmark calculations. Simulations in full-dimensional potential energy surfaces involve the propagation of a 24-dimensional wave packet to describe the S(1)S(2) interconversion of pyrazine after S(0)-->S(2) photoexcitation. The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems.

Computer Simulation↗

PubMed2006

Matching-pursuit split-operator Fourier-transform simulations of excited-state intramolecular proton transfer in 2-(2'-hydroxyphenyl)-oxazole.

The excited-state intramolecular proton-transfer dynamics associated with the keto-enolic tautomerization reaction in 2-(2(')-hydroxyphenyl)-oxazole is simulated according to a numerically exact quantum-dynamics propagation method and a full-dimensional excited-state potential energy surface, based on an ab initio reaction surface Hamiltonian. The reported simulations involve the propagation of 35-dimensional wave packets according to the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method by Wu and Batista. The underlying propagation scheme recursively applies the time-evolution operator as defined by the Trotter expansion to second order accuracy in dynamically adaptive coherent-state expansions. Computations of time-dependent survival amplitudes, photoabsorption cross sections, and time-dependent reactant(product) populations are compared to the corresponding calculations based on semiclassical approaches, including the Herman-Kluk semiclassical initial value representation method. The reported results demonstrate the capabilities of the MP/SOFT method as a valuble computational tool to study ultrafast reaction dynamics in polyatomic systems as well as to validate semiclassical simulations of complex (nonintegrable) quantum dynamics in multidimensional model systems.

Journal Article↗

PubMed2006

Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields.

We apply density functional theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew-Burke-Ernzerhof exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an electronvolt. The DFT+U technique, parametrized to B3LYP-predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than that of PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP and approximately 0.1 A changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first-row transition metal ion complexes in a condensed-matter setting.

Journal Article↗

PubMed2006

Characterization of synthetic oxomanganese complexes and the inorganic core of the O2-evolving complex in photosystem II: evaluation of the DFT/B3LYP level of theory.

The capabilities and limitations of the Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional are investigated as applied to studies of mixed-valent multinuclear oxomanganese complexes. Benchmark calculations involve the analysis of structural, electronic and magnetic properties of di-, tri- and tetra-nuclear Mn complexes, previously characterized both chemically and spectroscopically, including the di-mu-oxo bridged dimers [Mn(III)Mn(IV)(mu-O)(2)(H(2)O)(2)(terpy)(2)](3+) (terpy=2,2':6,2''-terpyridine) and [Mn(III)Mn(IV)(mu-O)(2)(phen)(4)](3+) (phen=1,10-phenanthroline), the Mn trimer [Mn(3)O(4)(bpy)(4)(H(2)O)(2)](4+) (bpy=2,2'-bipyridine), and the tetramer [Mn(4)O(4)L(6)](+) with L=Ph(2)PO(2)(-). Furthermore, the density functional theory (DFT) B3LYP level is applied to analyze the hydrated Mn(3)O(4)CaMn cluster completely ligated by water, OH(-), Cl(-), carboxylate and imidazole ligands, analogous to the '3+1 Mn tetramer' of the oxygen-evolving complex of photosystem II. It is found that DFT/B3LYP predicts structural and electronic properties of oxomanganese complexes in pre-selected spin-electronic states in very good agreement with X-ray and magnetic experimental data, even when applied in conjunction with rather modest basis sets. However, it is conjectured that the energetics of low-lying spin-states is beyond the capabilities of the DFT/B3LYP level, constituting a limitation to mechanistic studies of multinuclear oxomanganese complexes where until now the performance of DFT/B3LYP has raised little concern.

Biomimetics↗

PubMed2006

Computational studies of the primary phototransduction event in visual rhodopsin.

This Account addresses recent advances in the elucidation of the detailed molecular rearrangements due to the primary photochemical event in rhodopsin, a prototypical G-protein-coupled receptor (GPCR) responsible for the signal transmission cascade in the vertebrate vision process. The reviewed studies provide fundamental insight on long-standing problems regarding the assembly and function of the individual residues and bound water molecules that form the rhodopsin active site, a center that catalyzes the 11-cis/all-trans isomerization of the retinyl chromophore in the primary step of the phototransduction mechanism. Emphasis is placed on the authors' recent computational studies, based on state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, addressing the structural refinement of the retinyl chromophore binding site in high-resolution X-ray structures of bovine visual rhodopsin, the energy storage mechanism, and the molecular origin of spectroscopic changes due to the primary photochemical event.

Isomerism↗

PubMed2005

Influence of thermal fluctuations on interfacial electron transfer in functionalized TiO2 semiconductors.

The influence of thermal fluctuations on the dynamics of interfacial electron transfer in sensitized TiO2-anatase semiconductors is investigated by combining ab initio DFT molecular dynamics simulations and quantum dynamics propagation of transient electronic excitations. It is shown that thermal nuclear fluctuations speed up the underlying interfacial electron transfer dynamics by introducing nonadiabatic transitions between electron acceptor states, localized in the vicinity of the photoexcited adsorbate, and delocalized states extended throughout the semiconductor material, creating additional relaxation pathways for carrier diffusion. Furthermore, it is shown that room-temperature thermal fluctuations reduce the anisotropic character of charge diffusion along different directions in the anatase crystal and make similar the rates for electron injection from adsorbate states of different character. The reported results are particularly relevant to the understanding of temperature effects on surface charge separation mechanisms in molecular-based photo-optic devices.

Journal Article↗

PubMed2005

The mechanism of photosynthetic water splitting.

Oxygenic photosynthesis, which provides the biosphere with most of its chemical energy, uses water as its source of electrons. Water is photochemically oxidized by the protein complex photosystem II (PSII), which is found, along with other proteins of the photosynthetic light reactions, in the thylakoid membranes of cyanobacteria and of green plant chloroplasts. Water splitting is catalyzed by the oxygen-evolving complex (OEC) of PSII, producing dioxygen gas, protons and electrons. O(2) is released into the atmosphere, sustaining all aerobic life on earth; product protons are released into the thylakoid lumen, augmenting a proton concentration gradient across the membrane; and photo-energized electrons pass to the rest of the electron-transfer pathway. The OEC contains four manganese ions, one calcium ion and (almost certainly) a chloride ion, but its precise structure and catalytic mechanism remain unclear. In this paper, we develop a chemically complete structure of the OEC and its environment by using molecular mechanics calculations to extend and slightly adjust the recently-obtained X-ray crystallographic model with reference to this structure and to some important recent experimental results.

Computer Simulation↗

PubMed2005

Model study of coherent quantum dynamics of hole states in functionalized semiconductor nanostructures.

Functionalization of semiconductor nanocrystals can be achieved by anchoring organic ligands to the surface dangling bonds. The resulting surface complexes often introduce electronic states in the semiconductor band gap. These interband states sensitize the host material for photoabsorption at frequencies characteristic of the molecular adsorbates, leading to the well-known process of photoexcitation and subsequent femtosecond interfacial electron transfer. This paper investigates the relaxation dynamics of hole states, energetically localized deep in the semiconductor band gap, after the ultrafast electron-hole pair separation due to interfacial electron transfer. Mixed quantum-classical methods, based on mean-field nuclear dynamics approximated by ab initio density functional theory molecular dynamics simulations, reveal superexchange hole tunneling between adjacent adsorbate molecules in a model study of functionalized TiO2-anatase nanostructures. It is shown that electronic coherences can persist for hundreds of picoseconds under cryogenic and vacuum conditions, despite the partial intrinsic decoherence induced by thermal ionic motion, providing results of broad theoretical and experimental interest.

Journal Article↗

PubMed2005

Matching-pursuit/split-operator Fourier-transform simulations of nonadiabatic quantum dynamics.

A rigorous and practical approach for simulations of nonadiabatic quantum dynamics is introduced. The algorithm involves a natural extension of the matching-pursuitsplit-operator Fourier-transform (MPSOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] recently developed for simulations of adiabatic quantum dynamics in multidimensional systems. The MPSOFT propagation scheme, extended to nonadiabatic dynamics, recursively applies the time-evolution operator as defined by the standard perturbation expansion to first-, or second-order, accuracy. The expansion is implemented in dynamically adaptive coherent-state representations, generated by an approach that combines the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting propagation method are demonstrated as applied to the canonical model systems introduced by Tully for testing simulations of dual curve-crossing nonadiabatic dynamics.

Journal Article↗

PubMed2005

Is the Filinov integral conditioning technique useful in semiclassical initial value representation methods?

The utility of the Filinov integral conditioning technique, as implemented in semiclassical initial value representation (SC-IVR) methods, is analyzed for a number of regular and chaotic systems. For nonchaotic systems of low dimensionality, the Filinov technique is found to be quite ineffective at accelerating convergence of semiclassical calculations since, contrary to the conventional wisdom, the semiclassical integrands usually do not exhibit significant phase oscillations in regions of large integrand amplitude. In the case of chaotic dynamics, it is found that the regular component is accurately represented by the SC-IVR, even when using the Filinov integral conditioning technique, but that quantum manifestations of chaotic behavior was easily overdamped by the filtering technique. Finally, it is shown that the level of approximation introduced by the Filinov filter is, in general, comparable to the simpler ad hoc truncation procedure introduced by Kay.

Journal Article↗

PubMed2005

Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions.

A rigorous and practical methodology for evaluating thermal-equilibrium density matrices, finite-temperature time-dependent expectation values, and time-correlation functions is described. The method involves an extension of the matching-pursuit/split-operator-Fourier-transform method to the solution of the Bloch equation via imaginary-time propagation of the density matrix and the evaluation of Heisenberg time-evolution operators through real-time propagation in dynamically adaptive coherent-state representations.

Journal Article↗

PubMed2004

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision.

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.

Animals↗

PubMed2004

Quantum tunneling dynamics in multidimensional systems: a matching-pursuit description.

Rigorous simulations of quantum tunneling dynamics in model systems with up to 20 coupled degrees of freedom are reported. The simulations implement an extension of the recently developed matching-pursuit/split-operator Fourier-transform method to complex-valued coherent-state representations. The resulting method recursively applies the time-evolution operator, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state representations generated by an approach that combines the matching-pursuit algorithm with a gradient-based optimization method.

Journal Article↗

PubMed2003

Quantum dynamics simulations of interfacial electron transfer in sensitized TiO2 semiconductors.

Ab initio DFT molecular dynamics simulations are combined with quantum dynamics calculations of electronic relaxation to investigate the interfacial electron transfer in catechol/TiO(2)-anatase nanostructures under vacuum conditions. It is found that the primary process in the interfacial electron-transfer dynamics involves an ultrafast (tau(1) approximately 6 fs) electron-injection event that localizes the charge in the Ti(4+) surface ions next to the catechol adsorbate. The primary event is followed by charge delocalization (i.e., carrier diffusion) through the TiO(2)-anatase crystal, an anisotropic diffusional process that can be up to an order of magnitude slower along the [-101] direction than carrier relaxation along the [010] and [101] directions in the anatase crystal. It is shown that both the mechanism of electron injection and the time scales for interfacial electron transfer are quite sensitive to the symmetry of the electronic state initially populated in the adsorbate molecule. The results are particularly relevant to the understanding of surface charge separation in efficient mechanisms of molecular-based photovoltaic devices.

Journal Article↗

PubMed2002

Coherent control in the presence of intrinsic decoherence: proton transfer in large molecular systems.

An efficient semiclassical approach is developed and used to calculate the coherent-control map and time dependent decoherence measure for the excited-state proton transfer dynamics associated with the keto-enolic tautomerization reaction of 2-(2'-hydroxyphenyl)-oxazole. The method extends the usual bichromatic coherent-control scenario to simulate control at finite times after photoexcitation of the system. Extensive coherent control is demonstrated in a large molecule despite the ultrafast decoherence phenomena, providing results of broad theoretical and experimental interest.

Journal Article↗

PubMed2002

Proton-transfer dynamics in the activation of cytochrome P450eryF.

Molecular dynamics simulations are combined with quantum chemistry calculations of instantaneous proton-transfer energy profiles to investigate proton-transfer events in the transient pathway of cytochrome P450eryF (6-deoxyerythronolide B hydroxylase; CYP107A1), from the oxyferrous species to the catalytically active ferryl oxygen species (compound I). This reaction is one of the most fundamental unresolved aspects in the mechanism of oxidation that is common to all cytochrome P450s. We find that this process involves an ultrafast proton transfer from the crystallographic water molecule W519 to the distal oxygen bound to the heme group, and a subsequent proton-transfer event from W564 to W519. Both proton-transfer events are found to be endothermic in the oxyferrous state, suggesting that the oxyferrous reduction is mechanistically linked to the proton-transfer dynamics. These findings indicate that the hydrogen bond network, proximate to the O(2)-binding cleft, plays a crucial functional role in the enzymatic activation of P450s. Our results are consistent with the effect of mutations on the enzymatic efficacy.

Bacterial Proteins↗