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James T Hynes

Publications and source records attributed to James T Hynes.

13 recordsLinked to original sources
PubMed2006

Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations.

Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.

Base Sequence↗
PubMed2006

Excited-state charge transfer at a conical intersection: effects of an environment.

The influence of a polar and polarizable environment on charge transfer processes at a conical intersection (CI) can be described by a diabatic free energy model yielding coupled surfaces as a function of both molecular coordinates and a solvent coordinate. We extend and apply this model for the S1-S0 CI in protonated Schiff bases, representing a model for retinal isomerization (Faraday Discuss. 2004, 127, 395, 2004). A dielectric continuum description of the solvent is combined with a minimal, two-electron-two-orbital electronic structure model according to Bonacić-Koutecký, Koutecký, and Michl (Angew. Chem. 1987, 26, 170), which characterizes the charge translocation effects at the CI. The model predicts that the nonequilibrium solvent state resulting from the S0-->S1 Franck-Condon transition can entail the disappearance of the CI, such that solvent motion is necessary to reach the CI seam. The concerted evolution of the intramolecular coordinates and the solvent coordinate is illustrated by an excited-state minimum energy path.

Electrons↗
PubMed2006

Entropy of water in the hydration layer of major and minor grooves of DNA.

Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.

Biophysics↗
PubMed2006

On the ultrafast infrared spectroscopy of anion hydration shell hydrogen bond dynamics.

Molecular Dynamics simulations are used to examine the title issue for the I-/HOD/D2O solution system in connection with recent ultrafast infrared spectroscopic experiments. It is argued that the long "modulation time" associated with the spectral diffusion of the OH frequency, extracted in these experiments, should be interpreted as reflecting the escape time of an HOD from the first hydration shell of the I- ion, i.e., the residence time of an HOD in this solvation shell. Shorter time features related to the oscillation of the OH ...I- hydrogen bond and the breaking and making of this bond are also discussed.

Journal Article↗
PubMed2006

Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase.

The generalized Langevin equation (GLE)-based Grote-Hynes (GH) theory is used to calculate the transmission coefficients, kappa, for the methyl transfer from S-adenosylmethionine to catecholate both in aqueous solution and in the catechol O-methyltransferase active site. Values of kappa, which measures the deviation of the rate constants from the Transition State Theory (TST) predictions, are obtained by means of rare event molecular dynamics simulations. The results are 0.62 +/- 0.04 and 0.83 +/- 0.03 for the aqueous and enzymatic environments, respectively, while the Grote-Hynes predictions are 0.58 +/- 0.09 and 0.89 +/- 0.03, respectively. The Kramers theory estimates are much smaller, about 0.01 and 0.1, respectively. Thus, the enzymatic transmission coefficient is closer to TST predictions than the value obtained in solution. In addition, our results show that the enzymatic coefficient is also closer to its nonadiabatic (or frozen environment) limit than is the solution coefficient. These findings can be understood considering that, during the passage over the barrier top, there is a smaller coupling between the reactive system and the environment in the enzyme than in solution, as well as a smaller reorganization suffered by the enzyme. Analysis of the transition state friction kernel leads to the identification of some key vibrational modes governing the coupling between the two different environments and the reacting solute in the transition state region and insights on their relevance for the reaction dynamics' influence on the transmission coefficient.

Catechol O-Methyltransferase↗
PubMed2006

Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics.

We have investigated the photodissociation dynamics of NaI(H(2)O)(n) [n = 1-4] clusters using the molecular dynamics with quantum transitions method and a quantum mechanics/molecular mechanics description of NaI(H(2)O)(n), which involves a semiempirical valence-bond approach to describe the NaI electronic structure and classical solvent-solvent and solute-solvent interaction potentials. Our simulation results show that the NaI(H(2)O)(n) excited-state population decay upon reaching the NaI curve-crossing region increases with cluster size due to the stabilization of the ionic branch of the NaI excited state by the surrounding water molecules, and the resulting increase in nonadiabatic transition probability. After reaching the curve-crossing region for the first time, however, the excited-state population decay resembles that of bare NaI because of rapid evaporation of 99% and 95% of the water molecules for NaI(H(2)O) and NaI(H(2)O)(n) [n = 2-4], respectively. This extensive evaporation is due to the reversed NaI polarity in the Franck-Condon region of the NaI first excited state, which causes strong repulsive NaI-H(2)O forces and induces rapid nonstatistical water evaporation, where product water molecules are formed more rotationally than translationally hot. A few water molecules (5% or less) remain transiently or permanently bound to NaI, forming long-lived clusters, when NaI remains predominantly ionic, i.e., remains in the excited state, after reaching the curve-crossing region. To connect simulation results with experiment, we have simulated femtosecond probe signals resulting from two-photon and one-photon excitation to the X and I NaI(+) probe states. In agreement with experimental findings, the probe signals resulting from the two-photon probe scheme, where excitation occurs from the covalent branch of the excited state, decay exponentially over the NaI first excited-state vibrational period, with very little evidence of long-time dynamics. The one-photon probe scheme (not used for experimental cluster studies) is shown to be less sensitive to solvation, in that excitation energies will remain similar over a range of cluster sizes, as the ionic branch of the excited state and the NaI(+) probe states are stabilized to the same extent by the presence of water molecules. The resulting probe signals are also more revealing of the NaI(H(2)O)(n) photodissociation dynamics than the two-photon probe signals, as they may allow monitoring of solvation effects on the NaI nonadiabatic dynamics and of successive evaporation of water molecules. Time-resolved photoelectron spectra provide limited additional information regarding the NaI(H(2)O)(n) photodissociation dynamics. A key consequence of the rapid water evaporation demonstrated here is that experimentally observed signals may arise from the photodissociation of much larger NaI(H(2)O)(n) parent clusters.

Computer Simulation↗
PubMed2006

A molecular jump mechanism of water reorientation.

Despite long study, a molecular picture of the mechanism of water reorientation is still lacking. Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor. The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered. This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive.

Journal Article↗
PubMed2006

Heterogeneous reactions important in atmospheric ozone depletion: a theoretical perspective.

Theoretical studies of the mechanisms of several heterogeneous reactions involving ClONO(2), H(2)O, HCl, HBr, and H(2)SO(4) important in atmospheric ozone depletion are described, focused primarily on reactions on aqueous aerosol surfaces. Among the insights obtained is the active chemical participation of the surface water molecules in several of these reactions. The general methodology adopted allows reduction of these complex chemical problems to meaningful model systems amenable to quantum chemical calculations.

Aerosols↗
PubMed2005

Theoretical study of the first acid dissociation of H2SO4 at a model aqueous surface.

Electronic structure calculations on the H2SO4.(H2O)(4,6) model system embedded at the surface of an aqueous layer have been performed to examine the feasibility of the first acid dissociation of H2SO4 to an H2SO4-.H3O+ contact ion pair over a wide temperature range, with a special focus on the 190-250 K range relevant for atmospheric sulfate aerosols. The results indicate that the acid dissociation can be either thermodynamically favored or disfavored depending on the degree of solvation of the acid and the produced ions, as well as on the temperature.

Journal Article↗
PubMed2005

On the coupling between molecular diffusion and solvation shell exchange.

The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li(+) and Na(+) ions, and for liquid argon. First, two methods are proposed which allow, by means of simulation, to extract the quantitative speed-up in diffusion induced by the exchange events. Second, it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for nontrivial systems.

Journal Article↗
PubMed2004

Environmental effects on a conical intersection: a model study.

Excited-state processes at conical intersections (CIs) involving charge transfer phenomena can depend sensitively on the influence of a polar and polarizable environment. We propose here a formulation to describe the chromophore-environment interaction for such situations. In a model study, we focus on an extension of the two-electron two-orbital model by V. Bonacić-Koutecký, J. Koutecký, and J. Michl [Angew. Chem., Int. Ed. Engl., 1987, 26, 170], which yields a diabatic model for the S1-S0 CI in protonated Schiff bases and related systems, and describes the charge properties and charge translocation phenomena associated with this CI. The electrostatic effects of the environment, which are expected to strongly affect the CI topology, are accounted for by a dielectric continuum model. This translates to the image of free energy surfaces for the coupled chromophore-environment system represented by molecular coordinates plus a solvent coordinate. The environment's impact on the location and character of the CI is investigated. The limiting situations of "frozen" and equilibrium solvation effects are examined.

Journal Article↗
PubMed2003

On the dissociation of aromatic radical anions in solution.

A new theoretical formulation is given for the reaction rate and path for the important reaction class of aromatic radical anion dissociation in solution [Ar-X]-.-->Ar. + X-, and is illustrated for the case of the cyanochlorobenzene radical anion [CN-phi-CI]-. in dimethylformamide. Among the theory's novel features is the inclusion of the conical intersection aspect of this ground electronic state problem, which is key in allowing the reaction to occur and which has a significant impact on the reaction barrier height. Reasonable agreement with the experimental rate is found.

Journal Article↗