Development of a Potential Surface for Simulation of Proton and Hydride Transfer Reactions in Solution:  Application to NADH Hydride Transfer

Hurley, Margaret M.; Hammes‐Schiffer, Sharon

doi:10.1021/jp970269d

Cited by 20 publications

(15 citation statements)

References 55 publications

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“…For the rest of the molecular and solvent system we have used the function developed by Hurley and Hammes-Schiffer. 32 (This function has the desirable property that the structure of the substrate changes as the hydride moves along the reaction coordinate.) This hybrid potential was needed because the calculations of ref 32 did not include a metal ion.…”

Section: Resultsmentioning

confidence: 99%

Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling

2001

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The standard view of the origin of the catalytic properties of enzymes focuses on the binding energy differences between the ground state and the transition state arising from the arrangement of residues in the active site (i.e., statics). There is an alternative view that suggests that protein motions (i.e., dynamics) might play a role in catalysis. Klinman and co-workers recently published (Kohen, A.; Cannio, R.; Bartolucci, S.; Klinman, J. Nature 1999, 399, 496-499) findings on rate measurements in thermophilic alcohol dehydrogonase (ADH). At lower temperatures (below 30 °C), this enzyme undergoes a transition to a more rigid structure, and it was found that the corresponding apparent activation energy increases and the primary kinetic isotope effect (KIE) increases and becomes temperature-dependent. Explaining these results presents a challenge to theory. We show that a model of the reaction coordinate for the rate-determining step, coupled to an enzymatic environment and a specific strongly coupled active complex mode, can simultaneously explain a tunneling-dominated mechanism and the experimental trends reported by Klinman and co-workers. We propose a specific protein internal motion for the rate-promoting vibration and discuss other systems in which such motions might be dominant.

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Section: Resultsmentioning

confidence: 99%

Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling

2001

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“…As noted earlier, the MD model that is used here explicitly includes only those intramolecular vibrations associated with relative rotational motions of the rings of the molecule. The remaining degrees of freedom are frozen out by the use of constraints . Further, a quantum mechanical description of the remaining modes is evidently required, based on model calculations. , A complete quantum mechanical description of the internal modes and their dynamics would require expanding the wave function in eq 10 in internal coordinates q , as where the total wave function is expanded in internal vibrational state basis functions in addition to the electronic basis functions.…”

Section: Methodsmentioning

confidence: 99%

Computer Simulation of the Excited State Dynamics of Betaine-30 in Acetonitrile

Lobaugh

Rossky

1999

J. Phys. Chem. A

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Time-dependent studies of the excited state dynamics of betaine-30 in acetonitrile at room temperature have been carried out using a mixed classical/quantum molecular dynamics simulation methodology. The π-electron system of the solute molecule is treated quantum mechanically using the semiempirical Pariser−Parr−Pople Hamiltonian, including the solvent influence on electronic structure. The remaining interactions are treated via empirical potentials. Transition probabilities between adiabatic electronic states are evaluated using surface hopping methods, including all nuclear degrees of freedom in the coupling. The dynamics treats the (rigid) solvent and the dihedral angles for relative rotation of rings of an otherwise rigid solute classically. The contribution of all remaining solute intramolecular vibrations is included in the nonadiabatic coupling via an approximate, but purely quantum mechanical, treatment. Analysis of the dynamics reveals that, after excitation to the first excited state, the energy gap between ground and first excited states of the molecule exhibits an ultrafast (∼100 fs) decrease due to the inertial response of the solvent that accounts for about 70% of the solvent response, followed immediately by a further subpicosecond solvent component. The times and amplitudes of these solvation components are in accord with the results inferred from resonance Raman spectra, and the solvent contribution to the Stokes shift observed is in accord with values inferred from ground state absorption spectral line shape analysis. However, we also find that the energy gap exhibits a slower picosecond time scale response of comparable magnitude due to relative rotation of the central phenolate and pyridinium rings. This relaxation has not been previously noted or incorporated in corresponding electron transfer models. Analysis of contributions to the electronic nonadiabatic coupling shows that this is dominated by a small set of high-frequency intramolecular modes of the betaine-30 molecule, with the solvent making a relatively very small contribution, also in agreement with previous experimental inference.

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“…Blacker et al 19 argued that the two fluorescence lifetimes observed in NADH depend mostly on nonradiative decay which can be treated as conformational relaxation by activated barrier crossing and described by the Kramers' hydrodynamic theory and that the heterogeneity in the nonradiative decay is due to small scale motions such as ring puckering. 37,38 This paper aims to address further important questions on the NADH excited state dynamics under the excitation of the NA moiety within the first absorption band that despite many studies done still remain controversial. These are: the role of NADH conformations in excited state dynamics, the role of cis and trans configurations of the NA ring in the heterogeneity in the measured lifetimes, the influence of solution viscosity and polarity on the measured decay times and rotational diffusion time.…”

Section: Introductionmentioning

confidence: 99%

“…This approach has recently been described by Blacker et al , who suggested that the two fluorescent states correspond to alternate cis and trans configurations of the NA ring. Blacker et al argued that the two fluorescence lifetimes observed in NADH depend mostly on nonradiative decay which can be treated as conformational relaxation by activated barrier crossing and described by the Kramers’ hydrodynamic theory and that the heterogeneity in the nonradiative decay is due to small scale motions such as ring puckering. , …”

Section: Introductionmentioning

confidence: 99%

Two-Photon Excited Fluorescence Dynamics in NADH in Water–Methanol Solutions: The Role of Conformation States

et al. 2020

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The dynamics of polarized fluorescence in reduced nicotinamide adenine dinucleotide (NADH) at 460 nm under two-photon excitation at 720 nm by femtosecond laser pulses in water−methanol solutions has been studied experimentally and theoretically as a function of methanol concentration. A number of fluorescence parameters have been determined from experiment by means of the global fit procedure and then compared with the results reported by other authors. A comprehensive analysis of experimental errors was made. Ab initio calculations of the structure of NADH in water and methanol and of β-nicotinamide mononucleotide (NMNH) in vacuum have been carried out for clarifying the role of decay time heterogeneity. The main results obtained are as follows. An explanation of the heterogeneity in the measured fluorescence decay times in NADH has been suggested based on the influence of the internal molecular electric field in the nicotinamide ring on nonradiative decay rates. We suggest that different charge distributions in the cis and trans configurations result in different internal electrostatic field distributions that lead to the decay time heterogeneity. A slight but noticeable rise of the fluorescence decay times τ 1 and τ 2 with methanol concentration was observed and treated as a minor effect of a nonradiative relaxation slowing due to the decrease in solution polarity. Relative concentrations of the folded and unfolded NADH conformations in solutions have been determined using a new method of analysis of the rotational diffusion time τ r as a function of methanol concentration on the basis of the Stokes−Einstein−Debye equation. The analysis of the fluorescence anisotropy parameters obtained under linearly and circularly polarized excitation and the parameter Ω has been carried out and resulted in the determination of the two-photon excitation tensor components and suggested the existence of two excitation channels with comparable intensities. These were the longitudinal excitation channel dominated by the diagonal tensor component S zz and the mixed excitation channel dominated by the off-diagonal tensor components |S xz 2 + S yz 2 | 1/2 .

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Development of a Potential Surface for Simulation of Proton and Hydride Transfer Reactions in Solution: Application to NADH Hydride Transfer

Cited by 20 publications

References 55 publications

Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling

Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling

Computer Simulation of the Excited State Dynamics of Betaine-30 in Acetonitrile

Two-Photon Excited Fluorescence Dynamics in NADH in Water–Methanol Solutions: The Role of Conformation States

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