Dynamics of Proton Transfer in Mesoscopic Clusters

Proton transfer rates and mechanisms are studied in mesoscopic, liquid-state, molecular clusters. The proton transfer occurs in a proton-ion complex solvated by polar molecules comprising the cluster environment. The rates and mechanisms of the reaction are studied using both adiabatic and non-adiabatic molecular dynamics. For large molecular clusters, the proton-ion complex resides primarily on the surface of the cluster or one layer of solvent molecules inside the surface. The proton transfer occurs as the complex undergoes orientational fluctuations on the cluster surface or penetrates one solvent layer into the cluster leading to solvent configurations that favor the transfer. For smaller clusters the complex resides mostly on the surface of the cluster and proton transfer is observed only when the complex penetrates the cluster and solvent configurations that favor the proton transfer are achieved. Quantitative information on the cluster reaction rate constants is also presented.Comment: To appear in JCP (March). Postscript figures available on request ([email protected]

An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations

Time-dependent fluctuations in the catalysis rate ({delta}k(t)) observed in single-enzyme experiments were found in a particular study to have an autocorrelation function decaying on the same time scale as that of spectral diffusion {delta}{omega}0(t). To interpret this similarity, the present analysis focuses on a factor in enzyme catalysis, the local electrostatic interaction energy (E) at the active site and its effect on the activation free energy barrier. We consider the slow fluctuations of the electrostatic interaction energy ({delta}E(t)) as a contributor to {delta}k(t) and relate the latter to {delta}{omega}0(t). The resulting relation between {delta}k(t) and {delta}{omega}0(t) is a dynamic analog of the solvatochromism used in interpreting solvent effects on organic reaction rates. The effect of the postulated {delta}E(t) on fluctuations in the radiative component ({delta}{gamma}Formula(t)) of the fluorescence decay of chromophores in proteins also is examined, and a relation between {delta}{gamma}Formula(t) and {delta}{omega}0(t) is obtained. Experimental tests will determine whether the correlation functions for {delta}k(t), {delta}{omega}0(t), and {delta}{gamma}Formula are indeed similar for any enzyme. Measurements of dielectric dispersion, {varepsilon}({omega}), for the enzyme discussed elsewhere will provide further insight into the correlation function for {delta}E(t). They also will determine whether fluctuations in the nonradiative component {gamma}Formula of the lifetime decay has a different origin, fluctuations in distance for example

Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene

Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we explain how path integrals can be employed to evaluate the equilibrium (EIE) and kinetic (KIE) isotope effects, and the temperature dependence of the rate constant. The methodology is applied to the [1,5] sigmatropic hydrogen shift in pentadiene. Both the KIE and the temperature dependence of the rate constant confirm the importance of tunneling and other nuclear quantum effects as well as of the anharmonicity of the potential energy surface. Moreover, previous results on the KIE were improved by using a combination of a high level electronic structure calculation within the harmonic approximation with a path integral anharmonicity correction using a lower level method.Comment: 9 pages, 4 figure

Kinetics and mechanism of proton transport across membrane nanopores

We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across the membrane diffusively in single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier along the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube.Comment: 4 pages, 4 figure

A network model to investigate structural and electrical properties of proteins

One of the main trend in to date research and development is the miniaturization of electronic devices. In this perspective, integrated nanodevices based on proteins or biomolecules are attracting a major interest. In fact, it has been shown that proteins like bacteriorhodopsin and azurin, manifest electrical properties which are promising for the development of active components in the field of molecular electronics. Here we focus on two relevant kinds of proteins: The bovine rhodopsin, prototype of GPCR protein, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer disease. Both these proteins exert their functioning starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different electrical response associated with the different configurations. The model resolution of the electrical response is found able to monitor the structure and the conformational change of the given protein. In this respect, rhodopsin exhibits a better differential response than AChE. This result gives room to different interpretations of the degree of conformational change and in particular supports a recent hypothesis on the existence of a mixed state already in the native configuration of the protein.Comment: 25 pages, 12 figure

Time-dependent fluorescence in nanoconfined solvents: Linear-response approximations and Gaussian statistics

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/135/8/10.1063/1.3626825.The time-dependent fluorescence of a model dye molecule in a nanoconfined solvent is used to test approximations based on the dynamic and static linear-response theories and the assumption of Gaussian statistics. Specifically, the results of nonequilibrium molecular-dynamics simulations are compared to approximate expressions involving time correlation functions obtained from equilibrium simulations. Solvation dynamics of a model diatomic dye molecule dissolved in acetonitrile confined in a spherical hydrophobic cavity of radius 12, 15, and 20 Å is used as the test case. Both the time-dependent fluorescence energy, expressed as the normalized dynamic Stokes shift, and the time-dependent position of the dye molecule after excitation are examined. While the dynamic linear-response approximation fails to describe key aspects of the solvation dynamics, assuming Gaussian statistics reproduces the full nonequilibrium simulations well. The implications of these results are discussed

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein/water interface allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On the top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line.Comment: 9 pages, 8 figure

A QM/MM approach for the study of monolayer-protected gold clusters

We report the development and implementation of hybrid methods that combine quantum mechanics (QM) with molecular mechanics (MM) to theoretically characterize thiolated gold clusters. We use, as training systems, structures such as Au25(SCH2-R)18 and Au38(SCH2-R)24, which can be readily compared with recent crystallographic data. We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment. As an example, we demonstrate that calculations of the 1H and 13C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude increase in computational efficiency.Comment: Journal of Materials Science, 201