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

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

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 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

First-principles calculations of the structural, electronic, vibrational and magnetic properties of C_{60} and C_{48}N_{12}: a comparative study

In this work, we perform first-principles calculations of the structural, electronic, vibrational and magnetic properties of a novel ${\rm C}_{48}{\rm N}_{12}$ azafullerene. Full geometrical optimization shows that ${\rm C}_{48}{\rm N}_{12}$ is characterized by several distinguishing features: only one nitrogen atom per pentagon, two nitrogen atoms preferentially sitting in one hexagon, ${\rm S}_{6}$ symmetry, 6 unique nitrogen-carbon and 9 unique carbon-carbon bond lengths. The highest occupied molecular orbital of ${\rm C}_{48}{\rm N}_{12}$ is a doubly degenerate level of $a_{g}$ symmetry and its lowest unoccupied molecular orbital is a nondegenerate level of $a_{u}$ symmetry. Vibrational frequency analysis predicts that ${\rm C}_{48}{\rm N}_{12}$ has in total 116 vibrational modes: 58 infrared-active and 58 Raman-active modes. ${\rm C}_{48}{\rm N}_{12}$ is also characterized by 8 $^{13}{\rm C}$ and 2 $^{15}{\rm N}$ NMR spectral signals. Compared to ${\rm C}_{60}$, ${\rm C}_{48}{\rm N}_{12}$ shows an enhanced third-order optical nonlinearities which implies potential applications in optical limiting and photonics.Comment: a long version of our manuscript submitted to J.Chem.Phy

Dynamical aspects of quantum entanglement for weakly coupled kicked tops

We investigate how the dynamical production of quantum entanglement for weakly coupled, composite quantum systems is influenced by the chaotic dynamics of the corresponding classical system, using coupled kicked tops. The linear entropy for the subsystem (a kicked top) is employed as a measure of entanglement. A perturbative formula for the entanglement production rate is derived. The formula contains a correlation function that can be evaluated only from the information of uncoupled tops. Using this expression and the assumption that the correlation function decays exponentially which is plausible for chaotic tops, it is shown that {\it the increment of the strength of chaos does not enhance the production rate of entanglement} when the coupling is weak enough and the subsystems (kicked tops) are strongly chaotic. The result is confirmed by numerical experiments. The perturbative approach is also applied to a weakly chaotic region, where tori and chaotic sea coexist in the corresponding classical phase space, to reexamine a recent numerical study that suggests an intimate relationship between the linear stability of the corresponding classical trajectory and the entanglement production rate.Comment: 16 pages, 11 figures, submitted to Phys. Rev.

The evolution of multiple active site configurations in a designed enzyme

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis