1,721,045 research outputs found
Influence of Site-Dependent Pigment-Protein Interactions on Excitation Energy Transfer in Photosynthetic Light Harvesting
No full textA site-dependent spectral density system-bath model of the Fenna-Matthews-Olsen (FMO) pigment-protein complex is developed using results from ground-state molecular mechanics simulations together with a partial charge difference model for how the long-range contributions to the chromophore excitation energies fluctuate with environmental configuration. A discussion of how best to consistently process the chromophore excitation energy fluctuation correlation functions calculated in these classical simulations to obtain reliable site-dependent spectral densities is presented. The calculations reveal that chromophores that are close to the protein water interface can experience strongly dissipative environmental interactions characterized by reorganization energies that can be as much as 2-3 times those of chromophores that are buried deep in the hydrophobic protein scaffolding. Using a linearized density matrix quantum propagation method, we demonstrate that the inhomogeneous system bath model obtained from our site-dependent spectral density calculations gives results consistent with experimental dissipation and dephasing rates. Moreover, we show that this model can simultaneously enhance the energy-transfer rate and extend the decoherence time. Finally, we explore the influence of initially exciting different chromophores and mutating local environments on energy transfer through the network. These studies suggest that different pathways, selected by varying initial photoexcitation, can exhibit significantly different relaxation times depending on whether the energy-transfer path involves chromophores at the protein solvent interface or if all chromophores in the pathway are buried in the protein. RI Masia, Marco/A-5571-2010 OI Masia, Marco/0000-0003-2257-310
Transferability of polarizable models for ion-water electrostatic interaction Marco Masia
No full textEstimating chloride polarizability in a water solution
No full textThe evaluation of the hydrated chloride anion polarizability is hereby addressed by using density functional theory based calculations in the condensed phase. In this study, the quantum probability associated with maximally localized Wannier functions is included to account for the spatial extent of the electronic density. It is shown that the anion polarizability is not appreciably influenced upon solvation.
The method could be applied to systems where the quantum
state is separable; issues related to system size dependence and about its applicability to other systems are discussed
based polarizable force field parametrization
No full textExperimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ∼ 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car–Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations
Reaction rate theory approach to thermodynamic state dependence of hydration shell exchange for Li+(Aq)
No full textStructural Stabilization and Onset of Acid Dissociation in Hydrogen Halide-Water Aggregates
No full textComputational study of γ-butyrolactone and Li+/γ-butyrolactone in gas and liquid phases
No full textA comprehensive study of structural and dynamical properties of γ-butyrolactone (GBL) and the extent to which they are affected in the vicinity of a lithium ion, both in gas and liquid phases, is reported. The isolated GBL molecule is found to be nonplanar, with a barrier of ≈9 kJ/mol to ring inversion. As expected, the lithium ion coordinates the carbonyl oxygen with an almost collinear configuration relative to the carbon−oxygen bond but with a slight tilting toward the lactone oxygen. This configuration holds for clusters of up to four molecules and in the liquid phase as well (where a tetrahedral first solvation shell is found). A high level ab initio vibrational analysis, with a new assignment of bands has been performed, which shows substantial red and blue shifts upon lithium solvation, which decrease in a nontrivial way upon increasing the cluster size. To study the solvent effect of the vibrational spectrum, an accurate intramolecular force field has been developed, based on the concept of relaxed potential energy profiles. The inclusion of stretch and bend anharmonicity is shown to be essential in order to explain, not only the absolute value, but the sign of the shifts, particularly for the carbonyl stretching which is substantially downshifted. The shifts obtained for the rest of the bands, together with the diffusion coefficients for bulk GBL and for lithium, are in fair agreement with experimental results
On the performance of molecular polarization methods. II. Water and carbon tetrachloride close to a cation
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