1,720,991 research outputs found
Mixed Quantum-Classical Description of Excitation Energy Transfer in a Model Fenna-Matthews-Olsen Complex
No full textThe Fenna-Matthews-Olsen (FMO) complex has recently become a paradigmatic model system in terms of understanding the long-lived electronic quantum coherence that has been experimentally observed in photosynthetic systems. In this article we investigate the quantum dynamics of an FMO model within a mixed quantum-classical dynamics approach known as the Poisson bracket mapping equation (PBME), and explore the consequences of adopting this approximate description by simulating population transfer and electronic coherence. The results obtained via the Poisson bracket mapping formalism are explicitly compared with a selection of recent results on the FMO complex. The PBME is shown to be in excellent agreement with benchmark computational results at physiological temperature, and thus provides a computationally efficient and physically consistent algorithm that may be easily integrated in all-atom molecular dynamics simulations.X114137sciescopu
Development of Force Field Parameters for Oxyluciferin on its Electronic Ground and Excited States
No full textConstruction of force field parameters of the oxyluciferin molecule on its electronic ground and excited states is presented. Several new approaches are introduced for more reliable parameterization: argon-scanning, Hessian matching, and constrained-group parameterization. The Ar-scanning approach is for fitting Lennard-Jones parameters so that the constructed force field can mimic the changes in ab initio energy of oxyluciferin-argon pair at various argon positions. The Hessian matching procedure is to closely reproduce the second derivative matrix of the bonded interaction terms of the force field functions, in comparison with the quantum chemically obtained results. The constrained-group algorithm is applied for both of these approaches to enable an automated atom-type-based parameterization. For complete description of the force field of the oxyluciferin molecule, we have also adopted the second order perturbatively corrected one-particle density matrices to obtain the atomic partial charges within the conventional framework of the restrained electrostatic potential fit. With the availability of the full force field parameter sets, the differences in condensed-phase dynamics on the two states can be investigated. As a simple demonstration, molecular dynamics simulations of aqueous oxyluciferin solution have been performed. The surrounding water structures for the two cases are analyzed by inspecting both the static solvent distribution functions as well as time variation of solvent-solute interaction. The contributions of charge-charge and dispersive interactions toward the solvation dynamics are also discussed. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 4091-4105, 2011X112524sciescopu
Dispersion-Oriented Soft Interaction in a Frustrated Lewis Fair and the Entropic Encouragement Effect in its Formation
No full textThe origin of the stability of a frustrated Lewis pair (FLP) tBu(3)P:B-(C6F5)(3) is investigated computationally to demonstrate the importance of the dispersion interaction. To this end, the interaction between alkyl-substituted phosphines (Me3P and tBu(3)P) and hexafluorobenzene (C6F6) is first investigated. Driven by the lone-pair to pi-orbital interaction, the binding energy is found to be even larger than usual pi-pi interaction energies between small aromatic compounds. This character, which is inherited to fluorophenyl-substituted B(C6F5)(3) in the FLP, induces large flexibility in the FLP over the molecular surface of B(C6F5)(3). This soft interaction, in turn, causes an entropic stabilization of the FLP formation in comparison with classical Lewis pairs based on close and tight P-B dative bonds. It also suggests a diverse nature of the FLP when it is involved in chemical reactions. Even with the cooperative participation of the perfluorophenyl groups, a detailed inspection of the FLP interaction potential energy surface indicates that the boron atom is still the major interaction site for the pair formation. This non-negligible direct P-B interaction, which is related also to the soft nature of the borane frontier orbital, is further supported by substantial spatial overlap between the frontier orbitals on the phosphine/borane fragments and their interaction energy estimations.X113631sciescopu
Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model
No full textRecently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. (c) 2012 Wiley Periodicals, Inc.X1144sciescopu
Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase-Oxyluciferin System
No full textDynamics of the firefly luciferase-oxyluciferin complex in its electronic ground and excited states are studied using various theoretical approaches. By mimicking the physiological conditions with realistic models of the chromophore oxyluciferin, the enzyme luciferase, and solvating water molecules and by performing real time simulations with a molecular dynamics technique on the model surfaces, we reveal that the local chromophore-surrounding interaction patterns differ rather severely in the two states. Because of the presence of protein, the solvation dynamics of water around the chromophore is also peculiar and shows widely different time scales on the two terminal oxygen atoms. In addition, simulations of the emission with the quantum-mechanics/molecular-mechanics approach show a close relationship between the emission color variation and the environmental dynamics, mostly through electrostatic effects from the chromophore-surrounding interaction. We also discuss the importance of considering the time scales of the luminescence and the dynamics of the interaction.X114138sciescopu
Interpolated Mechanics-Molecular Mechanics Study of Internal Rotation Dynamics of the Chromophore Unit in Blue Fluorescent Protein and Its Variants
No full textThe excited state dynamics of the blue fluorescent protein (BFP) and its variants, azurite, EBFP1.2, and EBFP2.0, are studied using molecular dynamics (MD) simulations on potential energy surfaces (PESs) generated with the interpolated mechanics-molecular mechanics (IM/MM) scheme. This IM/MM strategy adopts the interpolated PES for an important area of the complex and the conventional force field for the remaining part. We focus on the internal rotation dynamics of the chromophore unit, which is directly related to its fluorescence property, and analyze the time evolutions of the nonrotated chromophore fractions based on trajectories over 10 mu s of aggregate simulation time. The characteristics obtained from the calculated time progresses of the nonrotated chromophore fractions in BFP and other variants agree well with experimentally observed properties. The results show that the MD simulation with an IM/MM potential is an attractive approach for studying excited state dynamics of fluorescent proteins in consideration of its efficiency and reliability. We also attempt to investigate the detailed roles that the mutated residues play in delaying the excited state chromophore twisting and thus improving the fluorescence property, and discuss the contributions by the Coulombic and the steric interactions between the chromophore and the mutated residues.X111312sciescopu
Behavior of Poisson Bracket Mapping Equation in Studying Excitation Energy Transfer Dynamics of Cryptophyte Phycocyanin 645 Complex
No full textRecently, it has been shown that quantum coherence appears in energy transfers of various photosynthetic light-harvesting complexes at from cryogenic to even room temperatures. Because the photosynthetic systems are inherently complex, these findings have subsequently interested many researchers in the field of both experiment and theory. From the theoretical part, simplified dynamics or semiclassical approaches have been widely used. In these approaches, the quantum-classical Liouville equation (QCLE) is the fundamental starting point. Toward the semiclassical scheme, approximations are needed to simplify the equations of motion of various degrees of freedom. Here, we have adopted the Poisson bracket mapping equation (PBME) as an approximate form of QCLE and applied it to find the time evolution of the excitation in a photosynthetic complex from marine algae. The benefit of using PBME is its similarity to conventional Hamiltonian dynamics. Through this, we confirmed the coherent population transfer behaviors in short time domain as previously reported with a more accurate but more time-consuming iterative linearized density matrix approach. However, we find that the site populations do not behave according to the Boltzmann law in the long time limit. We also test the effect of adding spurious high frequency vibrations to the spectral density of the bath, and find that their existence does not alter the dynamics to any significant extent as long as the associated reorganization energy is changed not too drastically. This suggests that adopting classical trajectory based ensembles in semiclassical simulations should not influence the coherence dynamics in any practical manner, even though the classical trajectories often yield spurious high frequency vibrational features in the spectral density.X115sciescopuskc
Performance of Quasi-Degenerate Scaled Opposite Spin Perturbation Corrections to Single Excitation Configuration Interaction for Excited State Structures and Excitation Energies with Application to the Stokes Shift of
No full textThe quasi-degenerate scaled opposite spin perturbation correction to single excitation configuration interaction (SOS-CIS(D-0)) is a promising electronic structure method that can describe electronically excited states of sizable molecular systems. In this article, we report an assessment of the performance of SOS-CIS(DD0) for adiabatic electronic transition energies and excited state equilibrium geometries for various small molecules. These tests allow optimization of the empirical scaling parameter in SOS-CIS(DD0), and it is shown that one universal scaling parameter (chosen as 1.4) can satisfactorily reproduce the experimental results for all the tested molecules. The method is then applied to examine the large Stokes shift observed with a dihydrosilaphenanthrene derivative. The main features of the experimental absorption and emission spectra of this molecule are well reproduced by SOS-CIS(D-0).X111718sciescopu
Quartic-Scaling Analytical Gradient of Quasidegenerate Scaled Opposite Spin Second-Order Perturbation Corrections to Single Excitation Configuration Interaction
No full textQuasidegenerate scaled second-order perturbation correction to single excitation configuration interaction (SOS-CIS(D-0)) is a viable method that can describe excited-state potential energy surfaces of various chemical systems both reliably and efficiently [J. Chem. Phys. 2008, 128, 164106]. In this work, its analytical gradient theory is developed and implemented into an efficient quartic-scaling algorithm. This low order scaling, as opposed to the traditional quintic scaling of various second-order perturbation methods, is attained by using the resolution-of-the-identity approximation and the Laplace transform. The efficiency of the method is demonstrated by calculating the excited-state gradients of molecules with varying sizes. The proposed gradient method will thus be useful in studying various chemical systems, ranging from finding the optimized stable geometry on the excited surface to elucidating interesting excited-state dynamics around the avoided crossing region.X112323sciescopu
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