58 research outputs found
Development and Application of Efficient Methods for the Simulation of Charge Transport in Complex Biomolecules
Charge transport through bio-molecular wires in a solvent: Bridging molecular dynamics and model Hamiltonian approaches
We present a hybrid method based on a combination of quantum/classical
molecular dynamics (MD) simulations and a mod el Hamiltonian approach to
describe charge transport through bio-molecular wires with variable lengths in
presence o f a solvent. The core of our approach consists in a mapping of the
bio-molecular electronic structure, as obtained f rom density-functional based
tight-binding calculations of molecular structures along MD trajectories, onto
a low di mensional model Hamiltonian including the coupling to a dissipative
bosonic environment. The latter encodes fluctuat ion effects arising from the
solvent and from the molecular conformational dynamics. We apply this approach
to the c ase of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show
that the DNA conformational fluctuations are essential in determining and
supporting charge transport
Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach
Charge transport through a short DNA oligomer (Dickerson dodecamer) in
presence of structural fluctuations is investigated using a hybrid
computational methodology based on a combination of quantum mechanical
electronic structure calculations and classical molecular dynamics simulations
with a model Hamiltonian approach. Based on a fragment orbital description, the
DNA electronic structure can be coarse-grained in a very efficient way. The
influence of dynamical fluctuations arising either from the solvent
fluctuations or from base-pair vibrational modes can be taken into account in a
straightforward way through time series of the effective DNA electronic
parameters, evaluated at snapshots along the MD trajectory. We show that charge
transport can be promoted through the coupling to solvent fluctuations, which
gate the onsite energies along the DNA wire
Tight-binding parameters for charge transfer along DNA
We systematically examine all the tight-binding parameters pertinent to
charge transfer along DNA. The molecular structure of the four DNA bases
(adenine, thymine, cytosine, and guanine) is investigated by using the linear
combination of atomic orbitals method with a recently introduced
parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are
discussed and then used for calculating the corresponding wavefunctions of the
two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO
and LUMO energies of the bases are in good agreement with available
experimental values. Our results are then used for estimating the complete set
of charge transfer parameters between neighboring bases and also between
successive base-pairs, considering all possible combinations between them, for
both electrons and holes. The calculated microscopic quantities can be used in
mesoscopic theoretical models of electron or hole transfer along the DNA double
helix, as they provide the necessary parameters for a tight-binding
phenomenological description based on the molecular overlap. We find that
usually the hopping parameters for holes are higher in magnitude compared to
the ones for electrons, which probably indicates that hole transport along DNA
is more favorable than electron transport. Our findings are also compared with
existing calculations from first principles.Comment: 15 pages, 3 figures, 7 table
Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation
Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals
Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation
Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist
Charge Transfer in E. coli DNA Photolyase: Understanding Polarization and Stabilization Effects via QM/MM Simulations
We study fast hole
transfer events in E. coli DNA photolyase,
a key step in the photoactivation process, using
a multiscale computational method that combines nonadiabatic propagation
schemes and linear-scaling quantum chemical methods with molecular
mechanics force fields. This scheme allows us to follow the time-dependent
evolution of the electron hole in an unbiased fashion; that is, no
assumptions about hole wave function localization, time scale separation,
or adiabaticity of the process have to be made beforehand. DNA photolyase
facilitates an efficient long-range charge transport between its flavin
adenine dinucleotide (FAD) cofactor and the protein surface via a
chain of evolutionary conserved Trp residues on the sub-nanosecond
time scale despite the existence of multiple potential trap states.
By including a large number of aromatic residues along the charge
transfer pathway into the quantum description, we are able to identify
the main pathway among alternative possible routes. The simulations
show that charge transfer, which is extremely fast in this protein,
occurs on the same time scale as the protein response to the electrostatic
changes; that is, time-scale separation as often presupposed in charge
transfer studies seems to be inappropriate for this system. Therefore,
coupled equations of motion, which propagate electrons and nuclei
simultaneously, appear to be necessary. The applied computational
model is shown to capture the essentials of the reaction kinetics
and thermodynamics while allowing direct simulations of charge transfer
events on their natural time scale
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