We present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters.
In order to study
Förster resonance energy transfer (FRET),
the fragment molecular orbital (FMO) method is extended to compute
electronic couplings between local excitations via the excited state
transition density model, enabling efficient calculations of nonlocal
excitations in a large molecular system and overcoming the previous
limitation of being able to compute only local excitations. The results
of these simple but accurate models are validated against full quantum
calculations without fragmentation. The developed method is applied
to a very important photosynthetic pigment–protein complex,
the Fenna–Matthews–Olson complex (FMOc), that is responsible
for the energy transfer from a chlorosome to the reaction center in
the green sulfur bacteria. Absorption and circular dichroism spectra
of FMOc are simulated, and the role of the molecular environment on
the excitations is revealed.
An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.