Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian

Park, Jae Woo; Rhee, Young Min

doi:10.1002/cphc.201402226

Cited by 14 publications

(52 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…35 The data set contained energy and derivative information at 1500 chromophore conformations and covered a wide range of configurational space. 32 The environment that surrounded the chromophore was described with the conventional molecular mechanics model. The chromophore−environment interaction was handled by adopting the interpolation mechanics/molecular mechanics (IM/MM) approach.…”

Section: Methods: Overviewmentioning

confidence: 99%

“…32,36−38 Indeed, IM/MM aims to follow the accuracy of the more demanding quantum mechanics/molecular mechanics (QM/MM) at a much reduced computational cost. 32 This approach models the interactions between the IM and the MM regions based on Coulomb and Lennard-Jones potentials together with linked hydrogen atoms over covalently bonded interfaces. The atomic partial charges of the chromophore were generated with our diabatic population matrix formalism 39 based on natural population analyses (NPA) 40 of the electron distributions in multiple electronic states.…”

Section: Methods: Overviewmentioning

confidence: 99%

“…where e k and e l are the corresponding column vectors of R. 32,34,76 In the condensed phase simulations using the interpolated diabatic Hamiltonian, the electrostatic interactions can also be described based on diabatic states. With this, it becomes possible to describe geometrydependent charge migration in the chromophore on each adiabatic potential energy surface.…”

Section: Journal Of the American Chemical Societymentioning

confidence: 99%

“…82 Protein Simulation Details. Interpolated mechanics/molecular mechanics (IM/MM) simulations with the diabatic Hamiltonian 32 was employed toward the MD simulations of the whole protein. The GROMACS 4.0.7 program package 86 with in-house external libraries for the diabatic Hamiltonian interpolation and the surface hopping algorithms was used for all simulations with the protein.…”

Section: Journal Of the American Chemical Societymentioning

confidence: 99%

See 3 more Smart Citations

Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

2016

Self Cite

View full text Add to dashboard Cite

The green fluorescent protein and its designed variants fluoresce efficiently. Because the isolated chromophore is not fluorescent in a practical sense, it is apparent that the protein environment plays a crucial role in its efficiency. Because of various obstacles in studying excited state dynamics of complex systems, however, the detailed mechanism of this efficiency enhancement is not yet clearly elucidated. Here, by adopting excited state nonadiabatic molecular dynamics simulations together with an interpolated quantum chemical potential model of the chromophore, we find that the strong electric field from the protein matrix contributes dominantly to the motional restriction of the chromophore. The delay in twisting motion subsequently obstructs the nonradiative decay that competes with fluorescence, leading naturally to an enhancement in light-emitting efficiency. Surprisingly, steric constraints make only a minor contribution to these aspects. Through residue specific analyses, we identify a group of key residues that control the excited state behavior. Testing a series of mutant GFPs with different brightnesses also supports the view regarding the importance of protein electrostatics. Our findings may provide a useful guide toward designing new fluorescent chemical systems in the future.

show abstract

Section: Methods: Overviewmentioning

confidence: 99%

Section: Methods: Overviewmentioning

confidence: 99%

Section: Journal Of the American Chemical Societymentioning

confidence: 99%

Section: Journal Of the American Chemical Societymentioning

confidence: 99%

See 2 more Smart Citations

Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…I do not use the prefix quasior other conditionals to refer to diabatic states that are not adiabatic with respect to nuclear displacements, such as has been done elsewhere, the phrase "diabatic" being reserved for representations that are adiabatic with respect to nuclear displacements. 16,24,25 In typical SA-CASSCF, where the variational objective is the state-averaged energy (2.1), self-consistency is only preserved within degenerate subspaces of the CAS-CI ensemble density matrix. In the general case, SA-CASSCF solutions are not invariant to transformations of the CAS-CI Hilbert space.…”

Section: Sa-casscf Ensembles and Their Invariancesmentioning

confidence: 99%

Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: Charge-bond resonance in monomethine cyanines

Olsen

2015

The Journal of Chemical Physics

View full text Add to dashboard Cite

This paper reviews basic results from a theory of the a priori classical probabilities (weights) in state-averaged complete active space self-consistent field (SA-CASSCF) models. It addresses how the classical probabilities limit the invariance of the self-consistency condition to transformations of the complete active space configuration interaction (CAS-CI) problem. Such transformations are of interest for choosing representations of the SA-CASSCF solution that are diabatic with respect to some interaction. I achieve the known result that a SA-CASSCF can be self-consistently transformed only within degenerate subspaces of the CAS-CI ensemble density matrix. For uniformly distributed ("microcanonical") SA-CASSCF ensembles, self-consistency is invariant to any unitary CAS-CI transformation that acts locally on the ensemble support. Most SA-CASSCF applications in current literature are microcanonical. A problem with microcanonical SA-CASSCF models for problems with "more diabatic than adiabatic" states is described. The problem is that not all diabatic energies and couplings are self-consistently resolvable. A canonical-ensemble SA-CASSCF strategy is proposed to solve the problem. For canonical-ensemble SA-CASSCF, the equilibrated ensemble is a Boltzmann density matrix parametrized by its own CAS-CI Hamiltonian and a Lagrange multiplier acting as an inverse "temperature," unrelated to the physical temperature. Like the convergence criterion for microcanonical-ensemble SA-CASSCF, the equilibration condition for canonical-ensemble SA-CASSCF is invariant to transformations that act locally on the ensemble CAS-CI density matrix. The advantage of a canonical-ensemble description is that more adiabatic states can be included in the support of the ensemble without running into convergence problems. The constraint on the dimensionality of the problem is relieved by the introduction of an energy constraint. The method is illustrated with a complete active space valence-bond (CASVB) analysis of the charge/bond resonance electronic structure of a monomethine cyanine: Michler's hydrol blue. The diabatic CASVB representation is shown to vary weakly for "temperatures" corresponding to visible photon energies. Canonical-ensemble SA-CASSCF enables the resolution of energies and couplings for all covalent and ionic CASVB structures contributing to the SA-CASSCF ensemble. The CASVB solution describes resonance of charge- and bond-localized electronic structures interacting via bridge resonance superexchange. The resonance couplings can be separated into channels associated with either covalent charge delocalization or chemical bonding interactions, with the latter significantly stronger than the former.

show abstract

Surface Hopping Dynamics on Vibronic Coupling Models

et al. 2021

View full text Add to dashboard Cite

See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles.vibronic coupling (LVC)-parametrized potential energy surfaces.• Zobel, J. P.; Knoll, T.; González, L. Ultrafast and longtime excited-state kinetics of an NIR emissive vanadium-(III) complex. II. Elucidating triplet-to-singlet excitedstate dynamics. Chem. Sci. 2021, 12, 10791−10801. 2 This work showcases SH/LVC simulations of an open-shell metal complex with a degenerate triplet ground state for several picoseconds in f ull dimensionality.

show abstract

Towards the Realization of Ab Initio Dynamics at the Speed of Molecular Mechanics: Simulations with Interpolated Diabatic Hamiltonian

Cited by 14 publications

References 77 publications

Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: Charge-bond resonance in monomethine cyanines

Surface Hopping Dynamics on Vibronic Coupling Models

Contact Info

Product

Resources

About