Excited State Dynamics in Biomolecules

Abstract

Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption. These reactions typically occur at femto‐ to picosecond timescales. As the relevant time and spatial resolutions are notoriously hard to access experimentally, molecular dynamics (MD) simulations are the method of choice to study such ultrafast processes. In the simulations, a multiconfigurational quantum mechanical (QM) description (CASSCF, CASPT2) is required to model the electronic rearrangement of those parts of the system that are involved in the absorption. For the remainder, typically consisting of the apoprotein and the solvent, a simple forcefield model (MM) suffices. QM/MM gradients have to be computed on‐the‐fly, and surface hopping procedures are needed to model the excited state decay. In this chapter, the computational framework underlying the atomistic simulation of photochemical events is reviewed and a few representative applications are discussed that demonstrate the validity of hybrid QM/MM approaches for photobiological reactions.

Generalized trajectory surface-hopping method for internal conversion and intersystem crossing

“…In our implementation, only the QM components of the derivative coupling vectors are used in QM/MM GTSH dynamics simulations because the MM components are expected to be very small; in addition, they are available only numerically so that their evaluation is expensive. Similar approximations have been used in previous QM/MM FSSH applications 7,12,14,24,[76][77][78] and in QM/MM optimizations of conical intersections. 79,80 In the same spirit, the spin-orbit couplings between electronic states I and J with different spin are determined from the QM wavefunctions obtained in the QM/MM calculations with electronic embedding,…”

“…[1][2][3] It is attractive because it is easy to implement and offers an intuitive interpretation, and it has thus been adopted by many groups. [4][5][6][7][8][9][10][11][12][13][14][15][16] It has been applied to study many ultrafast photophysical and photochemical processes in the gas phase and the condensed phase. [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33] Despite the growing popularity and success of the trajectory-based FSSH method, it remains approximate and has some well-known drawbacks.…”

Optimizing conical intersections of solvated molecules: The combined spin-flip density functional theory/effective fragment potential method

“…Finally, the gradient of the excitation energy obtained above is added to that of the ground-state energy (22) where D μνσ is a ground-state density matrix element and μνσ , κλτ is the DFT two-particle density matrix…”

“…9 Several studies have been reported in which CI points including environmental effects have been located. [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] Burghardt et al 10,11 have evaluated solvent effects on a CI point within the dielectric continuum model and applied the nonequilibrium free energy formulation to a model protonated Schiff base. Using the reference interaction site model selfconsistent field (RISM-SCF) method, Yamazaki and Kato 12,13 determined the CI points of ethylene, CH 2 NH 2 + , and 9H-adenine in polar solvents.…”

Conical intersections in solution: Formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method

“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] Conical intersections are not a single point but a multidimensional seam of 3N−8 degrees of freedom where N is the number of atoms in a system. These conical intersections are usually formed between electronic states with same spatial symmetries and spins, which are defined as seams of the true degeneracy between electronic states.…”