Automatized protocol and interface to simulate QM/MM time‐resolved transient absorption at TD‐DFT level with COBRAMM

Abstract

We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.

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“…To evaluate ESA, the double residue of the first hyperpolarizability (Equation ()) 73 give direct access to state‐to‐state transition dipole moments 24,182–184 . ESA can also be obtained from real‐time methods.…”

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“…A successful method to simulate wave packet dynamics is TSH, which represents the wave packet by a swarm of independent trajectories, obtained through sampling the phase space around the ground state (GS) equilibrium, subject to the Newtonian laws of motion along the PES calculated on the fly. The package is an interface to electronic structure codes to facilitate such simulation up to the ps time scale. ,, …”

“…The COBRAMM package is an interface to electronic structure codes to facilitate such simulation up to the ps time scale. 472,518,519 In the context of a very recent global restructuring of COBRAMM, an automated workflow was implemented to perform transient electronic spectroscopy simulations within the TSH framework exploiting OpenMolcas as the QM software. The OpenMolcas/COBRAMM interface facilitates nonadiabatic dynamics simulations, in gas-phase and in an explicit environment through a QM/MM hybrid scheme, with various RASSCF/RASPT2 flavors and makes use of the recently implemented analytical gradients.…”

The Protein Environment Restricts the Intramolecular Charge Transfer Character of the Luciferine/Luciferase Complex

“…Instead, an accurate conformational sampling of the chromophore is obtained by propagating short QM/MM trajectories, starting from geometries extracted from the classical MD, well separated in time (every ns), in order to also guarantee a statiscally-accurate thermal distribution of the solvent molecules interacting with the chromophore. Each of these snapshots were processed with the recently developed tools included in the CO-BRAMM 2 software 90,91 in order to define three different regions for the simulation: (i) the high layer, composed by the chromophore and treated with the CAM-B3LYP 66 /6-31+G(d) 60,[92][93][94][95][96][97] level of theory (with 3 roots in the case of the S 1 simulation); (ii) the medium layer, formed by the protein and the water molecules within 4 Å from the chromophore treated classically; and (iii) the low layer, including the rest of the water molecules and frozen during the simulation. All the QM/MM dynamics were run with COBRAMM 2 90,91 , using its interfaces with Gaussian16 and AM-BER20 suites to calculate QM and MM energies and gradients and the internal routines to build QM/MM potentials and gradients within the electrostatic embedding scheme, and to propagate the adiabatic dynamics on S 0 and S 1 with the velocity-Verlet algorithm.…”