Dataset Information

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

ABSTRACT: A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (? a max) have been measured. The results indicate that MC-PDFT may be employed to calculate ? a max values for this important class of photoresponsive proteins.

SUBMITTER: Marin MDC

PROVIDER: S-EPMC7096677 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

Marín María Del Carmen MDC De Vico Luca L Dong Sijia S SS Gagliardi Laura L Truhlar Donald G DG Olivucci Massimo M

Journal of chemical theory and computation 20190220 3

A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-ord ...[more]

PMID: 30721054

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Project description:THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect MM to QM (or QM/MM) levels of theory in FES.

Dataset Information

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

Publications

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

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