A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour

Overview

Journal J Comput Chem

Publisher Wiley

Specialties Biology
Chemistry

Date 2024 Dec 24

PMID 39718467

Authors

Tommaso Nottoli

Mattia Bondanza

Filippo Lipparini

Benedetta Mennucci

Affiliations

Soon will be listed here.

Abstract

We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite. The implementation supports both single-point energy evaluations and geometry optimizations, facilitated by the availability of analytical gradients. We demonstrate the methodology by applying it to two distinct photoreceptors, exploring the impact of the protein environment on the structural and photophysical properties of their embedded chromophores.

References

Mizuno H, Mal T, Walchli M, Kikuchi A, Fukano T, Ando R . Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. Proc Natl Acad Sci U S A. 2008; 105(27):9227-32. PMC: 2453726. DOI: 10.1073/pnas.0709599105. View

Li Q, Mennucci B, Robb M, Blancafort L, Curutchet C . Polarizable QM/MM Multiconfiguration Self-Consistent Field Approach with State-Specific Corrections: Environment Effects on Cytosine Absorption Spectrum. J Chem Theory Comput. 2015; 11(4):1674-82. DOI: 10.1021/ct5010388. View

Loco D, Polack E, Caprasecca S, Lagardere L, Lipparini F, Piquemal J . A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations. J Chem Theory Comput. 2016; 12(8):3654-61. DOI: 10.1021/acs.jctc.6b00385. View

Warshel A, Levitt M . Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol. 1976; 103(2):227-49. DOI: 10.1016/0022-2836(76)90311-9. View

Lu Z, Zhang Y . Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions. J Chem Theory Comput. 2009; 4(8):1237-48. PMC: 2640839. DOI: 10.1021/ct800116e. View

Brunk E, Rothlisberger U . Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev. 2015; 115(12):6217-63. DOI: 10.1021/cr500628b. View

Loco D, Lagardere L, Adjoua O, Piquemal J . Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity. Acc Chem Res. 2021; 54(13):2812-2822. PMC: 8264944. DOI: 10.1021/acs.accounts.0c00662. View

van der Kamp M, Mulholland A . Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry. 2013; 52(16):2708-28. DOI: 10.1021/bi400215w. View

Nifosi R, Mennucci B, Filippi C . The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation. Phys Chem Chem Phys. 2019; 21(35):18988-18998. DOI: 10.1039/c9cp03722e. View

10.

Boulanger E, Thiel W . Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model. J Chem Theory Comput. 2015; 8(11):4527-38. DOI: 10.1021/ct300722e. View

11.

Sala J, Guardia E, Masia M . The polarizable point dipoles method with electrostatic damping: implementation on a model system. J Chem Phys. 2010; 133(23):234101. DOI: 10.1063/1.3511713. View

12.

Roeggen I, Johansen T . Cholesky decomposition of the two-electron integral matrix in electronic structure calculations. J Chem Phys. 2008; 128(19):194107. DOI: 10.1063/1.2925269. View

13.

Matthews D, Cheng L, Harding M, Lipparini F, Stopkowicz S, Jagau T . Coupled-cluster techniques for computational chemistry: The CFOUR program package. J Chem Phys. 2020; 152(21):214108. DOI: 10.1063/5.0004837. View

14.

Morzan U, Alonso de Armino D, Foglia N, Ramirez F, Gonzalez Lebrero M, Scherlis D . Spectroscopy in Complex Environments from QM-MM Simulations. Chem Rev. 2018; 118(7):4071-4113. DOI: 10.1021/acs.chemrev.8b00026. View

15.

Bondanza M, Nottoli T, Nottoli M, Cupellini L, Lipparini F, Mennucci B . The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics. J Chem Phys. 2024; 160(13). DOI: 10.1063/5.0198251. View

16.

Lipparini F, Cappelli C, Barone V . Linear Response Theory and Electronic Transition Energies for a Fully Polarizable QM/Classical Hamiltonian. J Chem Theory Comput. 2015; 8(11):4153-65. DOI: 10.1021/ct3005062. View

17.

Helmich-Paris B . Benchmarks for Electronically Excited States with CASSCF Methods. J Chem Theory Comput. 2019; 15(7):4170-4179. PMC: 6620717. DOI: 10.1021/acs.jctc.9b00325. View

18.

Wu X, Teuler J, Cailliez F, Clavaguera C, Salahub D, de la Lande A . Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput. 2017; 13(9):3985-4002. DOI: 10.1021/acs.jctc.7b00251. View

19.

Bondanza M, Jacquemin D, Mennucci B . Excited States of Xanthophylls Revisited: Toward the Simulation of Biologically Relevant Systems. J Phys Chem Lett. 2021; 12(28):6604-6612. PMC: 8311646. DOI: 10.1021/acs.jpclett.1c01929. View

20.

Riahi S, Rowley C . The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. J Comput Chem. 2014; 35(28):2076-86. DOI: 10.1002/jcc.23716. View