Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics

Macaluso, Veronica; Hashem, Shaima; Nottoli, Michele; Lipparini, Filippo; Cupellini, Lorenzo; Mennucci, Benedetta

doi:10.1021/acs.jpcb.1c05753

Cited by 11 publications

(10 citation statements)

References 66 publications

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“…All residues beyond 22 Å from the flavin were kept frozen, and their AMOEBA polarizabilities were neglected to speed up the calculations. Simulations were propagated in the NVT ensemble using the Bussi thermostat with a time constant of 0.1 ps and an integration step of 0.5 fs, as done in our previous work. , The system was equilibrated classically at room temperature, so no zero-point energy has been included. Each GS QM/AMOEBA MD (from now on denoted with the letters A··· J) was run for 12 ps to allow equilibration and to sample initial conditions.…”

mentioning

confidence: 99%

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

Mazzeo

Hashem

Lipparini

et al. 2023

J. Phys. Chem. Lett.

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The excited-state dynamics of molecules embedded in complex (bio)matrices is still a challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be an effective strategy, but an optimal combination of accuracy and computational cost still has to be found. Here, we present a method which combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method. The newly implemented method is applied to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein. We show that the proton-coupled electron transfer (PCET) process suggested for other BLUF proteins is still valid also for AppA.

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confidence: 99%

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

Mazzeo

Hashem

Lipparini

et al. 2023

J. Phys. Chem. Lett.

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“…Effective normal modes can be obtained as linear combination of Cartesian coordinates, using a variational principle that minimizes the frequency spread of the corresponding power spectrum 107 . Recently, a signal‐processing technique called second‐order blind identification (SOBI) 108–111 was applied on the basis of internal coordinates to obtain effective normal modes in larger molecules 112 …”

Section: Qm/amoeba Dynamics At Workmentioning

confidence: 99%

“…Simulation of the transient IR spectra of AppA‐BLUF 112 . (a) Structure of the FMN chromophore, with the largest bond length variations upon excitation (excited‐minus‐ground) highlighted.…”

Section: Qm/amoeba Dynamics At Workmentioning

confidence: 99%

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QM/AMOEBA description of properties and dynamics of embedded molecules

Nottoli

Bondanza

Mazzeo

et al. 2023

WIREs Comput Mol Sci

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We describe the development, implementation, and application of a polarizable QM/MM strategy, based on the AMOEBA polarizable force field, for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. We show that polarizable QM/MM is a well‐understood, mature technology that can be deployed using a state‐of‐the‐art implementation that combines efficient numerical methods and linear scaling techniques. Thanks to these numerical advances and to the availability of parameters for a wide manifold of systems in the AMOEBA force field, polarizable QM/AMOEBA can be used for advanced production applications, that range from the prediction of spectroscopies to ground‐ and excited‐state multiscale ab initio molecular dynamics simulations.This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Combined QM/MM Methods

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“…For hybrid QM/MM coupling schemes based on mechanical and electrostatic embedding, such spectra can also be calculated [35][36][37][38][39][40][41][42][43]. However, there are fewer studies exploring the calculation of IR and Raman intensities using fully polarizable hybrid QM/MM methods [44][45][46][47][48].…”

Section: Introductionmentioning

confidence: 99%

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

Guan

Lü

Sen

et al. 2023

Phil. Trans. R. Soc. A.

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Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms. This article is part of a discussion meeting issue ‘Supercomputing simulations of advanced materials’.

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Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics

Cited by 11 publications

References 66 publications

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor

QM/AMOEBA description of properties and dynamics of embedded molecules

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

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