Polarizable Embedding for Excited-State Reactions: Dynamically Weighted Polarizable QM/MM

Hagras, Muhammad A.; Glover, William J.

doi:10.1021/acs.jctc.8b00064

Cited by 24 publications

(40 citation statements)

References 31 publications

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“…Previous theoretical and experimental studies ( Park and Rhee, 2016 ; Hagras and Glover, 2018 ; Langeland et al, 2018 ; Jin et al, 2020 ; Romei et al, 2020 ) on the GFP have emphasized the significant influence of the electrostatic effect from the protein environment on the fluorescence of the chromophore. Here, the two-body fragments constructed using the GMFCC method were utilized to further investigate the possible physical origins of the influence of the environment.…”

Section: Resultsmentioning

confidence: 99%

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Chenfei

Wang

2021

Front. Chem.

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Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.

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Section: Resultsmentioning

confidence: 99%

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Chenfei

Wang

2021

Front. Chem.

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“…Although the initial focus of the method has been on solvated systems, the bias function can be easily modified to describe surface geometries, allowing a description of heterogeneous interfaces. Furthermore, since the FlexiBLE bias potential is a function of nuclear coordinates only, and has an MMforcefield-like computational cost, the approach is entirely compatible with other embedding schemes, such as polarizable, [58][59][60][61] density, 22,23 and mean-field embedding theories. 24 We thus believe that constrained QM/MM partitioning, as in FlexiBLE, is a promising alternative to adaptive QM/MM.…”

Section: Discussionmentioning

confidence: 99%

Flexible boundary layer using exchange for embedding theories. I. Theory and implementation

Shen

Glover

2021

Preprint

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Embedding theory is a powerful computational chemistry approach to exploring the electronic structure and dynamics of complex systems, with QM/MM being the prime example. A challenge arises when trying to apply embedding methodology to systems with diffusible particles, e.g. solvents, if some of them must be included in the QM region, for example in the description of solvent supported electronic states or reactions involving proton transfer or charge-transfer-to-solvent: without a special treatment, inter-diffusion of QM and MM particles will lead eventually to a loss of QM/MM separation. We have developed a new method called Flexible Boundary Layer using Exchange (FlexiBLE) that solves the problem by adding a biasing potential to the system that maintains QM/MM separation. The method rigorously preserves ensemble averages by leveraging their invariance to exchange of identical particles. With a careful choice of the biasing potential, and the use of a tree algorithm to include only important QM and MM exchanges, we find the method has an MM-forcefield-like computational cost and thus adds negligible overhead to a QM/MM simulation. Furthermore, we show that molecular dynamics with the FlexiBLE bias conserves total energy and remarkably, dynamical quantities in the QM region are unaffected by the applied bias. FlexiBLE thus widens the range of chemistry that can be studied with embedding theory.

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“…The second strategy is that of employing a state-averaged polarization in the vicinity of crossings and a state specific approach elsewhere. Hagras and Glover proposed an algorithm to interpolate between the two descriptions, in terms of a switching function depending on the energy difference between a reference state and the other electronic states considered (101). This strategy, contrary to the first, has the advantage of being the most natural for multireference QM approaches, such as CASSCF, which are often required in nonadiabatic simulations.…”

Section: Extension To Multiscale Approachesmentioning

confidence: 99%

Multiscale Models for Light-Driven Processes

Nottoli

Cupellini

Lipparini

et al. 2021

Annu. Rev. Phys. Chem.

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Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Polarizable Embedding for Excited-State Reactions: Dynamically Weighted Polarizable QM/MM

Cited by 24 publications

References 31 publications

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs

Flexible boundary layer using exchange for embedding theories. I. Theory and implementation

Multiscale Models for Light-Driven Processes

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