Vibronic and environmental effects in simulations of optical spectroscopy

TJ Zuehlsdorff, SV Shedge, SY Lu… - Annual Review of …, 2021 - annualreviews.org
Including both environmental and vibronic effects is important for accurate simulation of
optical spectra, but combining these effects remains computationally challenging. We outline …

OpenMM 8: molecular dynamics simulation with machine learning potentials

P Eastman, R Galvelis, RP Peláez… - The Journal of …, 2023 - ACS Publications
Machine learning plays an important and growing role in molecular simulation. The newest
version of the OpenMM molecular dynamics toolkit introduces new features to support the …

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

F Santoro, JA Green, L Martinez-Fernandez… - Physical Chemistry …, 2021 - pubs.rsc.org
We concisely review the main methodological approaches to model nonadiabatic dynamics
in isotropic solutions and their applications. Three general classes of models are identified …

Adiabatic-molecular dynamics generalized vertical hessian approach: a mixed quantum classical method to compute electronic spectra of flexible molecules in the …

J Cerezo, D Aranda, FJ Avila Ferrer… - Journal of Chemical …, 2019 - ACS Publications
We present a general mixed quantum classical method that couples classical molecular
dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible …

Elucidating the role of hydrogen bonding in the optical spectroscopy of the solvated green fluorescent protein chromophore: Using machine learning to establish the …

MS Chen, Y Mao, A Snider, P Gupta… - The Journal of …, 2023 - ACS Publications
Hydrogen bonding interactions with chromophores in chemical and biological environments
play a key role in determining their electronic absorption and relaxation processes, which …

[HTML][HTML] Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches

TJ Zuehlsdorff, A Montoya-Castillo, JA Napoli… - The Journal of …, 2019 - pubs.aip.org
Simulating optical spectra in the condensed phase remains a challenge for theory due to the
need to capture spectral signatures arising from anharmonicity and dynamical effects, such …

Nonadiabatic molecular dynamics with extended density functional tight-binding: Application to nanocrystals and periodic solids

M Shakiba, E Stippell, W Li… - Journal of Chemical …, 2022 - ACS Publications
In this work, we report a new methodology for nonadiabatic molecular dynamics calculations
within the extended tight-binding (xTB) framework. We demonstrate the applicability of the …

Cost-effective simulations of vibrationally-resolved absorption spectra of fluorophores with machine-learning-based inhomogeneous broadening

EF Petrusevich, MHE Bousquet… - Journal of Chemical …, 2023 - ACS Publications
The results of electronic and vibrational structure simulations are an invaluable support for
interpreting experimental absorption/emission spectra, which stimulates the development of …

[HTML][HTML] Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue

AJ Dunnett, D Gowland, CM Isborn, AW Chin… - The journal of …, 2021 - pubs.aip.org
Modeling linear absorption spectra of solvated chromophores is highly challenging as
contributions are present both from coupling of the electronic states to nuclear vibrations and …

Nonadiabatic absorption spectra and ultrafast dynamics of DNA and RNA photoexcited nucleobases

JA Green, MY Jouybari, D Aranda, R Improta… - Molecules, 2021 - mdpi.com
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is
based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time …