Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^*/n\pi ^*$$ π π ∗ / n π ∗ decay of thymine

Liu, Yanli; Cerezo, Javier; Lin, Na; Zhao, Xian; Improta, Roberto; Santoro, Fabrizio

doi:10.1007/s00214-018-2218-z

Cited by 14 publications

(23 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Then, the vibronic absorption spectrum is obtained by Fourier transform of the sum of the correlations functions weighted by the scalar products of the transition dipoles (as reported in Equation ( 9 )). Cross-correlations functions usually have a very small effect and have been neglected [ 21 , 30 ].…”

Section: Methodsmentioning

confidence: 99%

“…We checked convergence by monitoring the populations at the beginning and end of the grid using the rdgpop tool provided in Quantics, and ensuring that they did not exceed 10

. For the ML tree, we chose the number of single particle functions (SPFs) for each node based on the magnitude of the on-diagonal vibronic coupling

at the FC point, with modes with larger couplings assigned larger numbers of SPFs, as we have done in previous studies [ 6 , 29 , 30 , 31 ]. Mode combination was also utilised for modes with similar character.…”

Section: Computational Detailsmentioning

confidence: 99%

“…We have recently proposed [ 29 ] a general scheme for the parameterisation of LVC Hamiltonians from TD-DFT calculations, based on a maximum overlap criterion, that is effective enough to generate automatically the parameters for systems with dozens of normal modes and 10–20 coupled electronic states [ 21 ]. Besides their interest for spectroscopy, LVC Hamiltonians can reliably describe the photodynamics in semi-rigid systems, such as in the DNA/RNA bases, on the ∼100 fs time scale, i.e., before large amplitude motions are likely to take place [ 6 , 29 , 30 , 31 ]. Therefore, they offer a powerful tool to investigate the initial steps of the intricate dynamics triggered in heterocyclic compounds by light absorption.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

et al. 2021

Self Cite

View full text Add to dashboard Cite

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 Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.

show abstract

Section: Methodsmentioning

confidence: 99%

“…We checked convergence by monitoring the populations at the beginning and end of the grid using the rdgpop tool provided in Quantics, and ensuring that they did not exceed 10

. For the ML tree, we chose the number of single particle functions (SPFs) for each node based on the magnitude of the on-diagonal vibronic coupling

Section: Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…As already done in previous works ref. 25,29 tight SCF convergence with 10 −6 au convergence threshold is used for TD-DFT energy calculations. Full-dimensionality QD calculations considering all the 51 normal modes were performed with the multilayer version of the multiconfigurational time dependent Harthee (ML-MCTDH) method.…”

Section: Computational Detailsmentioning

confidence: 99%

“…33 As a primitive basis set we adopted an Hermite DVR representation as we already did for similar systems. 25,29,34,35 ML-trees and convergence tests of the ML-MCTDH propagation with respect to the dimension of the primitive basis set and the number of single particle functions are reported in the section S3.1 of the ESI. LVC model assumes that all diabatic PES are harmonic with the same vibrational frequencies of S 0 .…”

Section: Computational Detailsmentioning

confidence: 99%

Quantum dynamics of the ππ/nπ decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase

Jouybari

Improta

et al. 2020

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

show abstract

Ab‐initio molecular dynamics and hybrid explicit‐implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

et al. 2020

View full text Add to dashboard Cite

Solute–solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non‐bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical–physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute–solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

show abstract

Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^/n\pi ^$$ π π ∗ / n π ∗ decay of thymine

Cited by 14 publications

References 39 publications

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

Quantum dynamics of the ππ/nπ decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase

Ab‐initio molecular dynamics and hybrid explicit‐implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Contact Info

Product

Resources

About

Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^*/n\pi ^*$$ π π ∗ / n π ∗ decay of thymine

Cited by 14 publications

References 39 publications

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

Quantum dynamics of the ππ*/nπ* decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase

Ab‐initio molecular dynamics and hybrid explicit‐implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Contact Info

Product

Resources

About

Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^/n\pi ^$$ π π ∗ / n π ∗ decay of thymine

Quantum dynamics of the ππ/nπ decay of the epigenetic nucleobase 1,5-dimethyl-cytosine in the gas phase