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

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1743
Author(s):  
James A. Green ◽  
Martha Yaghoubi Jouybari ◽  
Daniel Aranda ◽  
Roberto Improta ◽  
Fabrizio Santoro
Keyword(s):  
Absorption Spectra ◽  
Excited States ◽  
Quantum Dynamics ◽  
Density Functional ◽  
Basis Set ◽  
Ultrafast Dynamics ◽  
Effective Population ◽  
Dna And Rna ◽  
Vibronic Spectra ◽  
Effective Wave

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.

Vibronic absorption spectra and excited states of acridine red dye in aqueous solution: TD-DFT/DFT study

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Victor V. Kostjukov
Keyword(s):  
Aqueous Solution ◽  
Absorption Spectrum ◽  
Hydrogen Bonds ◽  
Absorption Spectra ◽  
Excited States ◽  
Dipole Moments ◽  
Basis Set ◽  
Calculated Spectrum ◽  
Solvent Model ◽  
Acridine Red

Abstract The vibronic absorption spectra of acridine red (AR) xanthene dye in an aqueous solution using 40 hybrid functionals, the 6-31++G(d,p) basis set, and the IEFPCM solvent model were calculated. It turned out that the O3LYP functional provided the best agreement with the experiment in the positions of the main maximum and the short-wavelength subband (shoulder). The calculations showed that this shoulder is vibronic. At the same time, the shoulder intensity in the calculated spectrum turned out to be lower than in the experimental one. Apparently, insignificant dimerization, which occurs even at low concentrations of the dye in solution, contributes to the shoulder of the experimental absorption spectrum. Various parameters of the AR cation in the ground and excited states (IR spectra, atomic charges, dipole moments, and transition moment) were calculated. Maps of the distribution of electron density and electrostatic potential have been built. The influence of the strong hydrogen bonds of the dye with three water molecules on the absorption spectrum was analyzed. It has been shown that these bonds are strengthened upon AR excitation. The strengthening of two hydrogen bonds with water upon excitation leads to a lowering of the potential energy surface of the excited state, which causes a decrease in the excitation energy (i.e., an increase in the wavelength of the absorbed photon) as compared to a purely implicit specification of the water environment. Therefore, explicit assignment of waters strongly bound to the dye leads to spectrum redshift.

scholarly journals Chemically Accurate Excitation Energies With Small Basis Sets

2019 ◽  
Author(s):  
Emmanuel Giner ◽  
Anthony Scemama ◽  
Julien Toulouse ◽  
Pierre-Francois Loos
Keyword(s):  
Excited States ◽  
Configuration Interaction ◽  
Density Functional ◽  
Chem Phys ◽  
Basis Set ◽  
Basis Sets ◽  
Excitation Energies ◽  
Functional Correction ◽  
The One ◽  
Range Density

<p>By combining extrapolated selected configuration interaction (sCI) energies obtained with the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm with the recently proposed short-range density-functional correction for basis-set incompleteness [Giner et al., J. Chem. Phys. 2018, 149, 194301], we show that one can get chemically accurate vertical and adiabatic excitation energies with, typically, augmented double-ζ basis sets. We illustrate the present approach on various types of excited states (valence, Rydberg, and double excitations) in several small organic molecules (methylene, water, ammonia, carbon dimer and ethylene). The present study clearly evidences that special care has to be taken with very diffuse excited states where the present correction does not catch the radial incompleteness of the one-electron basis set.</p>

scholarly journals A theoretical study on photo absorption in silicon decorated boron clusters (BnSi, n=7-10)

2021 ◽  
Vol 2070 (1) ◽  
pp. 012051
Author(s):  
Ankita Jaiswal ◽  
Shakti S Ray ◽  
Sridhar Sahu
Keyword(s):  
Optical Absorption ◽  
Oscillator Strength ◽  
Absorption Spectra ◽  
Density Functional ◽  
Visible Region ◽  
Basis Set ◽  
Functional Study ◽  
Strength Analysis ◽  
Optical Absorption Spectra ◽  
Boron Clusters

Abstract In this work, we have studied the optical absorption spectra of small boron clusters doped with single silicon atom (BnSi, n=7-10) and is reported employing CAM-B3LYP functional with 6-311+G(d) basis –set within the framework of time dependent density functional study (TD-DFT). We have computed excitation energy, oscillator strength, wavelength and the corresponding orbital transitions associated with a given oscillator strength. Analysis of optical absorption spectra of studied clusters shows that most of the absorption peaks are found in the ultraviolet-visible (UV-Vis) region (200 nm-700 nm). The major peaks are found to fall in UV region along with some weaker peaks at visible region. The most intense peak is recorded for B8Si cluster at 232 nm and oscillator strength of 0.084. This peak is associated with the orbital transition from H-4→L+1.

scholarly journals Broadband X-Ray Absorption Spectra from Time-Dependent Kohn-Sham Calculations

2021 ◽  
Author(s):  
Ying Zhu ◽  
Bushra Alam ◽  
John Herbert
Keyword(s):  
Absorption Spectra ◽  
Density Functional ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Propagation Time ◽  
Edge Structure ◽  
X Ray ◽  
The Cost ◽  
X Ray Absorption

We present a protocol for calculation of K-edge x-ray absorption spectra using time-dependent Kohn-Sham (TDKS) calculations, also known as "real-time" time-dependent density functional theory (TDDFT). In principle, the entire absorption spectrum (at all wavelengths) can be computed via Fourier transform of the time-dependent dipole moment function, following a perturbation of the ground-state density and propagation of time-dependent Kohn-Sham molecular orbitals. In practice, very short time steps are required to obtain an accurate spectrum, which increases the cost, but the use of Pade approximants significantly reduces the length of time propagation that is required. Spectra that are well converged with respect to the corresponding linear-response (LR-)TDDFT result can be obtained with < 10 fs of propagation time. Use of complex absorbing potentials helps to remove artifacts at high energies that otherwise result from the use of a finite atom-centered Gaussian basis set. Benchmark results, comparing TDKS to LR-TDDFT, are presented for several small molecules at the carbon and oxygen K-edges, demonstrating good agreement with experiment without the need for specialized basis sets. Whereas LR-TDDFT is a reasonable approach to obtain the near-edge structure, that approach requires hundreds of states and quickly becomes cost prohibitive for large systems, even when the core\slash valence separation approximation is used to remove most of the occupied states from the excitation manifold. We demonstrate the cost-effective TDKS approach by application to a copper dithiolene complex, where binding of a ligand is detectable via shifts in the sulfur K-edge.

scholarly journals Chemically Accurate Excitation Energies With Small Basis Sets

2019 ◽  
Author(s):  
Emmanuel Giner ◽  
Anthony Scemama ◽  
Julien Toulouse ◽  
Pierre-Francois Loos
Keyword(s):  
Excited States ◽  
Configuration Interaction ◽  
Density Functional ◽  
Chem Phys ◽  
Basis Set ◽  
Basis Sets ◽  
Excitation Energies ◽  
Functional Correction ◽  
The One ◽  
Range Density

<p>By combining extrapolated selected configuration interaction (sCI) energies obtained with the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm with the recently proposed short-range density-functional correction for basis-set incompleteness [Giner et al., J. Chem. Phys. 2018, 149, 194301], we show that one can get chemically accurate vertical and adiabatic excitation energies with, typically, augmented double-ζ basis sets. We illustrate the present approach on various types of excited states (valence, Rydberg, and double excitations) in several small organic molecules (methylene, water, ammonia, carbon dimer and ethylene). The present study clearly evidences that special care has to be taken with very diffuse excited states where the present correction does not catch the radial incompleteness of the one-electron basis set.</p>

scholarly journals Broadband X-Ray Absorption Spectra from Time-Dependent Kohn-Sham Calculations

2021 ◽  
Author(s):  
Ying Zhu ◽  
Bushra Alam ◽  
John Herbert
Keyword(s):  
Absorption Spectra ◽  
Density Functional ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Propagation Time ◽  
Edge Structure ◽  
X Ray ◽  
The Cost ◽  
X Ray Absorption

We present a protocol for calculation of K-edge x-ray absorption spectra using time-dependent Kohn-Sham (TDKS) calculations, also known as "real-time" time-dependent density functional theory (TDDFT). In principle, the entire absorption spectrum (at all wavelengths) can be computed via Fourier transform of the time-dependent dipole moment function, following a perturbation of the ground-state density and propagation of time-dependent Kohn-Sham molecular orbitals. In practice, very short time steps are required to obtain an accurate spectrum, which increases the cost, but the use of Pade approximants significantly reduces the length of time propagation that is required. Spectra that are well converged with respect to the corresponding linear-response (LR-)TDDFT result can be obtained with < 10 fs of propagation time. Use of complex absorbing potentials helps to remove artifacts at high energies that otherwise result from the use of a finite atom-centered Gaussian basis set. Benchmark results, comparing TDKS to LR-TDDFT, are presented for several small molecules at the carbon and oxygen K-edges, demonstrating good agreement with experiment without the need for specialized basis sets. Whereas LR-TDDFT is a reasonable approach to obtain the near-edge structure, that approach requires hundreds of states and quickly becomes cost prohibitive for large systems, even when the core\slash valence separation approximation is used to remove most of the occupied states from the excitation manifold. We demonstrate the cost-effective TDKS approach by application to a copper dithiolene complex, where binding of a ligand is detectable via shifts in the sulfur K-edge.

scholarly journals Comparison of Linear Response Theory, Projected Initial Maximum Overlap Method, and Molecular Dynamics Based Vibronic Spectra: The Case of Methylene Blue

2021 ◽  
Author(s):  
Ali Abou Taka ◽  
Shao-Yu Lu ◽  
Duncan Gowland ◽  
Tim J. Zuehlsdorff ◽  
Hector H. Corzo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Absorption Spectra ◽  
Linear Response ◽  
Density Functional ◽  
Normal Modes ◽  
Vertical Gradient ◽  
Linear Response Theory ◽  
Response Theory ◽  
Vibronic Spectra ◽  
Overlap Method

Simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited states. In this report, we show that utilization of such a procedure within an adiabatic linear response theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent eld method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical excitation procedures, such as those computed from a vertical gradient or molecular dynamics trajectory-based approach. For the methylene blue chromophore, we compare vibronic absorption spectra computed with: an adiabatic Hessian approach with linear response theory optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method optimized structures, and excitation energy time correlation functions generated from a molecular dynamics trajectory. Due to mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with linear response theory time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in linear response theory strongly couples to the optical excitation while showing S1/ S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited state adiabatic Hessian of linear response theory optimized structures and also showcases three alternatives that are not as subject to adiabatic state mixing effects.

scholarly journals An investigation of the excitation and emission properties of fluorescence compounds using DFT and TD-DFT methods

2018 ◽  
Vol 127 (1A) ◽  
pp. 43
Author(s):  
Duong Tuan Quang
Keyword(s):  
Density Functional Theory ◽  
Excited States ◽  
Density Functional ◽  
Basis Set ◽  
Excitation Energies ◽  
Dft Methods ◽  
Functional Theory ◽  
Emission Properties ◽  
Experimental Values ◽  
Optimized Geometries

<p class="03Abstract">The density functional theory and time-dependent density functional theory methods were used for investigation of the excitation and emission properties of some fluorophores. The calculations were based on the optimized geometries of ground states and excited states at the B3LYP functional and LanL2DZ basis set. The results clarified the nature of the optical properties of the compounds and agreed well with the experimental data. The approximate values of excitation energies and emission energies of compounds were also identified. The calculated excitation energies were about 0.01 to 0.56 eV higher than experimental values. Meanwhile, the emission energies were from 0.34 to 0.89 eV higher than experimental values. These large errors occurred when there were great variations between the optimized geometries of ground state and excited states. They could be due to the presence of components of solvent in real solution that stabilized the excited states, leading to reduce the excitation and emission energies in the experiments.</p>

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