Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation

Gabas, F.; Conte, Riccardo; Ceotto, Michele

doi:10.1021/acs.jpclett.1c04087

Cited by 8 publications

(12 citation statements)

References 72 publications

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“…We did not assign two signals at around 3100 cm –1 because we think they are due to bending combinations. To better characterize them, we should employ a semiclassical approach − able to reproduce anharmonic overtones and combination bands, which is beyond the scope of this paper.…”

Section: Discussionmentioning

confidence: 99%

Anharmonic Assignment of the Water Octamer Spectrum in the OH Stretch Region

et al. 2023

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We interface the quasi-classical trajectory approach with an ab initio potential energy surface for water to assign the vibrational spectroscopical features of the OH stretch region of the water octamer cluster, which is considered to be a precursor of ice. An attempt by Li et al. to assign their recent reference experiment involved lower-level calculations based on an ad hoc scaled harmonic approach. Differently from the conclusions of this previous assignment, which invoked the contribution of 5 conformers and a solvated form of the water heptamer in the spectrum, we find out that the spectroscopic features can be related to the 4 conformers of the octamer lying lower in energy.

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Section: Discussionmentioning

confidence: 99%

Anharmonic Assignment of the Water Octamer Spectrum in the OH Stretch Region

et al. 2023

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“…Our quantum mechanical vibrational levels are determined though the Divide-and-Conquer Semiclassical Initial Value Representation (DC-SCIVR) method that we developed recently. ,,− Here we report only the working equations of the DC-SCIVR approach for the calculation of vibrational spectra. The reader can find further details in ref , and further details can be found in regard to the DC-SCIVR application to adsorption studies in ref .…”

Section: Methodsmentioning

confidence: 99%

Quantum Anharmonic Calculations of Vibrational Spectra for Water Adsorbed on Titania Anatase(101) Surface: Dissociative versus Molecular Adsorption

et al. 2022

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The interaction of water molecules and hydroxyl groups with titanium dioxide (TiO 2 ) surfaces is ubiquitous and very important in anatase nanoparticle photocatalytic processes. Infrared spectroscopy, assisted by ab initio calculations of vibrational frequencies, can be a powerful tool to elucidate the mechanisms behind water adsorption. However, a straightforward comparison between measurements and calculations remains a challenging task because of the complexity of the physical phenomena occurring on nanoparticle surfaces. Consequently, severe computational approximations, such as harmonic vibrational ones, are usually employed. In the present work we partially address this complexity issue by overcoming some of the standard approximations used in theoretical simulations and employ the Divide and Conquer Semiclassical Initial Value Representation (DC-SCIVR) molecular dynamics. This method allows to perform simulations of vibrational spectra of large dimensional systems accounting not only for anharmonicities, but also for nuclear quantum effects. We apply this computational method to water and deuterated water adsorbed on the ideal TiO 2 anatase(101) surface, contemplating both the molecular and the dissociated adsorption processes. The results highlight not only the presence of an anharmonic shift of the frequencies in agreement with the experiments, but also complex quantum mechanical spectral signatures induced by the coupling of molecular vibrational modes with the surface ones, which are different in the hydrogenated case from the deuterated one. These couplings are further analyzed by exploiting the mode subdivision performed during the divide and conquer procedure.

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“…The correlated/coupled motion of the nuclei in a molecular system is an ultrafast phenomenon, and, as such, it must be studied using either experimental ultrafast techniques, which include pulse probe methods, or computer simulation methods aimed at the interpretation and simulation of two-dimensional spectra. ,− In theoretical chemistry, the identification of the uncoupled degrees of freedom is useful for computational methodologies that calculate the vibrational spectrum in reduced dimensionality, such as, for instance, semiclassical approaches, − QM/MM calculations, tensor-trains and sum of products of basis functions methods − and also the Multi-Configuration Time-Dependent Hartree method (MCTDH) − and methods based on MCTDH-like ansatz . Applications of all the aforementioned methods imply either that part of a system is partially independent of another or that the two parts have an artificial interaction.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of Artificially Pair-Decoupled Systems: An Accurate Tool for Investigating the Importance of Intramolecular Couplings

Gandolfi,

Ceotto

2023

J. Chem. Theory Comput.

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We propose a numerical technique to accurately simulate the vibrations of organic molecules in the gas phase, when pairs of atoms (or, in general, groups of degrees of freedom) are artificially decoupled, so that their motion is instantaneously decorrelated. The numerical technique we have developed is a symplectic integration algorithm that never requires computation of the force but requires estimates of the Hessian matrix. The theory we present to support our technique postulates a pair-decoupling Hamiltonian function, which parametrically depends on a decoupling coefficient α ∈ [0, 1]. The closer α is to 0, the more decoupled the selected atoms. We test the correctness of our numerical method on small molecular systems, and we apply it to study the vibrational spectroscopic features of salicylic acid at the Density Functional Theory ab initio level on a fitted potential. Our pair-decoupled simulations of salicylic acid show that decoupling hydrogen-bonded atoms do not significantly influence the frequencies of stretching modes, but enhance enormously the out-of-plane wagging and twisting motions of the hydroxyl and carboxyl groups to the point that the carboxyl and hydroxyl groups may overcome high potential energy barriers and change the salicylic acid conformation after a short simulation time. In addition, we found that the acidity of salicylic acid is more influenced by the dynamical couplings of the proton of the carboxylic group with the carbon ring than with the hydroxyl group.

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Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation

Cited by 8 publications

References 72 publications

Anharmonic Assignment of the Water Octamer Spectrum in the OH Stretch Region

Anharmonic Assignment of the Water Octamer Spectrum in the OH Stretch Region

Quantum Anharmonic Calculations of Vibrational Spectra for Water Adsorbed on Titania Anatase(101) Surface: Dissociative versus Molecular Adsorption

Molecular Dynamics of Artificially Pair-Decoupled Systems: An Accurate Tool for Investigating the Importance of Intramolecular Couplings

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