On-the-fly adiabatically switched semiclassical initial value representation molecular dynamics for vibrational spectroscopy of biomolecules

Botti, Giacomo; Ceotto, Michele; Conte, Riccardo

doi:10.1063/5.0075220

Cited by 18 publications

(19 citation statements)

References 83 publications

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“…Calculation of ethanol ( trans and gauche ) ZPEs and those of its deuterated isotopologues can be performed from a dynamical point of view by means of the adiabatically switched semiclassical initial value representation (AS SCIVR) technique. The goal is to corroborate DMC findings employing a completely different, but still full-dimensional, technique. − AS SCIVR is a recently developed two-step semiclassical approach able to regain quantum effects starting from classical trajectories. In this it is quite similar to standard semiclassical techniques, − but it differs in the way the starting conditions of the semiclassical dynamics run are selected.…”

Section: Theory and Computational Detailsmentioning

confidence: 99%

Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers

Nandi

Conte

Qu³

et al. 2022

J. Chem. Theory Comput.

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Ethanol is a molecule of fundamental interest in combustion, astrochemistry, and condensed phase as a solvent. It is characterized by two methyl rotors and trans ( anti ) and gauche conformers, which are known to be very close in energy. Here we show that based on rigorous quantum calculations of the vibrational zero-point state, using a new ab initio potential energy surface (PES), the ground state resembles the trans conformer, but substantial delocalization to the gauche conformer is present. This explains experimental issues about identification and isolation of the two conformers. This “leak” effect is partially quenched when deuterating the OH group, which further demonstrates the need for a quantum mechanical approach. Diffusion Monte Carlo and full-dimensional semiclassical dynamics calculations are employed. The new PES is obtained by means of a Δ-machine learning approach starting from a pre-existing low level density functional theory surface. This surface is brought to the CCSD(T) level of theory using a relatively small number of ab initio CCSD(T) energies. Agreement between the corrected PES and direct ab initio results for standard tests is excellent. One- and two-dimensional discrete variable representation calculations focusing on the trans – gauche torsional motion are also reported, in reasonable agreement with experiment.

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Section: Theory and Computational Detailsmentioning

confidence: 99%

Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers

Nandi

Conte

Qu³

et al. 2022

J. Chem. Theory Comput.

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“…In a very preliminar and partial simulation, two of us employed a type II proline while developing the on-the-fly adiabatically switched semiclassical initial value representation (AS SCIVR) method for spectroscopy. [21] However, there was no agreement between AS SCIVR, scaled harmonic, and previously assigned OH str frequencies. Due to this controversial result, we found it interesting to study the vibrational spectrum of proline in details by performing a thorough spectral analysis using AS SCIVR.…”

Section: Introductionmentioning

confidence: 82%

The complex vibrational spectrum of proline explained through the adiabatically switched semiclassical initial value representation

Botti

Aieta

Conte

2022

The Journal of Chemical Physics

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Proline, a 17-atom amino acid with a closed-ring side chain, has a complex potential energy surface characterized by several minima. Its IR experimental spectrum, reported in the literature, is of difficult and controversial assignment. In particular, the experimental signal at 3559 cm−1 associated with the OH stretch is interesting because it is inconsistent with the global minimum, trans-proline conformer. This suggests the possibility that multiple conformers may contribute to the IR spectrum. The same conclusion is obtained by investigating the splitting of the CO stretch at 1766 and 1789 cm−1 and other, more complex spectroscopic features involving CH stretches and COH/CNH bendings. In this work, we perform full-dimensional, on-the-fly adiabatically switched semiclassical initial value representation simulations employing the ab initio dft-d3-B3LYP level of theory with aug-cc-pVDZ basis set. We reconstruct the experimental spectrum of proline in its main features by studying the vibrational features of trans-proline and cis1-proline, and provide a new assignment for the OH stretch of trans-proline.

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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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On-the-fly adiabatically switched semiclassical initial value representation molecular dynamics for vibrational spectroscopy of biomolecules

Cited by 18 publications

References 83 publications

Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers

Quantum Calculations on a New CCSD(T) Machine-Learned Potential Energy Surface Reveal the Leaky Nature of Gas-Phase Trans and Gauche Ethanol Conformers

The complex vibrational spectrum of proline explained through the adiabatically switched semiclassical initial value representation

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

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