Tautomeric contributions to the absorption spectrum of [2,2′-bipyridyl]-3,3′-diol in water unveiled by molecular dynamics with accurate quantum mechanically derived force-fields

Prampolini, Giacomo; Porwal, Vishal K.; Carof, Antoine; Ingrosso, Francesca

doi:10.1016/j.molliq.2023.123898

Cited by 2 publications

(1 citation statement)

References 62 publications

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“…The quality of computed spectral signals thus depends on the accuracy of the QM level, the quality of treatment of the QM/MM interaction, which should include polarization to get a physically consistent picture, ,,− and the reliable sampling of the solute’s configurational space. While the refinement of QM/MM interactions and the QM level has attracted much interest in the context of computational spectroscopy, the role of accurate configurational sampling has generally been overlooked and performed employing classical molecular dynamics (MD) simulations. , The latter is a good compromise between computational cost and the accuracy of the sampling ,,,, and, along with density functional theory (DFT), has been used in multiple works to obtain spectra in solution. − However, anytime a molecular system is characterized by multiple metastable states in equilibrium, the exploration of the whole phase space can result frustrated by the presence of kinetic bottlenecks . Since reactive events may need high activation energies to happen, crossing these energy barriers can occur on a time scale that is hardly reachable with standard MD simulations, thus leading to incorrect sampling …”

Section: Introductionmentioning

confidence: 99%

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Sepali,

Gómez,

Grifoni

et al. 2024

J. Phys. Chem. B

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Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute−solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.

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Section: Introductionmentioning

confidence: 99%

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Sepali,

Gómez,

Grifoni

et al. 2024

J. Phys. Chem. B

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Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects

Vautrin,

Lambert,

Mahdhaoui

et al. 2024

Molecules

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Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide–water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes’ properties within their environment, accounting for finite temperature effects.

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Tautomeric contributions to the absorption spectrum of [2,2′-bipyridyl]-3,3′-diol in water unveiled by molecular dynamics with accurate quantum mechanically derived force-fields

Cited by 2 publications

References 62 publications

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects

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