New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics

Ensing

2018

J. Phys. Chem. A

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The enol form of dibenzoylmethane has been the subject of many experimental and theoretical studies, yet the symmetry and the spectral response of the OHO intramolecular hydrogen bond remains mysterious due to conflicting assignments. In order to qualitatively understand the complex proton dynamics, it is necessary to probe the neighborhood of stationary points on the potential energy landscape. Here, we employ density functional theory-based molecular dynamics (DFT-MD) simulations to sample the coupling between the intermolecular proton transfer and all other molecular modes. To account for the quantum nature of the proton motion, we employ the path integral formalism within the DFT-MD simulations. Our results reveal that the hydrogen-bonded proton is delocalized between two oxygen atoms with sightly higher probability to be observed in the asymmetric than the symmetric position. The simulated infrared spectrum is found to be in a reasonably good agreement with the experimental spectrum. The computed ν band is remarkably broad and centered around 2640 cm. The origin of the discrepancy between the simulated and experimental intensities of the ν band is discussed.

Section: ■ Computational Detailsmentioning

confidence: 99%

Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations

Ensing

2018

J. Phys. Chem. A

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“…In this contribution, we restricted our analysis to the gas phase structures. If one wants to mimic physiological conditions, it is necessary to incorporate explicit solvent molecules . Such large systems cannot be treated with the IQF approach.…”

Section: Discussionmentioning

confidence: 99%

Theoretical scrutinization of nine benzoic acid dimers: Stability and energy decomposition analysis

Petrović

Milovanovic

Int J of Quantum Chemistry

et al. 2019

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Aromatic carboxylic acids are able to form diverse dimers and multimers due to their hydrogen bond donor and acceptor cites, as well as the aromatic rings. In this work, we examine nine benzoic acid dimers stabilized by hydrogen bonding and stacking interactions. Interacting quantum atoms methodology revealed that dominant attractive interactions in all of them, including hydrogen bonded systems, are due to exchange-correlation. Coulomb interactions are significant only in the most stable dimer with a double hydrogen bond, although the corresponding energy term is almost two times lower compared to the nonclassical one. Since interacting quantum atoms approach treats monomers binding by considering electronic energy only, in order to examine dissociation kinetics we performed density functional theory-based molecular dynamics simulations of selected stacked dimers: in 40% of the studied systems at 300 K thermal energy was sufficient to overpower barrier for dissociation within 1 ps, which resulted in the separation of the monomers, whereas 20% of them remained in the stacked position even after 5 ps. These results highlight the importance of noncovalent interactions, particularly weak stacking interactions, on the structure and dynamics of carboxylic acids and their derivatives.benzoic acid dimer, density functional theory-based molecular dynamics, interacting quantum fragments, noncovalent interactions

“…DFT-based molecular dynamics (MD) simulations of the F2F uracil dimer were reported in ref. 30, but the structure of the dimer was denoted as F2B. The present MD simulations of the F2B uracil dimer in bulk water were carried out following the same procedure.…”

Section: Theoretical Methods and Computational Detailsmentioning

confidence: 99%

“…29 We should mention, however, that there is certain confusion in the literature and that the alternative definition is adopted in a number of papers. 12,25,30 According to the DFT study of Hunter and van Mourik, 29 F2F and F2B uracil stacks are characterized by several almost isoenergetic minima separated by low (1-2 kcal mol À1 ) barriers. The yields of the formation of different CUD diastereoisomers in various solvents have been investigated by Shetlar and Basus.…”

Section: Introductionmentioning

confidence: 99%

On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution

Milovanovic

Novak

Phys. Chem. Chem. Phys.

et al. 2022

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