Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine

Sun, Shuai; Brown, Alex

doi:10.1016/j.comptc.2016.12.014

Cited by 7 publications

(6 citation statements)

References 83 publications

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“…These complexes have already been reported in the literature. 21,23,24,26,27,[48][49][50][57][58][59][60][61][62][63][64][65] However, information on the single H-bonded (either OÁ Á ÁHO w or NHÁ Á ÁO w ), most likely local minimum structures of uracilwater, is not available in the H-bond literature. Ramondo and co-workers 27 reported IR spectra of four double H-bonded UW structures.…”

Section: Uracil-water (Uw) Double H-bonded Cyclic Complexesmentioning

confidence: 99%

Uracil–water interaction revisited – in search of single H-bonded secondary minima

Buczek,

Rzepiela,

Kupka

et al. 2024

Phys. Chem. Chem. Phys.

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Section: Uracil-water (Uw) Double H-bonded Cyclic Complexesmentioning

confidence: 99%

Uracil–water interaction revisited – in search of single H-bonded secondary minima

Buczek,

Rzepiela,

Kupka

et al. 2024

Phys. Chem. Chem. Phys.

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“…In simulation of RR spectra of uracil within STA, implicit polarizable continuum solvation model has been employed to account for bulk dielectric constant of water, 34 and the role of explicit solvation was also investigated in the case of uracil and thymine by Sun and Brown. 101 These authors investigated sitespecific role of solvents and found that explicitly H-bonded water molecule was necessary to predict the relative intensities of two carbonyl stretching modes (at 1623 and 1664 cm −1 ) with respect to the strongest mode at 1235 cm −1 of uracil in 266 nm excited RR spectrum. GMP has complex structure of the surrounding solvents due to the presence of six hydration sites, leading to a cage structure of the solvation shell, where explicit waters are H-bonded among themselves.…”

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation

Mondal

Narayana

2019

J. Phys. Chem. B

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In short-time dynamics approximation, relative resonance Raman (RR) intensity of a vibrational mode primarily depends on the magnitude of square of the excited-state gradient along the corresponding normal coordinate, ground-state normal mode eigenvector, and harmonic vibrational wavenumbers. In this study, through simulation of RR spectra of guanosine-5′-monophosphate (GMP) in two ππ* singlet excited states, we analyze how the explicitly hydrogen-bonded local solvation structure of the chromophore dictates intensities of the RR active modes in an unprecedented manner. We show that the accuracy of the structural model of solvated chromophore plays a decisive role in determining an optimal theoretical method for prediction of the Franck−Condon region of the ππ* excited states. 9-Methylguanine (9-meG) in complex with six water molecules (9-meG• 6H 2 O) is found out to be the most accurate one for describing GMP in two different bright electronic states. We find that explicit hydrogen-bonded water molecules strongly influence computed RR intensities of GMP by modulating both the ground-state normal mode vectors and the excited-state energy gradients. We find that simultaneous inclusion of six explicit waters to describe the solute−solvent interaction near all hydration sites is essential for reliable prediction of the features of RR spectra in L b and B b electronic states of GMP.

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“…The nucleobases decay mechanisms depend strongly on the embedding environment [ 8 , 9 , 10 , 11 , 12 ]. Indeed, when nucleobases are stacked in a DNA polymer, internal non-radiative decay competes with several charge- and proton transfers which ultimately lead to cyclobutane dimers or 6-4 photoadducts [ 13 , 14 , 15 , 16 , 17 , 18 ], at the origin of DNA mutations.…”

Section: Introductionmentioning

confidence: 99%

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

Huix‐Rotllant

2021

Molecules

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Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.

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Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine

Cited by 7 publications

References 83 publications

Uracil–water interaction revisited – in search of single H-bonded secondary minima

Uracil–water interaction revisited – in search of single H-bonded secondary minima

Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

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