Interaction of triplet uracil and thymine with water

Zhang, Ru Bo; Zeegers‐Huyskens, Th.; Ceulemans, Arnout; Nguyen, Minh Tho

doi:10.1016/j.chemphys.2005.04.028

Cited by 24 publications

(37 citation statements)

References 40 publications

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“…This substantial shift to lower frequency parallels the shift seen previously for the triplet state of an aromatic carbonyl compound [44]. Our B3LYP calculations (and also those of Zhang et al [43]) predict a 125 cm −1 shift for gas-phase thymine, based on scaled harmonic frequencies. At the PBE0/aug-cc-pVDZ level this shift is reduced to 111 cm −1 , which is still larger than the experimental red shift of 80 cm −1 in acetonitrile.…”

Section: Assignment Of Carbonyl Stretch Frequencies In the Lowest Trisupporting

confidence: 62%

“…Preliminary density-functional calculations on uracil-(H 2 O) 4 indicate a 20-30 cm −1 red shift in both C=O stretching frequencies, for both the singlet and triplet states. Calculations by Zhang et al for thymine solvated by explicit water molecules show a 30 cm −1 red shift when one water molecule is hydrogen bonded to the oxygen of either carbonyl [43]. Calculations taking solvation by acetonitrile into account are not yet available, so we simply scaled the isolated molecule frequencies in calculating the theoretical difference spectra for comparison with experiment, as discussed above.…”

Section: Assignment Of Carbonyl Stretch Frequencies In the Lowest Trimentioning

confidence: 99%

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Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

et al. 2008

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Vibrational spectra of the lowest energy triplet states of thymine and its 2'-deoxyribonucleoside, thymidine, are reported for the first time. Time-resolved infrared (TRIR) difference spectra were recorded over seven decades of time from 300 fs -3 µs using femtosecond and nanosecond pumpprobe techniques. The carbonyl stretch bands in the triplet state are seen at 1603 and ~1700 cm −1 in room-temperature acetonitrile-d 3 solution. These bands and additional ones observed between 1300 and 1450 cm −1 are quenched by dissolved oxygen on a nanosecond time scale. Density-functional calculations accurately predict the difference spectrum between triplet and singlet IR absorption cross sections, confirming the peak assignments and elucidating the nature of the vibrational modes. In the triplet state, the C4=O carbonyl exhibits substantial single-bond character, explaining the large (~70 cm −1 ) red shift in this vibration, relative to the singlet ground state. Femtosecond TRIR measurements unambiguously demonstrate that the triplet state is fully formed within the first 10 ps after excitation, ruling out a relaxed 1 nπ* state as the triplet precursor.

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Section: Assignment Of Carbonyl Stretch Frequencies In the Lowest Trisupporting

confidence: 62%

Section: Assignment Of Carbonyl Stretch Frequencies In the Lowest Trimentioning

confidence: 99%

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

et al. 2008

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“…E-mail: mirzaei_m@modares.ac.ir; hadipour@modares.ac.ir nucleobase, and its derivatives to HB interactions have been previously studied due to importance of 5-derivatives of uracil in pharmaceutical and biological activities in living systems [5][6][7][8][9][10][11][12]. 5-Nitrouracil (5NU) is the 5-nitro derivative of uracil whose contribution to HB interactions was reported by earlier X-ray study of Kennedy et al [13].…”

Section: Introductionmentioning

confidence: 99%

Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters

Mirzaei

Hadipour

2009

JICS

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Hydrogen bond interaction properties of backbone uracil was studied in crystalline structure of 5-nitrouracil. To this aim the electric field gradient tensors were calculated at the level of density functional theory in two single (non-hydrogen bonded) and cluster (hydrogen-bonded four-molecule) models of 5-nitrouracil. The electric field gradient tensors at the sites of O-17, N-14, and H-2 nuclei were converted to the experimentally measurable nuclear quadrupole resonance spectroscopy parameters, quadrupole coupling constant and asymmetry parameter. The results indicated different hydrogen bond interaction properties at the sites of various nuclei and also the protective role of -NO 2 group for contribution of O1 to hydrogen bond interactions in comparison with uracil. The density functional theory calculations were performed using GAUSSIAN 98 package employing B3LYP method and 6-311G** and 6-311++G** basis sets.

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“…32,33 Also, based on the reviewing literature the uracil-water interaction has been explored by means of the natural bond orbital analysis that provides supplementary information of the relative stability ordering. 31 In two CUA, nH 2 O and GAT, nH 2 O local minima structures, water molecules are bonded to the uracil of CUA as well as to the adenine of GAT by several hydrogen bonds. The oxygen and hydrogen atoms of water that are involved in forming the hydrogen bonds are in the same plane of uracil and adenine, while the free water hydrogen atoms are outside the plane.…”

Section: Hydration Models Of Cua and Gat Sequencesmentioning

confidence: 99%

Solvent effects on structural and thermochemical properties of p53 tumor-suppressor gene: a molecular modeling approach in drug design

Irani

Atyabi²,

Mivehchi³

et al. 2011

IJN

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Abstract:The p53 tumor-suppressor protein is a cellular phosphoprotein and a negative regulator of cell growth. Most p53 mutations occur in exons 5-8 within the DNA-binding domain. Therefore, p53 can potentially be targeted with novel drugs designed to bind to a mutation and restore its stability or wild-type conformation. For the current study, Hartree-Fock calculations were used to investigate the solvent-induced effects of five different solvent media (acetone, ethanol, methanol, dimethyl sulfoxide, and water) on the thermochemical parameters and relative energies, and on the multinuclear nuclear magnetic resonance shielding tensors of oxygen, nitrogen, and phosphorus nuclei, of GAT. To understand how the solvent affects the mutation region (the "hot spot") of p53, the relative energies of GAT in selected solvent media were determined. Some biological evidence suggested the structural stabilities of hot spots of GAT have the optimum temperature and solvent type for mutation. All the authors' findings are in accordance with common biological phenomena. Another important objective of this study was to compare the hydration Gibbs free energies of CUA and GAT in water using two different approaches where the solvent was treated as a continuum of the constant at different levels of Hartree-Fock theory. The Gibbs hydration energy values obtained in water with the polarized continuum model directly applied on the isolated CUA and GAT sequences were compared with those determined from the hydrated models with four, six, and eight water molecule clusters around the hot spots uracil and adenine. The clustered structures of water molecules around the hot spots of GAT (in DNA level) and CUA (in transcriptional level) were found to be energetically favored. The results of this study provide a reliable insight into the nature of mutation processes, which is of utmost importance for the study of biochemical structures, and provide a basis for drug design.

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Interaction of triplet uracil and thymine with water

Cited by 24 publications

References 40 publications

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine

Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters

Solvent effects on structural and thermochemical properties of p53 tumor-suppressor gene: a molecular modeling approach in drug design

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