Inelastic neutron scattering, Raman spectroscopy and periodic DFT study of purine

Parker, Stewart F.; Jeans, Richard; Devonshire, R.

doi:10.1016/j.vibspec.2004.01.003

Cited by 17 publications

(15 citation statements)

References 13 publications

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“…It is also in harmony with γ(NH) assignments in solid imidazole, optically at 958 cm -1 15 and INS at 961 cm -1 , 14 and agrees reasonably with the observation of γ(NH) at 888 and 900 cm -1 in purine. 16 In the isolated molecule γ(NH) is calculated about 440 cm -1 , in line with other reports, 3,17 and it is assigned in this region in matrix isolation experiments, 459 or 449 cm -1 . 1,17 However, in a Here, see Figure 1 for the atom numbering; the bond between atoms 1 and 2 is a; its lattice the molecule is known to be hydrogen bonded to its neighbors.…”

Section: Methodssupporting

confidence: 89%

Reassignment of the Vibrational Spectrum of Benzimidazole

Tomkinson

2008

J. Phys. Chem. A

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Section: Methodssupporting

confidence: 89%

Reassignment of the Vibrational Spectrum of Benzimidazole

Tomkinson

2008

J. Phys. Chem. A

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“…Parker et al [24] have performed neutron inelastic scattering (NIS) studies combined with DFT calculations on the parent molecule purine to confirm the identity of the tautomer in solution and to make satisfactory band assignments. NIS spectra computed using a hybrid DFT method, B3LYP/6-31G, for both N 7 -H and N 9 -H tautomers were in poor agreement.…”

Section: Purinementioning

confidence: 99%

“…Purine IR [115] 1584s, 1577s 871 w 513 vs 788 w NIS [24] 929 vs 788 w 6-Hydroxypurine [27] IR 1697s 1619m 779 w 809 m Raman 1695 ms 1590 m 790 vs 976 s 6-Methoxypurine [37] IR 750 w 874s…”

Section: Modementioning

confidence: 99%

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

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Purines, pyrimidines, and the corresponding ribose monophosphates are ubiquitous biomolecules involved in several cellular processes-in DNA and RNA, signaling, and energy transactions. In the new and exciting field of DNA-inspired nanostructures, they are used as fundamental building blocks. Unique features of the nucleobases are that several tautomeric states are close in energy and the tautomeric equilibria are sensitive to exocyclic substitution and pH. Knowing the exact structure and tautomer(s) at physiological conditions is crucial to understand the substrate specificities and catalytic mechanisms of the many enzymes for which these nucleobases are substrates. Very few spectroscopic methods can distinguish between tautomers and provide solution structures. Vibrational spectroscopy has long been known to be an excellent tool to obtain reliable information on nucleic acids. However, even when good-quality spectra are available, isotope editing is required to make reliable band assignments and identify structures unequivocally. Density functional theoretical (DFT) methods have become indispensible in assisting the assignment of observed spectra to normal modes, identification of tautomers, and modeling of spectra of isotope-edited molecules. We review the performance of DFT methods in the prediction of nucleobases and their analogs. We find that even with modest basis sets, trends in vibrational spectra can be predicted adequately and guide assignments to normal modes of the molecule. Shifts in band positions induced upon isotope labeling are reproduced more reliably than the band positions. Scaling considerably improves the agreement between the computed and experimental spectra, but accurate prediction of vibrations of exocyclic groups like C O requires that solvent effects are taken into account.

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“…Crystal neutral purine prefers the N7H tautomer due to strong intermolecular interactions [7]. Applications of the inelastic neutron scattering (INS) and Raman spectroscopy to solid purine [8] confirmed the preference of the N7H tautomer. These spectroscopic investigations have been performed in parallel to DFT calculations.…”

Section: Introductionmentioning

confidence: 99%

“…In this case, the interpretation has been based on comparison of the UV photoelectron spectra for purine and for its 7- and 9-methyl derivatives. The CH tautomers have been usually neglected in the tautomeric mixture of neutral purine [8–31]. However, it has been found recently that they become very important for anionic forms of nucleobases, adenine and guanine [34–36], and for uric acid [37, 38].…”

Section: Introductionmentioning

confidence: 99%

Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM)

Raczyńska

Kamińska

2013

J Mol Model

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Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6−311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6−311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.Electronic supplementary materialThe online version of this article (doi:10.1007/s00894-013-1926-5) contains supplementary material, which is available to authorized users.

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Inelastic neutron scattering, Raman spectroscopy and periodic DFT study of purine

Cited by 17 publications

References 13 publications

Reassignment of the Vibrational Spectrum of Benzimidazole

Reassignment of the Vibrational Spectrum of Benzimidazole

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM)

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