Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

Ghomi, Mahmoud; Aamouche, A.; Cadioli, Beniamino; Berthier, G.; Grajcar, L.; Baron, M. H.

doi:10.1016/s0022-2860(96)09471-9

Cited by 25 publications

(45 citation statements)

References 10 publications

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“…We note that both models predict experimental wavenumbers better than the uracil dihydrate model. This is also observed in some bands by Aamouche et al [103] and Ghomi et al, [101] where both the Onsager model and the uracil dihydrate model were used. Also, the use of much higher basis sets in the present work as well as by Giese and McNaughton [100] have yielded better results as against those of Aamouche et al [103] The use of much smaller basis sets MINI-1, STO-3G, and the PM3 method by Florian and Hrouda [98] has reproduced accurately the IR and Raman wavenumbers reported by them in the solid state; this has been achieved through the consideration of a set of scale factors used for different types of force constants.…”

Section: Uracilsupporting

confidence: 62%

“…A wealth of information on the vibrational spectroscopic properties is available for uracil. The IR [98] and Raman [98 -100] spectra in the solid state and aqueous solution, [99,100] NIS spectra, [101] and SERS spectra [99,100] have all been reported. Raman spectroscopic studies of free uracil and modified uracil (2 -β-fluorodeoxyuridine) complexes with uracil-DNA glycosylase (UDG) repair enzyme have been reported.…”

Section: Uracilmentioning

confidence: 99%

“…[102] Supporting theoretical work is done on isolated uracil and uracil-Ag/Au complexes [99,100] in the gas phase [98 -101,103,104] and solvent phase using the Onsager solvation model, as well as a uracil dihydrate complex. [100,101,103] A range of methods like semiempirical and DFT in conjunction with small basis sets like MINI1 and STO-3G to higher basis sets like 6-31++G(d,p) were employed. In addition, IR and Raman spectra of uridine in aqueous solution as well as NIS spectra in solid state [96] and UVRR spectra of deoxyuridine monophosphate (dUMP) at different excitation wavelengths [51] are available.…”

Section: Uracilmentioning

confidence: 99%

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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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Section: Uracilsupporting

confidence: 62%

Section: Uracilmentioning

confidence: 99%

Section: Uracilmentioning

confidence: 99%

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Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Shanmugasundaram¹,

Puranik²

2009

J Raman Spectroscopy

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“…The stability of the superwater systems has been explained according to the binding energies. On the other hand, some relevant vibrational frequencies of uracil have also been calculated for the uracil-water (1/2) supersystem (Ghomi et al, 1997). Fig.…”

Section: Analysis Of Thiazolidine-24-dione-water Complexmentioning

confidence: 99%

A theoretical study on the structure of thiazolidine-2,4-dione and its 5-substituted derivatives in the gas phase. Implications for the thiazolidine-2,4-dione -water complex

Safi

2016

Arabian Journal of Chemistry

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The results of a detailed DFT (B3LYP) investigation on five tautomers of thiazolidine-2,4-dione and their 5-substituted derivatives (ACH 3 , ANH 2 , ACl, AF, ACN-and NO 2 ) are presented here. The energy, geometrical parameters, topological parameters of all species in the gas phase have been calculated at B3LYP6-311++G(3df,2p)//B3LYP/311 + G(d,p) level of theory. The proton affinities (Pas), molecular electrostatic potential (MEP), natural valence atomic orbital energies (NNAO) of the basic center exist in the title compound in the gas phase have been calculated at the same level of theory. The specific hydration of the title compound by one water molecule has been also investigated at the same level of theory. Among the thiazolidine-2,4-dione tautomers and its derivatives, the most stable tautomer corresponds to the diketo forms (A), regardless of the substituent type. Results reveal that the oxygen atom of the carbonyl group at position 2 is more basic than the one at position 4. The existence of different hydrogen bond donor and acceptor centers in these molecules led to different kinds of intermolecular hydrogen bonds (CHAEAEAEO, NAHAEAEAEO and C‚OAEAEAEH) and different kinds of complexes. The stability of the cyclic complexes has been investigated using the analysis of Natural Bond Orbital (NBO), Atoms In Molecules topology, and the thermodynamic data. Results suggest that the water molecule prefers to bind with the oxygen atom, which has low intrinsic character. ª 2015 The Author. Production and hosting by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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“…Higher level methods [Møller-Plesset (MP) calculations] were applied mainly to base residues. 30,32,38,39 Density functional theory (DFT) methods were used for calculations on bases, 40,41 and they have begun to be applied to vibrational calculations on nucleosides. 33,42 Pioneering structural studies on a whole nucleotide were performed with DFT.…”

Section: Introductionmentioning

confidence: 99%

Ab initio Hartree–Fock/6‐31G** calculation on 9‐β‐D‐arabinofuranosyladenine‐5′‐monophosphate molecule: Application to the analysis of its IR and Raman spectra

et al. 2002

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9-beta-D-arabinofuranosyaldenine-5'-monophosphate (5'-ara-AMP) is an arabinonucleotide that has antiviral and antitumor activity. The accurate knowledge of the nature of its vibrational modes is a valuable step for the forthcoming elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT Raman spectra (4000-30 cm(-1)) of 5'ara-AMP and two deuterated derivatives ara-AMP-d(C8) (deuteration in C8) and ara-AMP-d7 (deuteration in C8, amino and hydroxyl groups) are reported. Theoretical vibrational calculations were performed using the Hartree-Fock/6-31G** method. An assignment of the observed spectra is proposed considering the scaled potential energy distribution of the vibrational modes of the 5'ara-AMP molecule and the observed band shifts by deuteration. The scaled ab initio frequencies are in good agreement with the experimental data (<3 cm(-1) SD).

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Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

Cited by 25 publications

References 10 publications

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

A theoretical study on the structure of thiazolidine-2,4-dione and its 5-substituted derivatives in the gas phase. Implications for the thiazolidine-2,4-dione -water complex

Ab initio Hartree–Fock/6‐31G** calculation on 9‐β‐D‐arabinofuranosyladenine‐5′‐monophosphate molecule: Application to the analysis of its IR and Raman spectra

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