Vibrational spectroscopy investigation using <i>ab initio</i> and density functional theory on flucytosine

Sujatha, S.; Gunasekaran, S.; Muthu, S.; Kumaresan, S.; Arunbalaji, R.

doi:10.1002/jrs.1808

Cited by 51 publications

(10 citation statements)

References 17 publications

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“…[113] In flucytosine, the fluoride substitution has a pronounced effect, upshifting the band by 38 cm −1 (Raman). [112] However, opposite shifts are seen in the NH 2 scissoring band upon substitution at different positions. There is coupling in this vibration to the phosphate group as well.…”

Section: Cytosinementioning

confidence: 89%

“…Seshadri et al [112] have reported a vibrational spectroscopic analysis of flucytosine for the first time, using HF and DFT methods with the 6-31G(d,p) and 6-311G(d,p) basis sets to characterize its IR and Raman spectra. The C 2 O carbonyl stretching mode has been predicted at 1682 cm −1 by B3LYP/6-311G(d,p).…”

Section: Flucytosinementioning

confidence: 99%

“…a UVRR wavenumber from Wen and Thomas. [59] Guanine [52,56] Raman 1675 w --1602vw 1542 m 879vw 603vw 649 vs Guanosine [58,59] UVRR 1685 w --1643 w 1575 m 670 w GMP [60] UVRR 1681 w --1602 m 1576 m 671vw 8-oxodG [60] UVRR 1677vw -1715 w 1610s 1601s 1455 m 1445 m -IR 1681 vs -1705s 1594 vs -605vw 7-Allyl-8-oxodG [60] UVRR 1674 w -1706 m 1605 vs 1455 m 1433 m 613vw IR 1676 vs -1704 vs 1596s 611 w Xanthine [92] IR 1658 1700 vs --1567 ms 538s Raman 1600 ms 1685 ms --1560s 547 ms Hypoxanthine [74,77] Raman 1691m ---735 vs Inosine [80] UVRR 1688 ---2 -Deoxyinosine [85] IR 1719s ---1592vw 843 w 719vw 725vw,sh Raman 1689 m ---1591vw 842 vs 719 vs 724 vs IMP [116] UVRR 1684 w ---1462 w 724 m Allopurinol [78,79] IR 1701s ---1434 w -536m Raman 1696 m ---719 vs Caffeine [87,92] IR [51] UVRR 1652 m 1605 w -782 vs anionic HO 5 dCyt [15] UVRR 1628 m 1615 m -1-Methylcytosine [118] Raman 1648 w -777 vs 5-Methylcytosine [118] Raman 1655 m 1,5-Dimethylcytosine [118] Raman 1665 w -Flucytosine [112] IR 1683 vs, 1671 vs 1651ov 898 m Raman 1679 m 1646 w 901 w 4-Aminopyrimidine [109] IR -1611 w 1584 817 w -988s ADHP [110] IR 1698s 840 m -DAHNP [111] Raman -1693 w, 1664vw --Coupled mode is given in bold face. ν, stretching; γ , out of plane bending; bre, breath; vs, very strong; s, strong; m, medium; w, weak; vw, very weak; sh, shoulder; ov, overlapped.…”

Section: Modementioning

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: Cytosinementioning

confidence: 89%

Section: Flucytosinementioning

confidence: 99%

Section: Modementioning

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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“…Literaturesurvey, points out that a complete quantum mechanical calculation for the selected title compound has not yet been reported so far. Quantum chemical calculations, and molecular modeling are playing a major role for drug design and research vibrational spectroscopy [ 8 , 9 , 10 , 11 ]. To find the structural information, functional groups, and other quantum level parameters, FT-IR, FT-Raman, NMR,UV-Visspectroscopyusing density functional theory (DFT) approaches are followed.…”

Section: Introductionmentioning

confidence: 99%

Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies

Rahuman¹,

Muthu²,

Raajaraman

et al. 2020

Heliyon

Self Cite

101

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Extensive quantum chemical calculation have been carried out to investigate the Fourier Transform Infrared(FT-IR), Fourier Transform Raman(FT-RAMAN) and Nuclear magnetic resonance(NMR), and Ultra Violet-Visible(UV-vis) spectra of 2-(4-Cyanophenylamino) acetic acid. The molecular structure, fundamental vibrational frequencies and intensities of the vibrational bands were interpreted with the aid of optimizations and normal coordinate force field calculations based on density functional theory (DFT) and ab initio HF methods with 6–311++G(d,p) basis set. The theoretical vibrational wavenumbers are compared with the experimental values. The calculated HOMO-LUMO energies were found to be-6.2056 eV and -1.2901 eV which indicates the charge transfer within the molecule. Natural bond orbital analysis has been carried out to explain the charge transfer (or) delocalization of charge due to the intra molecular interactions. Molecular Electrostatic Potential (MEP), First order hyperpolarizability, and Fukui functions calculation were also performed. The thermodynamic properties of the title compound were studied for different temperatures. Molecular docking studies were made on the title compound to study the hydrogen bond interactions and the minimum binding energy was calculated.

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“…In addition, SERS was employed to determine the orientation of molecules on a metal surfaces. Such fundamental molecular structure studies were carried out for: 3,5-pyrazoledicarboxylic acid and its Ce(III) and Nd(III) complexes, 94 the bis(perfluoroethanesulfonyl)imide anion (BETI , 95 5-aminoorotic acid and its new lanthanide(III) complexes, 96 5-sulphosalicylic acid dihydrate, 97 3,5-dinitrosalicylic acid, 98 self-assembly complexes of bis(pyrrol-2-ylmethyleneamine) ligands linked by alkyl spacers with Cu(II) 99 thymine, uracil and their isotopomers, 100 the nonlinear optical chromophore p-bromoacetanilide, 101 1,3-disilabutane (SiH 3 CH 2 SiH 2 CH 3 , 102 dihaloheptasilanes X 2 Si[SiMe(SiMe 3 2 ] 2 with X = F, Cl, Br, 103 5-bromouracil, 104 uracilyl-pyridinium mesomeric betaine, 105 flucytosine, 106 the food additivesˇ-hydroxy-ˇ-methylobutanoic acid (HMB), L-carnitine, and N-methylglycocyamine (creatine), 107 clioquinol and its Cu(II) complex, 108 4-mercaptopyridine aqueous solution and 4-mercaptopyridine/Ag complex system. 109…”

Section: Vibrational Studies In Chemistry Combined Raman Infrared Smentioning

confidence: 99%

Recent advances in linear and nonlinear Raman spectroscopy II

Kiefer

2008

J Raman Spectroscopy

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Following the first review on recent advances in linear and nonlinear Raman spectroscopy, the present review summarizes papers mainly published in the Journal of Raman Spectroscopy during 2007. This serves to give a fast overview of recent advances in this research field as well as to provide readers of this journal a quick introduction to the various subfields of Raman spectroscopy. It also reflects the current research interests of the Raman community. Similar reviews of highly active areas of Raman spectroscopy will appear in future issues of this journal.

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Vibrational spectroscopy investigation using ab initio and density functional theory on flucytosine

Cited by 51 publications

References 17 publications

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies

Recent advances in linear and nonlinear Raman spectroscopy II

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