Molecular Vibrations of Solvated Uracil. Ab Initio Reaction Field Calculations and Experiment

Ilich, Predrag; Hemann, Craig; Hille, Russ

doi:10.1021/jp9706285

Cited by 35 publications

(60 citation statements)

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“…Protonations at the N and C atoms in 1 are less favorable than at the O atoms. According to in vacuo calculations [30], the ratio of equilibrium constants of the formation of protonated uracil-O 8 and uracil-O 7 is ϳ 10 8 , while in an aqueous medium this ratio is predicted to be in the range (1.4 -2) ϫ 10 4 . This may suggest that 1a would be the predominant structure formed by electrospray and in equilibrium measurements.…”

Section: Uracil and Thymine And Their Nucleosidesmentioning

confidence: 99%

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Wincel

2009

J. Am. Soc. Mass Spectrom.

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Thermochemical data, ⌬H o n , ⌬S o n , and ⌬G o n , for the hydration of protonated nucleic acid bases and protonated nucleosides have been experimentally studied by equilibrium measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion-beam reaction chamber. For protonated nucleobases the hydration enthalpies were found to be similar for all studied systems and varied between 12.4 -13.1 kcal/mol for the first and 11.2-11.5 kcal/mol for the second water molecule. While for protonated nucleosides the water binding enthalpies (11.7-13.3 kcal/mol) are very close to those for protonated nucleobases, the entropy values are "more negative." The structural and energetic aspects of hydrated ions are discussed in conjunction with the available theoretical data. (J Am Soc Mass Spectrom 2009, 20, 1900 -1905) © 2009 American Society for Mass Spectrometry N ucleic acid bases are amongst the primary building blocks of DNA and RNA, and water is generally considered to be their integral part. Hydration of nucleobases is crucially important for the structure, stability, and biologic functions of DNA [1,2]. Interaction between the DNA constituents and water molecules is important for a better understanding of the mechanistic role of water molecules in conformational transitions and mechanisms of DNA's bioactivity. The effect of hydration of the DNA bases is very local and only a limited number of water molecules contribute to it significantly [1,2]. Many studies on the gas-phase interactions of neutral and anionic forms of nucleic acid bases [3][4][5][6][7][8][9][10][11][12][13] [19] of hydrated adenine and thymine cations. Much less attention has been paid to the hydration of protonated DNA components, although these forms are of considerable interest in view of their potential formation in radiation-induced damage of DNA and RNA, and interaction with a water environment. To our best knowledge, the stabilities of protonated adenine tautomers and their complexes with water molecules [20] have only been investigated computationally, while there have been some experimental and theoretical studies on the hydration of protonated and deprotonated forms of the four mononucleotides (dAMP, dCMP, dGMP, and dTMP) [21]. More recently, the possible tautomeric forms of the monohydrated protonated uracil have been examined in the gas phase by using IR multiple-photon dissociation spectroscopy (IR-MPD) in combination with computational study [22].In this paper, we present the first experimental results on the energetics of hydration of protonated nucleic acid bases, NABs (uracil, Ura; thymine, Thy; adenine, Ade; and hypoxanthine, Hyp), and protonated nucleosides, NSDs (uridine, Urd; thymidine, Thd; adenosine, Ado; and inosine, Ino). These results were obtained from high-pressure mass spectrometry equilibria measurements in the gas phase. Previously, we measured the energetics of hydration of protonated and deprotonated amino acids [23][24][25]. ExperimentalAll experiments were performed on a high-pressure (HP...

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Section: Uracil and Thymine And Their Nucleosidesmentioning

confidence: 99%

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Wincel

2009

J. Am. Soc. Mass Spectrom.

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“…[23][24][25] For Uracil and lumazine were purchased from SIGMA. Violapterin was isolated as product from the cases of lumazine and violapterin anions, 8w16…”

Section: Methodsmentioning

confidence: 99%

“…24 Accordingly, we assumed the latter frequency ordering for carThe program's output includes ground and excited state potential surfaces, a minimum energy geombonyl stretches of lumazine and violapterin anions. While we were able to maintain the same etry, vibrational frequencies, IR intensities, and normal mode descriptions.…”

Section: Ftir Ftir Spectra Of Dmso Solution Samples Dmso Solution Ftimentioning

confidence: 99%

“…In all cases, pargroups, respectively, of uracil, lumazine, and violapterin. 24 from a structural analogue, uracil. in the program was wrong and corrected this.…”

Section: Ftir Ftir Spectra Of Dmso Solution Samples Dmso Solution Ftimentioning

confidence: 99%

“…5 Thus, the extent to which the results In order to properly represent the structures of the anionic species in the QCFF/PI calculation, are comparable, and the question of whether vibrations of the Mo-pterin itself are also present it is also important to determine the most acidic of the amide hydrogens in both lumazine and in the result of Oertling and Hille, 5 are not yet established, and will also be facilitated by the violapterin. Ab initio calculations by Ilich et al [24][25] on heterocycles uracil, lumazine, and xanpresent study.…”

Section: Introductionmentioning

confidence: 95%

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FTIR characterization of heterocycles lumazine and violapterin in solution: Effects of solvent on anionic forms

Michaud¹,

Herrick²,

Duplain³

et al. 1998

Biospectroscopy

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Fourier transform infrared (FTIR) spectra have been obtained from solution samples of the heterocycles uracil, lumazine, and violapterin and reveal interpretable carbonyl stretching frequencies. Spectra of conjugate bases of lumazine and violapterin demonstrate decreases in these carbonyl stretching frequencies upon ionization. Based on isotopic shifts from amide deuterated analogs, semiempirical QCFF/PI calculations were used to assign the vibrational frequencies in the region 1100–1800 cm−1 observed from samples in dimethylsulfoxide (DMSO) and aqueous solutions to specific normal modes. The observed deuterium shifts and the calculations suggest that, in some cases, N—H bending motions are coupled to the C=O stretching motions of the pyrimidine ring. These data suggest that for lumazine anions a change in solvent can significantly change the mixing of the N—H bending and C=O stretching vibrational motions. This implies that vibrational analysis for lumazine species in relatively noninteracting media like nonpolar solvents, mulls or pellets cannot necessarily be transferred to the system when it is dissolved in a polar, hydrogen‐bonding solvent such as water. Although other explanations can be offered, our vibrational analysis suggests that the changes in normal mode composition of the predominantly C=O stretching vibrations of lumazine anion on going from dimethylsulfoxide to water solution are consistent with a change in the predominant tautomer of the heterocycle. This change appears to correspond to a shifting of the location of the remaining acidic proton to a different ring nitrogen atom. This interpretation is of interest in view of recent ab initio calculations which suggest that proton shifts may occur during the hydroxylation of lumazine as mediated by the enzyme xanthine oxidase. © 1998 John Wiley & Sons, Inc. Biospectroscopy 4: 235–256, 1998

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All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

2000

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Empirical force‐field calculations on biological molecules represent an effective method to obtain atomic detail information on the relationship of their structure to their function. Results from those calculations depend on the quality of the force field. In this manuscript, optimization of the CHARMM27 all‐atom empirical force field for nucleic acids is presented together with the resulting parameters. The optimization procedure is based on the reproduction of small molecule target data from both experimental and quantum mechanical studies and condensed phase structural properties of DNA and RNA. Via an iterative approach, the parameters were primarily optimized to reproduce macromolecular target data while maximizing agreement with small molecule target data. This approach is expected to ensure that the different contributions from the individual moieties in the nucleic acids are properly balanced to yield condensed phase properties of DNA and RNA, which are consistent with experiment. The quality of the presented force field in reproducing both crystal and solution properties are detailed in the present and an accompanying manuscript (MacKerell and Banavali, J Comput Chem, this issue). The resultant parameters represent the latest step in the continued development of the CHARMM all‐atom biomolecular force field for proteins, lipids, and nucleic acids. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 86–104, 2000

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Molecular Vibrations of Solvated Uracil. Ab Initio Reaction Field Calculations and Experiment

Cited by 35 publications

References 91 publications

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase

FTIR characterization of heterocycles lumazine and violapterin in solution: Effects of solvent on anionic forms

All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

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