Analysis of electronic-vibrational spectra of uracil,thymine, and cytosine

A theoretical analysis of absorption spectra of uracil, thymine, and cytosine—nucleic acid bases— is carried out. Structural dynamic models of these molecules in their electronically excited states are constructed. On the basis of the calculated vibrational structure of the electronic spectra, different tautomeric forms of these molecules are determined. The possibility of modeling the influence of hydrogen bonds on the electronic-vibrational spectra is shown.     

Fluorescence Properties of Intercalating Neutral Chromophores in Complexes with Polynucleotides of Various Base Compositions and Secondary Structures

Changes in the relative quantum yield and polarization degree of steady-state fluorescence of daunomycin (DM) on its binding to six synthetic single- and double-stranded polynucleotides of various nucleotide compositions were measured over a wide range of molar polymer-to-dye ratios, in solutions of low ionic strength. Guanine base was found to be an effective quencher of DM fluorescence [in the DM–poly(G) complex the intensity of residual emission was ~0.5% of the free dye intensity]. The quenching of DM fluorescence by another purine base, i.e., adenine, was also revealed. But, unlike guanine, adenine exhibits quenching activity when it is in close contact with the DM chromophore, as realized in the complex with single-stranded poly(A). In intercalative complexes with double-stranded nucleic acids, where such contact is lacking, the quenching ability of adenine does not manifest itself, which has been demonstrated with the DM–poly(A) · poly(U) complex. It was found that the interaction with pyrimidine bases does not substantially change the DM quantum yield. The quenching feature of DM fluorescence is identical to that observed earlier by us for a glycoside phenazine dye containing, like DM, a neutral chromophore.     

Investigations of Tautomeric Purine Forms by the Methods of Vibrational Spectroscopy and Resonance Raman Scattering. I. Modeling of the Purine Structure in Different Phase States

In the present work, the methods of vibrational spectroscopy are used to study the occurrence of two tautomeric purine forms in different phase states. It is demonstrated that the N₉H tautomeric purine form is dominant in the isolation matrix, the N₇H tautomer is dominant in the polycrystalline state, and both tautomeric forms coexist in the liquid phase (H₂O solution).     

Investigations of Tautomeric Purine Forms by the Methods of Vibrational Spectroscopy and Resonance Raman Scattering. II. Quantum-Mechanical Calculations of the Resonance Raman Scattering Spectra of Purine Tautomers

The quantum-mechanical analysis of the intensity distribution in the resonance Raman scattering (RRS) spectrum of the purine molecule is presented. Satisfactory agreement between the calculated results and the available experimental data is obtained, and a conclusion is made that both tautomeric forms (P–N₇H and P–N₉H) coexist in polar solvents.     

Quantum-mechanical calculations of the intensity distribution in spectra of adenine tautomers: II. Two-photon absorption spectra

We have performed quantum-mechanical calculations of the two-photon absorption spectra of three tautomeric forms of adenine in the gas phase and of four forms in the aqueous solution. Based on a comparison of the results of these calculations with experimental data, the occurrence of three structures, Ade-N₉,N₁H⁺, Ade-N₉H (am), and Ade-N₇H(am), in aqueous solution of adenine has been confirmed.     

Quantum-mechanical calculations of the intensity distribution in spectra of adenine tautomers: I. Spectra of resonant hyper-Raman scattering

The spectra of resonant hyper-Raman scattering of five tautomeric forms of adenine have been theoretically determined for the first time based on quantum-mechanical calculations in the Herzberg-Teller approximation. The occurrence of three structures, Ade-N₉,N₁H⁺, Ade-N₉H(am), and Ade-N₇H(am), in an aqueous solution of adenine has been established.     

A multinuclear magnetic resonance study of intramolecular hydrogen bonding in some Schiff and Schiff-Mannich bases in solution and in the solid state

Two Schiff bases; N, N′-bis(5-bromosalicylidene)-1,2-diaminoethane, BS, and 7-[(1-{5-bromo-2-hydroxyphenyl} methylidene)amino]-4-methylcoumarin, Sc, and two appropriate Schiff–Mannich bases, N, N′-bis{5-bromo-3-[(diethylamino)methyl]salicylidene}-1,2-diaminoethane, BSM, and 7-[(1-{5-bromo-3-[(diethylamino)methyl]-2-hydroxyphenyl} methylidene)amino]-4-methylcoumarin, SMc, capable of intramolecular hydrogen bonding have been investigated by multinuclear magnetic resonance methods in both solid and liquid phases. In all of the compounds under investigation tautomeric equilibrium involving an intramolecular hydrogen bond has been found. The Schiff–Mannich bases, which can form two different kinds of H bonds at room temperature, form relatively weak H bonds with the imino nitrogen atoms. At low temperatures the tautomeric proton exchange becomes slow on the NMR time scale and both hydrogen-bonded forms can be observed by ¹H, ¹³C, and ¹⁵N NMR methods. In the solid state the tautomeric process is frozen and only one H-bonded form is present. On the basis of 13C and ¹⁵N CPMAS NMR spectra this is identified as the form with hydrogen bonds involving the imino groups. This conclusion is in good agreement with previous results obtained by X-ray diffraction methods.

The investigated Schiff bases (BS and Sc) form relatively weak H bonds. The proton position in the hydrogen bridge, estimated from ¹⁵N and ¹³C chemical shifts, is very similar in both the solution and solid phases. In chloroform solution the observed tautomeric equilibria are almost insensitive to a temperature change within the range 223 to 303 K.     

Calculation and analysis of vibrational spectra of adenine–thymine,guanine–cytosine,and adenine–uracil complementary pairs in the condensed state

We have calculated the frequencies of the normal vibrations of the complementary nucleic acid base pairs adenine–thymine, guanine–cytosine, adenine–uracil, corresponding to the Watson–Crick structure, and the adenine–uracil pair, corresponding to the Hoogsteen structure, in condensed states and we interpret the spectra. We determine the contributions of hydrogen bonds to the vibrational modes of the complementary pairs. We have analyzed the nature of the relative displacements of the nucleic acid bases as integral molecular units along the hydrogen bonds. We show the role of hydrogen bonds in tautomeric interconversions of complementary nucleic acid base pairs. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 76, No. 1, pp. 84–92, January–February, 2009.     

The IR absorption spectrum of 2 - aminothiazolid - 4 - one

A mechanical model has been used to calculate the frequencies in the vibrational spectrum of the imine and amine tautomeric structures for this compound; the IR spectrum for the crystalline state has been deduced for the range 80–3500 cm^–1, and a discussion is given for the effect of the tautomeric prototropic forms on the vibrational spectrum.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii Fizika, No. 9, pp. 76–82, September, 1971.     

The attachment of amino fragment to purine: inner‐shell structures and spectra

The impact of the amino fragment (–NH₂) attachment on the inner‐shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site‐dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N₍₁₎ and C₍₅₎, demonstrate significant electrophilic reactivity (f^? > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C₍₆₎ position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C₍₆₎ position experiences substantial changes in energy and charge transfer, owing to the formation of the C—NH₂ bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH₂ fragment to purine exhibits deeply rooted influences to the inner‐shell structures of DNA/RNA bases. The present study suggests that some fragment‐based methods may not be applicable to spectral analyses in the inner shell.     

Calculation and Analysis of the IR Spectra of Cytosine in Various Phase States

Plane vibrations and intensities of the IR spectra of the ketone and enol forms of cytosine and deuterocytosine in various phase states are calculated and analyzed. It is shown that in a crystalline state and an aqueous solution cytosine forms a hydrogen bond of two types: C₂=O₈...HN₁ and C₂=O₈...HN₁₀, with a stronger intermolecular interaction in both phases being implemented by the hydrogen bonds between the O₈ and N₁ atoms. A satisfactory interpretation of the spectrum of the isolated molecules of cytosine, with the simultaneously existing ketone and enol tautomeric forms, is possible in the presence of the structural isomers of the enol form that differ in the position of multiple bonds.__________Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 72, No. 2, pp. 149–156, March–April, 2005.     

Determination of the tautomeric composition of adenine in the gas phase by vibrational spectroscopy methods: II. Analysis of resonance Raman spectra

The resonance Raman spectra of adenine in the gas phase under excitation with laser radiation at wavelengths of 266, 218, and 200 nm have been investigated experimentally. The quantum-mechanical calculations of the intensity distribution in the resonance Raman spectra of three adenine tautomers are performed in the Herzberg-Teller approximation with the inclusion of the Duschinsky and frequency effects. Conclusions regarding the tautomeric composition of adenine in the gas phase are drawn from comparison of the results of quantum-mechanical calculations with experimental data.     

核酸碱基和核苷的高效液相色谱——表面增强拉曼光谱在线联机分析研究

本文将反相高效液相色谱(RP——HPLC)与表面增强拉曼光谱(SERS)联机,对三个核嘧啶、四个核嘌呤和两个核嘧啶及其核苷混合物进行在线联机分析研究。在流动条件下,对影响 SERS 测定的因素,如激光照射、温度、pH 值、流速、记忆效应,以及联机系统的接口装置等进行了讨论。文中给出了联机测得的三维和二维 SERS 色谱图。     

pH dependent interaction of biofunctionalized CdS nanoparticles with nucleobases and nucleotides: A fluorimetric study

The interaction of DNA bases and corresponding nucleotides with CdS nanoparticles (NPs), biofunctionalized by cysteine, has been investigated by absorption and fluorescence spectroscopy. Unique enhancement effect of adenine, in contrast to other nucleobases, on the luminescence of cysteine capped CdS (cys-CdS) NPs at both pH 7.5 and 10.5 was found, the extent of enhancement being much higher at pH 10.5. At the latter pH, the difference optical absorption spectra show development of new peak at 278 nm with corresponding decrease in the absorption of adenine at 260 nm, which is attributed to binding of adenine anion to the CdS surface through N7 of the purine ring. Appearance of a new band at 478 cm⁻¹ and concomitant shift in the C₈-N₇ vibrations to 1610 cm⁻¹ in the FTIR spectra of cys-CdS NPs with adenine also suggest Cd-N7 binding on the particle surface. Amongst various nucleotides, ATP exhibited maximum luminescence enhancement on CdS NPs for a given change in concentration in the micro-molar range at physiological pH. A quantitative correlation between ATP concentration and PL enhancement of CdS NPs has been established, a step which in future might assist in developing new protocols for fluorescence sensing of adenine nucleotides under certain pathological conditions.     

IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine<Superscript>+</Superscript> with cytosine and thymine: Quantum-chemical study

Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine⁺ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.     

Inner‐shell chemical shift of DNA/RNA bases and inheritance from their parent purine and pyrimidine

Inner‐shell electronic structures, properties and ionization spectra of DNA/RNA bases are studied with respect to their parent pyrimidine and purine species. Density functional theory B3LYP/aug‐cc‐pVTZ has been employed to produce the geometries of the bases, whereas LB94/et‐pVQZ//B3LYP/aug‐cc‐pVTZ is used to calculate site‐related Hirshfeld charges and core (vertical) ionization energies, as well as inner‐shell spectra of C1s, N1s and O1s for DNA/RNA bases and their parent pyrimidine and purine species. The site‐dependent variations of properties indicate the changes and inheritance of chemical environment when pyrimidine and purine become substituted. In general, although the changes are site‐dependent, they are also ring‐dependent. Pyrimidine bases change less significantly with respect to their parent pyrimidine than the purine bases with respect to their parent purine. Pyrimidine bases such as uracil, thymine and cytosine inherit certain properties from their parent pyrimidine, such as the Hirshfeld charge distributions and the order of core ionization energy level etc. No particular sites in the pyrimidine derivatives are engaged with a dramatic chemical shift nor with energy crossings to other sites. For the core shell spectra, the purine bases inherit very little from their parent purine, and guanine exhibits the least similarities to the parent among all the DNA/RNA bases.     

6-Thioguanine luminescence probe to study DNA and low-molecular-weight systems

6-Thioguanine, an antitumor drug, has been tested as a luminescence probe to study DNA and cryoprotector solutions at temperatures between 4.2 and 273 K. The electronic structure of the tautomeric and ionic forms of 6-thioguanine is studied comprehensively both theoretically and experimentally. An excited-state diagram of 6-thioguanine N9H tautomer is proposed. The temperature behavior of 6-thioguanosine is examined in different cryoprotector solutions and with different aggregate states of solvents. Structure and phase transitions in low-molecular-weight cryoprotectors (glycerol, ethanol, propanediol, DMSO) and their water solution are investigated in the 4.2–273 K temperature range. New structural transitions in propanediol-water solutions are found in the temperature interval 10–180 K. DNA solutions are investigated by using 6-thioguanine incorporated in DNA by the method of biosynthesis. Phosphorescence intensity curves for 6-thioguanosine in native DNA manifest peculiarities at 21, 64, 87, 140, 180, and 268 K.     

Infra-Red Study of Tautomerism in Some Schiff Bases.

Infra-Red spectra of a series of substituted salicylaldehyde and 2-hydroxy-naphthaldehyde Schiff bases were used to investigate enol-keto tautomeric equilibrium. Two model compounds, namely, salicylidinaniline and naphthylidinequinolineamine Schiff bases were used to represent the enol and keto forms, respectively. From the IR spectra of the model compounds it was possible to assign the IR absorption for the C=O and the C=N groups in both the keto and the enol form. It was also possible to assign other absorptions which were either specific to the keto or the enol forms. Specific pattern were observed for all the studied compounds.     

Prototropy and π‐electron delocalization for purine and its radical ions – DFT studies

Complete tautomeric equilibria and π‐electron delocalization were studied at the B3LYP/6‐311+G** level for neutral purine ( P ) and its charged radicals ( P ^+? and P ^??). All possible nine tautomers (four NH and five CH forms) and all possible 36 tautomeric equilibria (six NⁱH → N^kH, twenty NH → CH, and ten CⁱH → C^kH conversions) were considered. The greatest variations of the tautomeric equilibrium constants (as pK_T) were observed for the NH → CH conversions when proceeding from neutral to reduced purine ( P + e → P ^??). These variations completely change the tautomeric preferences. One‐electron oxidation ( P ? e → P ^+?) has considerably smaller effect on the pK_T values and does not change the tautomeric preferences. π‐Electron delocalization depends on the position of the moving proton and on the type of the electron transfer. For individual tautomers, some linear relations between the relative stabilities and the HOMA (harmonic oscillator model of aromaticity) indices occur for neutral and oxidized purine. For reduced purine, a scatter plot is found. Copyright © 2010 John Wiley & Sons, Ltd.     

Computational prediction of vibrational spectra of normal and modified DNA nucleobases

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. Copyright © 2009 John Wiley & Sons, Ltd.