Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

A new theoretical prediction of the infrared spectra of cytosine tautomers

The infrared spectra of the cytosine amino-oxo and amino-hydroxy tautomers predicted theoretically at the ab initio Hartree—Fock level with a 6-31G** basis set are reported. These are compared with the experimental spectra obtained in an argon low-temperature matrix. The IR spectra computed at this level reproduce the experimental spectra closer than the previous predictions.     

Matrix isolation studies of cytosine: The separation of the infrared spectra of cytosine tautomers

The i.r. spectral studies of cytosine and its d₃-deuterated derivative isolated in Ar and Ne matrices are reported. The amino-hydroxy and the amino-oxo tautomeric forms dominate in matrices. Separation of the i.r. spectra of the two tautomers was based on observation of spectral changes following u.v. irradiation of the matrix. Detailed analysis and interpretation of the spectra was performed.     

Quantum chemical investigations of charge transfer interactions in relation to the electronic theory of cancer. IV. The interaction of formamide and the enol tautomers of several glyoxals

The results of ab initio “supermolecule” calculations of the charge transfer between formamide and the enol forms of methylglyoxal, ethylglyoxal, dimethylglyoxal, and propenylglyoxal are compared for several different conformations of the constituent molecules. The enols were found to be poorer electron acceptors than their respective keto isomers.     

The electronic absorption spectra and the electronic structures of cytosine,isocytosine, and their anions and cations

The electronic absorption spectra of cytosine and isocytosine have been measured in several solvents at room temperature, and the temperature and pH dependencies of the electronic absorption spectra in aqueous solution have also been examined, special attention being paid to the existence of tautomeric forms. Consequently, it is concluded that cytosine in aqueous solution takes 2-keto-6-amino (3H) form (I) at room temperature, but with rising temperature 2-keto-6-imino form (III) coexists with form I, the latter being determined to be more stable by 5.5 kcal/mole than the former, and that cytosine takes form I and form III in trimethyl phosphate and in acetonitrile, respectively. The change in stability of the tautomeric forms by different solvents has been discussed with regard to their calculated dipole moments due to-electrons and the polarity of the solvents.The-electron structures of several tautomeric forms of cytosine (5 tautomeric forms) and isocytosine (3 tautomeric forms) and of their ions have been calculated by combining the configuration interaction with the Pariser-Parr-Pople SCF MO method. The transition energies, oscillator strengths,-electron densities,-bond orders and dipole moments have been evaluated. Concerning the transition energy and oscillator strength, the comparison has been made between the theoretical and observed values, showing that the agreement between them is improved in the present calculation compared with previous calculations.

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Zusammenfassung Die Elektronen-Absorptionsspektren von Cytosin und Isocytosin wurden in verschiedenen Lösungsmitteln bei Raumtemperatur gemessen; in wäßriger Lösung wurden auch Temperatur und pH-Abhängigkeiten untersucht, wobei besonders auf die Existenz von Tautomeren geachtet wurde. Es ergab sich, daß Cytosin in wäßriger Lösung bei gewöhnlicher Temperatur in der 2-Keto-6-amino-Form vorliegt, aber bei steigender Temperatur daneben auch die 2-Keto-6-imino auftritt. Letztere dürfte etwa 5,5 Kcal/Mol stabiler sein. Cytosin in Trimethylphosphat und Acetonitril liegt in Form I bzw. Form II vor. Die unterschiedlichen Stabilitäten in verschiedenen Lösungsmitteln wurden in Hinblick auf die berechneten Dipolmomente, die vom-Elektronensystem und der Polarität des Lösungsmittels herrühren, diskutiert.Die-Elektronenstrukturen von fünf tautomeren Formen von Cytosin und von Isocytosin (drei tautomere Formen) sowie von deren Ionen wurden mittels einer Kombination von Konfigurationswechselwirkung und PPP-SCF-MO-Verfahren berechnet. Übergangsenergien, Oszillatorenstärken,-Elektronendichten und Bindungsordnungen sowie Dipolmomente wurden berechnet, wobei sich bei den beiden ersten Größen Verbesserungen gegenüber früheren Rechnungen ergaben.

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Résumé Les spectres d'absorption électronique de la cytosine et de l'isocytosine ont été obtenus à température ambiante dans différents solvants; en milieu aqueux la dépendance de la température et du pH a été étudiée, permettant des conclusions sur les problèmes de tautomérie. Il apparaît qu'en milieu aqueux, à température ordinaire, la cytosine se trouve sous la forme 2-céto, 6-amino, mais qu'à température plus élevée elle se trouve aussi sous la forme 2-céto,6-imino. Cette dernière est plus stable d'environ 5,5 Kcal/Mol. Un équilibre analogue se produit dans le triméthylphosphate et l'acétonitrile. Les différentes stabilités dans les différents solvants sont discutées en fonction des moments dipolaires calculés, qui proviennent du système d'électrons et de la polarité du milieu.La structure électronique de cinq formes tautomères de la cytosine et de trois formes tautomères de l'isocytosine ainsi que des ions correspondants a été calculée par une méthode S.C.F. M.O. P.P.P. avec I.C. Les énergies de transition, les forces d'oscillateur, les charges et les indices de liaison des électrons sont calculés, avec de meilleurs résultats que ceux obtenus précédemment pour les deux premières grandeurs.

     

Structure and electronic spectra of 2-phenylbenzimidazoles. Quantum chemical analysis of the intramolecular hydrogen bond

Institute of High-Molecular-Weight Compounds, Russian Academy of Sciences. Leningrad State University Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 5, pp. 20–27, September–October, 1992.     

C~6~0SiH~2的结构和电子光谱的量子化学研究

用INDO系列方法研究了C~6~0SiH~2的两种结构: 一是SiH~2加在两个六元环之间的键上形成C~2~v构型; 另一是SiH~2加在一个五元环和一个六元环之间的键上形成C~s构型。从总能量和LUMO-HOMO能级差看, C~6~0SiH~2的稳定结构应是C~2~v构型, 其中桥C(15)-C(30)的键长为0.1508nm, 键序为0.9369, 说明不开环, 形成类环丙烷结构。文中计算了两种构型的电子吸收光谱和NMR谱, 此类计算是基于对C~6~0SiH~2的等电子体C~6~0O和C~6~0CH~2的研究之上, 且后两者的研究结果与实验相一致。     

嘧啶及其异构体的密度泛函理论研究

胞嘧啶、尿嘧啶和胸腺嘧啶都有酮式和烯醇式互变异构。有人认为DNA的错配频率,与酮,烯醇或氨,亚氨的互变异构平衡有关。迄今,在相同理论水平上同时对三种嘧啶互变异构体进行理论计算研究的文献较少,     

Quantum chemical investigation of the electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene)

The electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene) molecule is calculated by the semiempirical CNDO/S3 method. The calculated Wiberg indices and the additive occupancies of interatomic bonds determine the structural formula, which includes the C=C and C=O conjugated double bonds and corresponds to the name of the compound. Polarization of C=O bonds and πelectron conjugation do not lead to a zwitterionic structure with positive aromatic fourmembered cycles. The indices and occupancies of carboncarbon bonds 1– 3 and 2– 4 are σelectronic, negative, and negligibly small. The band structure corresponds to strong electronaccepting properties of the polymer; the MO of the bottom of the lowlying vacant band contains 2pπorbitals of all atoms of the compound. The occupied π-electronic bands do not overlap, and their widths are relatively small. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 5, pp. 781–786, September–October, 1998.     

Disentangling intrinsic ultrafast excited-state dynamics of cytosine tautomers

Gas-phase ultrafast excited-state dynamics of cytosine, 1-methylcytosine, and 5-fluorocytosine were investigated in molecular beams using femtosecond pump-probe photoionization spectroscopy to identify the intrinsic dynamics of the major cytosine tautomers. The results indicate that, upon photoexcitation in the first absorption band, the cytosine enol tautomer exhibits a significantly longer excited-state lifetime than its keto and imino counterparts. The initially excited states of the cytosine keto and imino tautomers decay with sub-picosecond dynamics for excitation wavelengths shorter than 300 nm, whereas that of the cytosine enol tautomer decays with time constants ranging from 3 to 45 ps for excitation between 260 and 285 nm.     

The effect of hydrogen bonding on structural parameters I: An ab initio study of the keto and enol tautomers of formamide and their hydrogen bonded dimers

In order to study the variation of CO and CN bond lengths as functions of the hydrogen bond length, a series of ab initio calculations have been performed on the keto and enol tautomers of formamide. The formation of hydrogen bonds leads to an increase in the conjugation of the NCO fragment. This increase is expressed as a lengthening of the double bonds and a corresponding shortening of the single bonds. These changes are found to vary with the length of the hydrogen bonds and analytical expressions for these variations of the bond lengths have been derived. The potential functions for dimerization, i.e. formation of, respectively, two N-H ·· O and two O-H ·· N hydrogen bonds have also been found. The results obtained indicate significant differences between the two types of hydrogen bonds.     

Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine

In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86. We have also explored the correlations between the Kohn-Sham orbitals of the different tautomers at the BP86/QZ4P and SAOP/QZ4P levels. Finally, we discuss implications of the existence of the tautomeric forms of adenine for the DNA replication.     

Quantum chemical calculation of force constants and vibrational spectra

As a result of the development of direct derivative methods and improved computational facilities, ab initio quantum chemical calculations have become an increasingly important source of information for the determination of molecular force constants. Within the Hartree-Fock (H-F) SCF model and using moderate size basis sets such calculations are now economically feasible for molecules of up to 2o–3o atoms. At this level of theory, harmonic diagonal force constants are overestimated by 1o–3o%, corresponding to 5–15% in the frequencies. However, the largely systematic errors can be accounted for by simple empirical corrections. The resulting SQM (Scaled Quantum Mechanical) force fields are probably the most reliable ones available at present for larger molecules. Calculated infrared intensities are semi-quantitatively correct. Beyond the H-F model, large scale calculations including electron correlation give great improvements in the force constants, but there are still residual errors of a few percent.     

Optimum geometries and relative energies for cytosine,thymine, uracil,the imino tautomer of cytosine,the enol tautomer of thymine,and the enol tautomer of uracil by the MINDO/2 SCF MO method

A MINDO /2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, ?9.0, and ?14.2 kcal/mol for C?C*, T?T*, and U?U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO /2.     

DFT studies on the favored and rare tautomers of neutral and redox cytosine

The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311+G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo –OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino- and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.     

Fast atom bombardment mass spectra of keto acid and keto ester phosphoranes

Positive-ion fast atom bombardment mass spectra of 13 keto acid and keto ester phosphoranes were examined. All compounds gave a protonated molecular ion and characteristic peaks at m/z 303, 279, 262 and 201.     

Quantum chemical investigation on solvation of Ginkgolides

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气态烯丙醇光异构化反应的理论研究

本文采用自洽场分子轨道UHF/6-31G从头计算法, 辅以能量梯度法研究气相烯丙醇光异构化反应的机理。全部优化了T1态势能面上反应物、过渡态、中间体和产物的几何构型。基于Fukui提出的内禀反应坐标理论(IRC)计算这一体系的反应途径, 并针对各驻点进行MP2/6-31G的相关能校正, 得到该反应在激发态进行并为一经历双自由基中间体的分步反应的结论。支持了实验工作者提出的机理。