A computational study of azaphospholes: anions and neutral tautomers

One hundred and eleven azaphospholes (31 anions and 80 neutral compounds) have been studied theoretically at the B3LYP/6-311++G(d,p) level. Among the analyzed properties, there are the geometries, mainly the non-planarity of the PH tautomers, the isomerism of the anions, the NH/PH tautomerism of neutral compounds, the chemical shifts and spin–spin coupling constants. The aromaticity has been assessed through Schleyer’s NICS values, preferably NICS(1). Finally, we have compared our calculations with previous ones as well as with the available experimental data for the calculated compounds and for related ones.     

Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid bases

Anionic states of nucleic acid bases (NABs) are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated NAB parent anions probed mostly dipole-bound states, which are not present in condensed phase environments. Recently, we demonstrated that very rare tautomers of uracil (U), cytosine (C), adenine (A), and guanine (G), which are obtained from canonical tautomers through N-to-C proton transfers, support valence anionic states. Here we report the photoelectron spectrum of the final member of the NABs series: the valence state of the thymine (T) anion. Additionally, we summarized the work of all five NABs. All of the newfound anionic tautomers of the NABs may be formed via dissociative electron attachment followed by hydrogen atom reattachment to a carbon atom. Furthermore, these unusual tautomers may affect the structure and properties of DNA and RNA exposed to low-energy electrons. The new valence states observed here, unlike dipole bound states, could exist in condensed phases and may be relevant to radiobiological damage.     

A note on a non-empirical molecular orbital study of some cytosine and thymine tautomers

The relative stabilities of a series of cytosine and thymine tautomers have been investigated by means of non-empirical (ab initio) LCAO-MO-SCF Hartree-Fock-Roothaan calculations employing a small contracted Gaussian basis set (STO-3G) in all cases. The relative stabilities of the various tautomeric forms agree in general with the results of earlier empirical and semi-empirical calculations on these molecules. In particular, the “enol forms” of cytosine and thymine, within the isolated molecule approximation inherent in these MO calculations, are predicted to possess greater stability than the forms commonly assigned to these molecules in aqueous solution and found in the solid state by X-ray crystallographic studies.     

Selective conformer detection of short-lived base pair tautomers: A computational study of the unusual guanine-cytosine pairs using ultrafast resonance Raman spectroscopy

Base pair mismatch has been regarded as the main source of DNA point mutations, where minor short-lived tautomers were usually involved. However, the detection and characterization of these unnatural species pose challenges to existing techniques. Here, by using systematic structural and ultrafast resonance Raman (RR) spectral analysis for the four possible conformers of guanine-cytosine base pairs, the prominent marker Raman bands were identified. We found that the hydrogen bonding vibrational region from 2300 cm⁻¹ to 3700 cm⁻¹ is ideal for the identification of these short live species. The marker bands provide direct evidence for the existence of the tautomer species, thus offering an effective strategy to detect the short-lived minor species. Ultrafast resonance Raman spectroscopy would be a powerful tool to provide direct evidence of critical dynamical details of complex systems involving protonation or tautomerization.     

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,     

Theoretical study on the excitation energies of six tautomers of guanine: evidence for the assignment of the rare tautomers

The CASPT2//CASSCF method with the 6-31G basis set and an active space up to (16,12) was used to calculate the excitation energies for six tautomers of guanine. Our calculations provide further support on the recent reassignment of the near-UV resonant two-photon ionization (R2PI) spectrum, in which two rare tautomers of the 7H-oxo-imino form were proposed to replace the previously assigned 7H/9H-oxo-amino tautomers. The adiabatic excitation energies of the 7H-oxo-imino tautomers are calculated to be 0.3-0.5 eV higher than those of the 7H/9H-oxo-amino tautomers. Our calculations also indicate that the missing most stable tautomers (7H/9H-oxo-amino tautomers) in the R2PI experiment is possibly due to the existence of an ultrafast nonradiative deactivation process in the excited-state of these two tautomers.     

Gas-phase stability of tetrahedral multiply charged anions: a conceptual and computational DFT study

Multiply charged anions (MCA's) are unstable relative to electron autoejection; however, the repulsive Coulomb barrier (RCB) provides electronic stability. In view of their interest in biological systems, the behavior of isolated AsO(4)(3-), PO(4)(3-), SO(4)(2-), and SeO(4)(2-) in the gas phase and in solution has been studied. To calculate the RCB values, the electrostatic and point charge model-two methods currently used in the literature-are applied, together with a recently introduced Conceptual Density Functional Theory (DFT) based approach. The relative stability of the above-mentioned MCA's is compared. The trends of the RCB are analyzed by including analogous compounds from the second and third row and by passing from dianionic to trianionic systems. Considering the effect of solvent, using the SCI-PCM solvent model, the evolution of the RCB when passing to higher dielectric constants is evaluated. The RCB is related to the properties of the system as polarizability/softness. Both a numerical and a conceptual correlation between the RCB and the global softness is found.     

A non-empirical molecular orbital study of valence tautomers of C2H3N

The valence tautomers of C₂H₃N have been examined by non-empirical molecular orbital calculations using two split-valence shell basis sets. All geometries were fully optimized using the 4–31G basis set and these structures were then used in 6–31G basis set calculations. The order of stability of the three possible cyclic isomers is 1-azirine > cyclic carbene > 2-azirine. The profiles for conversion of vinylmethylene into cyclopropene, vinylnitrene into 1-arizine, and iminomethylene into 2-azirine have all been shown to have barriers.     

Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

Systematic theoretical investigations on the tautomers of thymine in gas phase and solution

The tautomers of thymine are systematically calculated using various methods. The order of the relative stability, dipole moment as well as solvent effect of the 13 isomers are investigated. The one-step transition process by proton transfer in gas phase and in solution (H₂O or CH₃OH), which acts as both proton donor and acceptor, are exhaustively studied, meanwhile, the internal rotation between two related isomers in the gas phase is also investigated. Furthermore, the energy barrier of each transition is calculated and the results show that both H₂O and CH₃OH could reduce the energy barrier. Comparisons between the activation energies of all the producing processes of each tautomer as well as temperature effect on the producing processes are made. The calculation results also indicated that the diketo is the most stable isomer both in gas phase and in solution, additionally, it is thermodynamically as well as dynamically favored.     

Relative stabilities of weakly coordinating anions: a computational study

This article describes BP86/SV(P) (DFT) calculations on a representative set of weakly coordinating anions (WCAs) of type [M(L)n]-, their parent neutral Lewis acids M(L)(n-1) and their ate complexes with fluoride, that is, [FM(L)(n)](n-1) (M=B, L=F, OTeF5, C6H5, C6F5, C6H3(CF3)2, CF3; M=P, As, Sb, L=F, OTeF5; M=Al, L=OC(CF3)3). Compounds with fluoride bridges, that is, Sb(n)F(5n) and [Sb(n)F(5n+1)]- (n=2, 3, 4), Al2(L)5F and [(L)3Al-F-Al(L)3]- (L=OC(CF3)3), (F4C6[1,2-B(L)2]2, [F4C6[1,2-B(L)2]2F]-, [F4C6[1,2-B(L)2]2OMe]- (L=C6F5) were also calculated. Based on these BP86/SV(P) and auxiliary MP2/TZVPP, G2, and CBS-Q calculations the relative stabilities and coordinating abilities of these WCAs were established with regard to the fluoride ion affinities (FIA) of the parent Lewis acids, the ligand affinity (LA) of the WCAs, the decomposition of a given WCA in the presence of a hard (H+, proton decomposition PD) and a soft electrophile (Cu+, copper decomposition CuD), the position of the HOMO, the HOMO-LUMO gap, and population analyses of the anions providing partial charges for all atoms. To obtain data that is more reliable, the assessed quantities were calculated through isodesmic reactions. If parts of the calculations could not be done isodesmically, higher levels such as MP2/TZVPP, G2, and CBS-Q were used to obtain reliable values for these reactions. Although the obtained results can not be taken as absolute, the relative ordering of the stabilities of all WCAs will undoubtedly be correct, since a single methodology was chosen for the investigation. To include media effects the decomposition reactions of a subset of 14 WCAs with the SiMe3+ and [Cp2ZrMe]+ ions were also calculated in PhCl and 1,2-F2C6H4 (COSMO solvation model). We found that in most cases gas-phase calculations and solution calculations give comparable results for the stability of the anion. Applications of the LA and FIA that allow one to decide, on thermodynamic grounds, which WCA or Lewis acid is the most suitable for a given problem are sketched.     

On isomers and tautomers of Nitro-1-deazapurine: A DFT study

The 1-deazapurine molecules substituted by the NO₂ group at three different positions of the six-membered ring were subject of computational study performed at the B3LYP/cc-pVTZ level. For each substitution three tautomers were considered. The N3H tautomers are relatively instable in the gas and water phases which is due to significant decrease in aromaticity of the N3H forms. In the gas phase, the equilibria between the N7H and N9H tautomers are determined by a competition of the repulsive and attractive intermolecular interaction of different moieties of Nitro-1-deazapurine. The close neighborhood of the two tertiary N atoms and attractive close neighborhood of the tertiary N atom and the NH group result in preference of the N9H tautomer over the N7H one by ca. 3.5 kcal/mol. By comparing energy of different forms and proposed isodesmic reaction we showed that the Gibbs free energy of the attractive interaction between the NO₂ and HN groups is equal to ca. 1.0 kcal/mol, whereas the repulsive interaction between the NO₂ group and the tertiary N atom of the imidazole is equal to ca. 6.4 kcal/mol. It was shown also that the increase in dipole moment in the water media is the crucial effect influencing the N7H/N9H tautomeric equilibria of Nitro-1-deazapurines. For the three isomers dissolved in water, the two tautomers, N7H and N9H, are predicted to be observed and the former should dominate slightly for the 2-Nitro isomer whereas the latter for the 6-Nitro and 1-Nitro isomers. The NBO analysis showed that the NO₂ group withdraws 0.3 e of the σ-electrons from the pyridine ring of 1-deazapurine and has no influence on the σ-electrons of the imidazole ring. The NBO analysis shows also that the ratio between number of π-electrons which are withdrawed from imidazole vs. pyridine ring is characteristic for position of the substitution. The isodesmic reaction used revealed also that the NO₂ group destabilizes the N3H-1-deazapurine system, whereas it stabilizes the N7H- and N9H-1-deazapurine systems.     

UV-induced generation of rare tautomers of 2-thiouracils: a matrix isolation study

Unimolecular photoisomerization reactions were studied for 2-thiouracil, 6-aza-2-thiothymine, 1-methyl-2-thiouracil, and 3-methyl-2-thiouracil isolated in low-temperature Ar matrixes. The IR spectra have revealed that before UV irradiation all the matrix-isolated compounds adopted exclusively the oxo-thione tautomeric form. Upon UV (lambda > 320 nm) irradiation of the matrixes, two oxo-thiol photoproducts were generated for monomeric 2-thiouracil as well as for monomeric 6-aza-2-thiothymine. Generation of these products corresponds to transfer of a proton from either the N(1)-H or N(3)-H group to the sulfur atom of the C(2)=S thiocarbonyl moiety. The first of the above reactions was photoreversible. As a consequence, after prolonged UV irradiation most of the material was transformed into the oxo-thiol-N(1)H form. The hydroxy-thiol tautomers of 2-thiouracil and 6-aza-2-thiothymine were also photogenerated as minor products. For 1-methyl-2-thiouracil and 3-methyl-2-thiouracil, thione --> thiol phototautomeric reactions yielded the oxo-thiol isomers of the compounds. Since these reactions were photoreversible, the final stages of the photoinduced processes corresponded, for both methylated 2-thiouracils, to photostationary states. All the products of the investigated photoreactions were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-311++G(2d,p) level.     

Understanding hydrogenation of the adenine‐thymine base pairs and their anions: A density functional study

The B3LYP/DZP++ approach has been used to investigate the properties of hydrogenated radicals and anions of adenine‐thymine (A‐T) base pairs. Our calculations show that the hydrogenated radicals and anions have relatively high stabilities compared with the single adenine and thymine base. The conformations and hydrogen‐bond interactions of A‐T base pairs have obviously changed once the hydrogen atoms attached to the A‐T base pairs and their anion. As for the hydrogenated A‐T radicals, all of them exhibit relatively high electron affinities and different hydrogenation properties with respect to their components. The process of the bond formations of (C6)‐H (adenine) and (C6)‐H (thymine) are the most favorable in energetics. The two hydrogenation channels have the reaction Gibbs free energies (ΔG°) of ?51.8 and ?54.2 kcal mol^?1, respectively. Also, the calculations on the basis of CPCM model imply that the solvent effect plays an important role in the electron attachment and hydrogenation reactions, and can stabilize the hydrogenated A‐T anions. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Ferrocenyl hetaryl thioketones: A computational study of their conformational stability

In this work, the conformational behavior of ferrocenyl- and hetaryl-functionalized thioketones was studied by means of computational quantum chemical methods. Four hetaryl substituents (furan-2-yl, thiophen-2-yl, selenophen-2-yl, and N-methylpyrrol-2-yl) were taken into account. The conformational space of the four ferrocenyl hetaryl thioketones was explored, and all found conformers were characterized using density functional (B3LYP) and wave function (SCS-MP2) theories. Their stability was explained in terms of intramolecular interactions. Such interactions were described using the methods of natural bond orbitals, “atoms in molecules,” noncovalent interaction index, and localized molecular orbital energy decomposition analysis. The identified conformations essentially differ in the arrangement of hetaryl heteroatom relative to the thiocarbonyl sulfur atom. The furan-2-yl substituent favors an s-trans-like arrangement of its heteroatom, while the remaining hetaryl substituents tend to adopt an s-cis-like arrangement. Such a conformational preference mainly results from the π → π* stabilization between the CS group and the hetaryl ring. Weak intramolecular hydrogen bonding of C H⋯O type was detected in the preferred conformer of ferrocenyl furan-2-yl thioketone. Low-polarity solvents, such as toluene, chloroform, and tetrahydrofuran, have a small effect on the preferred conformers of the four thioketones.     

Effects of microsolvation and aqueous solvation on the tautomers of histidine: a computational study on energy, structure and IR spectrum

Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined. The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent model shows that bare zwitterionic form is more stable than bare canonical form by 1.1 kcal/mol. This energy separation is increased to 2.2 and 3.4 kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with the experiments.     

On the unexpected stability of the dianion of perylene diimide in water--a computational study

It was recently reported (Shirman, J. Phys. Chem. B, 2008, 112, 8855) that the stable dianion of perylene diimide can be prepared in water. Herein, a computational study (using DFT at the M06-2X/6-31++G** level of theory) of this species is presented. It is shown that this dianion is aromatic and that its reaction with water is highly endergonic. The primary cause for this is the stabilization provided by the enhanced aromaticity of the dianion relative to its neutral counterpart. Comparison with other aromatic dianions is also presented.     

Electrochemical study of thymine dimer based on DNA charge transfer

Differential pulse voltammetry was used to study the formation and level of thymine dimer in DNA duplex modified on a gold electrode. The electrochemical signal of methylene blue coupled with ferricyanide can be obtained via DNA mediated electron transfer, which would be blocked during the formation of thymine dimer. DNA duplexes with different sequences differ in the level of thymine dimer under the same UV irradiation. Futhermore, the presence of guanine base directly preceding -TT- can effectively decrease the level of thymine dimer, possibly due to the self-repair process in which guanine participates. The proposed method can be further applied to DNA self-repair analysis.     

Origin of diastereocontrol in the oxy-Michael reactions of delta-lactol anions: a computational and experimental study

The diastereoselectivity in the alkylation and Michael addition of "naked" 6-substituted delta-lactolates has been studied by density functional (B3LYP) calculations with ab initio (MP2) energy refinements. The resulting proposed model for the origins of stereocontrol in this reaction has been tested by experiment. The reactions lead to a high cis diastereoselectivity across the THP ring due to the preference for both the alkoxide and the 6-substituent to sit equatorial in the alkylation transition structure. In the oxy-Michael addition of these lactolates to beta-substituted nitroolefins, we propose that the high diastereoselectivity beta- to the nitro group is a result of a combination of steric, stereoelectronic and solvation factors.