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 DFT study of the structures of pyruvic acid isomers and their decarboxylation

Pyruvic acid and its isomers, including the enol tautomers and enantiomeric lactone structures, have been investigated at the B3LYP/6-311 + + G(3df,3pd) level, and it is found that a keto form with trans C(methyl)C(keto)C(acid)O(hydroxyl) and cis C(keto)C(acid)OH, and with one methyl hydrogen in a synperiplanar position with respect to the keto oxygen, is the most stable. This agrees with previous theoretical and experimental determinations. However, no minimum corresponding to protonated pyruvate could be located, although previous semiempirical calculations had found such structures. Decarboxylation by different possible routes was then studied. It was found that the direct formation of acetaldehyde, the most stable of the resulting C2H4O isomers, via a four-center-like transition state is the most feasible, although there is a high activation barrier of 70 kcal mol(-1). In contrast to semiempirical calculations, it is found that no hydroxyethylidene-carbon dioxide complex exists as a product, and no transition state leading to the dissociation to hydroxethylidene could be located.     

Tautomerism and isomerism of guanine–cytosine DNA base pair: Ab initio and density functional theory approaches

The relative stabilities of guanine–cytosine (G–C) DNA base pairs are theoretically investigated with a focus on the keto–enol tautomerism as well as on the cis–trans enol isomerism by using both ab initio method and the density functional theory. The G–C pairs of the keto tautomers turn out to be in general more stable than those of the enol tautomers, 9H-guanine pair, 9KK (see the notation below), being the most stable one. The stability of the G–C pairs appears to be affected by various factors including the keto–enol tautomerization, cis–trans enol isomerization, and the steric hindrance between two tautomeric pairs. Although the B3LYP calculations tend to underestimate the binding energies, in addition, it is shown that the binding energy of G–C pairs interacting through hydrogen bonds can be reasonably calculated with the DFT method, contrary to the base pairs with stacked configurations.     

DFT,AIM, and NBO analyses of 1-methyl-2-thioxoimidazolidin-4-one tautomers and their complexes with iodine

Thioimidazoline derivatives can be used to treat hyperthyroidism due to their ability to make complexes with iodine. In this research designed to find new structures with the same ability, 1-methyl-2-thioxoimidazolidin-4-one (MTIO) and the structures of MTIO tautomers (5 tautomers), their isomers (total 9 isomers) and their complexes with iodine are optimized using the B3LYP method with two different basis sets to obtain their molecular parameters, relative energies, and vibrational frequencies. The relative energies show that in all tautomers and complexes, ketone and thione forms are more stable than enol and thienol forms, and also Z isomers are more stable than E isomers. Moreover, the NBO calculation is carried out for tautomers and complexes to obtain atomic charges and acceptor-donor interactions. These results confirm the ability of MTIO tautomers to form complexes and show that the planar complexes have more effective interaction than the perpendicular complexes. The essence and important complexation properties are also calculated and confirmed using the AIM analysis.     

Theoretical Study of the Intramolecular Proton Transfer in the Tautomers of Cytosine Assisted by Water

Ab initio MP2 and DFT studies on the tautomers of cytosine and the related hydrated tautomers have been carried out. The ground‐state structures of four tautomers of cytosine and related transition states were fully optimized. The vibrational frequency analysis was performed on all the optimized structures. Detailed intrinsic reaction coordinate (IRC) calculations were carried out to guarantee the optimized transition‐state structures being connected to the related tautomers. We obtained the relative stability order for the tautomers of cytosine and the related hydrated tautomers. In the isolated and hydrated condition, the bond types of C(2) O(7) and C(4) N(8) greatly affect the stability of the cytosine tautomers. Moreover, we have explored the influence of the water molecules on the intramolecular proton transfer between the keto and enol forms of the cytosine tautomers. The first water molecule obviously decreases the isomerization activation energy for the monohydrated cytosine tautomers. It is shown that the isomerization energy barrier changes only a little when the second and third water molecules are added in the reaction loop. The solvent effects have an obvious influence on the proton‐transfer barrier of the isolated cytosine. However, the solvent effects seem to be insignificant for the isomerization energy barriers of the monohydrated, dihydrated and trihydrated cytosine. The water molecule in these complexes can be looked on as the explicit water. Therefore, the explicit water model may be more credible to explore the intramolecular proton transfer, in comparison with the PCM which is the implicit water model.     

Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine

The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.     

Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: an ab initio study

High level ab initio calculations have been carried out to characterize the structure, bonding and energetics of Ag(I)-DNA base complexes, including adenine or cytosine, as well as Ag(I)-adenine-cytosine mispairs. The interactions of the Ag cation in all binding sites of all adenine and cytosine tautomers have been considered. The calculations show that in gas phase the canonical form of cytosine is stabilized upon metalation, whereas the lowest energy structure of Ag-adenine correspond to a rare tautomer. Interestingly, the theoretical inspection of metalated adenine-cytosine mispair reveals that the most stable structures are formed from the canonical cytosine and adenine tautomers. The lowest energy structure is planar with adenine and cytosine hydrogen-bonded. Within few kcal/mol nonplanar, conformationally very flexible structures are found, in which the Ag(I) crosslinks an endocyclic nitrogen of adenine and the oxygen of cytosine. Metalated reverse-Wobble type of structures, on the contrary, are predicted much higher in energy.     

Tautomer‐Specific Resonant Photoelectron Imaging of Deprotonated Cytosine Anions

Tautomers of the nucleobases play fundamental roles in spontaneous mutations of DNA. Tautomers of neutral cytosine have been studied in the gas phase, but much less is known about charged species. Here, we report the observation and characterization of three tautomers of deprotonated cytosine anions, [trans‐keto‐amino‐N3H‐H8b] (tKAN3H8b^?), [cis‐keto‐amino‐N3H‐H8a] (cKAN3H8a^?) and [keto‐amino‐H] (KAN1^?), produced by electrospray ionization. Excited dipole‐bound states (DBSs) are uncovered for the three anions by photodetachment spectroscopy. Excitations to selected DBS vibrational levels of cKAN3H8a^? and tKAN3H8b^? yield tautomer‐specific resonant photoelectron spectra. The current study provides further insight into tautomerism of cytosine and suggests a new method to study the tautomers of nucleobases using electrospray ionization and anion spectroscopy.     

FT-IR, FT-Raman, vibrational assignments, and density functional studies of 1,2,4-triazole-3-carboxylic acid, and its tautomers, dimers

The molecular geometry, relative energy, and vibrational properties (harmonic wavenumbers, total energy distributions) of several plausible tautomers and homodimers of 1,2,4-triazole-3-carboxylic acid (TCA) molecule were analyzed by applying the density functional theory (DFT), with the B3LYP functional and the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra of the biomolecule TCA were recorded in the regions 4000–100 cm⁻¹ and 3500–100 cm⁻¹, respectively. The calculated vibrational wavenumbers were compared with IR and Raman experimental data. The atomic charges and the dimer forms of the most stable tautomer were also discussed.     

密度泛函方法研究气相胞嘧啶的互变异构化

By comparing the ready experimental results with the calculated results obtained at 7 basis sets and 3 theoretical levels, respectively, for the tautomeric form Cyt1 of cytosine, the relatively accurate B3LYP/6-311+G** theoretical method to study the tautomerism of cytosine was chosen. The ground-state structures of 8 tautomers of cytosine were fully optimized at B3LYP/6-311+G** level, and the tautomerism of 6 relatively stable tautomers of cytosine was studied. The frequency analysis was performed on all the optimized structures. For the ground state geometries, all the calculated frequencies are real; for the transition-state geometries, there is only one imaginary frequency for each structure. Detailed Intrinsic Reaction Coordination calculations were carried out to guarantee the optimized transition-state structures being connected to the related tautomers. All the energies given include the zero-point energy corrections. The theoretical results can give a reasonable interpretation for the experimental results.     

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.     

Negatively charged xanthine. I. Anions formed by canonical isomers

The possibility of an excess electron binding to canonical isomers of xanthine in the gas phase was studied at the coupled-cluster level with single and double excitations using the 6-31++G** basis sets supplemented with the 4(sp)3d set of diffuse functions. It was found that xanthine should exist in the gas phase as one canonical tautomer while all the other tautomers are not likely to be detected experimentally because of their significant thermodynamic instability. On the other hand, all canonical tautomers (except one) were found to be capable of forming electronically stable anionic states of dipole-bound nature. However, the only thermodynamically stable anion (with vertical electron binding energy estimated to be 0.041 eV) based on xanthine tautomers is the one supported by the most stable neutral species.     

原子团簇Ge_7的结构与稳定性

用分子图形软件设计出多种锗原子团簇Ge7的模型,并进行B3LYP密度泛函几何构型优化和振动频率计算,得到8种稳定的同分异构体结构。在锗原子团簇中,大部分原子以三、四、五配位成键。根据分子的总能量,最稳定的Ge7构型为D5h构型。Ge7稳定结构中高配位原子越多,构型越稳定。     

Si_2C_(m-2)(m=4～15)团簇的结构与稳定性

用密度泛函理论(DFT)的B3LYP/6-31G*方法, 对Si2Cm-2(m = 4~15)团簇的几何构型、电子结构、振动频率等性质进行了研究, 讨论了化学键的特征和热力学稳定性, 比较了Si2Cm-2团中环状和线状结构的差异。结果表明, m = 4~13的团簇为线状结构, m=14~15的团簇为环状结构。在线状结构中, 随着m增大, 自旋多重度出现1、3交替变化, 并且Si原子倾向于在C链端部成键;环状结构中, C原子形成环状, 2个Si原子处于椭圆环状构型的两端。m 为奇数的Si2Cm-2团簇比m为偶数的更为稳定。     

鸟嘌呤红外光谱的密度泛函理论研究──标度量子力学(SQM)力场处理

用密度泛函理论DFT(B3LYP)/6-31G^*方法对鸟嘌呤分子的酮-胺式和醇-胺式异构体的几何结构、振动谐性力场和红外光谱进行了研究.理论力场由迁移自相关分子异胞嘧啶和咪唑的力常数标度因子进行标度.算得振动频率与鸟嘌呤的实验基质隔离IR光谱比较平均偏差对酮-胺式和醇-胺式分别为6.6和6.0cm^-1.根据振动频率的势能分布和DFT计算的光谱强度值对鸟嘌呤分子的实验振动基频进行了理论归属.     

Tautomerism and proton transfer in photoionized acetaldehyde and acetaldehyde–water clusters

Understanding the gas‐phase chemistry of acetaldehyde can be challenging because the molecule can assume several tautomeric forms, namely keto, enol and carbene. The two last forms are the most stable ionic forms. Here, insight into the gas‐phase cluster ion chemistry of homogeneous acetaldehyde and mixed water–acetaldehyde clusters is provided by mass spectrometry/vacuum ultraviolet photoionization combined with density functional theory calculations. (AA)_nH⁺ clusters (AA = acetaldehyde) and mixed (AA)_nH₃O⁺ clusters were detected using tunable vacuum ultraviolet photoionization. Barrierless proton transfers were observed during the geometry optimization of the most stable dimer structures and helped to explain the cluster ion chemistry induced by photoionization, namely the formation of deprotonated tautomers and protonated keto tautomers. Water was found to catalyze the keto–enol and keto–carbene isomerizations and facilitate the proton transfer from the ionized enol or carbene part of the cluster to the neutral keto part, resulting in protonated keto structures. The production of protonated keto structures was identified to be the main fragmentation channel following ionization of the homogeneous acetaldehyde cluster and a channel for ionized mixed clusters as well. These findings are significant for a broad range of fields, including current atmospheric models, because acetaldehyde is one of the most prominent organic species in the troposphere and ions play a crucial role in aerosol formation. Copyright © 2014 John Wiley & Sons, Ltd.     

Isomer structures of thioketene and its cyclic oligomers. <Emphasis Type="Italic">Ab initio</Emphasis> calculations

The thioketene molecule, as well as its isomer and dimer molecules, were calculated by the HF, MP2, and DFT (B3LYP) ab initio methods. The 6-31G (d) and 6-311G (2d, p) basis sets were used. The sequence of stable isomers is refined, and vibrational spectra are calculated for three most stable structures. The assignment of some absorption bands is changed. The most stable dimers and trimers of thioketene are calculated.     

Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase

Gas-phase metal affinities of DNA and RNA bases for the Na(+) and K(+) ions were determined at density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of nucleic acid bases and the alkali ions on the different binding sites, were considered. Structural features of the sodium and potassium complexes were found to be similar except in some uracil and thymine compounds in which the tendency of potassium ion toward monocoordination appeared evident. B3LYP bond energies for both metal ions were in agreement with the available experimental results in the cases of uracil and thymine for which the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base. For adenine, although the interaction of the ions with the most stable free tautomer generated the least stable molecular complex, the best agreement with experiment was found in just this case. For the remaining cytosine and guanine bases, our calculations indicated that the metal ion affinity value closest to experiment should be determined taking into account the role played by the different tautomers of the free bases with similar energy and all the possible complexes obtained by them.     

A theoretical study of solvent effects on tautomerism and electronic absorption spectra of 3-hydroxy-2-mercaptopyridine and 2,3-dihydroxypyridine

The tautomerization equilibria of 3-hydroxy-2-mercaptopyridine (HMP) and 2,3-dihydroxypyridine (DHP) in vacuo and in ethanol solution have been studied using the density functional theory (DFT) at B3LYP/6-31Gd level. The results indicate that the thione form of HMP and the keto form of DHP are the most stable tautomers in the equilibrium, and the energy barrier for the thiol-thione and enol-keto proton transfer decreases significantly when the tautomerism is mediated by a specific ethanol molecule in solution. The time-dependent density functional theory--polarizable continuum model (TDDFT-PCM) calculations on all tautomers of HMP and DHP in vacuo and in ethanol have assigned the lowest pi --> pi* excitations of thione and keto tautomers to the observed absorption bands of HMP and DHP in solutions. The solvation is predicted to have relatively small effect on these pi --> pi* excitations in ethanol.     

S2O2分子稳定结构的密度泛函理论研究

采用密度泛函理论中的B3LYP方法,在6-311+G(3df)和Aug-cc-pVTZ水平上,研究了单态S2O2分子的各种可能的异构体及其相对稳定性。结果表明,具有C2v对称性的三角平面分叉异构体的热力学稳定性要高于目前实验上唯一被发现的具有C2v对称性的cis-OSSO异构体,同时trans-OSSO的稳定性与顺式异构体十分接近,这2种异构体应该可以在实验上被观察到。同时本文还讨论了3个最稳定构型的前线分子轨道和链型OSSO的内扭转势能。