Tautomerism of pyrimidine bases—uracil,cytosine, isocytosine: Theoretical study with complete optimization of geometry

The semiempirical MINDO /3 method with complete optimization of geometry is employed to calculate the electronic ground-state properties (dipole moments and ionization potentials) and the energies of various tautomeric forms of uracil, uracil monoanion, cytosine, and isocytosine. The results are shown to be consistent with most of the experimental data. Accuracy of various quantum–mechanical methods is discussed. Particular attention is paid to the influence of the geometry optimization on energy differences between various tautomers. Some qualitative conclusions of biological importance are drawn from these calculations.     

喹唑啉酮互变异构的理论计算

采用密度泛函理论B3LYP/6-311+G(d,p)方法,计算并考察了喹唑啉酮进行结构互变的质子迁移过程的两种可能途径:(a)分子内质子迁移,(b)水助质子迁移.结果表明,途经b所需要的能垒小,氢键在降低反应能垒方面起重要作用.     

Uracil and the tautomer 4-hydroxyuracil: An ab initio study with geometry optimization

Ab initio STO -3G geometries and relative energies for uracil (U) and the tautomer 4-hydroxyuracil (U*) were obtained with the HONDO program utilizing the rapidly convergent method of Murtaugh and Sargent for geometry optimization. ΔE for U?U* is 6.61 kcal/mole. The reaction field continuum model for solvent effect indicates a preferential stabilization of U* by 1.0 kcal/mole. The calculated gas phase K_t and solution K_t for U?U* are 1.44×10^?5 and 1.3×10^?4, respectively.     

Combining genetic algorithm and simulated annealing: a molecular geometry optimization study

We introduce a new hybrid approach to determine the ground state geometry of molecular systems. Firstly, we compared the ability of genetic algorithm (GA) and simulated annealing (SA) to find the lowest energy geometry of silicon clusters with six and 10 atoms. This comparison showed that GA exhibits fast initial convergence, but its performance deteriorates as it approaches the desired global extreme. Interestingly, SA showed a complementary convergence pattern, in addition to high accuracy. Our new procedure combines selected features from GA and SA to achieve weak dependence on initial parameters, parallel search strategy, fast convergence and high accuracy. This hybrid algorithm outperforms GA and SA by one order of magnitude for small silicon clusters (Si₆ and Si₁₀). Next, we applied the hybrid method to study the geometry of a 20-atom silicon cluster. It was able to find an original geometry, apparently lower in energy than those previously described in literature. In principle, our procedure can be applied successfully to any molecular system.     

Tautomerism in the Sulfonamide Moiety: Synthesis,Experimental and Theoretical Characterizations

Following our previous work, we synthesized N-(7-methyl-5,6-diphenyl-2-m-tolyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)benzensulfonamides to study the sulfonylimine-sulfonamide tautomerism. This goal is performed using the density functional theory (DFT). Four plausible isomers including the keto and enol sulfonamide as well as Z and E sulfonimide are considered for each of compounds. The DFT calculations are carried out at the B3LYP/6-31+G(d,p) level of theory. The optimized geometric parameters such as bond lengths and bond angles are calculated. The computed IR vibrational frequencies and ¹H NMR chemical shifts are in good agreement with the experimental data. The structure of all compounds is confirmed on the basis of their full spectral data. In all three compounds, the Z-sulfonimide form is more stable than the other isomers. A high energy gap between the frontier orbitals confirms the stability of the compounds.     

Theoretical study of the [10]-annulenes geometry and stability

Five structures of [10]-annulene, proposed in the literature, namely the naphthalenic, planar, boat and helix forms have been studied by EHT, CNDO/2, MINDO/2 methods and the empirical method of Dashevskyi. Optimum geometries of the single structures were determined either from energy curves or from the coplanarity condition for bond groups of the ethylenic type. The relative stabilities of the structures were established by comparing their heats of formation with the values of the other stable cyclic polyenes. The most favourable boat form appears as an antiaromatic inverse to benzene.     

2，4-二硫基胸腺嘧啶的异构化和质子迁移的理论研究

采用密度泛函方法在B3LYP/6-31+G水平上研究了2，4-二硫基胸腺嘧啶孤立分 子和水合物的异构体的相对稳定性和可能的质子迁移反应，分析了水分子的参与对 2，4-二硫基胸腺嘧啶异构体的相对稳定性和质子迁移速率的影响。结果表 明，该分子在气相中只存在一种稳定构型，水分子的参与未改变2，4-二硫基胸腺 嘧啶各异构体的稳定性顺序，但大大降低了质子迁过程的活化能垒。     

A molecular orbital study of nitrogen inversion in aniline with extensive geometry optimization

The geometry and energy of aniline have been calculated using the 6-31G and 6-31G^*(5D) basis sets for the planar structure and various pyramidal structures, assuming that the ring and the N-atom bonded to it lie in the same plane, but otherwise with full geometry optimization. With the 6-31G basis set the planar structure is predicated to be the most stable, whereas the inclusion of polarization functions in the 6-31G^*(5D) basis set finds a pyramidal structure with the out-of-plane angle =42.3° to be most stable and the energy barrier to inversion via the planar transition state to be 1.59±0.02 kcal mol^–1, in close agreement with experiment. Completing the optimization, allowing the N-atom and the C- and H-atoms of the ring to take up equilibrium out-of-plane positions increases the calculated energy carrier to inversion by less than 0.1 kcal mol^–1 to 1.66 kcal mol^–1. The ring adopts a very shallow inverted boat-type conformation with N₇-C₁C₄ = 2.0°.     

Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol

The conformational behavior of 2-trifluoromethylphenol was investigated by means of theoretical calculations. Four characteristic structures have been found on the potential energy hypersurface of the compound: anti form (local minimum), in which the hydroxy hydrogen points away from the trifluoromethyl group; and three syn forms (the hydrogen points towards the trifluoromethyl group), with different trifluoromethyl torsions (global minimum, one low and another one high lying saddle-point). The geometry of these conformers were optimized by ab initio calculations using 6-31G** basis set. The effects of electron correlation were investigated by MP2 and various DFT methods. To investigate the intramolecular interaction in the syn forms, the electron density distribution was calculated at the MP2 level of theory. In the structure corresponding to the global minimum at the MP2/6-31G** level a bond critical point was found in Bader's sense between the hydroxy hydrogen and a fluorine of the trifluoromethyl group indicating hydrogen bonding interaction. The length of the hydrogen bond, 1.98 Å, corresponds to medium strength interaction. The O(SINGLE BOND)H bond is slightly twisted and the C(SINGLE BOND)F bond, interacting with it, is considerably twisted out of the plane of the benzene ring to the same side of the ring. The most pronounced geometrical consequence of the hydrogen bond is the 0.02-Å lengthening of the C(SINGLE BOND)F bond participating in its formation. All the other geometrical changes in 2-trifluoromethylphenol, as compared with trifluoromethylbenzene and phenol, are also consistent with the phenomenon of resonance-assisted hydrogen bonding. © 1996 by John Wiley & Sons, Inc.     

2-巯基苯并咪唑及其类似物互变异构的理论研究

采用B3LYP/6-311G**方法, 计算了2-巯基苯并咪唑及其类似物(2-巯基苯并噁唑、2-巯基苯并噻唑、2-羟基苯并咪唑、2-羟基苯并噁唑、2-羟基苯并噻唑以及2-巯基咪唑、2-巯基噁唑、2-巯基噻唑、2-羟基咪唑、2-羟基噁唑、2-羟基噻唑)的(硫)醇式与(硫)酮式结构进行质子迁移的3种可能途径: (a)分子内质子迁移; (b)水助质子迁移; (c)甲醇助质子迁移．结果表明, 途经b和c所需要的活化能较小, 氢键在降低反应活化能方面起重要作用．采用PCM方法研究了反应体系的溶剂化效应．结果表明孤立分子、一水合物和一甲醇合物的最稳定异构体相同, 都为(硫)酮式, 与气相结论一致．溶剂化效应对异构化能垒的影响较小.     

Tautomerism and thermal decomposition of tetrazole: high-level ab initio study

The mutual interconversion and decomposition reactions of four tetrazole isomers (1H-TZ, 2H-TZ, 5H-TZ, and an N-heterocyclic carbene 14H) have been studied theoretically using the W1 high-level procedure. Computations allowed resolution of the existing discrepancies in the mechanism and key intermediates of TZ thermolysis. The tautomeric equilibria between 1H-TZ, 2H-TZ, and 14H turned out to play a very important role in the mechanism of thermal decomposition. Although the barriers of monomolecular tautomeric transformations were found to be high (～50-70 kcal/mol), the concerted double H atom transfer reactions in the H-bonded complexes of TZ tautomers have profoundly lower barriers (～18-28 kcal/mol). These reactions lead to fast interconversion between 1H-TZ, 2H-TZ, and 14H. The carbene 14H has never been considered before; however, it was predicted to be a key intermediate in the mechanism of thermal decomposition of TZ. For all species considered, the unimolecular reactions of N(2) elimination were predicted to dominate over the elimination of hydrazoic acid. In agreement with existing experimental data, the effective activation energy of thermolysis was calculated to be 36.2 kcal/mol.     

A Theoretical Study on the Tautomerism of C-Carboxylic and Methoxycarbonyl Substituted Azoles

DFT calculations (B3LYP/6-31+G^**) have been carried out on 106 tautomers and conformers of NH-azoles bearing CO₂H and CO₂CH₃ groups. The following azoles systems have been studied: 2-substituted pyrroles, 2-substituted indoles, 2-substituted imidazoles, 2-substituted benzimidazoles, 4(5)-substituted imidazoles, 3(5)-substituted pyrazoles, 3-substituted indazoles (1H and 2H), 3,4(5)-substituted-1,2,3(5)-triazoles, 2,3(5)-substituted-1,2(3),4-triazoles, 4(5)-1,2,3,4(5)-tetrazoles. In the case of pyrazole, 3,5-disubstituted derivatives have also been computed, including four dimers.Dedicated to our friend Professor Vladimir I. Minkin on his 70th anniversary.     

Tautomerism of the antiepileptic drug Felbamate: A DFT study

The Felbamate is a novel anticonvulsant and neuropathic pain drug that can exist as three possible tautomers. Herein, employing density functional theory (DFT) and handling the solvent effects with the PCM model, the structural parameters, energy behavior, natural bond orbital analysis (NBO), as well as the tautomerism of Felbamate are investigated. F1 is the kinetically and thermodynamically most stable tautomer of Felbamate, which contains the amide group in each of the carbamate moieties. The calculated NMR chemical shifts and IR vibrational frequencies are in good agreement with the experimental values, confirming the suitability of the optimized geometry for Felbamate. The tautomerization reaction of F1 to each of the other tautomers occurs via an intramolecular proton transfer. This reaction affects considerably the structural parameters and atomic charges of the Felbamate molecule. A large HOMO-LUMO energy gap implies a high stability of the F1 tautomer.     

Tautomerism of peroxyacetic acid derivatives: a quantum chemical study

The electronic and molecular structures and the relative stabilities of organic peracids X=C(R)-COOH and their cyclic tautomers, dioxiranes

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, with R = Me, CF₃; X = O, NH, were studied using the ab initio Hartree-Fock method and the density functional theory (B3LYP version) as well as at the MP2-MP4 Møller-Plesset levels of perturbation theory. Geometry optimization was performed by the UHF and B3LYP methods with the 6-31G** basis set and at the MP2/cc-pvtz level of theory. The acyclic form of the peracid is more stable than the cyclic dioxirane form irrespective of the nature of the substituent. The energy difference between these tautomers increases as the CF₃ and NH groups are replaced by Me and O, respectively. Parameters of the activation barrier to tautomeric conversion increase in parallel with enhancement of the electron-accepting properties of both substituents. The transition state of tautomeric interconversion, which is topologically similar to the acyclic structure of the carbonyl oxide derivative R(HX)C=O⁺-O^?, was found and characterized taking peroxyacetic acid as an example. The characteristic features of the transition state are an intramolecular “multicenter” H-bond and the charge distribution that is inconsistent with the canonical structure mentioned above. An appropriate reaction coordinate for the transformation of the quasi-tetrahedral dioxirane structure into a planar peroxyacetic acid structure is provided by the dihedral angle. Deprotonated anionic systems are characterized by much smaller differences between the relative stabilities of the open and closed forms of isomers and by much lower activation barriers to isomeric conversions.

     

Projection operator method for geometry optimization with constraints

A new approach is presented for performing geometry optimization for stationary points on potential energy hypersurfaces with equality constraints on the internal coordinates of a polyatomic system. The working equations are the same as for unconstrained Newton–Raphson optimization in Cartesian coordinates except that projection operators are applied to the gradient and Hessian to enforce the constraints. Two reactive systems with different kinds of constraints are treated as examples: OH + H₂ → OH → H₂O + H with one constrained OH bond distance and CH₃ + H₂ → CH → CH₄ + H with one constrained H? C? H bond angle in the CH₃ group or with one constrained bond distance and one simultaneously constrained bond angle. In each case we optimized all reactants and products as well as the saddle point, all subject to the constraints.     

Tautomerism of anthraquinones: VIII. Tautomerism and conformations of 1,4-diamino-9,10-anthraquinone

The compound widely known as 1,4-diamino-9,10-anthraquinone is in fact an equilibrium mixture of 4,9-diamino-1,10-anthraquinone and tautomeric imino forms, 10-amino-9-hydroxy-1,4-anthraquinone 1-imine and its conformer, and 4-amino-1-hydroxy-9,10-anthraquinone 9-imine or 4,9-dihydroxy-1,10-anthraquinone diimine. Amino-imino tautomerism and rotational isomerism are responsible for fine structure of the π_l,π*-absorption of the title compound.     

4(3H)-嘧啶酮及其类似物互变异构的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了4(3H)-嘧啶酮及其类似物(5-氟-4(3H)-嘧啶酮、4-巯基嘧啶和5-氟-4-巯基嘧啶)醇式结构和酮式结构进行结构互变质子迁移过程中的2种可能途径:(a)分子内质子迁移;(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小.研究还表明,氢键在降低反应活化能方面起着重要的作用.     

Tautomerism of metal complexes with quinalizarin

The formation of complexes with quinalizarin was found to occur through the peri-hydroxycarbonyl groups with participation of tautomers and conformers. The diversity of the electronic absorption spectra of quinalizarin complexes is explained not only by the ligand ionization degree but also by the shifts in the tautomeric and conformer equilibria. The classification of the known quinalizarin complexes is suggested on the basis of spectrophotometric data and quantum-chemical calculations of the π _l ,π^*-band position by the Pariser-Parr-Pople method.