Hydration effect on the stability of the keto-enol tautomers of 5-hydroxy-6-methyluracil

The structure and energies of six tautomeric forms of 5-hydroxy-6-methyluracil (OMU) and their 1:n (n = 1−4) complexes with water were determined by the density functional theory (PBE/3z) method. The stability series of the tautomers and changes in it depending on the number of water molecules in the nearest environment of the tautomer were found. The effect of the water solvent was also included using the continuum (B3LYP/6-311+G(2d,p), COSMO) model. Both complex formation and medium effects significantly influenced the stability series of the tautomers. Although the decrease in the energy of the diketo form on hydration was smaller than for the enol states, diketo tautomer a remained the most stable form of OMU in solution. Inclusion of hydration in calculations suggests that the energies of three enol tautomers b–d were equalized (ΔH ≈ 5.5 kJ/mol). This should be taken into account for the conditions that facilitate the keto-enol tautomerism of OMU.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

Computational investigation of enol/keto chloramphenicol with β-cyclodextrin

PM3 and ONIOM2 were carried out to investigate the structures and properties for the inclusion complexes of chloramphenicol tautomers into β-cyclodextrin (at 1:1 stoichiometry). Two possible orientations into host cavity were considered for both enol and keto chloramphenicol. The PM3 results gives that B orientation is more preferred for enol and keto form, the preference is of 0.63 and 1.67 kcal/mol respectively. This preference is greater in the case of ONIOM2 calculations. Finally, the chemical shifts (ppm) of free and complexed chloramphenicol were calculated at B3LYP/6-31G(d) by (GIAO method) and compared with experimental data taken from the literature.     

Tautomeric and conformational properties of acetoacetamide: electron diffraction and quantum chemical study

The tautomeric properties of acetoacetamide, CH3C(O)CH2C(O)NH2, have been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-31G(d,p) and 6-311++G(3df,pd) basis sets). GED results in a mixture of 63(7)% enol tautomer and 37(7)% diketo form at 74(5) degrees C. Only one enol form with the O-H bond adjacent to the methyl group (CH3C(OH)=CHC(O)NH2) and only one diketo conformer (with dihedral angles tau(O=C(CH3)-C-C) = 31.7(7.5) degrees and tau(O=C(NH2)-C(H2)-C(O)) = 130.9(4.5) degrees ) are present. The calculated tautomeric composition varies in a wide range depending on the quantum chemical method and basis set. Only the B3LYP method with small basis sets reproduces the experimental composition correctly.     

Conformers and intramolecular hydrogen bonding of the oxalic acid monomer and its anions

Density functional theory, B3LYP/6‐31G** and B3LYP/6‐311+G(2d,p), and ab initio MP2/6‐31G** calculations have been carried out to investigate the conformers, transition states, and energy barriers of the conformational processes of oxalic acid and its anions. QCISD/6‐31G** geometrical optimization is also performed in the stable forms. Its calculated energy differences between the two most stable conformers are very near to the related observed value at 7.0 kJ/mol. It is found that the structures and relative energies of oxalic acid conformers predicted by these methods show similar results, and that the conformer L1 (C_2h) with the double‐interfunctional‐groups hydrogen bonds is the most stable conformer. The magnitude of hydrogen bond energies depends on the energy differences of various optimized structures. The hydrogen bond energies will be about 32 kJ/mol for interfunctional groups, 17 kJ/mol for weak interfunctional groups, 24 kJ/mol for intra‐COOH in (COOH)₂, and 60 kJ/mol for interfunctional groups in (COOH)COO⁻¹ ion if calculated using the B3LYP/6‐311+G(2d,p) method. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 541–551, 2000     

2-(2-巯苯基)苯并噁唑分子内质子转移的理论研究

在B3LYP/6-31G(d,p)水平上研究了2-(2-巯苯基)苯并噁唑气态中五种异构体(E1, E2, E3, E4和K)在气态中的稳定性及其在基态下的质子转移, 同时结合极化连续介质模型(PCM)研究了水、二甲亚砜、乙腈、乙醇、苯胺和环己烷等对2-(2-巯苯基)苯并噁唑溶剂化作用的影响. 研究结果表明, 醇式异构体E1为2-(2-巯苯基)苯并噁唑的优势构型; 在E1向K(酮式异构体)转变过程中, 存在一个较小的能垒; 当考虑零点振动能(ZPVE)后, 逆向能垒消失. 在溶液中, 随着溶剂极性的增强, 醇式异构体E1与K之间的反应平衡向K方向移动, 在非极性溶剂环己烷中, E1为优势构型, 而在强极性水溶液中, K为优势构型.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

过充电保护添加剂1,4-二甲氧基苯的反应机理

采用密度泛函理论(B3LYP/6-311+G(d,p))和MP2/6-311+G(d,p)方法,研究锂离子电池过充电保护添加剂1,4-二甲氧基苯(p-DMOB)的作用机理.计算结果表明,在过充时,p-DMOB优先于溶剂分子(乙基甲基碳酸酯、二甲基碳酸酯、碳酸乙酯)发生氧化反应.用B3LYP和MP2计算所得的p-DMOB理论氧化电位接近,分别为4.12和4.05V(vsLi/Li+).p-DMOB氧化时首先失去一个电子,生成p-DMOB+·正离子自由基,用B3LYP和MP2方法计算所得的相应能量变化分别为701.24和728.27kJ·mol-1.失去电子后苯环的共轭性受到破坏,随后p-DMOB+·苯环上的C―H键发生断裂,失去H+并形成p-DMOB·自由基.用B3LYP和MP2方法计算所得的相应能量变化分别为1349.78和1810.99kJ·mol-1.p-DMOB·自由基很不稳定,会在电极表面发生聚合反应形成聚合物膜,用B3LYP和MP2方法计算所得的相应能量变化分别为-553.37和-1331.20kJ·mol-1.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

A DFT study of uracil and 5-bromouracil in nanodroplets

The canonical (keto) and rare (enol) tautomers of uracil and 5-bromouracil in clusters comprising 50 and 100 water molecules (nanodroplets) were studied using density functional theory. The geometries of the various complexes were optimized at two different levels of theory, BLYP/6-31G(d,p) and B3LYP/6-31G(d,p). Tautomerization energies were computed using the BLYP, B3LYP and M05-2X density functionals. The gas-phase tautomerization energies of uracil and 5-bromouracil are very similar, favoring the keto tautomer. However, in the hydrated phase, the tautomeric preference of 5-bromouracil is reversed. This result is obtained for all four sets of clusters (BLYP or B3LYP optimized, containing 50 or 100 water clusters) and at all levels of theory employed, and indicates that a bromine atom in the 5-position considerably increases the proportion of the hydroxyl group present in uracil.     

Ab initio study of 2,4-substituted azolidines. II. Amino-imino tautomerism of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one in water solution

The relative stabilities of the tautomers of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one were calculated at the MP2/6-31+G(d,p) level by considering their mono- and trihydrated complexes. Single-point calculations at the MP4/6-31+G(d,p)//MP2/6-31+G(d,p) level of theory were performed to obtain more accurate energies. The values of proton transfer barriers in the isolated, mono- and trihydrated tautomers of 2-aminothiazolidine-4-one (2AT) and 4-aminothiazolidine-2-one (4AT) were calculated for two different mechanisms of tautomerisation. In the absence of water, the process of proton transfer should not occur. Addition of water molecules decreases the barrier making the process faster, as the participation of two water molecules in a proton transfer reaction is more favorable than the participation of only one water molecule. To estimate the effect of the medium (water) on the relative stabilities of the tautomers of the studied compounds we applied the polarizable continuum model (PCM). (13)C NMR chemical shieldings were calculated using the GIAO approach at MP2/6-31+G(d,p) optimized geometries. HF and the DFT B3LYP functional with 6-31+G(d,p) basis set were employed. The quantum chemical results for the chemical shifts in gas phase and in polar solvents (water and DMSO) were compared with experimental data. TD DFT B3LYP/aug-cc-pVTZ calculations were performed to predict the absorption maxima of tautomers A and B of 2AT and 4AT.     

苯并氧化呋咱稳定性和异构化的DFT和ab initio研究

运用B3LYP/6-31G(d)密度泛函理论（DFT）方法对苯并氧化呋咱、邻二亚硝基苯及其间的异构化反应进行了计算研究。结果表明,苯并氧化呋咱的分子总能量比邻二亚硝基苯的低;由苯并氧化呋咱异构为邻二亚硝基苯的正向反应活化能（Ea+=51.0kJ/mol）,与文献实测值（58.6kJ/mol）较接近,而其逆向反应活化能（Ea-=4.6kJ/mol）很小,从而揭示了苯并氧化呋咱比邻二亚硝基苯更稳定·此外,进行了HF/3-21G、HF/6-31G(d)和MP2/6-31G(d)//6-31G(d)水平下相应的计算,发现B3LYP-DFT的结果较abinitio为优。谐振动频率的B3LYP/6-31G(d)计算还支持了邻二亚硝基苯为苯并氧化呋咱“自-自”互变重排反应的中间体。     

2-(2-巯苯基)苯并噁唑分子内质子转移取代基电子效应的密度泛函理论研究

在B3LYP/6-31G(d,p)和TDB3LYP/6-31++G(d,p)//CIS/6-31G(d,p)水平上研究了2-(2-巯苯基)苯并噁唑及其衍生物基态和激发态分子内质子转移现象,并探讨取代基电子效应对分子内质子转移的影响,研究结果表明,在基态时,硫醇式异构体为优势构象,供电子取代基使基态分子内正向质子转移能垒(烯醇式→酮式)升高;而吸电子取代基则可降低能垒,有利于基态分子内质子转移并有助于硫酮式异构体的稳定.在激发态时,硫酮式结构为优势构象,所研究的2-(2-巯苯基)苯并噁唑化合物及衍生物均可以发生无能垒或低能垒(≤1.5kJ/mol)的激发态分子内质子转移.巯苯基部分是激发态失活的主要活性部分,供电子基团有利于激发态的质子转移,吸电子基团使激发态跃迁困难,不利于激发态的质子转移.     

Addition reactions of nitrones on the reconstructed C(1 0 0)-2 × 1 surfaces

In this paper, the reactions of nitrone, N-methyl nitrone, N-phenyl nitrone and their hydroxylamine tautomers (vinyl-hydroxylamine, N-methyl-vinyl-hydroxylamine and N-phenyl-vinyl-hydroxylamine) on the reconstructed C(1 0 0)-2 × 1 surface have been investigated using hybrid density functional theory (B3LYP), Møller–Plesset second-order perturbation (MP2) and multi-configuration complete-active-space self-consistent-field (CASSCF) methods. The calculations showed that all the nitrones can react with the surface “dimer” via facile 1,3-dipolar cycloaddition with small activation barriers (less than 12.0 kJ/mol at B3LYP/6-31g(d) level). The [2+2] cycloaddition of hydroxylamine tautomers on the C(1 0 0) surface follows a diradical mechanism. Hydroxylamine tautomers first form diradical intermediates with the reconstructed C(1 0 0)-2 × 1 surface by overcoming a large activation barrier of 50–60 kJ/mol (B3LYP), then generate [2+2] cycloaddition products via diradical transition states with negligible activation barriers. The surface reactions result in hydroxyl or amino-terminated diamond surfaces, which offers new opportunity for further modifications.     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

Theoretical study of the enol imine <--> enaminone tautomeric equilibrium in organic solvents

The tautomeric enol imine <--> enaminone (phenol <--> quinone) equilibrium of the 1-hydroxy-2-naphthaldehyde Schiff base (2-phenyliminomethyl-naphthalen-1-ol) was investigated by density functional theory (B3LYP) and ab initio (MP2) methods in the IEF-PCM polarizable continuum dielectric solvent approximation and by a combined ab initio + FEP/MC study by considering an explicit solvent model. Special emphasis was put on the effect of solvation on this equilibrium by using an apolar (CCl4), polar aprotic (CH3CN), and polar protic (CH3OH) solvent. Compared with experimental tautomerization Gibbs free energies, the IEF-PCM/B3LYP calculations apparently overestimate the stability of the quinone form both when the 6-31G(d,p) and the 6-311++G(d,p) basis sets are applied. IEF-PCM/MP2 studies with the above basis sets predict the preference of the aromatic phenol tautomer, in contrast to the experiment in methanol and acetonitrile solvent. Calculation of the total relative free energy as DeltaG(tot) = DeltaE(int)(IEF-PCM/QCISD(T)/6-31G(d)) + DeltaG(solv, FEP/MC) + DeltaG(thermal) provided agreement with the experimental values up to 0.6 kcal/mol in the three solvents, and the predominant tautomer was always correctly predicted. In-solution relevant atomic charges, derived by a fit to the molecular electrostatic potential generated by the IEF-PCM/B3LYP/6-31G(d,p) wave function, show strong dependence on the fitting procedure (CHELPG or RESP) and are fairly insensitive to the chemical nature of the actual solvent. Use of the CHELPG charges in FEP/MC simulations revealed to be superior in comparison with the use of the RESP charge set.     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

Effects of the ionization in the tautomerism of uracil: A reaction electronic flux perspective

The one‐step tautomerization processes of uracil and its radical cation and radical anion have been investigated in the light of the reaction force and reaction electronic flux (REF) formalisms. The relative energies of the different tautomers as well as the corresponding tautomerization barriers have been obtained through the use of the G4 high‐level ab initio method and by means of B3LYP/6‐311+G(3df,2p)//B3LYP/6‐311+G(d, p) calculations. Systematically, the enol radical cations are more stable in relative terms than the neutral, due to the higher ionization energy of the diketo forms with respect to the enolic ones. Conversely, the enol radical anions, with the only exception of the 2‐keto‐N1 anion, are found to be less stable than the neutral. The effects of the ionization are also sizable on the tautomerization barriers although this effect also depends on the particular tautomerization process. The reaction force analysis shows that all reactions are mainly activated through structural rearrangements that initiate the electronic activity. This electronic activity is monitored along the reaction coordinate through the REF that obeys a delicate balance between the acid and basic character of the atoms involved in the hydrogen transfer. © 2015 Wiley Periodicals, Inc.