6-巯基嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G水平下,对8种气相和水相中可能存在的6-巯基嘌呤异构体进行了几何构型的全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能．Onsager反应场溶剂模型用于水相的计算．计算结果表明,6-巯基嘌呤在气相和水相中主要以硫酮形式存在．在气相中,硫酮．N(7)(H)要比硫酮-N(9)(H)更稳定,而在水相中,则硫酮-N(9)(H)要比硫酮-N(7)(H)更稳定．计算结果同已有实验结果一致．6-巯基嘌呤的熵效应小,对互变异构平衡几乎没有显著的影响,而焓变对互变异构产生了主要的影响．较详细地讨论了水溶剂化作用对异构体的能量、几何结构、电荷分布和偶极矩的影响,溶剂化吉布斯自由能与异构体的气相偶极矩存在相关性．     

2-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平上,对14种气相和水相中可能存在的2-硫代黄嘌呤互变异构体进行了几何构型全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能.Onsager反应场溶剂模型用于水相的计算.计算结果表明,2-硫代黄嘌呤在气相和水相中主要以酮式结构形式存在,与已有实验结果一致.在气相和水相中,酮式结构—N(7)(H)均比酮式结构—N(9)(H)更稳定.2-硫代黄嘌呤互变异构的熵效应小,对互变异构平衡没有显著的影响,而焓变对互变异构却产生了主要的影响.水溶剂化自由能与异构体的气相偶极矩存在相关性.另外,较详细地考察了2-硫代黄嘌呤与6-硫代黄嘌呤的相对稳定性.     

MP2 Study on the Proton Transfer Mechanism of Glycine Assisted by Water

The geometries of glycine-nH2O （n = 1-5） complexes and the transition states of proton transfer in glycine-H2O system were calculated at the MP2/6-31＋＋G＊＊//MP2/6-31G＊ level, upon which we discovered the proton transfer mechanisms, including the number of water molecules necessary for the stabilization of zwitterions and the effect of increasing water molecules on the proton transfer. To our interest, we found that only one water molecule can stabilize the zwitterions; in addition, with the increment of water molecules, the activation energy of positive reaction decreases and that of reverse reaction increases gradually. Glycine will be ionized completely while the water molecules reach to a certain number.     

MP2, DFT and ab initio calculations on thioxanthone

Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. ¹³C and ¹H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties.     

5-氯尿嘧啶质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP/6-311+G**方法,对5-氯尿嘧啶分子内质子转移及水助催化质子转移引起的互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数。计算结果表明,5-氯尿嘧啶无论是孤立分子还是一水合物,其双酮式CU1是最稳定异构体,由双酮式向烯醇式异构化找到3条通道(P1,P2,P3),各通道速控步骤的活化能分别为177.85、177.05和197.58kJ/mol。当水分子参与反应以双质子转移机理异构化时,活化能显著降低,各通道速控步骤的活化能依次降为66.24、69.36和77.85kJ/mol,有利于双酮式向烯醇式或酮醇式转变。计算结果还表明,氢键作用在增大5-氯尿嘧啶一水复合物稳定性、降低质子转移异构化反应活化能等方面起着重要作用。     

2,6-二巯基嘌呤质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP方法, 在6-311＋G(d,p)基组水平上对2,6-二巯基嘌呤质子转移引起的硫醇式与硫酮式互变异构反应进行了计算研究, 获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等性质. 计算结果表明, 2,6-二巯基嘌呤无论是孤立分子还是一水合物, 其二硫酮式R是最稳定异构体. 由二硫酮式通过分子内质子转移向二硫醇式异构化共有6条反应通道, 其主通道(1)速控步骤的活化能为139.1 kJ•mol^－1, 速率常数为2.16×10^－12 s^－1; 当水分子参与反应以双质子转移机理异构化时, 活化能显著降低, 有利于硫酮式向硫醇式转变, 其主通道(7)速控步骤的活化能为61.3 kJ•mol^－1, 速率常数为1.33×10 s^－1. 计算结果还表明, 氢键作用在增大2,6-二巯基嘌呤氢键一水合物稳定性、降低质子转移异构化反应活化能等方面起着重要的作用.     

Halogen‐Bonding Interactions with π Systems: CCSD(T), MP2, and DFT Calculations

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X=F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller–Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.     

DFT and MP2 study of simple and water-assisted tautomerism in amidrazones

DFT and MP2 methods were used to calculate structural parameters, vibrational modes, solvent effect, and energetic properties of amidrazones. Amidrazones can be presented by three tautomeric forms and six isomers. All tautomers and transition states were optimized at the B3LYP/6-311++g** and MP2/6-311++G** levels of theory. The relative stabilities of amidrazone isomers in the gas phase were found to be as 1Z > 1E > 2E > 2Z > 3E > 3Z > TS(1–2) > TS(1–3). The calculated energy differences between E and Z isomers are very low and between different tautomers are nearly low, but the energy barriers for tautomerism interconversions at the gas phase are high. The kinetic and thermodynamic data in solvents (chloroform, tetrahydrofuran, acetone, and water) are nearly similar to those in the gas phase but their rate constants are slightly less than those in the gas phase. Moreover, equilibrium and rate constants of intermolecular tautomerism in presence of 1–3 molecules of water were calculated. Computed energy barriers show that the barrier energy of water-assisted tautomerism is very lower than that in simple tautomerism and also calculated binding energies show that water can stabilize transition states more than tautomers. Therefore, this water-assisted tautomerism can be performed fast, especially with the assistance of two molecules of water.     

胸腺嘧啶-BH3构型与性质的DFT和MP2研究

Geometries and combination energies are predicated at B3LYP / 6-31G（d）and MP2 / 6-31G（d）level for thymine-BH3 complexes and 5 geometries have been obtained. Then single point energy calculations using larger basis sets（6-311 + G（2df）and aug-cc-pVDZ）and vibrational analysis and natural bond orbital analysis are carried out on the 5 optimized conformers. The outcome indicates that the conformers with the boron atom combined with O directly are relatively stable ones,（a）and（b）,with the combination energies of 90. 4 and 88. 0 kJ / mol （B3LYP / 6-31G（d）,BSSE corrected）. The fact is that the nitrogen atom offers electron to the empty atomic orbital of boron which produces the conformers（c）and（d）. Only one conformer is found which is formed because two carbon atoms offer π electron to the empty orbital of boron. The charge transference exists in all the conformers. The combination energies have a good line relation with their charge transference. The calculated results show that when the complex forms their IR spectrum moved to the red side and the frequency shifts are relative to the stabilities of the complexes.     

Structure and stability of thiourea with water, DFT and MP2 calculations

The relative stabilities of thiourea in water are investigated computationally by considering thiourea–water complexes containing up to 1–6 water molecules (CS(NH₂)₂(H₂O)_n=1–6) using density functional theory and MP2 ab initio molecular orbital theory. The results show that the thiourea complex is stable and has an unusually high affinity for incoming water molecules. The clusters are progressively stabilized by the addition of water molecules, as indicated by the increasing of the binding energy. The binding energy of the cluster to each H₂O molecule is about 33 kJ mol⁻¹ for n=1–5.The C–S bond, N–C bond distance, Mulliken populations and binding energy keep approximately constant as the clusters increase in size with an increasing number of H₂O molecules. As the solvation progresses, the C–S distance increases monotonically while the Mulliken populations on the C–S bond reduces monotonically with the addition of each H₂O molecule, indicating that the C–S bond of the thiourea unit in the clusters is de-stabilized with an increasing number of H₂O molecules. Charge transfers for the clusters are mainly found at N, S atoms of the thiourea.     

Computational Study of Proton Transfer in Tautomers of 3‐ and 5‐Hydroxypyrazole Assisted by Water

The tautomerism of 3‐ and 5‐hydroxypyrazole is studied at the B3LYP, CCSD and G3B3 computational levels, including the gas phase, PCM–water effects, and proton transfer assisted by water molecules. To understand the propensity of tautomerization, hydrogen‐bond acidity and basicity of neutral species is approached by means of correlations between donor/acceptor ability and H‐bond interaction energies. Tautomerism processes are highly dependent on the solvent environment, and a significant reduction of the transition barriers upon solvation is seen. In addition, the inclusion of a single water molecule to assist proton transfer decreases the barriers between tautomers. Although the second water molecule further reduces those barriers, its effect is less appreciable than the first one. Neutral species present more stable minima than anionic and cationic species, but relatively similar transition barriers to anionic tautomers.     

2-巯基吡啶质子迁移过程的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了2-巯基吡啶分子硫醇式结构和硫酮式结构进行结构互变质子迁移过程中的4种可能途径:(a)分子内质子迁移,(b)水助质子迁移,(c)同种二聚体双质子迁移和(d)异种二聚体间双质子迁移.计算结果表明,途经c所需要的活化能最小(9.73 kJ.mol-1,逆反应则为55.28 kJ.mol-1),而过程a所需要的活化能最大(106.02 kJ.mol-1),途径b和d的活化能居中间(分别为32.05和15.91 kJ.mol-1).研究还表明,氢键在降低反应活化能方面起着重要的作用.     

Probing the Charge Transfer in a Frustrated Lewis Pair by Resonance Raman Spectroscopy and DFT Calculations

A classical Lewis adduct derives from a covalent bond between a Lewis acid and a base. When the adduct formation is precluded by means of steric hindrance the association of the respective acid-base molecular system is defined as a frustrated Lewis pair (FLP). In this work, the archetypal FLP Mes₃P/B(C₆F₅)₃ was characterized for the first time by resonance Raman spectroscopy, and the results were supported by density functional theory (DFT) calculations. The charge transfer nature of the lowest energy electronic transition, from phosphine to borane, was confirmed by the selective enhancement of the Raman bands associated to the FLP chromophore at resonance condition. Herein, we demonstrate the use of resonance Raman spectroscopy as a distinguished technique to probe the weak interaction involved in FLP chemistry.     

A Conformational Study on Silacyclohexane. Comparison of ab initio (HF,MP2), DFT,and Molecular Mechanics Calculations. Conformational Energy Surface of Silacyclohexane

The structures and relative energies for the basic conformations of silacyclohexane 1 have been calculated using HF, RI‐MP2, RI‐DFT and MM3 methods. All methods predict the chair form to be the dominant conformation and all of them predict structures which are in good agreement with experimental data. The conformational energy surface of 1 has been calculated using MM3. It is found that there are two symmetric lowest energy pathways for the chair‐to‐chair inversion. Each of them consists of two sofa‐like transition states, two twist forms with C₁ symmetry (twist‐C₁), two boat forms with Si in a gunnel position (C₁ symmetry), and one twist form with C₂ symmetry (twist‐C₂). All methods calculate the relative energy to increase in the order chair < twist‐C₂ < twist‐C₁ < boat. At the MP2 level of theory and using TZVP and TZVPP (Si atoms) basis sets the relative energies are calculated to be 3.76, 4.80, and 5.47 kcal mol^–1 for the twist‐C₂, twist‐C₁, and boat conformations, respectively. The energy barrier from the chair to the twisted conformations of 1 is found to be 6.6 and 5.7 kcal mol^–1 from MM3 and RI‐DFT calculations, respectively. The boat form with Si at the prow (C_s symmetry) does not correspond to a local minimum nor a saddle point on the MM3 energy surface, whereas a RI‐DFT optimization under C_s symmetry constraint resulted in a local minimum. In both cases its energy is above that of the chair‐to‐twist‐C₁ transition state, however, and it is clearly not a part of the chair‐to‐chair inversion.     

DFT Calculations on Hydrogen-Bonded Complexes Formed Between Guanine and Acrylamide

B3LYP/6-311+G* theoretical calculations have been employed to investigate the complexes involving hydrogen bonding between guanine and acrylamide. Nine stable conformers were obtained by geometry optimization without imaginary frequencies. The calculation results revealed that the stability of these complexes was accounted for by the intensity and numbers of hydrogen bonds between guanine and acrylamide, which was proved by the energy analysis and the topological properties at the critical points. In these optimized complexes, the complex with three hydrogen bonds was the most stable one because it offered the biggest binding energy. Clearly, the hydrogen bonds appear to be crucial in the stability of these complexes. This work will provide another nosogenetic interpretation besides the covalent interactions between DNA and acrylamide, which are of interest for studying DNA mutation.     

Vibrational Spectroscopic Investigation and DFT Calculations on the Decabromodiphenyl Ether

Decabromodiphenyl ether (BDE-209), the major congener in the high volume industrial flame retardant mixture "DecaBDE", has become a ubiquitous environmental contaminant. In the present work, combined experimental and theoretical studies have been undertaken on the structure and vibrational spectra of BDE-209. The FT-IR (400-4000 cm-1) and FT-Raman spectra (100-4000 cm-1) of BDE-209 were recorded, while density functional B3LYP calculations were employed in conjunction with the 6-31G(d) basis set for investigating the corresponding geometric structure and vibrational spectroscopic properties. Besides, the detailed interpretations of fundamental vibrations were performed on the basis of experimental results and potential energy distribution (PED) of the vibrational modes. Optimized structures of the title compound were interpreted and compared with the earlier reported experimental values, which yield good agreement. Finally, the measured and calculated harmonic vibrational wavenumbers were compared with each other, and they were found to be in good accordance.     

Hydrogen-bonding interaction of 5,6-dihydrouracil with RNA bases: DFT and MP2 studies

5,6-Dihydrouracil (DHU) is a rare pyrimidine base naturally occurring in tRNAs, it differs from the base uracil due to the saturation of the C₅–C₆ bond. This work presents the interaction energies of complexes formation involving DHU bound to the natural RNA bases adenine (A), uracil (U), guanine (G), and cytosine (C). Full geometry optimization has been performed for the studied complexes by B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) calculations. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. We find that the stability order is DHU:G > DHU:A > DHU:C  DHU:U.