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A theoretical study on the substituent effect of DNA-photocleavage by [Ru(phen)2(6-R-dppz)]2+ (R = H, OH, and NO2) [Ru(phen)2(6-R-dppz)]2+ (R = H, OH, NO2)光裂解dna取代基效应的理论研究
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.030
Lian-cai Xu , Qian-shu Li , Zhi-qiang Zhang , Ti-fang Miao , Kang-cheng Zheng , Liang-nian Ji

A theoretical study was conducted on the effects of three substituents in the Ru(II) polypyridyl complex, [Ru(phen)2(6-R-dppz)]2+, (R = H for complex 1, OH for complex 2, and NO2 for complex 3), on the photocleavage of DNA. The geometric and electronic structures of these complexes in the ground (S0), first singlet (S1), and triplet (T1) excited states, were calculated using the density functional theory (DFT), Hartree–Fock (HF), and configuration interaction singles (CIS) methods. The excited reduction potentials of the Ru(II) complexes in aqueous solution, which appear to be primarily responsible for the DNA-photocleavage behavior, were calculated by thermodynamic cycle, and determined to be higher than the oxidation potentials of some DNA-bases. The order of the reduction potentials changes from 3 > 2 > 1 in the ground state to 2 > 1 > 3 in the excited state, suggesting that the substituent on the main ligand has a significant effect on the electrochemical properties of the excited Ru(II) polypyridyl complexes. In addition, these theoretical results can explain two experimentally-observed phenomena: (a) the cleavage of DNA by complex 3 in the absence of light irradiation; (b) the inability of complex 3 to emit luminescence in its excited triplet state in aqueous solution.

对Ru(II)多吡啶配合物[Ru(phen)2(6-R-dppz)]2+(配合物1为R = H,配合物2为OH,配合物3为NO2)中三个取代基对DNA光裂解的影响进行了理论研究。利用密度泛函理论(DFT)、harree - fock (HF)和组态相互作用单态(CIS)方法计算了这些配合物在基态(S0)、第一单重态(S1)和三重态(T1)激发态的几何和电子结构。通过热力学循环计算了水溶液中Ru(II)配合物的激发还原电位,并确定其高于某些dna碱基的氧化电位,这似乎是dna光裂解行为的主要原因。还原电位的顺序从3 >2比;1在基态到2 >1比;表明主配体上的取代基对受激发的Ru(II)多吡啶配合物的电化学性能有显著影响。此外,这些理论结果可以解释两个实验观察到的现象:(a)在没有光照射的情况下,复合体3对DNA的切割;(b)配合物3在水溶液中不能以激发态发光。
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引用次数: 4
On the role of halogen bond in the halophilic reaction: A theoretical study 亲盐反应中卤素键作用的理论研究
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.039
Yu Zhang

Halophilic reactions have been modeled theoretically by employing CBr4, Cl3CCN, Cl3CCOCl, CCl4 and Cl3CF as substrates and Cl as a nucleophile. It was found that the formation of the strong halogen bond is a necessary but not sufficient condition for the occurring of the halophilic reaction: the strong red-shifting halogen bond facilitates the reaction whereas the strong blue-shifting halogen bond retards it. The theoretical results are in good agreement with the experimental results.

以CBr4、Cl3CCN、cl3cccl、CCl4和Cl3CF为底物,Cl−为亲核试剂,对亲盐反应进行了理论模拟。发现强卤素键的形成是发生亲盐反应的必要条件,但不是充分条件:强红移卤素键促进反应,而强蓝移卤素键阻碍反应。理论结果与实验结果吻合较好。
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引用次数: 7
Theoretical studies on the structures and properties of As-doped Sin (n = 1–8) clusters 掺as的Sin (n = 1-8)团簇结构与性质的理论研究
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.09.003
Aimei Gao, Guoliang Li, Yu Chang, Hongyu Chen, Qian-shu Li

The As-doped small silicon clusters AsSin/AsSin+/AsSin- (n = 1–8) have been systematically investigated at the B3LYP/6–311+G* level of theory. The most stable isomer of the neutral AsSi2 cluster has an isosceles triangle structure (2n  1). Edge-capping with a silicon atom to 2n  1, yields the lowest energy structure of the neutral AsSi3 cluster, a deformed planar rhombus structure (3n  1). The ground state structure of the neutral AsSi4 cluster is predicted to have a trigonal bipyramid form (4n  1). Adding one, two, or three Si atoms to different positions in this 4n  1 structure gives the lowest energy structures of the neutral AsSi5, AsSi6, and AsSi7 clusters (5n  1, 6n  1, and 7n  1), respectively. The global minimum of neutral AsSi8 (8n  1) can be gained by capping the most stable AsSi7 structure with a silicon atom. The ground states of the neutral AsSin clusters are all doublet. The three low-energy states of ionic AsSin+/AsSin- have very similar structures to those of their neutral AsSin counterparts, but their orders of stability are somewhat changed. Except for the smaller AsSi+, the most stable AsSin+/AsSin- isomers all have singlet electronic states. Based on the optimized geometries, various energetic properties, including the incremental binding energies, the gaps between the highest occupied molecular orbital and lowest unoccupied molecular orbital, the adiabatic ionization potentials, and electron affinities, are calculated for the most stable isomers of AsSin/AsSin+/AsSin<

在B3LYP/ 6-311 +G*理论水平上系统地研究了砷掺杂的小硅团簇AsSin/AsSin+/AsSin- (n = 1-8)。中性AsSi2簇的最稳定异构体具有等腰三角形结构(2n−1)。硅原子在2n−1上的边缘封顶产生中性AsSi3簇的最低能量结构,即变形的平面菱形结构(3n−1)。中性AsSi4簇的基态结构预计具有三角双棱锥体形式(4n−1)。在这个4n−1结构中,将三个Si原子放到不同的位置,分别得到中性的AsSi5、AsSi6和AsSi7簇(5n−1、6n−1和7n−1)的最低能量结构。中性AsSi8 (8n−1)的全局最小值可以通过用硅原子覆盖最稳定的AsSi7结构来获得。中性AsSin簇的基态都是重态。离子AsSin+/AsSin-的三个低能态与它们的中性AsSin对应物具有非常相似的结构,但它们的稳定顺序有所改变。除了较小的AsSi+外,最稳定的AsSin+/AsSin-异构体都具有单重态电子。基于优化的几何结构,计算了最稳定的AsSin/AsSin+/AsSin-异构体的各种能量性质,包括增量结合能、最高已占据轨道与最低未占据轨道之间的间隙、绝热电离势和电子亲和。结果表明,AsSi4-和AsSi7-具有最高的稳定性。自然键轨道分析表明,离域电子和多中心键可能是低能AsSin/AsSin+/AsSin-结构稳定的原因。
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引用次数: 9
Density functional modelling studies on N-2-Methoxyphenyl-2-oxo-5-nitro-1-benzylidenemethylamine n -2-甲氧基苯基-2-氧-5-硝基-1-苄基二甲基胺的密度泛函模型研究
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.035
Metin Yavuz , Hasan Tanak

Density functional calculations of the structure, molecular electrostatic potential and thermodynamic functions have been performed at B3LYP/6-31G(d) level of theory for the title compound of N-2-Methoxyphenyl-2-oxo-5-nitro-1-benzylidenemethylamine. To investigate the tautomeric stability, optimization calculations at B3LYP/6-31G(d) level were performed for the enol and keto forms of the title compound. Calculated results reveal that the enol form of the title compound is more stable than its keto form. The predicted non-linear optical properties of the title compound are much greater than ones of p-Nitroaniline. The changes of thermodynamic properties from the monomers to title compound with the temperature ranging from 200 K to 450 K have been obtained using the statistical thermodynamic method. At 298.15 K the change of Gibbs free energy for the formation reaction of the title compound is 30.654 kJ/mol. The title compound cannot be spontaneously produced from the isolated monomers at room temperature. The tautomeric equilibrium constant is computed as 0.0192 at 298.15 K for enol-imine  keto-amine tautomerization of the title compound. In addition, natural bond orbital analysis of the title compound were performed using the B3LYP/6-31G(d) method.

在B3LYP/6-31G(d)理论水平上对标题化合物n -2-甲氧基苯基-2-氧-5-硝基-1-苄基甲乙基胺的结构、分子静电势和热力学函数进行了密度泛函计算。为了研究该化合物的互变异构稳定性,在B3LYP/6-31G(d)水平上对烯醇和酮进行了优化计算。计算结果表明,标题化合物的烯醇形式比其酮形式更稳定。该化合物的非线性光学性质比对硝基苯胺大得多。用统计热力学方法得到了单体到标题化合物在200 ~ 450 K温度范围内的热力学性质的变化。298.15 K时,该化合物生成反应的吉布斯自由能变化为30.654 kJ/mol。所分离的单体在室温下不能自发生成标题化合物。该化合物的烯醇亚胺↔酮胺的互变异构平衡常数在298.15 K时计算为0.0192。此外,采用B3LYP/6-31G(d)方法对标题化合物进行天然键轨道分析。
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引用次数: 41
Structures, stabilities and electronic properties of C50 dimers C50二聚体的结构、稳定性和电子性质
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.033
Hongcun Bai, Ruiying Du, Weiye Qiao, Yuanhe Huang

The dumbbell-shaped dimers constructed from C50 cages are investigated using self-consistent field molecular orbital method based on density functional theory. Our study focuses on the structures, stabilities, electronic and vibrational properties of the C50 dumbbell-shaped dimers. It is found that the stability of these C50 dimers is related to bonding positions and linking patterns. For the dimers by [2 + 2] cycloaddition, a simple rule is proposed to predict the stabilities of these additive products of fullerenes according to the environment around the C–C bonds on the addition position. Moreover, higher thermodynamic stability is accompanied with larger HOMO–LUMO gaps for these dimers. The vibrational properties of the C50 dimers are also discussed in this paper.

采用基于密度泛函理论的自洽场分子轨道方法对C50笼构建的哑铃型二聚体进行了研究。本文主要研究了C50哑铃型二聚体的结构、稳定性、电子和振动性能。发现这些C50二聚体的稳定性与成键位置和连接模式有关。对于[2 + 2]环加成的二聚体,根据加成位置上C-C键周围的环境,提出了一个预测富勒烯加成产物稳定性的简单规则。此外,这些二聚体具有较高的热力学稳定性和较大的HOMO-LUMO间隙。本文还讨论了C50二聚体的振动性质。
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引用次数: 22
On tautomerism and substituent effect in 8-hydroxyquinoline-derived medicine molecules 8-羟基喹啉类药物分子的互变异构和取代基效应
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.09.006
Grażyna Karpińska , Aleksander P. Mazurek , Jan Cz. Dobrowolski

The 8-hydroxyquinoline (8HQ) molecule and its four derivatives used as medicines: chloroxine, clioquinol, iodoquinol, and nitroxoline (8HQ substituted in the benzene ring by 5,7-dichloro-, 5-chloro-7-iodo-, 5,7-diiodo-, and 7-nitro-, respectively), were studied using the DFT/B3LYP/6-311G∗∗ method. Three forms of each molecule were considered: (OH⋯N) with the intramolecular OH⋯N hydrogen bond, (OH;N) with the broken intramolecular hydrogen bond, and (NH), the tautomer with the H-atom attached to the pyridine N-atom. Regardless of the substitution, the (OH⋯N) form, with the intramolecular OH⋯N hydrogen bond, was the most stable form. Breaking the intramolecular bond led to the formation of (OH;N), which was less stable by at least 25 kJ/mol. The NH tautomer was higher in energy than the (OH⋯N) tautomer by at least 40 kJ/mol. Based on AIM analysis, it was found that the intramolecular OH⋯N bond was the weakest in 8HQ, stronger in chloroxine, clioquinol and iodoquinol, and it was the strongest in nitroxolin. The benzene ring aromaticity decreased from 8HQ, through halogenosubstituted 8HQ, to nitroxoline, which was in line with the decrease of the π-electron population in the benzene ring. The sum of aromaticities of the two rings was largest for the (OH⋯N) tautomers, significantly lower for the (OH;N) tautomers, and the smallest for (NH) tautomers. From the electron population in σ and π valence orbitals of the two quinoline rings it appears that, for the benzene ring, the halogens acted as σ-electron withdrawing and π-electron donating substituents, whereas NO2 was a σ- and π-electron withdrawing substituent. The σ substituent effect almost solely influenced the substitution site, i.e., the benzene ring, whereas the π substituent effect was extended to the pyridine ring. Here, we also present changes in the σ and π-electron populations resulting from tautomerization and breaking of the intramolecular OH⋯N hydrogen bonds.

采用DFT/B3LYP/6-311G∗∗方法研究了8-羟基喹啉(8HQ)分子及其4种药物衍生物:氯氧基、氯喹啉、碘喹啉和硝基喹啉(8HQ在苯环上分别被5,7-二氯、5-氯-7-碘、5,7-二碘和7-硝基取代)。每个分子都考虑了三种形式:(OH⋯N)与分子内OH⋯N氢键,(OH;N)与断裂的分子内氢键,以及(NH), h原子与吡啶N原子相连的互变异构体。无论取代与否,具有分子内OH⋯N氢键的(OH⋯N)形式是最稳定的形式。分子内键的断裂导致(OH;N)的形成,其稳定性降低了至少25 kJ/mol。NH互变异构体的能量比(OH⋯N)互变异构体至少高40 kJ/mol。基于AIM分析,发现分子内OH⋯N键在8HQ中最弱,在氯氯喹啉、氯喹啉和碘喹啉中最强,在硝基喹啉中最强。苯环芳香度由8HQ通过卤素取代8HQ下降到硝基喹啉,这与苯环上π电子占比的下降是一致的。(OH⋯N)互变异构体的两个环芳香性总和最大,(OH;N)互变异构体的芳香性总和显著低于(OH;N), (NH)互变异构体的芳香性总和最小。从两个喹啉环的σ价轨道和π价轨道上的电子占比可以看出,对于苯环,卤素是σ-吸电子和π-供电子取代基,而NO2是σ-吸电子和π-吸电子取代基。σ取代基效应几乎只影响取代位,即苯环,而π取代基效应扩展到吡啶环。在这里,我们还提出了由分子内OH⋯N氢键的变异构化和断裂引起的σ和π电子居群的变化。
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引用次数: 15
Theoretical studies and topological analysis of the electron density of clusters of O3 with HNCO and HCNO O3与HNCO和HCNO团簇电子密度的理论研究和拓扑分析
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.015
Abedien Zabardasti , Ali Kakanejadifard , Mozhgan Kikhaei , Mohammad Solimannejad

Ab initio and density functional calculations were used to analyze the O3–HNCO and O3–HCNO clusters in the gas phase. Interaction of O3 with HNCO and HCNO have been investigated at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. Three isomers were found for each system in both methods. The NH⋯O, CH⋯O, O⋯O, N⋯O and C⋯O interactions are predicted in the optimized structures. The atoms in molecules (AIM) theory were also applied to explain the nature of the interaction in predicted clusters.

采用从头算和密度泛函计算对气相中O3-HNCO和O3-HCNO团簇进行了分析。在B3LYP/6-311++G(d,p)和MP2/6-311++G(d,p)计算水平上研究了O3与HNCO和HCNO的相互作用。在两种方法中,每个体系都发现了三个异构体。在优化的结构中预测了NH⋯O, CH⋯O, O⋯O, N⋯O和C⋯O的相互作用。分子中的原子(AIM)理论也被用于解释预测团簇中相互作用的性质。
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引用次数: 11
C–N bond dissociation energies: An assessment of contemporary DFT methodologies 碳氮键离解能:当代DFT方法的评估
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.09.005
Cai Qi , Qiu-Han Lin , Ya-Yu Li , Si-Ping Pang , Ru-Bo Zhang

The assessment of the C–N bond dissociation energies is performed by using the various density functionals at 6-31+g(d,p) level. CBS-QB3 method was used to provide the theoretical benchmark values. The present results show that the three hybrid meta GGA functionals, BB1K, MPWB1K and M06 reproduce the experimental values well. M06-2X could normally overestimate the homolytic C–N bond dissociation energies. For the hybrid functionals, B3P86 and PBE1PBE can also behave almost as well as the above meta GGA functionals. Thus, they should be recommended as the most reliable method to estimate the energetic C–N bond dissociation energies.

利用6-31+g(d,p)水平的各种密度泛函来评估C-N键的离解能。采用CBS-QB3方法提供理论基准值。结果表明,混合元GGA泛函BB1K、MPWB1K和M06能较好地再现实验值。M06-2X通常会高估C-N键的均裂离解能。对于混合函数,B3P86和PBE1PBE也可以表现得几乎与上述元GGA函数一样好。因此,它们应该被推荐为估计C-N键能的最可靠的方法。
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引用次数: 25
Density functional theory calculations of the gas-phase elimination kinetics of 2-(dimethylamino)ethyl chloride and ethyl chloride 2-(二甲胺)氯乙酯和氯乙酯气相消除动力学的密度泛函理论计算
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.08.037
Alexis Maldonado , José R. Mora , Tania Cordova , Gabriel Chuchani

The kinetic and mechanism of the unimolecular gas-phase elimination of 2-(dimethylamino)ethyl chloride were examined by using density functional theory methods to explain the enhanced reactivity in gas-phase elimination compared to the parent compound ethyl chloride. The plausible anchimeric assistance of the dimethylamino proposed in the literature was investigated. The theoretical calculations were carried out at B3LYP/6-31G(d,p), B3LYP/6-31++G(d,p), MPW1PW91/6-31G(d,p), MPW1PW91/6-31++G(d,p), PBEPBE/6-31G(d,p), and PBEPBE/6-31++G(d,p) levels of theory. The previous proposed reaction path of anchimeric assistance has an energy of activation 60 kJ/mol higher than the experimental value. The located transition state in the minimum energy path is a four-centered cyclic configuration comprising chlorine, hydrogen and two carbon atoms. Calculation results give a lower energy of activation of 2-(dimethylamino)ethyl chloride when compared to the parent compound ethyl chloride. This result is due to the stabilization of the transition state because of electron delocalization involving the dimethylamino substituent.

采用密度泛函理论方法研究了2-(二甲氨基)氯乙酯气相消除反应的动力学和机理,以解释其气相消除反应活性较母体氯乙酯增强的原因。研究了文献中提出的二甲基胺的似是而非的对映辅助性。理论计算分别在B3LYP/6-31G(d,p)、B3LYP/6-31++G(d,p)、MPW1PW91/6-31G(d,p)、mpw1pw91 /6-31++G(d,p)、PBEPBE/6-31G(d,p)、PBEPBE/6-31G(d,p)理论水平下进行。先前提出的助嵌合反应路径的活化能比实验值高60 kJ/mol。位于最小能量路径上的过渡态是由氯、氢和两个碳原子组成的四中心环构型。计算结果表明,与母体化合物氯乙酯相比,2-(二甲胺)氯乙酯的活化能较低。这一结果是由于涉及二甲胺取代基的电子离域使过渡态稳定。
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引用次数: 3
High second-order NLO responses of dehydrogenated hydrogen cyanide borane(1) oligomers 脱氢氰化氢硼烷(1)低聚物的高二阶NLO反应
Pub Date : 2010-12-15 DOI: 10.1016/j.theochem.2010.09.001
Miroslav Medveď , Šimon Budzák , Ivan Černušák

Second-order non-linear optical (NLO) properties of dehydrogenated hydrogen cyanide borane(1) oligomers (up to dodecamers) are investigated by the Hartree–Fock, hybrid DFT (including long-range corrected functionals) and MP2 approaches. Due to one-dimensional extension of the systems the longitudinal component of the properties is addressed with focus on the electronic contributions. Direct and indirect electron correlation effects are evaluated at the MP2 level paying particular attention to the basis set effects. Unit-cell asymmetry and delocalization effects in the NLO responses are discussed in terms of the evolution of the bond-length alternation parameter, dipole moment and polarizability (reduced per unit cell) with the increasing chain length. It was found that suitable combination of the unit-cell asymmetry and electron delocalization leads to extremely large NLO response (MP2/6-311++G(d,p) value for the dodecamer is 43.7 × 103 a.u. per unit cell) what makes the conjugated BCN oligomers (if one takes into account their thermodynamic stability) a promising material for NLO applications.

采用Hartree-Fock、混合DFT(包括远程校正泛函)和MP2方法研究了脱氢氰化氢硼烷(1)低聚物(高达十二聚体)的二阶非线性光学(NLO)性质。由于系统的一维扩展,属性的纵向分量主要集中在电子贡献上。在MP2水平上评估直接和间接电子相关效应,特别注意基集效应。从键长交替参数、偶极矩和极化率随链长增加而变化的角度,讨论了NLO响应中的单胞不对称和离域效应。研究发现,单元胞不对称和电子离域的适当结合导致极大的NLO响应(MP2/6-311++十二聚体的G(d,p)值为43.7 × 103 a.u. /单元胞),这使得共轭BCN低聚物(如果考虑到它们的热力学稳定性)成为NLO应用的有前途的材料。
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引用次数: 10
期刊
Journal of Molecular Structure-theochem
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