Calculations of ionization energies and electron affinities for atoms and molecules: A comparative study with different methods

In the present work, we examined the performance of 36 density functionals, including the newly developed doubly hybrid density functional XYG3 (Y. Zhang, X. Xu, and W. A. Goddard III, Proc. Natl. Acad. Sci, USA, 2009, 106, 4963), to calculate ionization energies (IEs) and electron affinities (EAs). We used the well-established G2-1 set as reference, which contains 14 atoms and 24 molecules for IE, along with 7 atoms and 18 molecules for EA. XYG3 leads to mean absolute deviations (MADs) of 0.057 and 0.080 eV for IEs and EAs, respectively, using the basis set of 6-311 + G (3df,2p). In comparison with some other functionals, MADs for IEs are 0.109 (B2PLYP), 0.119 (M06-2X), 0.159 (X3LYP), 0.161 (PBE), 0.162 (B3LYP), 0.165 (PBE0), 0.173 (TPSS), 0.200 (BLYP), and 0.215 eV (LC-BLYP). MADs for EAs are 0.090 (X3LYP), 0.090 (B2PLYP), 0.102 (PBE), 0.103 (M06-2X), 0.104 (TPSS), 0.105 (BLYP), 0.106 (B3LYP), 0.126 (LC-BLYP), and 0.128 eV (PBE0).     

精确计算化学键解离能的ONIOM-G3B3方法及其在抗氧化剂研究中的应用

通过对179个有机化合物C—H,N—H,O—H键离解能的理论计算,系统评估了高精度组合从头算方法(ONIOM-G3B3)和密度泛函理论方法(B3LYP)在预测键离解能上的可靠性.研究发现ONIOM-G3B3方法可以准确预测各类有机化合物的键解离能,精度达到5.9 kJ/mol.运用ONIOM-G3B3方法成功预测了两类重要的天然抗氧化剂维生素E族和茶多酚族的键解离能,并进一步讨论了抗氧化活性、自由基清除机理及其构效关系.     

精确计算化学键解离能的ONIOM-G3B3方法及其在抗氧化剂研究中的应用

通过对179个有机化合物C—H, N—H, O—H键离解能的理论计算, 系统评估了高精度组合从头算方法(ONIOM-G3B3)和密度泛函理论方法(B3LYP)在预测键离解能上的可靠性. 研究发现ONIOM-G3B3方法可以准确预测各类有机化合物的键解离能, 精度达到5.9 kJ/mol. 运用ONIOM-G3B3方法成功预测了两类重要的天然抗氧化剂维生素E族和茶多酚族的键解离能, 并进一步讨论了抗氧化活性、自由基清除机理及其构效关系.     

常见三氟甲基源释放三氟甲基自由基能力的理论计算研究

三氟甲基自由基源（·CF₃）是发展自由基三氟甲基化反应的基础.采用密度泛函理论（M06-2X）,系统研究35个常见三氟甲基源释放CF₃自由基的能力（TR^·DA：trifluoromethyl radical donor ability）及可能的途径.计算结果表明,35个三氟甲基源通过化学键均裂释放三氟甲基自由基所需能量跨度为-21.5至95.2 kcal·mol^-1.单电子转移、卤键和硫键给体（halogen/chalcogen-bond donor）可促进CF₃自由基释放.相关研究结果将有助于理解和设计新自由基三氟甲基化试剂和反应.     

高位阻烷烃的C-C和C-H键的键离解能

本文使用ONIOM-G3B3的方法计算了一系列高位阻烷烃的C-C和C-H键离解能。研究还测定了它们的几何参数,如键长,键角,分子体积等,它们中的绝大多数分子目前还没有被合成。这些几何参数表征了位阻效应对键离解能产生的影响。研究确定了键离解能的迅速减小和分子体积的增大之间的一些关系。这些关系可以帮助使用理论方法预测很多高位阻化合物的合成。     

HCS自由基超精细结构的密度泛函理论计算

１９９８年,李远哲等［１］对ＨＣＳ自由基进行了傅里叶变换毫米波光谱实验研究,测定了质子的超精细耦合常数Ａ（Ｈ）为１２７．４２７ＭＨｚ．他们注意到此值远小于ＨＣＯ自由基的Ａ（Ｈ）值,并认为这与ＨＣＳ的键角比ＨＣＯ的键角大有关．我们用密度泛函理论中的（Ｕ）Ｂ３ＬＹＰ［２,３］方法对ＨＣＳ及有关的ＨＣＯ、ＨＳＩＳ和ＨＳＩＯ自由基进行了计算研究．本研究结果表明：Ｂ３ＬＹＰ方法计算的ＨＣＳ的Ａ（Ｈ）与实验值非常一致;键角的大小不足以解释ＨＣＳ的Ａ（Ｈ）值远小于ＨＣＯ这一事实;用自旋密度却可简明地加以解释．…     

Theoretical study on the hydrolytic deamination mechanism of adenosine

The hydrolytic deamination mechanism of adenosine to produce inosine was studied using density functional method on two models. One is adenine and the other is adenosine. Optimized geometries of reactants, intermediates, transition states, and products were determined at B3LYP/6-311G(d,p) level. IRC calculations were performed on the transition states to verify whether it is the real transition state that connects the corresponding intermediates. Single point calculations were carried out on the previous optimized geometries obtained during IRC calculations. Four pathways have been determined for the hydrolytic deamination of adenosine. Pathway d is the most favorable pathway. In this pathway a tetra-coordinated intermediate is formed through hydrolysis reaction, then the deamination reaction takes place, which causes the cleavage of C6–N10 bond and the creation of C=O bond. Unlike the deamination of adenine, the attacking side of water molecule has effect on the deamination of adenosine. The energy barriers of adenosine deamination are a little higher than those of adenine deamination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

Pd6簇与H2分子相互作用的密度泛函理论研究

通过相对论有效核势密度泛函理论计算,优化了Pd6(H)2和Pd6(H)4等簇的平衡几何结构,预测了氢分子在Pd6簇表面上的吸附行为与活化解离性质.计算结果表明,单态的Pd6簇可以活化两个氢分子;第一个H2和第二个H2吸附解离过程速率决定步骤的能垒分别是66.4和24.5kJ/mol、在形成的分子氢配合物Pd6(H2)和Pd（H)2H2中,H2主要作为给电子配体.在最稳定的二氢簇合物Pd6(H)2中,H倾向与3个Pd相互作用,形成面位氢的多核成键吸附方式.     

Bonding in germatranyl cation and germatranes

Equilibrium structures of silatranyl and germatranyl cations as well as corresponding fluoroatranes are obtained at the B3LYP/cc-pVDZ level of theory. Changes in the bonding on going from germatranyl cation to a neutral molecule are analyzed by using the NBO method. In contrast to three-coordinate planar germylium cations, germatranyl cation does not possess a vacant orbital which is involved in the formation of the transannular bond. However, in germatrane upon formation of an “external” bond with a fluorine anion the inversion of this orbital occurs to accept halogen electron pairs. The presence of the GeF bond drastically changes the scheme of bonding in the GeO₃N moiety compared to that of cation through the formation of interactions of a fluorine atom with equatorial oxygens.     

位阻效应对N-(4-脱氢苯基)吡啶离子与氮氧自由基反应的理论计算研究

应用量子化学密度泛函理论(DFT),在B3LYP/cc-pVDZ基组水平上,对N-(4-脱氢苯基)吡啶离子与不同结构的氮氧自由基反应进行了热动力学研究.优化了反应通道上反应物、中间体、过渡态和产物的几何构型并计算出它们的零点振动能( Ezpv)和焓值,分析数据研究位阻效应对反应的影响.研究表明3类氮氧自由基均与N-(4...     

平面型四核铜簇合物Cu4(CH2XMen)4桥键性质的密度泛函研究

采用密度泛函B3LYP方法，用LanL2DZ和6—31G^＊基组分别优化了平面型四核铜簇合物Cu4（CH2SiMe3）4和Cu4（CH2XMe2）4（X=P，As）的几何构型，并对B3LYP／LanL2DZ方法优化的结构进行了红外振动频率计算和自然键轨道分析．结果表明，簇合物均呈笼状结构，Cu—C—Cu三中心桥键之间电子的离域增强了Cu簇合物的稳定性，配位C原子的C—H平伏键与C—Cu配位键之间存在σ-超共轭效应．     

液态石油烃的脱砷及砷化物与亚铜探针的相互作用

采用密度泛函理论B3LYP方法, 在6-311+G(2df,2p)基组水平上研究了液态石油烃体系中甲基胂化合物与过渡金属探针Cu+和CuCl的相互作用. 结果表明, 甲基胂化物与亚铜离子作用的最稳定模式为四面体构型, 随着烃基取代数增加, 砷化物同Cu+或CuCl的相互作用能(E0)更负, 配合物更稳定, 同时二者的相互作用轨道的能级差(△E)与E0值线性相关(R2≥0.99). Cu+配合物中, As—Cu成键轨道向C—As和/或H—As反键轨道形成电子反馈, 但是CuCl配合物中类似电子反馈则没有形成. 烃基取代并不降低活性组分对砷化物的吸附活性, 在活性组分满足砷化物选择性吸附的条件下, 液态石油烃脱砷的主要控制因素为砷化物在脱砷剂内部孔道中的扩散传输. 有机硫化物噻吩并不影响砷化物的选择性吸附分离, 硫醇类化合物则会影响单烷基砷化物的选择性吸附. 在进行脱砷剂开发时, 应拓宽载体孔道以提高流体传输效率, 并选择活性相组分与砷化物作用的△E相对较小, 配合物容易形成电子反馈, 且对硫醇类化合物的作用能力相对较弱, 对单烷基砷化物的作用能力相对较强的过渡金属组分.     

溶液中甲醇和二氯亚砜的化学反应

用B3LYP方法和SCIPCM模型(模拟溶剂效应)研究了甲醇和二氯亚砜在两种非极性(ε<15)和两种极性(ε>15)溶剂中的反应(最终产物为氯代甲烷和二氧化硫). 反应过程由反应(1)和反应(2)组成, CH3OS(O)Cl是反应(1)的主要产物和反应(2)的反应物. 反应(2)有“前面取代”(经过渡态TS3f)和“背后取代”(先经CH3OS(O)Cl的电离, 再经过渡态TS3b)两种机理. 计算表明, 在气相和四种溶剂中反应(1)和(2)都是放热反应, 反应(1)具有相同的反应途径(经过渡态→中间体→过渡态), 溶剂的极性对反应(2)有很大的影响. 在气相和非极性溶剂中, TS3f的能量比(CH3OSO++Cl-)离子对(中间体IM2)的能量低, 反应(2)应为前面取代机理; 在极性溶剂中, IM2和TS3b的能量都比TS3f低, 反应(2)应为背后取代机理.     

Application of the DFT Theory to Study Cobalamin Complexes

The aim of present study is to select the best methodology in the frame of the Density Functional Theory (DFT), which may be employed to study the cobalamin complexes. Our discussion is limited to two approaches, one in which hybrid B3LYP and UB3LYP functionals are used, and the second in which geometry parameters are calculated within LDA-VWN functional, and energies of the investigated systems are computed within RPBE functional. Results of performed calculations show that both methodologies can be successfully applied to study cobalamin derivatives. Probably because of the small ligand binding energies in the studied complexes, the B3LYP and UB3LYP functionals may be used only to predict the pattern of changes in the binding energies. The use of the RPBE functional, originally parameterized to reproduce in a proper way the chemisorption energies of the small molecules on the metallic surfaces, allows to improve their values so as they fit into experimental data. Geometry parameters of the investigated complexes computed within both approaches are in good agreement with the experimental values. Interatomic distances are a little overestimated while calculated within both hybrid functionals, what is in contrast to VWN functional results. The latter, in general, gives shorter distances as observed experimentally.