Computational study of glycine–(water)3 complex by density functional method

Glycine–(water)₃ complexes have been studied by means of B3LYP density functional method using 6-311++G* basis set. In the complex considered here, the three water molecule are either attached to the carboxylic group or bridge between the amino group and carboxylic group of glycine. Four such complexes are studied. Relaxation energies, two-, three- and four-body interaction energies are obtained by applying many-body analysis to know their role in binding energy of the complex. The results are compared with recent work on glycine–(water)₃ complex with group as proton donor [A. Chaudhari, P.K. Sahu, S.L. Lee, J. Chem. Phys. 120 (2004) 170]. In the most stable structure of glycine–(water)₃ complex, the three water molecules are attached to the carboxylic group of glycine and it is 5.3 kcal/mol lower in energy than that of the most stable structure reported earlier. The three-body term from water–water–water interaction in the most stable in this work and that reported earlier is unique since the distances between the water molecules are almost same. The two-body term from water–water interaction has significant contribution to the total two-body term when the distance between water molecules is less than 3 Å.     

电场对金属串配合物M3(dpa)4Cl2 (M=Co,Rh, Ir; dpa=dipyridylamide)结构的影响

应用密度泛函理论PBE0 方法研究具有分子导线潜在应用的金属串配合物M₃(dpa)₄Cl₂ (1: M=Co, 2: M=Rh, 3: M=Ir; dpa=dipyridylamide)在电场作用下的几何和电子结构. 结果表明: 配合物基态均是二重态. 1和2的M₃⁶⁺金属链形成三中心三电子σ键, 3 中M₃⁶⁺形成三中心四电子σ键且存在弱的δ键. 随金属原子周期数增大其M―M键增强、LUMO与HOMO能隙减小、金属原子的反铁磁耦合减弱以至消失且自旋密度向配体的离域增强. 在Cl4→Cl5 电场作用下, 低电势端的M3－Cl5 键缩短, 高电势端的M2―Cl4 键增长, M―M平均键长略为缩短, M―M键增强, 有利于分子线的电子传递; 分子能量降低, 偶极矩线性增大. 低电势端Cl5的负电荷向高电势端Cl4 转移, 且3 中金属原子的正电荷由高电势端向低电势端的转移较明显, 自旋电子由低电势端向高电势端金属原子移动, 但桥联配体dpa^-与M和Cl 所在的分子轴间没有电荷转移. 电场使LUMO与HOMO能隙减小, 有利于分子的电子输运. 随金属原子周期数增大, 电场作用下M―M平均键长变化减小, LUMO、HOMO的能级交错现象减少.     

C56X10(X=F,Cl, Br,I)的结构稳定性和电子性质

采用密度泛函理论(DFT)中的广义梯度近似(GGA)方法对C56X10(X=F, Cl, Br, I)的结构稳定性和电子性质进行了计算研究. 结构稳定性计算表明: 对于C56X10(X=F, Cl, Br, I), 能隙、反应热、最大振动频率和最小振动频率都随着X原子序数的增加而减小, 表明C56X10(X=F, Cl, Br, I)的稳定性随着X原子序数的增加而逐渐降低, 其中C56F10最为稳定. 前人在实验上已成功合成出C56Cl10, 因此, 我们推测C56F10有望在实验上成功合成. 前线轨道计算发现, C56相邻的五边形公共顶点以及两个六边形-五边形-六边形公共顶点是笼子中化学活性最强的部位, 有利于卤族元素的外部吸附. 此外, 计算结果还显示, C56X10(X=F, Cl, Br, I)的电负性随着X原子序数的增大而逐渐减弱, C—X基团的电负性因位置的不同而不同.     

Density functional study of lanthanide complexes (η-C5H5)2LnX·OC4H8 (Ln=La-Lu; X=F, Cl, Br and I)

Density functional calculations were performed on a series of mixed-ligand organolanthanide complexes, (η⁵-C₅H₅)₂LnX·OC₄H₈ (η⁵-C₅H₅=Cp; Ln=La-Lu; X=F, Cl, Br and I; OC₄H₈=THF). The calculated geometrical parameters are in reasonable agreement with the experimental data. The distances between Ln and ligands follow linearity along the ionic radius of lanthanide metal, as the same as that observed in experiment. In the mixed-ligand complexes, Ln-Cp and Ln-THF bonds are more covalent compared to Ln-X. The lanthanide contraction of various bond and the metal-ligand interaction energy followed the order of Ln-X>Ln-Cp>Ln-OC₄H₈. The orbital population and dipole moment were also discussed.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

The interaction between C28 (Td) and X (X=H and F)

Hydrogen and fluorine addition reactions with C₂₈(T_d) have been investigated by the density function theory method at B3LYP/6-31G level. The interaction potential between C₂₈(T_d) and atom X (X=H and F) shows that there are three possible stable isomers of C₂₈(T_d)X (X=H and F) and the average binding energy calculations suggest that C₂₈(T_d)H₄ is the most stable hydrogen adduct among C₂₈(T_d)H_n (n=1–28). Furthermore, by comparisons of the energy between C₂₈(T_d)H and C₂₈(C_s)H we found that the former are more stable than the later, and the structural and energy analysis further indicate that C₂₈(C_s)H is only with a small distortion of C₂₈(T_d)H symmetry. In addition, the transition states, as well as reaction pathways of X transfer reactions between different key points on C₂₈(T_d) representative patch are given to explore the possible reaction mechanism.     

Structure and conformational stability of CH2CHCH2X (X=F, Cl and Br) molecules—post Hartree–Fock and density functional theory methods

The molecular structure and conformational stability of CH₂CHCH₂X (X=F, Cl and Br) molecules were studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 3-fluoropropene were optimized employing BLYP and B3LYP levels of theory of DFT method implementing 6-311+G(d,p) basis set. The MP2/6-31G^*, BLYP and B3LYP levels of theory of ab initio and DFT methods were used to optimize the 3-chloropropene and 3-bromopropene molecules. The structural and physical parameters of the molecules are discussed with the available experimental values. The rotational potential energy surface of the above molecules were obtained at MP2/6-31G^* and B3LYP/6-311+G(d,p) levels of theory. The Fourier decomposition of the rotational potentials were analyzed. The HF/6-31G^* and MP2/6-31G^* levels of theory have predicted the cis conformer as the minimum energy structure for 3-fluoropropene, which is in agreement with the experimental values, whereas the BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory reverses the order of conformation. The ΔE values calculated for 3-chloropropene at MP2/6-31G^*, BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory show that the gauche form is more stable than the cis form, which is in agreement with the experimental value. The same levels of theory have also predicted that the gauche form is stable than cis for 3-bromopropene molecule. The maximum hardness principle has been able to predict the stable conformer of 3-fluoropropene at HF/6-31G^* level of theory, but the same level of theory reverses the conformational stability of 3-chloropropene and 3-bromopropene molecules and MP2/6-31G^* level of theory predicted the stable conformer correctly.     

Theoretical studies of the oxidative addition of PhBr to Pd(PX3)2 and Pd(X2PCH2CH2PX2) (X = Me, H, Cl)

The density functional theory calculations were used to study the influence of the substituent at P on the oxidative addition of PhBr to Pd(PX₃)₂ and Pd(X₂PCH₂CH₂PX₂) where X = Me, H, Cl. It was shown that the C_ipso-Br activation energy by Pd(PX₃)₂ correlates well with the rigidity of the X₃P-Pd-PX₃ angle and increases via the trend X = Cl < H < Me. The more rigid the X₃P-Pd-PX₃ angle is, the higher the oxidative addition barrier is. The exothermicity of this reaction also increases via the same sequence X = Cl < H < Me. The trend in the exothermicity is a result of the Pd(II)-PX₃ bond strength increasing faster than the Pd(0)-PX₃ bond strength upon going from X = Cl to Me. Contrary to the trend in the barrier to the oxidative addition of PhBr to Pd(PX₃)₂, the C_ipso-Br activation energy by Pd(X₂PCH₂CH₂PX₂) decreases in the following order X = Cl > H > Me. This trend correlates well with the filled d_π orbital energy of the metal center. For a given X, the oxidative addition reaction energy was found to be more exothermic for the case of X₂PCH₂CH₂PX₂ than for the case of PX₃. This effect is especially more important for the strong electron donating phosphine ligands (X = Me) than for the weak electron donating phosphine ligands (X = Cl).     

Quantum-chemical Study on the Structures and Properties of Uracil-BX3 （X = F, Cl） Complexes

1 INTRODUCTION The intermolecular interaction of bases in DNA or RNA is of immense interest and significance to che- mists and biologists alike. The interactions of these bases with metal cations, solvent molecules and other small molecules or ions would affect the struc- ture and biological properties or recognition process,which has been investigated widely[1～8]. Boron contained compounds are electron deficient com- pounds and have been extensively used as catalysts in chemical react…     

Theoretical determination of the favorable mechanism of the reaction between AlX and HX (X = Br, Cl, and F)

The reaction mechanism between AlX and HX (X = Br, Cl, and F) have been characterized in detail using DFT as well as the ab initio method. The reaction yielding AlX₃ and molecular hydrogen was calculated to be highly exothermic. The present calculations also show that the possible routes to the trihalides species start more favorable with the primary insertion product AlX₂H than with the biadduct AlX(HX)₂ one.      

硅苯与HX (X=F,OH, NH2)的1,2-及1,4-加成反应

采用密度泛函理论方法在B3LYP/6-311++G(d,p)水平上, 研究了硅苯与HX (X=F, OH, NH₂)的1,2-及1,4-加成反应的微观机理和势能剖面, 考察了Si 原子上的取代基及四氢呋喃溶剂对反应势能剖面的影响. 研究结果表明, 标题反应有两种可能的机理: (1) 硅苯与一个HX (X=F, OH, NH₂)分子先形成中间复合物, 然后经过四元环过渡态(机理1)生成最终产物; (2) 硅苯与两个HX分子先形成中间复合物, 然后经过六元环过渡态(机理2)生成另一中间复合物, 该中间复合物脱去一个HX分子形成最终产物. 机理2 在动力学上远较机理1 有利. 1,2-及1,4-加成产物哪种优先形成由动力学控制且与X基团的种类有关. HX在气相中参与加成反应从易到难的次序为: HF>H₂O>NH₃. Si 原子上具有较强供电子和吸电子性质的取代基, 在热力学和动力学上均有利于反应的进行, 但具有较大体积的2,4,6-三甲基苯基取代基对反应反而不利. 四氢呋喃溶剂在热力学上不利于硅苯与HX的1,2-及1,4-加成反应, 在动力学上对HF或H₂O作为加成试剂的反应也不利, 但对NH3作为加成试剂的反应反而有利.     

Density functional theory of the iron–nitrosyl (S = 3/2) complex

On the basis of density functional theory (DFT), the iron–nitrosyl complex Fe[Me₃TACN](NO)(N₃)₂ (S = 3/2) is studied via the B3LYP hybrid method. Its Raman vibrational frequencies, atomic net charges, and spin densities are analyzed. The related complexes Fe(NH₃) (n = 1, 2, and 3) are employed as reference compounds to determine the characteristics of the central iron. Our results indicate that the S = 3/2 spin ground state of Fe[Me₃TACN](NO)(N₃)₂ is best described by the presence of Fe^II (S = 2) anti‐ferromagnetically coupled to NO⁰ (S = 1/2) yielding Fe^II[Me₃TACN](NO⁰)(N)₂. This is clearly different from the previous Fe^III‐NO^? theoretical assignment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

苯-卤素(X2, X=F, Cl, Br, I)相互作用本质的对称性匹配微扰理论研究

在MP2水平下对被定义为"电荷转移复合物(CTC)"的苯(C6H6)-卤素分子X2(X＝F, Cl, Br, I)相互作用体系进行了量子化学研究. 在优化所得C6H6-X2(X＝F, Cl, Br, I)复合物的平衡几何结构中, 卤素分子X2接近垂直指向苯环上碳-碳双键的中心. 自然键轨道(NBO)分析结果表明, 苯-卤素体系中电荷转移的数量很少. 对称性匹配微扰理论(Symmetry-adapted perturbation theory, SAPT) 能量分解结果显示, 在4个复合物体系中, 静电作用的贡献相对较小(只占总吸引作用的20%左右), 对于C6H6-F2体系, 色散作用是其主要吸引作用, 对于C6H6-Cl2, C6H6-Br2和C6H6-I2 体系, 诱导作用则是其主要的吸引作用, 从F到I, 色散作用逐渐减弱, 诱导作用逐渐增强, 表明在电子相关水平上将苯-卤素体系称为"电荷转移复合物"的说法并不确切.     

Thermochemistry of the higher chlorine oxides ClOx (x=3, 4) and Cl2Ox (x=3–7)†

Heats of formation for ClO₃, ClO₄, Cl₂O₃, Cl₂O₄, Cl₂O₅, Cl₂O₆ and Cl₂O₇ molecules are determined at the B3LYP, B3PW91, mPW1PW91 and B1LYP levels of the density functional theory employing a series of extended basis sets, and using Gaussian-3 model chemistries. Modified Gaussian-3 calculations, which employ accurate B3LYP/6-311+G(3d2f) molecular geometries and vibrational frequencies, were also performed. Heats of formation were calculated from both total atomization energies and isodesmic reaction schemes. The latter method in conjunction with Gaussian-3 models leads to the most reliable results. The best values at 298 K for ClO₃, ClO₄, Cl₂O₃ and Cl₂O₄ as derived from an average of G3//B3LYP and G3//B3LYP/6-311+G(3d2f) calculations are 43.1, 54.8, 31.7 and 37.4 kcal mol⁻¹. From calculations carried out at the G3(MP2)//B3LYP and G3(MP2)//B3LYP/6-311+G(3d2f) levels, heats of formation for Cl₂O₅, Cl₂O₆ and Cl₂O₇ are predicted to be 53.2, 52.2 and 61.5 kcal mol⁻¹. All best values are reproduced within 1 kcal mol⁻¹ by using mPW1PW91/6-311+G(3d2f) isodesmic energies. Enthalpy changes for relevant Cl–O bond fission reactions are reported. Comparisons with previous thermodynamics data are made.     

Theoretical study on the structure and UV–visible spectrum of pyridine–chloranil charge-transfer complex

The ground-state structure of the charge-transfer complex formed by pyridine (Py) as electron donor and chloranil (CA) as acceptor has been studied by full geometry optimization at the MP2 and DFT levels of theory. Binding energies were calculated and counterpoise corrections were used to correct the BSSE. Both MP2 and DFT indicate that the pyridine binds with chloranil to form an inclined T-shape structure, with the pyridine plane perpendicular to the chloranil. The CP and ZPE corrected binding energies were calculated to be 14.21 kJ/mol by PBEPBE/6-31G(d) and 23.21 kJ/mol by MP2/6-31G(d). The charge distribution of the ground state Py–CA complex was evaluated with the natural population analysis, showing a net charge transfer from Py to CA. Analysis of the frontier molecular orbitals reveals a σ–π interaction between CA and Py, and the binding is reinforced by the attraction of the O₇ atom of CA with the H₂₃ atom of Py. TD-DFT calculations have been performed to analyze the UV–visible spectrum of Py–CA complex, revealing both the charge transfer transitions and the weak symmetry-relieved chloranil π–π^* transition in the UV–visible region.     

Theoretical Studies on Dehydrogenation Reactions in Mg2(BH4)2(NH2)2 Compounds

Borohydrides have been recently hightlighted as prospective new materials due to their high gravimetric capacities for hydrogen storage. It is, therefore, important to under-stand the underlying dehydrogenation mechanisms for further development of these ma-terials. We present a systematic theoretical investigation on the dehydrogenation mecha-nisms of theMg₂(BH₄)₂(NH₂)₂ compounds. We found that dehydrogenation takes place most likely via the intermolecular process, which is favorable both kinetically and thermo-dynamically in comparison with that of the intramolecular process. The dehydrogenation of Mg₂(BH₄)₂(NH₂)₂ initially takes place via the direct combination of the hydridic H in BH₄^- and the protic H in NH₂^-, followed by the formation of Mg-H and subsequent ionic recombination of Mg-H^δ- …H^δ+N.     

Density functional theory analysis of CaRgn complexes: (Rg=He, Ne, Ar; n=1–4)

CaRg_n⁺ (Rg=He, Ne, Ar) complexes with n=1–4, are investigated by performing using the B3LYP/6-311+G (3df) density functional theory calculations. The CaHe_n⁺ (n=1–4) complexes are found to be stable. In the case of CaNe_n⁺ and CaAr_n⁺, stable structures and stationary point were found only for n=1 and 2. For n=3 in the C_3V and the D_3h point group as well as for n=4 in the T_d (tetrahedral) point group a saddle point (imaginary frequency) is observed and global minimum could be obtained along the potential energy surface.     

Ph3PAuX和Ph3AsAuX(X=Cl,Br)的最低三重激发态

分子水平上的激发态理论研究能够用来解释分子材料的多色发光机理. 采用单组态相互作用方法, 计算研究了四种二配位的Au(I)配合物Ph3PAuCl, Ph3PAuBr, Ph3AsAuCl和Ph3AsAuBr的分子结构限制的三重激发态(T1a)和分子结构松弛的三重激发态(T1b)的分子结构与光物理性质. 由于θ(PAuX)/θ(AsAuX)从180°扭曲到120°左右, T1b态的能量在单线态组态相互作用(CIS)水平上降低了0.805-1.124 eV, 在密度泛函理论(DFT)水平上降低了0.820-0.947 eV. 自然键轨道电荷布居数分析表明, 在T1a态中两个单电子主要分布在一个苯基上, 而在T1b态中两个单电子分布在PAuX/AsAuX 上. 因此, 在晶体中观察到的较高能磷光归属于T1a态的苯基之间的3π*→1π电子跃迁, 而较低能磷光主要起源于T1b态的Au 的3σ*→1σ电子跃迁.