Intramolecular Nonbonded Interactions Between Oxygen and Group VIA Elements: An Ab Initio Molecular Orbital and Density Functional Theory Investigation of the Structures of HX—CH2—COOH (X=S,Se, and Te)

Ab initio molecular orbital and density functional methods have been used to study the potential energy surfaces of the substituted acetic acids HX—CH₂—COOH, where X is one of the Group VIA Chalcophiles S, Se, or Te. The various conformers adopted by these compounds provide information regarding the energetic importance of nonbonded and hydrogen bonding interactions involving oxygen atoms with different hybridizations. Density functional and ab initio molecular orbital methods yield similar structural and energetic trends for these compounds. Calculations show that the structure of the lowest-energy conformer of each of these acids has the X—C—C—O backbone substantially twisted from planarity, similar to that previously observed for the corresponding aldehydes, HX—CH₂—CHO. In the twisted acid structures the shortest distance is within about 0.1 Å of the sum of the X and O van der Waals radii, which reduces overcrowding of the lone pairs of electrons on these atoms. In conformers where the heavy atom backbone is planar, one of the distances is significantly shorter than the sum of the van der Waals radii, and the total molecular energy of these conformers is higher than that of the twisted forms. The variation of X—H vibrational frequencies among conformers reflects the extent of X—H hydrogen bonding, and indicates that formation of this hydrogen bond is not the dominant factor in determining the lowest-energy conformation. When X is oxygen (HO—CH₂—COOH), the lowest-energy conformer is also nonplanar, whereas for the corresponding aldehyde, HO—CH₂—CHO, the lowest-energy conformer is a planar structure with C_S symmetry. The conformational preferences of these simple species provide reference points for inter- and intramolecular interactions in more complex systems of biological interest.     

A theoretical study of five nitrates: Electronic structure and bond dissociation energies

Three density-functional methods (B3P86, B3PW91, and B3LYP) are employed to investigate the O–NO₂ bond lengths, frontier orbital energies, and O–NO₂ bond dissociation energies (BDEs) of n-propyl nitrate (NPN), isopropyl nitrate (IPN), 2-ethylhexyl nitrate (EHN), triethylene glycol dinitrate (Tri-EGDN), and tetraethylene glycol dinitrate (Tetra-EGDN). It is found that the O–NO₂ bond lengthens (destabilizes) in the order of IPN, NPN, EHN, Tetra-EGDN, and Tri-EGDN. From the data of frontier orbital energies (E_HOMO, E_LUMO), and energy gaps (ΔE), we estimate the relative thermal stability ordering of five nitrates and their corresponding radicals. The predicted BDEs of O–NO₂ bond in NPN, IPN, EHN, Tri-EGDN, and Tetra-EGDN, are 176.6, 174.5, 168.1, 156.1, and 159.3 kJ mol⁻¹, respectively. Based on the finding that the present results of BDEs are well coincident with the experimental results of apparent activation energies from the literature, we can draw a conclusion that the experimental thermolysis of five nitrates is only unimolecular homolytical cleavage of the O–NO₂ bonds.     

C30卡宾三叶结分子结构与稳定性的理论研究

三叶结分子是最简单的非平凡纽结分子, C₃₀卡宾三叶结分子是由一条闭合的(C≡C—)₁₅ sp杂化碳链组成的, 是具有D₃对称性的拓扑手性分子. 本文用密度泛函方法[DFT/RB3LYP/6-31G(D)]对分子结构和光谱性质进行了研究, 在优化构型的基础上通过自然键轨道(NBO)方法和轨道能级研究了它的共轭性、成键情况和稳定性, 并与平面型C₃₀卡宾环分子进行了比较. 计算结果表明三叶结分子的三叶弧上形成了非平面的C≡C共轭和扭曲的内螺旋结构, 交叉处具有弱成键作用, 且分子轨道也发生了扭曲; 三叶结分子比卡宾环的共轭性和赝Jahn-Teller效应都明显小, 而总能量高. 因此, 分子打结是一个能量升高的过程.     

d9配合物MOSE曲面和几何构型的研究

d~9电子构型的金属离子所形成的配合物几何构型一般为拉长八面体或平面正方形,晶体场理论和角重叠模型都对此作出了较满意的描述,但就该电子构型的中心离子与指定配体配位时易形成配合物的配位数、配体所处的位置等问题,至今尚无满意解释.本文通过分子轨道稳定化能(MOSE)的计算及其曲面的绘制,形象地解释了上述问题.     

Basis Set Orbital Relaxation in Atomic and Molecular Hydrogen Systems

Orbital relaxation (OR) amounts to variation of the orbital exponents in hydrogen molecules and ions relative to the exponents of the isolated atom; it is represented as the sum of the one- and two-center contributions depending on the effective atomic charge and on the presence of other atoms in the molecule. The procedure for isolating the contributions of the exponent includes treatment of the OR of hydrogen in a special set of neutral and charged atoms and molecules with certain multiplicities of their electronic states. Within the framework of the spin-unrestricted Hartree-Fock method, we found and discussed the optimal values of the exponents of the basis orbitals of hydrogen atoms and molecules using the minimal split valence-shell basis set, the basis set that includes the polarization function, and the expanded set of grouped natural orbitals. A simple energy model is suggested for OR. Expressions are derived for evaluating the exponents of the relaxed orbitals in hydrogen-containing systems.Original Russian Text Copyright © 2004 by A. I. Ermakov, A. E. Merkulov, A. A. Svechnikova, and V. V. Belousov__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 973–978, November–December, 2004.     

Hydrogen bonding and dimeric self-association of 2-pyrrolidinone: An ab initio study

Ab initio calculations on the different associated structures of 2-pyrrolidinone with water and with itself were carried out using 3-21G and 6-31G^* basis sets at the Hartree–Fock level, including electron correlation using second-order Møller–Plesset perturbation theory. The calculated free energy changes for the intermolecular hydrogen bonded dimer and hydrated species indicated that the molecular systems with cyclic dimerization and association with two water molecules are dominant. The results are compared to the available experimental data in the literature.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

分子的模糊对称性

将模糊数学方法引入对分子对称点群的研究,建立描述具有不完整分子对称性的模糊点对称群(集合).建立具有模糊对称性分子轨道的模糊表示及其模糊特征标(模糊广义宇称).通过对典型的线状分子、平面分子以及非平面的立体分子等进行分析,展示了一个新的理论化学园地.初步探讨了具有模糊对称性的动态反应体系.从模糊对称性出发,探讨了分子轨道对称守恒原理的半定量特征.     

聚合物{[CuII(Hpb) (mal)]H2O}n :单体的量子化学计算和磁性研究

{[Cu^Ⅱ（Hpb）（mal）]H=O}n （Hpb=2-2＇-pyridylbenzimidazole, mal=maleic acid） is a helical chain-like polymer complex. In order to investigate the electronic structure of the complex, the monomer Cu^Ⅱ（Hpb）（mal） was obturated with different functional groups respectively. For these selective segments, the geometry optimizations were conducted by using hybrid DFT （B3LYP）methods to find that the structure obturated with H2O was better consistent with the experiment, and then this model would be used to latter calculations, such as the frontier molecular orbital and the NBO charge population analysis. In addition the magnetic behaviors of this complex were analyzed by experiments and the weak antiferromagnetic couple between copper（Ⅱ） ions was observed. The exchange coupling constant was calculated by DFT based on the spin broken symmetry formalism. The calculated coupling constants were in good agreement with the experimental data.     

硝酸酯分子几何构型的量子化学研究

运用MINDO / 3、MNDO 和AM1 三种半经验分子轨道(MO)方法, 通过SCF计算, 首次系统地获得了32个硝酸酯化合物分子的全优化几何构型。三种方法的计算结果与已报道的四个化合物(硝酸甲酯、吉纳、硝化甘油和太安)的实验结果相比, AM1法较好。所有硝酸酯的酯基(-ONO~2)具有近似不变的几何参数。直链烷基硝酸酯的键长和键角极为相近, 全部重原子均共平面。二元直链和四元硝酸酯具有对称的分子构型。