Computational study of epoxy-amine reactions

Density functional theory calculations were carried out for the title reactions. Ethylene oxide and methylamine were adopted as reactants. Amine clusters (dimer, trimer, tetramer, and pentamer) were considered, because the combination of one oxide and one amine molecule gave a large activation energy. An amine tetramer was found to react favorably with the oxide via various zwitterionic intermediates. A back-side S(N)2 nucleophilic attack of one amine and the subsequent proton relay up to the front side provide a stabilized reaction field. The amine-alcohol mixed reactant may react readily with the oxide, because the alcoholic O-H group is in contact with the oxide oxygen with the strong hydrogen-bond stabilization.     

Long‐range π‐type hydrogen bond in dimers CH2?HF,CH2O?H2O,and CH2O?NH3

Using four basis bets, (6‐311G(d,p), 6‐31+G(d,p), 6‐31++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for the dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. In contrast with the above three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD (T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

四唑及其衍生物的理论研究Ⅷ: 硝氨四唑衍生物的从头算

运用从头计算法,在HF/6-31G^*水平下,全优化计算了7种硝氨四唑衍生物的分子几何和电子结构。结果表明,标题物的四唑环近似为平面构型;2H式中性分子的芳香性大于相应的1H式异构体。5-硝氨-1H四唑分子内氢键使硝氨基与环共面;其余标题物中硝氨基与环垂直。不同水平下的总能量计算表明,标题物中电子相关效应显著;1H式中性分子较2H式的能量高,5-硝氨四唑负离子在三个负离子中最稳定。根据电荷分布阐明了四唑环质子化位置和标题物与金属的配位方式。此外还计算了各标题物的红外光谱及热力学性质。     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Rg—HX(Rg=He,Ne;X=F,Cl,Br)分子间势的精确量子化学从头计算研究III.He—HBr

在用非迭代的三重激发项来校正CCSD的CCSD（T）理论水平下，采用aug-cc- pVQZ基函数对He—HBr的分子间势进行了系统的研究。结果表明：He—HBr以线型结 构存在。在极限基的情况下，复合物两种线型极小点结构He—H—Br和He—Br—H势 阱深分别为28.792 cm~(-1)和35.707 cm~(-1)，对应He原子到HBr分子质心的距离 R分别为0.407 nm和0.343 nm。讨论了不同的基函数和理论方法在研究此类弱束缚 态复合物的分子间势时的可靠性及其对结果的影响，同时也给出了热函数的解析形 式。     

甲醛与乙醛,甲醚,硝基甲烷相互作用的从头算研究

用6-31G、全构型优化,研究了甲醛与乙醛、甲醚、硝基甲烷的相互作用。结果表明所有超分子稳定构型都包含2个C—H—O氢键的平面环状结构。H—O距离为0.228～0.264 nm,作用能为—19～—24 kJ/mol,与二聚水的作用能接近。稳定性主要取决于甲基上取代基Y吸电子能力以及环状结构中氢键张力。STO-3G不很适用于研究这类分子的相互作用。     

Computationally-assisted approach to the vibrational spectra of molecular crystals: study of hydrogen-bonding and pseudo-polymorphism.

A new computationally-assisted methodology (PiMM), which accounts for the effects of intermolecular interactions in the crystal, is applied to the complete assignment of the Raman and infrared vibrational spectra of room temperature forms of crystalline caffeine, theobromine, and theophylline. The vibrational shifts due to crystal packing interactions are evaluated from ab initio calculations for a set of suitable molecular pairs, using the B3LYP/6-31G* approach.The proposed methodology provides an answer to the current demand for a reliable assignment of the vibrational spectra of these methyl-xanthines, and clarifies several misleading assignments. The most relevant intermolecular interactions in each system and their effect on the vibrational spectra are considered and discussed. Based on these results, significant insights are obtained for the structure of caffeine in the anhydrous form (stable at room temperature), for which no X-ray structure has been reported. A possible structure based on C((8))--H...N((9)) and C((1,3))--H...O intermolecular interactions is suggested.     

Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra

The infrared (IR) and Raman spectra of eight substitutional carbon defects in silicon are computed at the quantum mechanical level by using a periodic supercell approach based on hybrid functionals, an all electron Gaussian type basis set and the CRYSTAL code. The single substitutional C _s case and its combination with a vacancy (C _sV and C _sSiV) are considered first. The progressive saturation of the four bonds of a Si atom with C is then examined. The last set of defects consists of a chain of adjacent carbon atoms C, with i = 1–3. The simple substitutional case, C _s, is the common first member of the three sets. All these defects show important, very characteristic features in their IR spectrum. One or two C related peaks dominate the spectra: at 596 cm⁻¹ for C _s (and C _sSiV, the second neighbor vacancy is not shifting the C _s peak), at 705 and 716 cm⁻¹ for C _sV, at 537 cm⁻¹ for C and C (with additional peaks at 522, 655 and 689 for the latter only), at 607 and 624 cm⁻¹, 601 and 643 cm⁻¹, and 629 cm⁻¹ for SiC, SiC, and SiC, respectively. Comparison with experiment allows to attribute many observed peaks to one of the C substitutional defects. Observed peaks above 720 cm⁻¹ must be attributed to interstitial C or more complicated defects.     

Study of spectral analytical data using fingerprints and scaled similarity measurements

A new chemoinformatic model has been developed for enlarging the differences between spectra and applied to differentiation of wines according to the criteria grape origin and variety and ageing process. The model is based on generation of fingerprints from normalised spectra, using empirical parameters and a set of 120 samples. After generation of the fingerprints, similarity matrixes were built on the basis of the Tanimoto similarity index between the fingerprints of the samples. Calculation of the Tanimoto index was modified to adapt the index to the characteristics of the analytical measurements. Thus, scaling factors taking into account pattern fingerprints generated from a group of samples with common characteristics were used. In addition, a modified expression for calculating the Tanimoto index was employed. Principal-components analysis (PCA) and soft independent modelling of class analogy (SIMCA) were applied to the similarity matrixes. The results obtained are discussed as a function of the normalisation method employed, the empirical factor used in generation of the fingerprints, and selection of samples for building the pattern fingerprint, etc. Finally, results from differentiation of wines are compared with those obtained by applying PCA to the unprocessed spectra as stated by the proposed model.     

Novel platinum-catalysed cascade reactions: cyclisation, ring expansion and 1,2-oxygen shift reaction of a camphor-derived diyne

2,3-Bis(ethynyl)-3-hydroxy-camphorsultam was converted in one step into a novel tetracyclic cyclopentenone derivative, in an unprecedented platinum-catalysed cascade reaction. In the course of this reaction, cyclisation of the alkynes takes place, together with a ring expansion of the camphor skeleton and 1,2-migration of an oxygen atom. The structure of the unexpected product was analysed in detail by one- and two-dimensional NMR spectroscopy, and validated with the help of quantum mechanical calculations (B3LYP/6-31G^∗∗ and B3LYP/6-31+G(2df)) of the IR vibrational frequencies and the ¹H and ¹³C isotropic chemical shifts.