Silabenzene through divalent precursors at theoretical levels

Abstract  

Based on geometries and relative energies, three different mechanisms are proposed for the rearrangements of five isomers of silacyclohexadienylidenes to silabenzene at B3LYP and MP2 levels: (1) [1,2]-hydrogen migration through a planar transition state, (2) [1,4]-hydrogen migration through a boat transition state, and (3) zip-zap mechanism, comprised of three successive [1,2]-hydrogen migrations. The above results are compared and contrasted to rearrangements of the corresponding cyclohexadienylidenes to benzene.     

On the selenepin/benzene selenide valence tautomerizations: electronic and steric effects at theoretical levels

Tautomerization in selenepin (1) benzene⇌selenide (2) binary system is found to favor, 2, at HF, MP2, and B3LYP levels, using 6-311G* basis set. Electronic effects appear to have small effects on 1⇌2 equilibria and show little impact on the conformational ring inversions of 1, at the same levels. In contrast, steric effects effectively decrease ∆H values in an order inversely proportional to the size of the substituents employed (Me > Et > i-Pr). A possible Se extrusion is suggested to be the main reason why no 2 has ever been detected experimentally. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of fused benzene rings on tautomerizations and inversions of benzo, azabenzo, and oxabenzocycloheptatrienes at theoretical levels

Biologically important bicyclic species, including 6H-, 6H-6-aza-, and 6-oxabenzocycloheptatrienes (in which the benzene moiety is fused meta with respect to the tetrahedral constituents: –CH₂–, –NH–, and –O–, respectively), show strong shifts of tautomerizations in favor of the corresponding tricyclic benzonorcaradienes (with ΔH values of −11.49, −14.55, and −19.20 kcal mol⁻¹, respectively), at B3LYP/6-311++G**//B3LYP/6-31G*, and MP2/6-311++G**//MP2/6-31G* levels, and at 298 K. In contrast, such shifts are strongly disfavored by the isomeric bicyclic species in which the benzene moieties are fused ortho or para with respect to –CH₂–, –NH–, and –O–, respectively. Hence for species with ortho benzene rings including 5H-, 5H-5-aza- and 5-oxabenzocycloheptatrienes, tautomerization ΔH values are 30.76, 31.89, and 25.27 kcal mol⁻¹, respectively, while for species with para fused benzene moieties including 7H-, 7H-7-aza-, and 7-oxabenzocycloheptatrienes, tautomerization ΔH values are 24.12, 26.00, and 19.55 kcal mol⁻¹, respectively. NICS calculations are successfully used to rationalize these results. The calculated energy barriers for inversion of the seven-membered rings of bicyclic species predict a dynamic nature for all the structures except for the virtually planar 6H-6-aza- and 6-oxabenzocycloheptatrienes. Finally, our theoretical data are compared to the experimental results where available. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

An Ab Initio Molecular Orbital Study of Valence Bond Isomers of Silabenzene and Phosphabenzene

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single point total energy calculation are reported for silabenzene ( 7 ), phosphabenzene ( 8 ) and 16 valence bond isomers of silabenzene and phosphabenzene ( 9-24 ). The calculated energy difference (19.78 kcal mol m 1 ) between silabenzene and the most stable valence bond isomer of silabenzene (1-silabenzvalene, 9 ) is much smaller than the difference (73.60 kcal mol m 1 ) between benzene and benzvalene ( 2 ). The energy difference between phosphabenzene and the most stable valence bond isomer of phosphabenzene (1-phosphabenzvalene, 17 ) is calculated to be 43.29 kcal mol m 1 .     

Kinetic study of the reaction H2O2+H→H2O+OH by ab initio and density functional theory calculations

Theoretical investigations on the kinetics of the elementary reaction H₂O₂+H→H₂O+OH were performed using the transition state theory (TST). Ab initio (MP2//CASSCF) and density functional theory (B3LYP) methods were used with large basis set to predict the kinetic parameters; the classical barrier height and the pre-exponential factor. The ZPE and BSSE corrected value of the classical barrier height was predicted to be 4.1 kcal mol⁻¹ for MP2//CASSCF and 4.3 kcal mol⁻¹ for B3LYP calculations. The experimental value fitted from Arrhenius expressions ranges from 3.6 to 3.9 kcal mol⁻¹. Thermal rate constants of the title reaction, based on the ab initio and DFT calculations, was evaluated for temperature ranging from 200 to 2500 K assuming a direct reaction mechanism. The modeled ab initio-TST and DFT–TST rate constants calculated without tunneling were found to be in reasonable agreement with the observed ones indicating that the contribution of the tunneling effect to the reaction was predicted to be unimportant at ambient temperature.     

Investigation of the effects of ionic hydrogen bonds (COH–C and N–HOC) in crystalline dl-proline by ab initio and DFT calculated NQR parameters

In this paper, we have calculated the nuclear quadrupole resonance (NQR) parameters of the quadrupole nuclei involved in the hydrogen bonds (CO⁻H–C and ⁺N–H⁻OC) in the monomer and pentameric cluster of dl-proline by HF and B3LYP methods and basis sets of 6-311+G^* and 6-311++G^**. These computations are performed on the basis of X-ray diffraction structural data of dl-proline. The results indicate that the calculations including hydrogen-bonding (HB) interactions (in pentamer) are in better agreement with the experimental data than those in which these interactions are neglected (in monomer). The quantum chemical calculations show that the intermolecular hydrogen-bonding interactions play an important role in determination of the NQR parameters of ¹⁴N, ²H of group and ¹⁷O.     

Self-assembly of DMF with chloromethane and their structures: a theoretical study

The stability of hydrogen-bonded complexes, DMF–H _n CCl_4−n (n = 1–3), has been investigated by several theoretical methods including the MP2 level of ab initio theory at various basis sets from 6-31+G* to 6-311++G**. Two stable configurations (respectively a and b) were obtained for each complex with no imaginary frequencies. The minimum energy structure of these complexes has also been analyzed by means of the atoms in molecule theory at MP2/6-311++G** level. It is found that C–H···O hydrogen bonding exists in these systems and that the intensity of HB interaction gradually increases with successive chlorination. Computed results indicate that these complexes automatically assemble into different stable configurations. For the complexes under consideration, their stabilities can be mainly ascribed to the intermolecular HB interaction. The present work is helpful to clearly understand the interaction mechanism of these complexes in theory.     

Binding mechanism of RGD and its mimetics to receptor GPIIb/IIIa. A theoretical study

In order to better understand, at a sub-molecular level, the minimal structural requirements for the recognition process in the platelet aggregation inhibitory activity, a series of RGD mimetics were examined as fibrinogen receptor antagonists variants. We simulate the electronic interactions between RGD with its biological receptor in terms of smaller molecules. MeCOO⁻ was used to mimic the side chain of deprotonated Asp and Meguanidinium group mimicked the side chain of the protonated Arg. Alternative moieties present on the RGD mimetics were also studied in this report. AM1; RHF/3-21G; B3LYP/6-31++G^** in the gas phase. Also, B3LYP/6-31++G^** calculations using the IPCM solvation model were carried out for all the complexes. Our results indicate that high level of theory calculations and the inclusion of solvent effects are crucial in order to obtain satisfactory of accuracy in the electronic distributions of these compounds.     

Hydrogen bonds and ionic interactions in Guanidine/Guanidinium complexes: a computational case study

It is frequently said that hydrogen bonds (HBs) are enhanced by ionic interactions and in this article we intend to determine the degree at which this reinforcement happens. Considering our interest in the Guanidine(neutral)/Guanidinium(cation) system and its particular nature, all the possible 1:1 complexes with the Chloride(anion)/Hydrochloric acid(neutral) system have been studied at different levels of computation (B3LYP with 6-31+G* and TZVP basis sets; MP2 with 6-31+G*, 6-311++G** and aug-cc-pVDZ basis sets; CBS-QB3 and G3MP2). The nature of these interactions established in all the systems and, when possible, at all the levels of computation used in this study, has been analyzed using Atoms in Molecules and Natural Bond Orbital methodologies. By examining the interaction energy, the electron density at the bond critical bonds, the atomic energy, the charge transfer, the orbital energy, and the deformation energy we can conclude that HBs are stronger when the ionic interaction is stronger. Thus, both interactions do not work in an independent manner but one reinforces the other to different degrees depending on the nature of the charges present. Several correlations with the interaction energy have been found and a partition of the contributions of both the HB and ionic forces to the total interactions is proposed.     

Cl_2 2HI=2HCl I_2反应机理的理论研究

分别在MP2/3-21G!!、CCSD(T)/3-21G!!//MP2/3-21G!!和B3LYP/3-21G!!3种水平上,计算研究了气相反应Cl2 2HI=2HCl I2的机理,求得一系列四中心和三中心的过渡态.通过比较六种反应通道的活化能大小,得到了相同的结论:双分子基元反应Cl2 HI"HCl ICl和ICl HI"I2 HCl的最小活化能小于Cl2、HI和ICl的解离能,从理论上证明了反应Cl2 2HI=2HCl I2将优先以分子与分子作用形式分两步完成.用内禀反应坐标(IRC)验证了MP2/3-21G!!方法计算得到的过渡态.     

Cl2+2HI=2HCl+I2反应机理的理论研究

分别在MP2/3-21G**、CCSD(T)/3-21G**//MP2/3-21G**和B3LYP/3-21G**3种水平上, 计算研究了气相反应Cl₂+2HI=2HCl+I₂的机理, 求得一系列四中心和三中心的过渡态. 通过比较六种反应通道的活化能大小, 得到了相同的结论：双分子基元反应Cl₂+HIHCl+ICl和ICl+HII₂+HCl的最小活化能小于Cl₂、HI和ICl的解离能, 从理论上证明了反应Cl₂+2HI=2HCl+I₂将优先以分子与分子作用形式分两步完成. 用内禀反应坐标(IRC)验证了MP2/3-21G**方法计算得到的过渡态.     

A computational study of AlN nanotube as an oxygen detector

Interaction of O2 molecule and a zigzag aluminum nitride nanotube(AlNNT) was studied based on the density functional theory.The O2 molecule is adsorbed on the surface of AlNNT with the adsorption energies in the range of 11.0 to 12.1 kJ/mol.Geometrical structure of the AlNNT remains intact in the presence of oxygen molecule while its electronic structure dramatically changes so that its HOMO(or SOMO)-LUMO gap is approximately reduced to half of its original value.It suggests that the AlNNT may be used as a gas sensor for the O2 detection.     

Substituent effect on diastereoselectivity in Type-II ene cyclisation: a theoretical study

Methyl and methoxy substituted transition states (TS) of Type-II ene cyclisation have been optimized by ab-initio method and relative stability of the diastereomeric TSs have been calculated. In all TSs, equatorial substituent positions have been found to be preferred over the axial positions except for the 4′-substituted methoxy derivative, in which the methoxy group prefers to retain axial position. It has also been noted that the presence of the methoxy group(s) in other position(s) may affect the stability of axially oriented TS and thus alters the overall stereoselectivity of the reaction.     

Synthesis, characterization, and DFT studies of a novel azo dye derived from racemic or optically active binaphthol

We present a new azo reactive dye from racemic or optically active BINOL. This dye was characterized by UV-vis, FTIR, mass, ¹H NMR, and ¹³C NMR spectroscopic techniques and elemental analysis. The structure and spectrometry of this azo dye have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G^∗ basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FTIR spectra are assigned based on the results of the theoretical calculations. The theoretical electronic absorption spectra have been calculated using CIS, TD-DFT, and ZINDO methods. In addition, a good agreement between calculated and experimental NMR data is observed.     

Theoretical study for the HNSi–HSiN isomerization: ab initio and DFT calculations

Ab initio and density functional theory (DFT) calculations using the GAUSSIAN 94 program have been performed to investigate the molecular structures of HNSi and HSiN in the ground state as well as the transition state for the HNSi–HSiN isomerization reaction at the 6-311G(d,p), 6-311+G(2d,p) and 6-311+G(2df,p) basis sets. The results show that DFT calculations at higher levels of theory reproduce experimental vibrational frequencies of both HNSi and HSiN better than ab initio methods including electron correlation effects. Those calculated geometries are accurate enough to predict the rotational constant of HNSi. The barrier height for the isomerization reaction is found to be about 10 kcal/mol.     

Complete basis set ab initio computational study of three-dimensional aromaticity in highly symmetric hydrogen clusters

The aromaticity of planar and highly symmetric three-dimensional hydrogen clusters were evaluated with the complete basis set ab initio computational method. The energy of formation of the hydrogen clusters from the hydrogen molecule and hydrogen molecular ions were used in comparison to their relative stabilities. The aromaticity of planar hydrogen clusters, as well as hydrogen clusters in the three dimensions, arranged as highly symmetric regular polyhedra (Plato's polyhedras), were discussed with respect to the Hückel and Möbius aromatic rules.     

A theoretical study of the Si-O bond in disiloxane and related molecules

Summary A comparison of semi-empirical (MNDO) and ab initio (GAUSSIAN) calculations for disiloxane and related molecules is given. The STO-3G^* basis set well reproduced the observed geometries of disiloxane (*), DZP, TZVP) gave much poorer agreement with the observed geometries.Comparison of the STO-3G^* and the STO-3G basis sets demonstrates the necessity of including d-orbitals on the silicon. However, the semi-empirical MNDO program gave, despite the absence of d-orbitals, a better approximation to the molecular geometry than the complex ab initio basis sets.Force field parameters have been calculated for k_SiOSi, k_OSiO, 0.089 and 0.73 mdyneÅ/rad², and the SiOSiO torsion which has a V₁ potential of –0.68 kcal/mol. In addition, the HSiOH torsion is shown to have a three-fold potential of 0.78 kcal/mol. These are profoundly different from the analogous carbon-oxygen force constants, demonstrating that C-O parameters cannot be transferred to the corresponding Si-O systems.     

淀粉系高吸水性树脂反应中间体稳定性及反应活性的量子化学研究

运用abinitioUHF方法和DFTUB3LYP方法在6-31G基组水平下对淀粉系高吸水性树脂反应中间体的模型体系进行几何构型优化.针对每类自由基对应得到的两种典型的构象异构体(1_a,1_b和2_a,2_b),进行稳定性和反应活性分析.构型1_a和2_b的总能量相对较低.比较4个模型体系的前线分子轨道,构型1_a的能隙较小,同时HOMO能量较高,易给出电子,LUMO能量较低,易得电子,有利于电子转移,因而有较好的反应活性.自由基自旋密度主要集聚在C2或C3上,未有较大弥散,同时也是前线MO主要布居位置和重要的反应活性部位.对构型1_a与丙烯酸模型分子形成的复合物分析表明,两者的反应未经过过渡态,在瞬间即可完成.