Kinetic Study and NBO Analysis of the Dehydrogenation Mechanism of Five‐membered Ring Heterocyclic 2,5‐Dihydro‐[furan,thiophene, selenophene

The theoretical study of the dehydrogenation of 2,5‐dihydro‐[furan ( 1 ), thiophene ( 2 ), and selenophene ( 3 )] was carried out using ab initio molecular orbital (MO) and density functional theory (DFT) methods at the B3LYP/6‐311G**//B3LYP/6‐311G** and MP2/6‐311G**//B3LYP/6‐311G** levels of theory. Among the used methods in this study, the obtained results show that B3LYP/6‐311G** method is in good agreement with the available experimental values. Based on the optimized ground state geometries using B3LYP/6‐311G** method, the natural bond orbital (NBO) analysis of donor‐acceptor (bond‐antibond) interactions revealed that the stabilization energies associated with the electronic delocalization from non‐bonding lone‐pair orbitals [LP(e)_X3] to δ*_{C(1)  H(2)} antibonding orbital, decrease from compounds 1 to 3 . The LP(e)_X3→δ*_{C(1)  H(2)} resonance energies for compounds 1 – 3 are 23.37, 16.05 and 12.46 kJ/mol, respectively. Also, the LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the decrease of occupancies of LP(e)_X3 non‐bonding orbitals in ring of compounds 1 – 3 ( 3 > 2 > 1 ). The electronic delocalization from LP(e)_X3 non‐bonding orbitals to δ*_{C(1)  H(2)} antibonding orbital increases the ground state structure stability, Therefore, the decrease of LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the kinetic of the dehydrogenation reactions of compounds 1 – 3 (k ₁ >k ₂ >k ₃ ). Also, the donor‐acceptor interactions, as obtained from NBO analysis, revealed that the (_C(4)C(7)→δ*_{C(1)  H(2)} resonance energies decrease from compounds 1 to 3 . Further, the results showed that the energy gaps between (_C(4)C(7) bonding and δ*_{C(1)  H(2)} antibonding orbitals decrease from compounds 1 to 3 . The results suggest also that in compounds 1 – 3 , the hydrogen eliminations are controlled by LP(e)→δ* resonance energies. Analysis of bond order, natural bond orbital charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and synchronous six‐membered cyclic transition state type of mechanism.     

Ab initio through‐space/bond interaction analysis of the long C–C bonds in Bi(anthracene‐9,10‐dimethylene) photoisomers

The bi(anthracene‐9,10‐dimethylene) photoisomer has remarkably long C–C single bonds. To examine the lengthening of the C–C bond, we propose a novel procedure for quantitatively analyzing orbital interactions in a molecule at the level of the ab initio molecular orbital method. In this procedure, we can cut off the specific through‐space/bond interactions in a molecule by artificially increasing the absolute magnitude of the exponents in a Gaussian function. Then, the spatial orbital interactions were perfectly cut off, and, each term that makes up the total energy, that is, the nuclear–electron attractions, the electron–electron repulsions, and the nuclear–nuclear repulsions cancel each other. Several model molecules of the photoisomer were analyzed by this procedure. It was found that the orbital interaction between the p orbital on the benzene ring and the σ* orbital on the C–C bond in question, σ→σ* electron transfer through π orbital, weakens the C–C bond efficiently when these orbitals were located in the “periplanar” conformation. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.04, and 8.19 kcal mol(-1), respectively, at BP86/6-311++G(3df,3pd)//B3LYP /6-311++G(3df,3pd) level). Their origin of the cis-preferred difference in energy was investigated with natural bond orbital (NBO) analysis to show that the "cis effect" came mainly from antiperiplanar interactions (AP effect) between the nitrogen lone pair and the neighboring antibonding orbital of the N-X bond (n(N) --> sigma(N'X'*)). The delocalization of halogen lone-pair into the antibonding orbital of the N=N bonds (the LP effects) was also found to enhance the cis preference by 1.20 to 6.58 kcal mol(-1), depending on the substituted halogen atom. The total amount of the AP effect increased as the halogen atom became larger, and the increased AP effect promoted the triple-bond-like nature of the N=N bond (shorter N=N bond length and wider NNX angle). The greater AP effect also made the N'-X' bond easier to cleave (longer N-X bond length), and a higher energy level than that of the nitrogen lone pair was found in the N-Br bonding orbital in 1,2-dibromodiazenes, thus indicating the significant instability of this molecule. The degradability of the N-Cl bond in 1,2-dichlorodiazenes and the fair stability of the N-F bond in 1,2-fluorodiazenes were also confirmed theoretically, and were found to be consistent with the previous experimental and theoretical reports. These results clearly indicate the dominance of lone-pair-related hyperconjugations on the basic electronic structure and energetic natures of 1,2-dihalodiazene systems.     

3-(9-芴甲氧羰基)四氢噻唑-2-硫酮的合成及其晶体结构

在吡啶存在下, 由9-芴甲氧羰酰氯与四氢噻唑-2-硫酮反应得到3-(9-芴甲氧羰基)四氢噻唑-2-硫酮, 产率为78.0%。用X射线衍射法测定晶体结构, 属正交晶系, Pca21空间群, 晶体学参数:a=0.9654(2), b=2.8032(1), c=0.6069(2)nm, Z=4。分子中的C=O与C=S基团处在C(3)-N-C(4)键的同侧, 为顺式结构。用PM3分子轨道方法研究该化合物的电子结构、电荷和键序分布、前线轨道性质。     

A Gaussian-3 investigation on the stabilities and bonding of the nine N10 clusters

A Gaussian-3 investigation has been performed to examine the stabilities of the nine N₁₀ isomers. G3 energies at 0K, enthalpies and heats of formation at 298K have been calculated. The most stable structure is VIII, which consists of three five-membered rings with a bowl-shape structure. The thermodynamic stability trend of the nine N₁₀ clusters is VIII > V > IX > VII > IV > VI > III > I > II, which is different from the previous theoretical results. Natural bond orbital (NBO) and atom in molecules (AIM) analysis have been carried out to study the bonding of these isomers.     

Purification and antioxidant capacity analysis of anthocyanin glucoside cinnamic ester isomers from Solanum nigrum fruits

In a recent study, anthocyanins, which have a strong free radical‐scavenging activity, were examined for their potential to effectively prevent cancer. However, clinical trials are limited by the purity of the anthocyanin. Multiple methods are used to extract and purify anthocyanins. Based on previous work on Solanum nigrum, which is a widely distributed plant, in this study, DM130 macroporous resin, Sephadex LH20, and a C18 column were used to separate cis–trans anthocyanin isomers. These anthocyanins constitute the majority of total S. nigrum anthocyanins. The results showed that this “DM130‐LH20‐C18 system” can be used to obtain a cinnamic acid‐derived cis–trans anthocyanin, petunidin‐3‐(p‐coumaroyl)‐rutinoside‐5‐glucoside, with a purity of 98.5%, for effective quantitation. In order to determine the antioxidant ability of the petunidin‐3‐(p‐coumaroyl)‐rutinoside‐5‐glucoside cis–trans isomers, three ordinary methods were adopted. The maximum antioxidant ability of the cis–trans anthocyanin was dozens of times higher than that of vitamin C.     

14顶点闭合型碳硼烷异构体的结构和稳定性的密度泛函理论研究

采用密度泛函理论(DFT) B3LYP/6-31G(d)方法对14顶点闭合型碳硼烷异构体的几何结构进行优化, 分析了它们的稳定性、电荷分布以及前线分子轨道能级. 结果表明, C₂B₁₂H₁₄碳硼烷的9个异构体都有对应的稳定构型, 并基本保持了B₁₄H₁₄^2－的骨架构型; 除两个C原子取代轴顶点位置B原子的1,14-C₂B₁₂H₁₄外, 其稳定性均随着两个C原子之间距离的增大而增加, 但C原子取代高配位数的B原子不利于其构型的稳定性. 各异构体的负电荷主要分布在C原子上, 同时处于轴向位置的B原子也有部分负电荷, 它们可能成为反应的亲核活性中心. 异构体的HOMO能级的高低与其稳定性相对应, HOMO能级低的异构体稳定性好.     

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 study of the inhibitive properties of a group of benzimidazoles

In this work, a group of benzimidazoles, namely benzimidazole (BIM), 2‐hexyl benzimidazole (2‐HBIM), and 2‐benzyl chloride benzimidazole (2‐ClBBIM), have been studied using density functional theory (DFT) at the level of B3LYP with the 6‐31G (d) and 6‐311G (d, p) base sets in order to elucidate the different inhibition efficiencies and reactive sites of these compounds as corrosion inhibitors. Based on the calculated results, the studied molecules interact with Fe‐atoms mainly in their stable pyridine‐N protonated forms. It is found that the inhibition efficiencies of the stable protonated molecules involved in this study have a certain relation with some parameters, such as the highest occupied molecular orbital energy (E_HOMO) and the global hardness (η). The results indicate that the C (7) atoms, as the reactive sites, receive electrons from Fe‐atoms, benzene ring denote electrons to vacant orbital of Fe‐atoms. Additionally, Fukui indices and the orbital analyses suggest that 2‐ClBBIM has the highest reaction activity among the three molecules, the efficiency order of three inhibitors is found to be 2‐ClBBIM > 2‐HBIM > BIM, which accords with experimental results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

On the mechanism of intramolecular nitrogen‐atom hopping in the carbon chain of C6N radical: A Plausible 3c−4e crossover Long‐Bond

Linear isomers of C₆N radical differ in the position of the nitrogen atom in the carbon chain of C₆N. Reaction routes, involving intramolecular nitrogen atom insertion at varying position in the carbon chain of C₆N, are analyzed for the isomerisation between linear isomers of C₆N. Through an automated and systematic search performed with global reaction route mapping of the potential energy surface, thermal isomerisation pathways for C₆N radical are proposed based on the computations carried out at CASSCF/aug‐cc‐pVTZ, and CCSD(T)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) levels of the theory. Notably, a high lying linear isomer, centrosymmetric with respect to the nitrogen atom, is observed to be stabilized by a unique crossover three center‐four electron π long bond between the carbon atoms that are spatially separated by a nitrogen atom in a natural bond orbital. This long bond is concluded to be responsible for the predicted thermal isomerisation to be more feasible than the dissociation during the isomerisation pathway of a linear isomer of C₆N. © 2014 Wiley Periodicals, Inc.     

The π‐Bonding Trend in VIB M(CO)6 Observed by NMR Spectroscopy — A Natural Bond Orbital View

Analysis of carbonyl's 2π orbital populations, [2π], obtained by NMR relaxation time experiments of VIB M(CO)(?⁶‐C₆H₆) reveals the 3d < 4d < 5d trend for M r? CO back‐donation, as reported values of [2π] for VIB M(CO)₅(quinuclidine). The same analysis performed on Mn(CO)₃(?⁵C₅H₅) and Re(CO)₃(?⁵‐C₅H₅) also gives 3d < 5d order of back‐donation. The distinctive 3d ～ 5d > 4d trend reported for VIB M(CO)₆ has been investigated by second‐order perturbation theory analysis within the natural bond orbital (NBO) scheme to search for orbital‐based explanations. Besides the conventional d_π r? 2π donor‐acceptor (DA) interaction in the trend 3d < 4d < 5d, the other DA interaction arising from three‐center‐hyperbond (3CHB) hyperconjugation has been found in the trend 3d >> 5d ～ 4d. Within the VIB M(CO)₆ family, this 3CHB hyperconjugation is so much higher in Cr(CO)₆ than in W(CO)₆ as to render the overall 2π populations exhibiting the 3d ～ 5d > 4d trend.     

Structures,energetics, and isomerism of [Be,C,O,S]: Stability of triply bonded sulfur

Multiply bonded sulfur has continued to attract attention both experimentally and theoretically. Triply sulfur‐bonded compounds are still rare, due to either the lack of suitable generation precursors or the conversion instability toward doubly sulfur‐bonded structures. A detailed computational study was performed on the structures and stability of various [Be,C,O,S] isomers at the coupled cluster singles doubles (triple excitations) (CCSD(T))/aug‐cc‐pVTZ//B3LYP/6‐311+G(d)+ZPVE level to predict intrinsically stable isomers with triply bonded sulfur. The molecular orbital, bond distance, and harmonic vibrational frequency analysis were carried out at aug‐cc‐pVTZ‐B3LYP, M06‐2X, and CCSD(T) levels to investigate the bonding nature of linear structures. It was shown that two low‐lying isomers are linear SBeCO 01 (0.0 kcal/mol) and SBeOC 02 (15.7 kcal/mol), both of which possess the SBe triple bonding. The Lewis acid–base association of SBe + CO can barrierlessly form 01 and 02, with the former more abundant, while the insertion reaction of SCO + Be might generate more 02 than 01 via photochemical processes. By contrast, formation of the SC‐bearing isomer SCBeO 04 (39.4 kcal/mol) seems unlikely due to its higher energy and less kinetic competition than that of 01 and 02, via either simple association or insertion reactions. The new stable isomers SBeCO 01 and SBeOC 02 add to the number of SBe triply bonded species. Their unique structures and varied branching ratios under association and insertion processes deserve future experimental study. © 2013 Wiley Periodicals, Inc.     

Assessment of substituent effects on the parameters of 35Cl nuclear quadrupole resonance in para‐substituted benzene‐sulphenyl chloride via quantum chemical calculations

In this research, substituent effects on the parameters of ³⁵Cl nuclear quadrupole resonance (NQR) in para‐substituted benzene‐sulphenyl chloride were studied at M062X/6‐311G(d,p) theory level. The ³⁵Cl NQR parameters of the quadrupole coupling constant (QCC) and electric‐field gradient (EFG) tensor, as well as an asymmetric parameter, were shown to be correlated with Hammett constant following their calculations. The frontier orbital energy levels, HOMO‐LUMO gaps, hardness, electrophilicity, and chemical potential values of these molecules were calculated as well. natural bond orbital (NBO) analysis was applied for calculating natural populations at chlorine atoms.     

反式-1,4,5,8-四硝基-1,4,5,8-四氮杂萘烷异构体热解机理与稳定性的理论研究

运用密度泛函理论和半经验分子轨道方法,对一系列高能杂环硝胺—反式-1,4,5,8-四硝基-1,4,5,8-四氮杂萘烷异构体的热解机理和稳定性进行了系统地计算研究。在B3LYP/6-31G**和PM3水平上,分别计算了标题物的化学键离解能(BDE)和热解反应活化能(Ea),并根据BDE和Ea数值考察了硝胺取代基对化合物稳定性和热解机理的影响;同时,还详细考察了BDE与Ea、化学键重叠布居数、前线轨道能级以及能隙之间的相关性。结果表明,由BDE、Ea和静态电子结构参数推断的标题物热稳定性和热解机理的结论基本是一致的,N-NO2键均裂是标题物的热解引发步骤,间位取代异构体较对位取代异构体稳定,而邻位取代的异构体稳定性最差。     

Peroxide linkage N2O4 molecule: Prediction of new ONOONO isomers

Ab initio and density functional theory (DFT) have been applied to predict the existence of the ONOONO molecules. Two new isomers, cis‐perp‐cis and cis‐perp‐trans ONOONO, are found to be minima on the potential energy hypersurface calculated at MP2 level with 6‐311G(d) basis set and Becke3P86 and Becke3LYP levels with the cc‐PVDZ basis set. Vibrational frequencies are calculated at the optimized structures. Calculations at both ab initio and DFT methods show that cis‐perp‐cis is energetically favored in all three O O bonded ONOONO isomers. © 1999 John Wiley & Sons, Inc. Int J Quant Chem 76: 77–82, 2000     

Intramolecular hydrogen bond in the hydroxycyclohexadienyl peroxy radicals

The hydroxycyclohexadienyl peroxy radicals (HO? C₆H₆? O₂) produced from the reaction of OH‐benzene adduct with O₂ were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical II_s and 4‐hydroxycyclohexadienyl peroxy radical III_s were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical II_s is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical III_s, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

3-苄氧羰基四氢噻唑-2-硫酮的晶体结构与量子化学研究

苄氧羰酰氯与四氢噻唑-2-硫酮在三乙胺存在下反应生成了3-苄氧羰基四氢噻唑-2-硫酮。在甲醇中培养了标题化合物单晶,用X射线衍射法进行了结构表征。晶体结构属三斜晶系,P1间群,晶体学参数:a=0.6274(2)nm,b=0.7340(3)nm,c=1.2976(4)nm;α=100.73(3)°,β=94.53(3)°,γ=103.28(3)°,Z=2,M_μ=4.30cm^-1.分子中的>C=O与>C=S基团处于C(4)-N-C(1)键的同侧,为顺式。用PM₃分子轨道方法研究了该化合物的电子结构,得到电荷和键序分布以及前线轨道等性质。     

配合物[Ni(Pht)(Medpq)(H2O)3]n的水热合成、表征及自然键轨道(NBO)分析

采用水热法合成了一种新型金属配合物[Ni(Pht)(Medpq)(H2O)3]n(1)(Pht=phthalic acid,Medpq=2-methyldipyrido[3,2-f∶2′,3′-h]quinoxaline),并对其进行了元素分析、红外光谱、热重表征、X射线单晶衍射测定和理论计算。在晶体中,Ni(Ⅱ)与来自于Medpq分子上的2个氮原子,邻苯二甲酸上的1个氧原子及来自于3个不同的配位水分子上的3个氧原子配位,形成畸变的八面体构型。整个晶体由Pht-Ni-Medpq单元组成零维结构。应用Guassian03W程序,在HF/LANL2DZ水平上对标题化合物的自然键轨道(NBO)进行了分析,结果表明Ni(Ⅱ)与配位原子间的价键类型都属于共价键范畴。     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006