Atranes

The conformational energy of the 1-methylsilatrane molecule for sp³ and sp³d hybridization of the silicon atom was calculated. The known data on the structure of the atrane portion of the molecule are in good agreement with the results of the calculation for sp³d hybridization and differ radically from the results of the calculation for sp³ hybridization of the silicon atom. The conformational factors constitute a considerable contribution (11.4 kcal/mole) to the forced change in the hybridization of the silicon atom. An analysis of the dependence of the energy of the 1-methylsilatrane molecule on the distance between the Si and N atoms shows that a stable exo form, isolated to any extent by a considerable conformational barrier from the real structure with an SiN transannular interaction, does not exist.See [1] for communication XXXIV.Translated from Khimiya Geterotsiklicheskikh Soedinenii. No. 5, pp. 613–617, May, 1974.     

Chemical bonding in the crystal structure of 1-hydrosilatrane

A study has been made of the crystal and molecular structure of 1-hydrosilatrane HSi(OCH_2CH₂)₃N. The quantum chemical calculations of its crystal structure have been carried out. According to an estimate of the energy, the coordination bond N→Si is by 5 kcal mol^?1 stronger than that in the crystal of 1-methylsilatrane. The charge values calculated within the framework of the topological analysis of the electron density demonstrate that the electron density of the coordination bond N→Si is primarily transferred to the region of the equatorial bonds Si—O and, to a lesser extent, to the bond Si—H. On going from the isolated molecule of 1-hydrosilatrane to its crystal, the interatomic distance N—Si decreases, mainly owing to the weak intermolecular interaction C—H...O.     

Pyridazine based scorpionate ligand in a copper boratrane compound

Reaction of potassium tris(mercapto-tert-butylpyridazinyl)borate K[Tn(tBu)] with copper(II) chloride in dichloromethane at room temperature led to the diamagnetic copper boratrane compound [Cu{B(Pn(tBu))(3)}Cl] (Pn = pyridazine-3-thionyl) (1) under activation of the B-H bond and formation of a Cu-B dative bond. In contrast to this, stirring of the same ligand with copper(I) chloride in tetrahydrofuran (THF) gave the dimeric compound [Cu{Tn(tBu)}](2) (2) where one copper atom is coordinated by two sulfur atoms and one hydrogen atom of one ligand and one sulfur of the other ligand. Hereby, no activation of the B-H bond occurred but a 3-center-2-electron B-H···Cu bond is formed. The reaction of copper(II) chloride with K[Tn(tBu)] in water gave the same product 2, but a formal reduction of the metal center from Cu(II) to Cu(I) occurred. When adding tricyclohexyl phosphine to the reaction mixture of K[Tn(R)] (R = tBu, Me) and copper(I) chloride in MeOH, the distorted tetrahedral Cu complexes [Cu{Tn(R)}(PCy(3))] (R = tBu 3, Me 4) were formed. Compound 4 is exhibiting an "inverted" κ(3)-H,S,S, coordination mode. The copper boratrane 1 was further investigated by density functional theory (DFT) calculations for a better understanding of the M→B interaction involving the d(8) electron configuration of Cu.     

Quantumchemical investigation of borabenzene adduct with pyridine

Atomic charges and structural parameters of borabenzene, pyridine and their adduct in free state, in liquid argon and in tetrahydrofuran are calculated by the quantum-chemical method B3LYP/6-311G(3d5f7,p) &; PCM. Mutual polarization of the adduct and medium results in small increase in boron-nitrogen interatomic distance and dihedral angle between the aromatic heterocycles. Calculated dipole moment of the adduct (7.17 D) is by 4.55 D over than the sum of dipole moments of the free components. Internal rotation barriers are not high: 1 kcal mol^?1 (0° and 180°) and 4 kcal mol^?1 (90°). The borabenzene-pyridine bonding energy (46 kcal mol^?1) is higher than that with dinitrogen (19 kcal mol^?1) and xenon atom (6 kcal mol^?1). The B-N bond length in the little stable adduct with dinitrogen is by 0.08 Å shorter than in the stable adduct with pyridine. The Lewis acid properties inherent in borabenzene are transferred on the π-electron system of pyridine fragment in the adduct. The electron transfer wavelength from borabenzene to pyridine fragment in argon matrix is by 109 nm higher than in tetrahydrofuran, as calculated by CIS CNDO/S method.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

Novel pyridazine based scorpionate ligands in cobalt and nickel boratrane compounds

Heating of 6-methylpyridazine-3-thione (HPn(Me)) and 6-tert-butylpyridazine-3-thione (HPn(tBu)) with potassium borohydride in diphenylmethane in a 3:1 ratio gave two new scorpionate ligands K[HB(Pn(Me))(3)] and K[HB(Pn(tBu))(3)]. Single crystal X-ray diffraction analysis of the methyl derivative K[HB(Pn(Me))(3)] revealed a dimeric species with one potassium atom coordinated by six sulfur atoms of two scorpionate ligands and a second potassium atom coordinated by three nitrogen atoms of one of the two ligands as well as by three water molecules. The reaction of K[HB(Pn(tBu))(3)] with nickel(II) chloride or cobalt(II) chloride in CH(2)Cl(2) led to the new boratrane compounds [M{B(Pn(tBu))(3)}Cl] (M = Ni 1, Co 3) where a formal reduction of the metal ions to Ni(I) and Co(I), respectively, and activation of the B-H bond occurred. Similar reactivity was observed by employing K[HB(Pn(R))(3)] (R = Me, tBu) and nickel(II) chloride in water. Reaction with cobalt(II) chloride in water also gave boratrane compounds [Co{B(Pn(R))(3)}(Pn(R))] (R = tBu 4, Ph 5), but instead of a chloride a bidentate pyridazinethionate ligand from a defragmentated scorpionate is found in the molecules. The molecular structures of all nickel and cobalt compounds were determined by single crystal X-ray diffraction analyses confirming the formation of boratranes in compounds 1-5. Magnetic measurements confirm the reduced oxidation states and the paramagnetic character of the Ni(I) and Co(I) complexes. Supportive DFT studies were carried out for a better understanding of the electronic nature of the metal-boron bond of the boratrane complexes.     

Hydrogen-atom abstraction from the adenine-uracil base pair

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.     

The role of nucleobase carboradical and carbanion on DNA lesions: a theoretical study

DNA base release induced by H and OH radical addition to thymine and their corresponding electron adducts is studied at the DFT B3LYP/6-31+G(d,p) level in gas phase and in solution. H atom transfer after radical formation from C2' on the sugar to the C6 site on the base is shown to be prohibited for the radical species. Their corresponding electron adducts, albeit minor events in cellular systems, show excellent capabilities to proton transfer from C2' on the sugar to the C6 site on the base. The barriers for subsequent N-glycosidic bond dissociation range from 0.1 to 1.6 kcal mol(-1) at the B3LYP level and around 5 kcal mol(-1) using the BB1K functional, implying that these reactions can serve as a source to abasic sites. Analysis of bond dissociation energies show that all the reactions are exothermic, which is consistent with the changes in N-glycosidic bond lengths during the proton-transfer reactions. Bulk solvation plays a reverse influence on proton transfer and the bond rupture reactions. Molecular orbitals, NPA charges, and electron affinities are calculated to shed further light on the properties leading up to the intramolecular reactions.     

Study of the dative bond in 2-aminoethoxydiphenyl borate at various levels of theory: another poor performance of the B3LYP method for B-N dative bonds

Aminoethoxydiphenyl borate (2-APB), 1, is a potent inhibitor of store-operated calcium entry channels (SOCCs). Other SOCC inhibitors are being investigated as promising pharmacological agents for a variety of conditions. Though toxic, 2-APB could be useful in the development of additional inhibitors, but its preferred binding structure must first be determined. Thus, we performed ab initio calculations to study the conformers and the strength of the dative bond of 2-APB. As a first step, we performed a series of computations at various levels of theory. We obtained vastly different dissociation energies for the dative bond depending on whether we used MP2 or B3LYP (7-10 kcal/mol different). This discrepancy has previously been observed for other B-N dative bonds by Gilbert, who found that the MP2 values were in much better agreement with experimental values (Gilbert, T. M. J. Phys. Chem. A 2004, 108, 2550-2554). Since we lacked experimental data for comparison, we performed CCSD(T) calculations and found them to have similar results to those from MP2. Thus, we conclude that MP2 is more accurate for 2-APB. The dissociation free energy at the MP2 level is 7 kcal/mol and indicates that the dative bond conformer will be the predominant structure in the gas phase. The dissociation energy is comparatively low due to the electron donation from the oxygen atom to the boron atom and due to the ring strain in the dative bond conformer.     

Structures and Electronic Properties of HOCl···HCOCl Complexes

B3LYP/6-311++G** and MP2/6-311++G** calculations were used to analyze the interaction between hypochlorous acid (HOCl) and formyl chloride (HCOCl). The results showed that there were four equilibrium geometries (S1, S2, S3, and S4) optimized at B3LYP/6-311++G** level, and all the equilibrium geometries were confirmed to be in stable states by analytical frequency calculations. Complexes S1 and S3 use the 5H atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift hydrogen bond systems. However, the blue-shifted hydrogen bond (2C-3H···6O) coexists with 4Cl···5O interaction in structures S2. As for S4, it uses the 7Cl atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift halogen bond system. Interaction energies between monomers in the four complexes corrected with basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE) lie in the range from −5.05 to −14.76 kJ·mol⁻¹ at MP2/6-311++G** level. The natural bond orbital (NBO) and atoms in molecules (AIM) theories have also been applied to explain the structures and the properties of the complexes.     

卤素氮氧化物的结构和光谱性质的理论研究

通过DFT/B3LYP计算,优化了卤素氮氧化物XNO_2及其异构体XONO（X = F,Cl ,Br,I）的平衡几何构型,预测了异构体的相对稳定性及其相互转化的活化能垒 。在B3LYP和QCISD（T）计算水平上,确定了X-NO_2键的解离能。应用与时间有关 的密度泛函理论（TD-B3LYP）计算了XNO_2低激发态的跃迁能,并讨论了这些激发 态与卤素氮氧化物光诱导解离过程的关联。     

Comparative density functional theory and post-Hartree-Fock (CCSD, CASSCF) studies on the electronic structure of halogen nitrites ClONO and BrONO using quantum chemical topology

In this paper, the electronic structures of cis- and trans-ClONO and BrONO are studied at the CCSD∕aug-cc-pVTZ, CASSCF(14,12)/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ computational levels. For the Cl-O bond, topological analysis of the electron density field, ρ(r), shows the prevalence of the shared-electron type bond (?(2)ρ((3,-1)) < 0). The Br-O bond, however, represents the closed-shell interaction (?(2)ρ((3,-1)) > 0). Topological analysis of the electron localization function, η(r), and electron localizability indicator (ELI-D), (D) (σ)(r), shows that the electronic structure of the central N-O bond is very sensitive to both electron correlation improvements (coupled-cluster single double (CCSD), CASSCF, density functional theory (DFT)) and bond length alteration. Depending on the method used, the N-O bond can be characterized as a "normal" N-O bond with a disynaptic V(N,O) basin (DFT); a protocovalent N-O bond with two monosynaptic, V(N) and V(O), basins (CCSD, CASSCF); or a new type, first discovered for FONO, characterized by a single monosynaptic, V(N) basin (CCSD, DFT). The total basin population oscillates between 0.46-0.96 e (CCSD) and 0.86-1.02 e (CASSCF). The X-O bond is described by the single disynaptic basin, V(X,O), with a basin population between 0.76 and 0.81 e (CCSD) or 0.77 and 0.85 e (CASSCF). Analysis of the localized electron detector distribution for the cis-Cl-O1-N=O2 shows a manifold in the Cl···O2 region, associated with decreased electron density.     

Co-doping with boron and nitrogen impurities in T-carbon

Previously, Ren et al. [Chem. Phys. 518, 69–73, 2019] reported the failure of Boron-Nitrogen (B-N) co-doping as inter B-N bond in T-carbon. In present work, a B-N atom pair is introduced in T-carbon as p-n co-dopant to substitute two carbon atoms in the same carbon tetrahedron and form an intra B-N bond. The stability of this doping system is verified from energy, lattice dynamic, and thermodynamic aspects. According to our B3PW calculations, B-N impurities in this situation can reduce the band gap of T-carbon from 2.95 eV to 2.55 eV, making this material to be a promising photocatalyst. Through the study of its transport properties, we can also conclude that B-N co-doping cannot improve the thermoelectric performance of T-carbon.     

A-T碱基对单羟基自由基加成产物的单电子氧化还原性质

采用密度泛函理论在B3LYP/DZP++//B3LYP/6-31 ++G(d,p)水平上研究A-T碱基对的单羟基加成产物的氧化还原性质.计算表明,所有8种加成复合物都表现出显著的氧化性,但其还原性却很弱.加成复合物AC2-T、AC4-T、AC5-T的俘获电子诱发T碱基N3位上的H原子向A碱基的N1位迁移,产生这种氢迁移的根源在于A碱基俘获电子后电子密度较大,有利于在A碱基上形成新的N-H键.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

铁原子与氮分子间的相互作用——单侧双配位构型

用密度泛函理论的B3LYP/6-311+G(d)方法对单侧双配位FeN2体系(简记为S-FeN2)不同自旋多重度的稳定态、范德华力作用态和过渡态的多个电子态的几何结构、电子结构、能量和振动频率进行了计算比较研究. 结果表明, S-FeN2体系三种自旋态间, Fe—N 距离R1和N—N 距离R2值均比较接近; 能量最低的是15B2态, 相近态有15B1、13B1和13B2, 彼此能差约25 kJ·mol-1. 三重态电子结构复杂, 单重态能量普遍偏高; 基组态Fe原子与N2间存在强的σ-π电子对排斥而无有效轨道重叠和电子转移, 其它组态4s13d7、4s13d64p1和3d74p1, Fe 和N2间发生σ(sd)-π和π-π*轨道重叠作用, 有少量电子转移, 体系呈现一定的离子性特征, 活化N2键长基本不超过120 pm. Fe 原子的电子单或双重被激发到由N2反键轨道为主要成分的分子轨道上时, 能使N2活化到单键程度甚至解离.     

Specific hydration effects on oxo-thio triazepine derivatives

The specific hydration of 2,7-dimethyl-1,2,4-triazepine oxo-thio derivatives by one water molecule has been investigated at the B3LYP/6-311++G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. The existence of different hydrogen bond (HB) donor and acceptor centers in these molecules led to different kinds of hydrogen bonds (CH-O, OH-S, NH-O, OH-N, and OH-O) and different kinds of complexes. Among them, the most stable structures correspond to complexes where the heteroatom X or Y at positions 3 and 5 behaves as HB acceptor and the hydrogen atom associated with the nitrogen atom at position 4 as HB donor. In accordance with previous studies, it has been shown that the thiocarbonyl group forms stronger HBs than the carbonyl group because the sulfur atom is a better HB acceptor than the oxygen one. With the help of the AIM (atoms in molecules) theory and ELF (electron localization function) analysis, it has been shown that, in the case of 3O5O, 3S5O, and 3S5S, the most basic site is the heteroatom at position 3, while in 3O5S species the most basic center is the sulfur atom.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1,S2,S3和S4).其中,在复合物S1和S3中,HOCl单体的5H原子作为质子供体,与HCOCl单体中作为质子受体的10原子相互作用,形成红移氢键复合物;在复合物S4中,HOCl单体的7Cl原子作为质子供体,与HCOCl单体中作为质子受体的IO原子相互作用,形成红移卤键复合物;而在复合物S2中,同时存在2C-3H…6O蓝移氢键和4Cl…5O相互作用.在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正,其值在-5.05与-14.76 kJ·mol-1之间.采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.