A B3LYP and QTAIM study of a new proton donor for dihydrogen bonds: the case of the C2H5 +···nBeH2 complexes (n = 1 or 2)

B3LYP/6-311++G(d,p) calculations and molecular integrations from the quantum theory of atoms in molecules (QTAIM) were performed for the purposes of studying a new class of dihydrogen-bonded hyperconjugation complexes formed by C₂H₅ ⁺···n(BeH₂), when n = 1 (bimolecular) or n = 2 (trimolecular). Whether bimolecular or trimolecular, when the hyperconjugation on the ethyl cation (C₂H₅ ⁺) is taken into account, this enables the earth alkaline hydride, BeH₂, to interact efficiently with the nonlocalized hydrogen (H⁺) of the C₂H₅ ⁺ . In addition to computation of QTAIM topological parameters, analysis of the infrared harmonic spectrum at the B3LYP/6-311++G(d,p) level of theory revealed the existence of red-shifts on BeH₂, and this effect is explained by means of the atomic charges derived from the ChelpG approach. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Uncommon hydrogen bonds between a non-classical ethyl cation and π hydrocarbons: a preliminary study

This study undertakes a theoretical investigation into uncommon hydrogen bonds between the ethyl cation (C₂H₅ ⁺) and π hydrocarbons. Firstly, it considers the hyperconjugation effect of the ethyl cation, in which the non-localized hydrogen (H⁺) is taken to be a pseudoatom bound to the carbons of the methyl groups. The goal of the research is to use this electronic phenomenon to gain a better understanding of the (H⁺···π) and (H⁺···p-π) hydrogen bonds, which are considered uncommon because they are formed through the interaction of the H⁺ of the ethyl cation with the π bonds of the acetylene (C₂H₂) and ethene (C₂H₄), as well as with the pseudo-π bond of the cyclopropane (C₃H₆). In view of this, B3LYP/6-311++G(d,p) calculations were used to determine the geometries of the C₂H₅ ⁺···C₂H₂, C₂H₅ ⁺···C₂H₄, and C₂H₅ ⁺···C₃H₆ hydrogen-bonded complexes. Deformations of the bond lengths and bond angles of these systems were analyzed geometrically. Examination of the stretch frequencies and absorption intensities of the (H⁺···π) and (H⁺···p-π) hydrogen bonds has revealed red-shifts in π and p-π bonds. After structural modeling and vibrational characterization, analysis of the charge transfer following the ChelpG approach and subsequently quantification of the hydrogen bond energies (basis sets superpostition error and zero point vibrational energies being considered) were used to predict the strength of the (H⁺···π) and (H⁺···p-π) hydrogen bonds. In addition, the molecular topography was estimated using the quantum theory of atoms in molecules (QTAIM). QTAIM was chosen because of a desire to understand the (H⁺···π) and (H⁺···p-π) hydrogen bonds chemically on the basis of the quantity of charge density and interpretation of Laplacian fields. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Bonding in germatranyl cation and germatranes

Equilibrium structures of silatranyl and germatranyl cations as well as corresponding fluoroatranes are obtained at the B3LYP/cc-pVDZ level of theory. Changes in the bonding on going from germatranyl cation to a neutral molecule are analyzed by using the NBO method. In contrast to three-coordinate planar germylium cations, germatranyl cation does not possess a vacant orbital which is involved in the formation of the transannular bond. However, in germatrane upon formation of an “external” bond with a fluorine anion the inversion of this orbital occurs to accept halogen electron pairs. The presence of the GeF bond drastically changes the scheme of bonding in the GeO₃N moiety compared to that of cation through the formation of interactions of a fluorine atom with equatorial oxygens.     

Quantum chemical calculations and X-ray crystallographic studies of cis-dioxomolybdenum(VI) Schiff base complex

Treatment of the Schiff base 2-((E)-(2-hydroxy propylimino)methyl)phenol with MoO₂(acac)₂ in dry methanol gave the mononuclear complex (methanol{6-[(2-oxidopropyl)iminometh-yl]phenolato}dioxidomolybdenum(VI), which was characterized by X-ray crystal analysis, and it has monoclinic space group p2₁/c, and a = 10.330(17) Å, b = 9.397(15) Å, c = 13.695(2) Å, V = 1252.1(3) Å³, and Z = 4. B3LYP theoretical method with DZP basis sets calculations nicely reproduces the X-ray experimental geometry, molecular orbital levels and the other structural properties for this complex.     

A theoretical analysis of topography and molecular parameters of the CFCl3···O3 complex: Linear and bifurcate halogen‐oxygen bonding interactions

A theoretical analysis of linear and bifurcate halogen‐oxygen bonds is presented in this work. B3LYP/6‐311++G(d,p) and MP2/6‐311++G(d,p) calculations were used to determine the optimized geometries of intermolecular systems formed by CFCl₃ and O₃. Molecular properties often analyzed in hydrogen‐bonded complexes were used here to describe the interaction between chlorine (CFCl₃) and oxygen (O₃). The halogen‐oxygen bond in the CFCl₃···O₃ complex was characterized using the topological parameters derived from the quantum theory of atoms in molecules. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

光合反应中心原初电子转移机理的理论研究

用量子化学密度泛函B3LYP方法在3-21G水平上计算细菌光合反应中心原初电子给体P960和绿色植物PSⅡ光合反应中心原初电子给体P680的电子结构,然后研究轴向配位的组氨酸残基和周围蛋白质环境的影响,最后探讨其原初电子转移机理。计算结果表明：(1)细菌光合作用反应中心原初电子给体P960-h的HOMO主要是由与M分支相连的组成单元上原子的原子轨道组成,而它的LUMO则两个组成单元上原子的原子轨道都有贡献;PSⅡ反应中心中原初电子给体P680的HOMO和LUMO均主要由与D1蛋白相连的组成单元上原子的原子轨道组成。这些计算结果能够从反应中心最核心的部分-原初电子给体的电子结构方面解释Rps.uiridis反应中心和PSⅡ反应中心原初电子转移只沿一个分支进行的的途径选择性。(2)虽然与细菌反应中心原初电子给体超分子P960的两个细菌叶绿素分子形成轴向配位的组氨酸残基His并未参与超分子P960-h的HOMO和LUMO的组成,但是由于其轴向配位,使得P960-h的ELUMO显著地升高到高于辅助细菌叶绿素和去镁细菌叶绿素的相应值,使得原初电子转移反应能够顺利进行。否则原初电子转移反应很难进行。PSⅡ反应中心的情况,与细菌反应中心十分相似。(3)细菌反应中心辅助细菌叶绿素(ABChlb)中的Mg离子与最近的组氨酸残基His中的N原子的距离和原初电子给体P960中的相应的Mg-N的距离相似,因此同样应该考虑此轴向配位的组氨酸残基,此时原初电子转移反应是沿L分支从P960-h经ABChlb到去镁细菌叶绿素(BPheob)的两步电子转移过程。而PSⅡ反应中心的辅助叶绿素不存在His的轴向配位,这应是与细菌反应中心的重要区别之一,此时原初电子转移应是沿Dl分支从P680-h到Pheoa的一步电子转移过程,但同时也不能完全排除从P680-h到AChla到Pheoa的二步电子转移过程。     

Quantum chemical study of effect on adsorption properties of antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide interaction with CNT(C56H16)

Tuberculosis is the most common disease that affects the lungs in humans. The electronic structural and chemical properties of the antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide have already been investigated. The adsorption properties of the antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide (CPPC) with single-wall carbon nanotube CNT(C56H16) are investigated using a combination of DFT/B3LYP method and 6-31G(d,p) basis set in both gaseous and water solvent, and calculated results are compared. By comparing CNT's corresponding optimized bond lengths with CNT@CPPC, the effect of CPPC adsorption on optimized drug delivery system parameters has been discussed. Based on topological parameters, the nonbonding interaction between CNT and CPPC drug is discussed using QTAIM analysis at BCP in both gas and water solvent. The thermodynamical stability of the CPPC@CNT adsorption process is also calculated, showing the adsorption of CPPC with CNT favors in both media. Natural bond analysis (NBO) was used to investigate the IR spectra, and the effect of charge transfer from CPPC to CNT in CNT@CPPC in both media provides information about how polarity changes from gas to water solvent. Because drug delivery action is done in blood plasma, the UV–Vis spectra of CNT are compared to CNT@CPPC in water solvent, providing insight into the adsorption of CPPC drug by CNT. We have compared the chemical shift isotropic (CS1) and chemical shift anisotropic (CSA) of CNT, CPPC, and CNT@CPPC to determine the change in electron density.     

Nature of closed‐ and open‐shell interactions between noble metals and rare gas atoms

Interactions between noble metals and rare gases have become an interesting topic over the last few years. In this work, a computational study of the open‐shell (d¹⁰s¹) and closed‐shell (d¹⁰s and d¹⁰s²) noble metals (M = Cu, Ag, and Au) with three heaviest rare gas atoms (Rg = Kr, Xe, and Rn) has been performed. Potential energy curves based on ab initio [MP2, MP4, QCISD, and CCSD(T)] and DFT functionals (M06‐2X and CAM‐B3LYP) were obtained for ionic and neutral AuXe complexes. Dissociation energies indicate that neutral metals have the lowest and cationic metals have the highest affinities for interaction with rare gas atoms. For the same metals, there is a continuous increase in dissociation energies (D_e) from Kr to Rn. The nature of bonding and the trend of D_e and equilibrium bond lengths (R_e) have been interpreted by means of quantum theory of atoms in molecules, natural bond orbital, and energy decomposition analysis. © 2013 Wiley Periodicals, Inc.     

Theoretical Studies on Intermolecular Hydrogen-bond Interactions between Hexamethylenetetramine and Nitric Acid

The structures of the complexes generated by hexamethylenetetramine and nitric acid have been fully optimized by B3LYP method at the 6-311++G** and aug-cc-pVTZ levels. The intermolecular hydrogen-bonding interactions have been calculated by the B3LYP/6-311++G**, B3LYP/aug-cc-pVTZ, MP2(full)/6-311++G** and CCSD(T)/6-311++G** methods, respectively. The NBO (nature bond orbital), AIM (atom in molecule), temperature effect and solvation effect have been analyzed to reveal the origin of the interactions. The results indicate that the stable hydrogen-bonded complexes could be generated by hexamethylenetetramine and nitric acid. The interactions follow the order of (a)>>(e)>(b)>(c)>(d)>(f)>(g). The C-N bonds which are adjacent to the methylene involving the hydrogen bonds tend to break in the chemical reaction. Due to the exothermic process, low temperature is conducive to the formation of the composition, which tallies with the experimental result.     

(CH2)2O, (CH2)2S与双卤分子间卤键的理论研究

运用量子化学密度泛函B3LYP方法, 采用6-311＋＋G(d,p)及aug-cc-pVDZ基组, 通过CP校正的几何梯度优化对(CH2)2O和(CH2)2S与双卤分子XY (XY＝Cl2, Br2, ClF, BrF, BrCl)形成的卤键复合物的几何构型、振动频率和相互作用能等进行了研究. 利用电子密度拓扑分析理论方法对卤键复合物的拓扑性质进行了分析研究, 探讨了该类分子间卤键的作用本质. 结果表明, (CH2)2O和(CH2)2S与双卤分子间的卤键介于共价键与离子键之间, 偏于静电作用成分为主. 形成卤键后, 双卤分子的键长增加, 振动频率减小, 原子积分性质发生改变. 卤键键长的变化、键能的强弱、键鞍点处的电子密度值与双卤分子的电负性有关.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

液态石油烃的脱砷及砷化物与亚铜探针的相互作用

采用密度泛函理论B3LYP方法, 在6-311+G(2df,2p)基组水平上研究了液态石油烃体系中甲基胂化合物与过渡金属探针Cu+和CuCl的相互作用. 结果表明, 甲基胂化物与亚铜离子作用的最稳定模式为四面体构型, 随着烃基取代数增加, 砷化物同Cu+或CuCl的相互作用能(E0)更负, 配合物更稳定, 同时二者的相互作用轨道的能级差(△E)与E0值线性相关(R2≥0.99). Cu+配合物中, As—Cu成键轨道向C—As和/或H—As反键轨道形成电子反馈, 但是CuCl配合物中类似电子反馈则没有形成. 烃基取代并不降低活性组分对砷化物的吸附活性, 在活性组分满足砷化物选择性吸附的条件下, 液态石油烃脱砷的主要控制因素为砷化物在脱砷剂内部孔道中的扩散传输. 有机硫化物噻吩并不影响砷化物的选择性吸附分离, 硫醇类化合物则会影响单烷基砷化物的选择性吸附. 在进行脱砷剂开发时, 应拓宽载体孔道以提高流体传输效率, 并选择活性相组分与砷化物作用的△E相对较小, 配合物容易形成电子反馈, 且对硫醇类化合物的作用能力相对较弱, 对单烷基砷化物的作用能力相对较强的过渡金属组分.     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

Comprehensive quantum chemical calculations and molecular docking analysis of uracil mustard by first principle

Uracil mustard belongs to the nitrogen mustard family and is primarily used in anticancer drugs. The research that follows, investigates many quantum chemical features such as the computation of global minimum energies with no negative wavenumber values using the Density Functional Theory (DFT) with Becke three functional and 6-311G (d, p)/6–311++G (d, p) basis sets. All the vibrational modes have been calibrated and justified in comparison to their experimental counterparts. Mustard's polarizability and hyperpolarizability components, Natural Bond Analysis (NBO), electronic properties, Fukui function analysis, various global parameters, Quantum Theory of Atoms In Molecule (QTAIM) analysis, ADMET analysis, and docking analysis have all been investigated using the same theory and basis sets, indicating its biochemical significance. The biological activity of the molecule is reported by using PASS software. The Full fitness score and binding affinity parameters are utilized to determine the binding strength with 6cq3 protein. The acidity of the title molecule is calculated in water solvent by polarizable continuum model (PCM) solvent effects (estimated in water). The HOMO, LUMO, and MESP plots are used to explore the nature of binding and surfaces. The Fukui functions are computed using Mulliken atomic charges for neutral atoms, cations, and anions. The Ultraviolet–visible (UV–vis) of the molecule is computed employing the TD-DFT method.     

含能材料六硝基六氮杂异伍兹烷分子的B3LYP研究

在B3LYP/6-31G^**水平上对六硝基六氮杂异伍兹烷(CL-20)分子进行结构优化、集居数分析、自然键轨道和振动频率计算,得到与实验值相符的稳定构型.根据计算结果,讨论了键特性对分子性质的影响.     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

Theoretical investigation on charge‐assisted halogen bonding interactions in the complexes of bromocarbons with some anions

A series of dimeric complexes formed between bromocarbon molecules and two anions (Br^? and CN^?) have been investigated by using MP2 method. The quantum theory of atoms in molecules (QTAIM) and the second‐order perturbation natural bond orbital (NBO) approaches were applied to analyze the electron density distributions of these complexes and to explore the nature of charge‐assisted halogen bonding interactions. As anticipated, these interactions are significantly stronger relative to the corresponding neutral ones. The results derived from ab initio calculations described herein reveal a major contribution from the electrostatic interaction on the stability of the systems considered. Beside the electrostatic interaction, the charge‐transfer force and the second‐order orbital interaction also play an important role in the formation of the complexes, as a NBO analysis suggested. The presence of halogen bonds in the complexes has been identified in terms of the QTAIM methodology, and several linear relationships have been established to provide more insight into charge‐assisted halogen bonding interactions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008