Understanding the electronic structure, reactivity, and hydrogen bonding for a 1,2-diphosphonium dication

The experimental charge density for hexamethyldiphosphonium ditriflate has been determined from low-temperature high-resolution X-ray diffraction data. These results have been compared with theoretically calculated values for the isolated gas-phase compound. Analysis of the topological and atomic basin properties has provided insight into the exact nature of the P-P bond in both the crystalline and the gas-phase structures. The rho(b)(r) and nabla2rho(b)(r) values highlight the covalent nature of the P-P bond, while the atomic charges indicate a localization of the positive charges on the two phosphorus atoms. This seems to indicate that a covalent bond is formed despite a strong electrostatic repulsion between these two heteroatoms. The topological properties and electrostatic potentials have also been shown to provide significant insight into the chemical reactivity of the title compound. A topological analysis of P2Me4, P2Me5(+), and P2Me6(+2) species has provided information about the progression of the P-P bond in the synthesis of the title compound. An investigation of the different hydrogen-bonding networks present in the crystalline and gas-phase structures, along with their affect on the electronic structure of the title compound has also been investigated. This has all led to significant new insight into the electronic structure, reactivity, and weak hydrogen bonding in prototypical 1,2-diphosphonium dications.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

ZSM-5分子筛催化1-己烯生成cis-2-己烯的理论研究

基于54T团簇模型, 采用ONIOM分层计算方法, 研究了1-己烯在ZSM-5分子筛上进行顺式双键异构的反应机理. 计算结果表明, 1-己烯的顺式双键异构反应通过只有分子筛Brønsted酸部分起作用的机理进行. 首先, 1-己烯与分子筛的Brønsted酸性位形成π配位复合物. 接着, 酸质子发生迁移使1-己烯的双键端基碳原子被质子化, 同时双键的另一碳原子与失去质子的Brønsted酸羟基的氧原子成键, 形成稳定的烷氧基中间体. 然后, 烷氧基中间体中的C―O共价键被打断, 同时Brønsted酸羟基的氧原子从C₆H₁₃基团提取一个氢原子还原分子筛的酸性位, 并且生成cis-2-己烯. 这一反应路径与借助于分子筛活性位的酸-碱双功能性质的反应路径是相互竞争的. 计算得到的表观活化能是59.37 kJ·mol^-1, 该值与实验值非常接近. 这一结果合理解释了双键异构过程中的能量特征, 并且扩展了对分子筛活性位本质的理解.     

(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.     

Theory of intermolecular interactions: The long range terms in the dipole–dipole,monopoles–dipole,and monopoles–bond polarizabilities approximations

The problem of evaluating the long range terms (electrostatic, polarization, dispersion) of the interaction energy between molecules at intermediate distances (i.e. distances of the order of magnitude of the molecular dimensions) is considered. Instead of being approximated by its dipole part, the exact interaction Hamiltonian is treated as proposed by Longuet-Higgins [11], i.e. the matrix elements are interpreted as electrostatic interactions between state and transition charge distributions. These charge distributions are approximated in a systematic way by sets of point charges (localized on the atoms) or sets of dipoles (localized on the bonds). The various contributions to the energy may then be expressed in terms of atomic net charges and bond polarizabilities. More refined approximations of the charge distributions could be used and correspondingly improved formulae could be derived: as an example, a formula for the σ-π dispersion energy is derived, where the σ charge distributions are approximated by bond transition dipoles (leading to σ bond polarizabilities in the final formula) while the π charge distributions are approximated by atomic charges.     

Conformational aspects of glutathione tripeptide: electron density topological & natural bond orbital analyses

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density $ \nabla^{2} $ ρ(r) from Bader’s atom in molecules theory. Charge transfer energies based on natural bond orbital analysis are also considered to interpret these intramolecular hydrogen bonds. Our results show that these hydrogen bonds are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the stabilization energy of hydrogen bond increases. Furthermore, the back bone and side chain (Ramachandran map) orientations of various ionic forms of glutathione have been studied and conformation of each constitution of glutathione tripeptide (i.e., Glu, Cys, and Gly moieties) was determined. In most species side chain conformation were found to be hindered gauche–gauche orientation by intramolecular hydrogen bonds.     

Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective

This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H₂ taken as a prototype for a covalent bond, excimer formation of He₂ to analyze non‐covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C₂H₄. The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one‐ and two‐electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states. © 2017 Wiley Periodicals, Inc.     

Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.     

Effects of Electronic Structure of Adjacent Carbon on the Strength of C─F⋯H─F Organofluorine Hydrogen Bonds

We investigate the effects of the electronic structure of carbon atom on the organofluorine hydrogen bonds, C─F⋯H─F. Our results show that we can modulate the strength of organofluorine hydrogen bonds by adjusting the volume of fluorine atom in C─F via changing the electronic structure of adjacent carbon atoms. Different with the conventional hydrogen bonds, we found that instead of carbon rehybridization and hyperconjugative effects, the magnitude of fluorine atomic volume plays important roles in determining the strength of the C─F⋯H─F organofluorine hydrogen bonds. The lone pair electrons at both the proximal and the vicinal carbon dramatically reinforce the strength of C─F⋯H─F organofluorine hydrogen bond with its interaction energy in the range of about 15–25 kcal/mol, that is, the carbanion-mediated organofluorine hydrogen bond could be very strong. Due to the high electronegativity of fluorine atom, it easily attracts the excess electron from the proximal and vicinal carbon, which results in the increase of its volume and negative charge. The enhanced volume of fluorine atom gives rise to the large polarization energy, and its enhanced negative charge favors the large electrostatic interaction, both of which substantially contribute to making the organofluorine hydrogen bonds strong. © 2019 Wiley Periodicals, Inc.     

Quantum chemistry aspects of the solvent effects on the ene reaction of 1‐Phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene

A density functional theory study was used to investigate the quantum aspects of the solvent effects on the kinetic and mechanism of the ene reaction of 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene. Using the B3LYP/6–311++ G(d,p) level of the theory, reaction rates have been calculated in the various solvents and good agreement with the experimental data has been obtained. Natural bond orbital analysis has been applied to calculate the stabilization energy of N18? H19 bond during the reaction. Topological analysis of quantum theory of atom in molecule (QTAIM) studies for the electron charge density in the bond critical point (BCP) of N18? H19 bond of the transition states (TSs) in different solvents shows a linear correlation with the interaction energy. It is also seen form the QTAIM analysis that increase in the electron density in the BCP of N18? H19, raises the corresponding vibrational frequency. Average calculated ratio of 0.37 for kinetic energy density to local potential energy density at the BCPs as functions of N18? H19 bond length in different media confirmed covalent nature of this bond. Using the concepts of the global electrophilicity index, chemical hardness and electronic chemical potentials, some correlations with the rate constants and interaction energy have been established. Mechanism and kinetic studies on 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene ene reaction suggests that the reaction rate will boost with interaction energy enhancement. Interaction energy of the TS depends on the solvent nature and is directly related to electron density of the bonds involved in the reaction proceeding, global electrophilicity index and electronic chemical potential. However, the chemical hardness relationship is reversed. Finally, an interesting and direct correlation between the imaginary vibrational frequency of the N18? H19 critical bond and its electron density at the TS has been obtained. © 2014 Wiley Periodicals, Inc.     

Study on the Cation-π Interactions between Ammonium Ion and Aromatic π Systems

The nature and strength of the cation-π interactions between NH4^＋ and toluene, p-cresol, or Me-indole were studied in terms of the topological properties of molecular charge density and binding energy decomposition. The results display that the diversity in the distribution pattern of bond and cage critical points reflects the profound influence of the number and nature of substituent on the electron density of the aromatic rings. On the other hand, the energy decomposition shows that dispersion and repulsive exchange forces play an important role in the organic cation （NH4^＋）-π interaction, although the electrostatic and induction forces dominate the interaction. In addition, it is intriguing that there is an excellent correlation between the electrostatic energy and ellipticity at the bond critical point of the aromatic π systems, which would be helpful to further understand the electrostatic interaction in the cation-π complexes.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

The possible covalent nature of N-H...O hydrogen bonds in formamide dimer and related systems: an ab initio study

The N-H...O hydrogen bonds are analyzed for formamide dimer and its simple fluorine derivatives representing a wide spectrum of more or less covalent interactions. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. To explain the nature of such interactions, the Bader theory was also applied, and the characteristics of the bond critical points (BCPs) were analyzed: the electron density at BCP and its Laplacian, the electron energy density at BCP and its components, the potential electron energy density, and the kinetic electron energy density. These parameters are used to justify the statement that some of the interactions analyzed are partly covalent in nature. An analysis of the interaction energy components for the systems considered indicates that the covalent character of the hydrogen bond is manifested by a markedly increased contribution of the delocalization term relative to the electrostatic interaction energy. Moreover, the ratio of stabilizing the delocalization/electrostatic contributions grows linearly with the decreasing lengths of the hydrogen bond.     

Density functional theory study of the carbonyl-ene reaction of encapsulated formaldehyde in Cu(I), Ag(I), and Au(I) exchanged FAU zeolites

Carbonyl-ene reactions, which involve C-C bond formation, are essential in many chemical syntheses. The formaldehyde-propene reaction catalyzed by several of the group 11 metal cations, Cu(+), Ag(+), and Au(+) exchanged on the faujasite zeolite (metal-FAU) has been investigated by density functional theory at the M06-L/6-31G(d,p) level. The Au-FAU exhibits a higher activity than the others due to the high charge transfer between the Au and the reactant molecules, even though it is located at a negatively charged site of the zeolite. This site enables it to compensate for the charge of the Au(+) ion. The NBO analysis reveals that the 6s orbital of the Au atom plays an important role, inducing a charge on the probe molecules. Moreover, the effect of the zeolite framework makes the Au-FAU more active than the others by stabilizing the high charge induced transition structure. The activation energy of the reaction catalyzed by Au-FAU is 13.0 kcal/mol whereas that of Cu and Ag-FAU is found to be around 17 kcal/mol. The product desorption needs to be improved for Au-FAU; however, we suggest that catalysts with high charge transfer might provide a promising activity.     

Theoretical Studies on the Halogen Bond between Propargyl Radical and Dihalogen Molecules

MP2/aug‐cc‐pVDZ calculations are carried out on the geometries, vibrational frequencies, interaction energies and topological properties for the π‐type halogen‐bonded complexes between propargyl radical and dihalogen molecules ClF, BrF and BrCl. There are two kinds of geometries: complex ( a ) involves the interaction between the X (X=Cl, Br) atom and the midpoint of C(1) –C(2) bond, complex ( b ) involves the interaction between the X atom and C(3) atom. The lengths of the halogen bond, the frequencies of the halogen bond, the elongation extent of the X–Y (XY=ClF, BrF, BrCl) bond, topological parameters at the BCPs of the halogen bond and X–Y bond are all well consistent with the interaction energies. The interaction of complex ( a ) is stronger than that of complex ( b ); the interaction of propargyl···BrF is stronger than that of propargyl···ClF and propargyl···BrCl. For the complexes ( a ) and ( b ), the charge transfer is observed from propargyl radical to XY, the atomic energy, the dipolar polarization, and the volume of the halogen atom X decrease upon complex formation.     

Binding of genistein to the estrogen receptor based on an experimental electron density study

In a continuing effort to determine a relationship between the biological function and the electronic properties of steroidal and nonsteroidal estrogens by analysis of the submolecular properties, an experimental charge density study has been pursued on the nonsteroidal phytoestrogen, genistein. X-ray diffraction data were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen-Coppens multipole model. Genistein packs in puckered sheets characterized by intra- and intermolecular hydrogen bonds while weaker intermolecular hydrogen bonds (O...H-C) exist between the sheets. A topological analysis of the electron density of genistein was then completed to characterize all covalent bonds, three O...H-O and four O...H-C intermolecular hydrogen bonds. Two O...H-O hydrogen bonds are incipient (partially covalent) type bonds, while the other O...H-O hydrogen bond and O...H-C hydrogen bonds are of the pure closed-shell interaction type. In addition, two intermolecular H...H interactions have also been characterized from the topology of the electron density. The binding of genistein to the estrogen receptor is discussed in terms of the electrostatic potential derived from the electron density distribution.     

Probing the structural and electronic factors affecting the adsorption and reactivity of alkenes in acidic zeolites using DFT calculations and multivariate statistical methods

Quantum mechanical (QM) cluster calculations have been performed on a model of ZSM-5 at DFT and MP2 levels. We investigated how the adsorption energies and the energetics of alkoxide intermediate formation of six different alkene substrates, ethene, propene, 1-butene, cis/trans butene, and isobutene, vary in this zeolite model. An analysis of the DFT geometric, electronic, and energetic parameters of the zeolite-substrate complexes, transition states, and alkoxide intermediates is performed using principal components analysis (PCA) and partial least squares (PLS). These deliver an insight into the correlated changes that occur between molecular structure and energy along the reaction coordinate between the physisorbed and chemisorbed species within the zeolite. To the best of our knowledge, this is the first occasion multivariate techniques such as PCA or PLS have been employed to profile the changes in electronics, distances, and angles in QM calculations of catalytic systems such as zeolites. We find the calculated adsorption and the alkoxide intermediate energies correlate strongly with the absolute charge on the substrate and the length of the substrate double bond. The transition states' energies are not affected by the zeolite framework as modeled, which explains why they correlate strongly with the gas-phase substrate protonation energy. Our cluster results show that for ethene, propene, 1-butene, and isobutene, the relative energetics associated with the formation of the alkoxide intermediate in ZSM-5 follow the same trends as calculations where the effects of the framework are included.     

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron‐oxo porphyrin π‐cation radical complex Por^·+Fe^IV?O (S? H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon–carbon bonds in porphyrin moiety. The double C?C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V_i=1,2(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)_i=1–20 after complexation with the Fe cation. The iron–nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)_i=1–4, where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron–oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe^δ+···O^δ?, as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge‐shift bond. The Fe? S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (?0.43e to 0.50e) and S? H bond (?0.55e to 0.52e). © 2012 Wiley Periodicals, Inc.