A computational investigation on the geometries,stabilities, antioxidant activity,and the substituent effects of the L‐ascorbic acid and their derivatives

The geometries, stabilities, and antioxidant activities of L‐Ascorbic acid (1a), D‐erythroascorbate (2a), and D‐erythroascorbate glucoside (3a) as well as their sulfur and selenium derivatives are systematically investigated by using density functional theory. Emphasis is placed on studies of the two main mechanisms, that is, hydrogen atom donation and single‐electron transfer, and the O—H bond dissociation enthalpy and the ionization potential are computed in the gas phase and water solution. The calculated results indicate that the 2‐OH group in the five‐membered ring acts as an important H atom donor to free radicals. The 2‐OH radical spin density distribution shows that the unpaired electron is mostly located at the C3 atom of the five‐membered ring and partially at the vicinal O atoms, proving that a certain delocalization of the odd electron is effective in the five‐membered ring. In water aqueous solution, the antioxidant capacity and the electron donating ability are increased as the O atom in the five‐membered ring of 1a, 2a, and 3a is replaced by S and Se, respectively, in good agreement with experimental measurements; Furthermore, their antioxidant capacities are enhanced as compared with the standard antioxidant (resveratrol). © 2013 Wiley Periodicals, Inc.     

Bonding charge density from atomic perturbations

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. In this work, we present a first‐principles approach to calculating the charge transfer. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, we determine unambiguously the amount of electron charge associated with a particular atom or a group of atoms. We computed the topological electron loss versus gain using ethylene, graphene, MgO, and SrTiO₃ as examples. Our results verify the nature of chemical bonds in these materials at the atomic level. © 2015 Wiley Periodicals, Inc.     

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.     

Topological Analysis of Electron Densities: Is the Presence of an Atomic Interaction Line in an Equilibrium Geometry a Sufficient Condition for the Existence of a Chemical Bond?

The structure, energetics, and electron density in the inclusion complex of He in adamantane, C10H16, have been studied by density functional theory calculations at the B3LYP6-311++G(2p,2d) level. Topological analysis of the electron density shows that the He atom is connected to the four tertiary tC atoms in the cage by atomic interaction lines with (3,-1) critical points. The calculated dissociation energy of the complex He@adamantane(g)=adamantane(g) + He(g) of DeltaE=-645 kJ mol(-1) nevertheless shows that the He-tC interactions are antibonding.     

Donor-Stabilized Silylene/Phosphine-Supported Carbon(0) Center with High Electron Density

An isolable donor-stabilized silavinylidene phosphorane was synthesized. This molecule, which can also be regarded as a new carbon(0) complex featuring a phosphine and a donor-stabilized silylene ligand, presents a central carbon atom with a remarkably high electron density (−1.82). Furthermore, the experimental electron-density study of this compound demonstrates the delocalization of the σ-lone pair at the central carbon atom toward the silicon center, a feature which is remarkably different from electronic situation of other bent-allene-type molecules. This result clearly demonstrates the powerful electron-donating ability of donor-stabilized silylene ligands, as well as their excellent electron-acceptor properties.     

Relativistic Spin–Orbit Electronegativity and the Chemical Bond Between a Heavy Atom and a Light Atom

Relativistic effects are known to alter the chemical bonds and spectroscopic properties of heavy-element compounds. In this work, we introduce the concept of spin–orbit (SO) electronegativity of a heavy atom, as reflected by an SO-induced change in the interatomic distance between the heavy atom (HA) and a neighboring light atom (LA). We provide a transparent interpretation of these SO effects by using the concept of spin–orbit electron deformation density (SO-EDD). Spin–orbit coupling at the HA induces rearrangement of the electron density for the scalar-relativistically optimized geometry that, in turn, exerts a new force on the LA. The resulting expansion or contraction of the HA−LA bond depends on the nature and electron configuration of the HA. In addition, we quantify the change in atomic electronegativity induced by SO coupling for a series of hydrides, thereby complementing the SO-EDD picture. The trends in the SO-induced electronegativity and the HA−LA bond length across the periodic table of elements are demonstrated and interpreted, and also linked, intuitively, with the SO-induced NMR shielding at the LA.     

开放骨架磷酸铝合成中碳链长度对乙二胺结构导向效应的影响

以乙二胺(EDA)和1,3-丙二胺(1,3-DAP)为结构导向剂,在180 ℃加热摩尔比n(Al₂O₃):n(P₂O₅):n(R):n(H₂O)=1:1:1:277(R=EDA,1,3-DAP)的混合物,分别得到了高结晶度的三维阴离子开放骨架磷酸铝AlPO₄-12和UiO-26。 利用X射线粉末衍射分析、元素分析和液相酸碱度测量等表征手段,研究了两个合成体系的晶化过程以及晶化过程中液相的Al、P浓度和pH值随时间的演化。 用Materials Studio中的“原子体积和表面”模块和Dmol3模块计算了双质子化乙二胺和1,3-丙二胺的体积以及Hirshfeld电荷。 结果表明,双质子化EDA和1,3-DAP中N原子上的Hirshfeld电荷分别为0.073 e和0.064 e,按Hirshfeld电荷计算的电荷密度分别为1.8573和1.3400 e/nm³,按形式电荷计算的电荷密度分别为25.44和20.94 e/nm³,而AlPO₄-12和UiO-26的骨架电荷密度分别为-6.1和-4.6 e/nm³。 结果表明,与氨基中N原子相连碳链长度的改变会影响其上的电荷量以及电荷密度,从而改变原有机胺的结构导向效应,导致晶化产物从AlPO₄-12变成了具有较小电荷密度的UiO-26。     

Experimental and theoretical charge density study of the neurotransmitter taurine

The experimental electron density distribution in taurine, 2-aminoethane sulfonic acid, 1, has been determined from high-resolution X-ray diffraction data collected at a temperature of 100 K. Taurine crystallizes as a zwitterion in the monoclinic space group P2(1)/c. Topological analysis of the experimental electron density and a comparison with high-level theoretical gas-phase calculations show that the crystal environment has a significant influence on the electronic configuration of the sulfonate moiety in 1, which in the crystal is more delocalized than in the gas phase. This crystal effect is mainly due to hydrogen bonding.     

A quantitative analysis of light‐driven charge transfer processes using voronoi partitioning of time dependent DFT‐derived electron densities

An analytical method is presented that provides quantitative insight into light‐driven electron density rearrangement using the output of standard time‐dependent density functional theory (TD‐DFT) computations on molecular compounds. Using final and initial electron densities for photochemical processes, the subtraction of summed electron density in each atom‐centered Voronoi polyhedron yields the electronic charge difference, Q ^VECD. This subtractive method can also be used with Bader, Mulliken and Hirshfeld charges. A validation study shows Q ^VECD to have the most consistent performance across basis sets and good conservation of charge between electronic states. Besides vertical transitions, relaxation processes can be investigated as well. Significant electron transfer is computed for isomerization on the excited state energy surface of azobenzene. A number of linear anilinepyridinium donor‐bridge‐acceptor chromophores was examined using Q ^VECD to unravel the influence of its pi‐conjugated bridge on charge separation. Finally, the usefulness of the presented method as a tool in optimizing charge transfer is shown for a homologous series of organometallic pigments. The presented work allows facile calculation of a novel, relevant quantity describing charge transfer processes at the atomic level. © 2017 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

自由基C59N及双体(C59N)2的理论研究

用INDO系列方法对自由基C59N及双体(C59N)2进行了理论研究,结果表明: N的掺入使C60笼发生畸变, N向笼外突出, 碳氮6-6键上的C自旋密度较大, 两C59N自由基在这个碳上以C-C单键连接形成双体为C2h, C2v对称性。其中C2v构型更稳定, 且N与附近的三个碳均以单键连接。理论计算的电子光谱与实验吻合较好。(C59N)2易分解为单体C59N。     

Novel properties from experimental charge densities: an application to the zwitterionic neurotransmitter taurine

The charge distribution of taurine (2-aminoethane-sulfonic acid) is revisited by using an orbital-based method that describes the density in a fixed molecular orbital basis with variable orbital occupation numbers. A new neutron data set is also employed to explore whether this improves the deconvolution of thermal motion and charge density. A range of molecular properties that are novel for experimentally determined charge densities are computed, including Weinhold population analysis, Mayer bond orders, and local kinetic energy densities, in addition to charge topological analysis and quantum theory of atoms-in-molecules (QTAIM) integrated properties. The ease with which a distributed multipole analysis can be performed on the fitted density matrix makes it straightforward to compute molecular moments, the lattice energy, and the electrostatic interaction energies of molecules removed from the crystal. Results are compared with high-level (QCISD) gas-phase calculations and band structure calculations employing density functional theory. Finally, the avenues available for extending the range of molecular properties that can be calculated from experimental charge densities still further using this approach are discussed.     

Theoretically Calculated Deformation Density of Small Molecules

Analysis of the theoretical electron deformation density based on EHMO and ab initio calculations has been applied to the simple molecules F₂, H₂O and SO₂ The effects from varied basis sets for such deformation density were sought. The accumulation of electron density between the bonded atoms calculated from EHMO and ab initio methods with STO-3G is generally under-estimated. Such phenomena are significantly improved by using split-valence basis sets e.g. 3–21G and 4–31G. The addition of d polarization functions is apparently important for the sulfur atom in sulfur-related bonding. 3–21G or 3–21G^* basis sets were found to provide not only valuable deformation density distributions of molecules but also comparable orbital energy states with respect to the experimental values.     

Continua of interactions between pairs of atoms in molecular crystals

The electron density distributions in crystals of five previously studied DMAN complexes and five Schiff bases (two new ones) have been analysed in terms of various properties of bond critical points (BCPs) found in the pair-wise interactions in their lattices. We analysed the continua of interactions including covalent/ionic bonds as well as hydrogen bonds and all other types of weak interactions for all pairs of interacting atoms. The charge density at BCPs and local kinetic and potential energy densities vary exponentially with internuclear distance (or other measures of separation). The parameters of the dependences appear to be characteristics of particular pairs of atom types. The Laplacian and the total (sum of kinetic and potential) energy density at BCPs show similar behaviour with the dependence being of the Morse type. The components lambda1, lambda2, lambda3 of the Laplacian at BCPs vary systematically with internuclear distance according to the type of atom pair. For lambda1 and lambda2 the distribution is of the exponential type, whereas lambda3 does not seem to follow any simple functional form, consistent with previous theoretical findings. Analytical nonlinear dependences of Laplacian on charge density have been found. They agree reasonably well with those obtained by least square fit of the Laplacian to charge density data. There are four distinct regions of the [symbol: see text]2rho(BCP)/rho(BCP) space, generated by E(BCP) = 0 and G(BCP)/rho(BCP) = 1 conditions. Two regions clearly correspond to the shared-shell and closed-shell interactions and the other two to some intermediate situation.     

Recognizing a triple bond between main group atoms

The electron pair density, in conjunction with the theory of an atom in a molecule, enables one to unambiguously determine the nature of the bonding between the gallium atoms in bent [HGa-GaH]²⁻. The Ga-Ga bonding in the dianion at the experimental bond length is found to be the result of the sharing of two electron pairs at the Hartree-Fock level of theory, the level consistent with the Lewis model of the electron pair. Received: 27 July 2000 / Accepted: 4 October 2000 / Published online: 19 January 2001     

Effect of substituent groups of diphenyl disulfide on novel cationic oxidative polymerization: examination of the electrophilic reaction of the cation by computational calculation

Substituent groups of the diphenyl disulfides (DPSs) influence the cationic oxidative polymerization in the formation of polyphenylene sulfides (PPSs). A semiempirical MO calculation (AM1) was performed on the model compounds of PPS, such as thioanisoles (TAs) and diphenyl sulfides (PSs), in order to elucidate the reactivity of the cation. Linear PPS is formed on polymerization because of the high electron density of the carbon in the para position. The ratios of the frontier electron density of the carbon in the para position on the disulfide to the sulfur atom are ordered as follows; 3,5-dimethyl-PS>2,5-dimethyl-PS-3-methyl-PS>nonsubstituted PS>2-methyl-PS>2,6-dimethyl-PS. The formation energies of the σ-complex, which is the intermediate of the reaction, also shows the same order. The theoretical calculation indicates that 3,5-dimethyl disubstituted disulfide and 3-methyl one are most preferable monomers of this cationic oxidative polymerization.     

Valence shell charge concentrations at pentacoordinate d0 transition-metal centers: non-VSEPR structures of Me2NbCl3 and Me3NbCl2

The molecular structures of the monomeric, pentacoordinated methylchloroniobium(IV) compounds Me3NbCl2 and Me2NbCl3 have been determined by gas electron diffraction (GED) and density functional theory (DFT) calculations, and, for Me3NbCl2, by single crystal X-ray diffraction. Each of the molecules is found to have a heavy-atom skeleton in the form of a trigonal bipyramid (TBP) with Cl atoms in the axial positions, in accord with their vibrational spectra. The TBP is somewhat distorted in the case of Me2NbCl3 with the two axial Nb--Cl bonds bent away from the equatorial, slightly shorter Nb--Cl bond. In the case of Me3NbCl2, moreover, the X-ray model suggests structural distortions away from the idealized C3h geometry, in line with the results of quantum chemical calculations. Structure optimizations by DFT calculations and least-squares refinement to the GED data yield the following structural parameters (calcd/exptl; eq=equatorial; ax=axial; distances in A, angles in degrees; average values in brackets): Me3NbCl2, in C(3v) symmetry, Nb--Cl 2.370/2.319(3), Nb--C 2.173/2.152(4), C--H 1.096/1.124(5), angle-spherical NbCH 109.3/105.2(8), angle-spherical ClNbC 92.2/93.3(2), angle-spherical CNbC 119.9/119.7(1); Me2NbCl3, in C(2v) symmetry, Nb--Cl(ax) 2.361/2.304(5), Nb--Cl(eq) 2.321/2.288(9), Nb--C 2.180/2.135(9), C--H 1.094/1.12(1), angle-spherical Cl(ax)NbCl(eq) 98.5/96.5(6), angle-spherical CNbC 121.0/114(2), angle-spherical NbCH 108.9/109(2). The electronic structures of Me2NbCl3 and Me3NbC(2 have been explored by rigorous analysis of both the wavefunction and the topology of the electron density, employing DFT calculations. Hence the structures of these compounds are shown to reflect repulsion between the Nb--C and Nb--Cl bonding electron density and charge concentrations induced by the methyl ligands in the valence shell of the Nb atom and arising mainly from use of Nb(4d) functions in the Nb--C bonds.     

Donor‐Stabilized Silylene/Phosphine‐Supported Carbon(0) Center with High Electron Density

An isolable donor‐stabilized silavinylidene phosphorane was synthesized. This molecule, which can also be regarded as a new carbon(0) complex featuring a phosphine and a donor‐stabilized silylene ligand, presents a central carbon atom with a remarkably high electron density (−1.82). Furthermore, the experimental electron‐density study of this compound demonstrates the delocalization of the σ‐lone pair at the central carbon atom toward the silicon center, a feature which is remarkably different from electronic situation of other bent‐allene‐type molecules. This result clearly demonstrates the powerful electron‐donating ability of donor‐stabilized silylene ligands, as well as their excellent electron‐acceptor properties.     

甲醇和甲氧基在Cu(111)表面吸附的第一性原理研究

Adsorption of methanol and methoxy at four selected sites(top,bridge,hcp,fcc)on Cu(111)surface has beeninvestigated by density functional theory method at the generalized gradient approximation(GGA)level.The cal-culation on adsorption energies,geometry and electronic structures,Mulliken charges,and vibrational frequenciesof CH_3OH and CH_3O on clean Cu(111)surface was performed with full-geometry optimization,and compared withthe experimental data.The obtained results are in agreement with available experimental data.The most favoriteadsorption site for methanol on Cu(111)surface is the top site,where C-O axis is tilted to the surface.Moreover,the preferred adsorption site for methoxy on Cu(111)surface is the fcc site,and it adsorbs in an upright geometrywith pseudo-C_(3v) local symmetry.Possible decomposition pathways also have been investigated by transition-statesearching methods.Methoxy radical,CH_3O,was found to be the decomposition intermediate.Methanol can be ad-sorbed on the surface with its oxygen atom directly on a Cu atom,and weakly chemisorbed on Cu(111)surface.Incontrast to methanol,methoxy is strongly chemisorbed to the surface.