Exploring the lower limit in hydrogen bonds: analysis of weak C-H...O and C-H...pi interactions in substituted coumarins from charge density analysis

Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H...O and C-H...pi interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-31G* method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H...O) and a van der Waals interaction (C-H...pi). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.     

Anisotropic interaction and stereoreactivity in a chemi-ionization process of OCS by collision with He*(2(3)S) metastable atoms

Ionic-state-resolved collision energy dependence of Penning ionization cross sections for OCS with He*(2(3)S) metastable atoms was measured in a wide collision energy range from 20 to 350 meV. Anisotropic interaction potential for the OCS-He*(2(3)S) system was obtained by comparison of the experimental data with classical trajectory simulations. It has been found that attractive potential wells around the O and S atoms are clearly different in their directions. Around the O atom, the collinear approach is preferred (the well depth is ca. 90 meV), while the perpendicular approach is favored around the S atom (the well depth is ca. 40 meV). On the basis of the optimized potential energy surface and theoretical simulations, stereo reactivity around the O and S atoms was also investigated. The results were discussed in terms of anisotropy of the potential energy surface and the electron density distribution of molecular orbitals to be ionized.     

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.     

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.     

Experimental and theoretical electron density study of estrone

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

From weak interactions to covalent bonds: a continuum in the complexes of 1,8-bis(dimethylamino)naphthalene

Experimental charge density distributions in a series of ionic complexes of 1,8-bis(dimethylamino)naphthalene (DMAN) with four different acids: 1,2,4,5-benzenetetracarboxylic acid (pyromellitic acid), 4,5-dichlorophthalic acid, dicyanoimidazole, and o-benzoic sulfimide dihydrate (saccharin) have been analyzed. Variation of charge density properties and derived local energy densities are investigated, over all inter- and intramolecular interactions present in altogether five complexes of DMAN. All the interactions studied [[O...H...O](-), C[bond]H...O, [N[bond]H...N](+), O[bond]H...O, C[bond]H...N, C pi...N pi, C pi...C pi, C[bond]H...Cl, N[bond]H(+)] follow exponential dependences of the electron density, local kinetic and potential energies at the bond critical points on the length of the interaction line. The local potential energy density at the bond critical points has a near-linear relationship to the electron density. There is also a Morse-like dependence of the laplacian of rho on the length of interaction line, which allows a differentiation of ionic and covalent bond characters. The strength of the interactions studied varies systematically with the relative penetration of the critical points into the van der Waals spheres of the donor and acceptor atoms, as well as on the interpenetration of the van der Waals spheres themselves. The strong, charge supported hydrogen bond in the DMANH(+) cation in each complex has a multicenter character involving a [[Me(2)N[bond]H....NMe(2)](+)....X(delta-)] assembly, where X is the nearest electronegative atom in the crystal lattice.     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Intermolecular electrostatic energies using density fitting

A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.     

乙烷在Pt/γ-Al2O3（001）模型催化剂上吸附行为的理论研究

本文采用密度泛函理论方法和周期性边界条件,考察了Pt原子与γ-Al2O3(001)表面上六种不同位点的相互作用,获得了最稳定吸附位的Pt/γ-Al2O3模型催化剂,建立了Pt原子负载在γ-Al2O3(001)表面的模型催化剂。同时,考查了乙烷分子在Pt/γ-Al2O3模型催化剂上的吸附行为。结果表明,在Pt/γ-Al2O3模型催化剂上,Pt原子转移了部分电子到载体γ-Al2O3。乙烷以分子态形式吸附在Pt/γ-Al2O3模型催化剂上,靠近Pt原子的C-H键受到一定程度地活化。     

Transition from moderate to strong hydrogen bonds: its identification and physical bases in the case of O-H...O intramolecular hydrogen bonds

A systematic investigation aimed at identifying the transition from moderate (M) to strong (S) hydrogen bonds (HBs) and the physical bases of the main geometry-based HB strength classifications reported in the literature has been undertaken using the quantum theory of atoms in molecules (QTAIM). Correlations between the Laplacian of the electron density (rho) at the O...H hydrogen bond critical points (HBCPs), nabla2rhohb, specifically between the more intuitive parameter Lhb = -nabla2rhohb and other QTAIM parameters, have also been explored. The transition from MHBs to SHBs has been identified as the minimum (maximum) in the geometric dependence of Lhb (nabla2rhohb). For O-H...O intramolecular (IM) HBs (including resonance-assisted HBs), the transition is obtained, in a truly remarkable agreement with the existing geometry-based HB strength classifications, when the O...O (O...H) distance is approximately 2.51 ( approximately 1.55) A and when the ratio of the potential energy density (|Vhb|) to the kinetic energy density (Ghb) approximately 1.3. Accordingly, the ranges of the |Vhb|/Ghb ratios are >2-1.3 and 1.3-1 for, respectively, SHBs and MHBs. When the O...O distance is not a genuine indicator of HB strength, the |Vhb|/Ghb ratio and other parameters should be considered to characterize the strength of the HBs. Rationalizations have been provided by way of decoding the physical bases of the transition in terms of the properties of rho and the mechanical characteristics of the interactions that created the HBCPs. Lhb was found to correlate, with a very high degree of fidelity, with at least three parameters (in addition to O...O and O...H distances and the IMHB energy), Vhb/Ghb, Hhb/rhohb (the ratio of the total energy density, Hhb, to the electron density, rhohb (the so-called bond degree parameter)), and deltahb(O,H) (the delocalization index), demonstrating the importance and utility of Lhb (nabla2rhohb) for the study of HB interactions. A new refined energetics-based classification of O-H...O IMHB strengths has been advanced. The approach taken in this investigation can be extended to other HB systems.     

NCO自由基与O和N反应的理论研究

采用密度泛函和量子化学从头算方法, 对NCO自由基和O, N原子反应的势能面进行了理论研究, 讨论了主要的反应通道. 这两种自由基反应的机理比较类似, 初始都有两种进攻方式. NCO与O的主反应通道是O原子从N端无势垒加合, 经过一低垒过渡态, 得到稳定产物P1(CO+NO), 而对NCO与N反应得到了一完整反应通道和无垒加合产物.     

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Topological analysis of the electronic charge density in the ethene protonation reaction catalyzed by acidic zeolite

In the present work, the distribution of the electronic charge density in the ethene protonation reaction by a zeolite acid site is studied within the framework of the density functional theory and the atoms in molecules (AIM) theory. The key electronic effects such as topological distribution of the charge density involved in the reaction are presented and discussed. The results are obtained at B3LYP/6-31G(**) level theory. Attention is focused on topological parameters such as electron density, its Laplacian, kinetic energy density, potential energy density, and electronic energy density at the bond critical points (BCP) in all bonds involved in the interaction zone, in the reactants, pi-complex, transition state, and alkoxy product. In addition, the topological atomic properties are determined on the selected atoms in the course of the reaction (average electron population, N(Omega), atomic net charge, q(Omega), atomic energy, E(Omega), atomic volume, v(Omega), and first moment of the atomic charge distribution, M(Omega)) and their changes are analyzed exhaustively. The topological study clearly shows that the ethene interaction with the acid site of the zeolite cluster, T5-OH, in the ethene adsorbed, is dominated by a strong O-H...pi interaction with some degree of covalence. AIM analysis based on DFT calculation for the transition state (TS) shows that the hydrogen atom from the acid site in the zeolitic fragment is connected to the carbon atom by a covalent bond with some contribution of electrostatic interaction and to the oxygen atom by closed shell interaction with some contribution of covalent character. The C-O bond formed in the alkoxy product can be defined as a weaker shared interaction. Our results show that in the transition state, the dominant interactions are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the concentration and accumulation of the charge density along the bond path between the nuclei linked increases.     

CIO自由基与CN自由基反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论（DFT）对CIO与CN的双自由基反应进行了研究．结果表明,CIO自由基的O原子进攻CN自由基的C原子是主要的进攻方式,并形成了中间体1 CIOCN．随后,中间体1发生异构化和分解反应得到热力学上可行的3种产物P4（CINCO）,P1（CO＋CIN）和P3（NO＋CCl）．其中P4是主要产物,P1和P3是次要产物．与单态势能面上相比,三态势能面对整个反应的贡献可以忽略．     

双自由基CF2与O3的反应机理

主要用作致冷剂和发泡剂的氯氟烃（CFCs）是破坏臭氧层的主要物质之一．对氯氟烃类化合物及其降解产物（包括光解、光氧化、化学反应产物等）在大气中行为问题的研究是大气化学研究的重要内容．前人[1-3]从理论和实验两方面研究了自由基与臭氧的反应机制，但是氯氟烃光解过程中     

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.     

On the interplay between CH...O and OH...O interactions in determining crystal packing and molecular conformation: an experimental and theoretical charge density study of the fungal secondary metabolite austdiol (C12H12O5)

The total experimental electron density rho(r), its Laplacian inverted delta(2)rho(r), the molecular dipole moment, the electrostatic potential phi(r), and the intermolecular interaction energies have been obtained from an extensive set of single-crystal X-ray diffracted intensities, collected at T = 70(1) K, for the fungal metabolite austdiol (1). The experimental results have been compared with theoretical densities from DFT calculations on the isolated molecule and with fully periodic calculations. The crystal structure of (1) consists of zigzag ribbons extended along one cell axis and formed by molecules connected by both OH...O and CH...O interactions, while in a perpendicular direction, adjacent molecules are linked by short CH...O intermolecular contacts. An extensive, quantitative study of all the intra- and intermolecular H...O interactions, based not only on geometrical criteria, but also on the topological analysis of rho(r), as well as on the evaluation of the pertinent energetics, allowed us (i) to assess the mutual role of OH...O and CH...O interactions in determining molecular conformation and crystal packing; (ii) to identify those CH...O contacts which are true hydrogen bonds (HBs); (iii) to determine the relative hydrogen bond strengths. An experimental, quantitative evidence is given that CH...O HBs are very similar to the conventional OH...O HBs, albeit generally weaker. The comparison between experimental and theoretical electric dipole moments indicates that a noticeable charge rearrangement occurs upon crystallization and shows the effects of the mutual cooperation of HBs in the crystal. The total intermolecular interaction energies and the electrostatic energy contribution obtained through different theoretical methods are reported and compared with the experimental results. It is found that the new approach proposed by Spackman, based on the use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies, predicts the correct relative electrostatic interaction energies in most of the cases.     

Energetic and geometrical evidence of nonbonding character of some intramolecular halogen···oxygen and other Y···Y interactions

We present high-level ab initio calculations for representative group of molecules possessing the intramolecular interaction of the X···O type (X = F, Cl, Br, and I). Few examples of molecules with intramolecular O···O and F···F interactions are also investigated. We show that, although most often investigated as bonding, all these interactions are nonbonding or repulsive, as indicated by positive values of interaction energies obtained by means of a few estimating methods, by thorough studies of geometrical changes that take place during the X···O contact formation and by the lateral contact of electron density isosurfaces of X and O atoms, which both are characterized by negative values of electrostatic potential. The presented conclusion about the repulsive nature of the intramolecular X···O and similar interactions is in opposition to the proclamation of the quantum theory of atoms in molecules of Bader that the presence of a bond path and a corresponding bond critical point is always to indicate the bonding, thus, stabilizing interaction.