改进的相对论量子化学计算ZORA方法

提出一种改进的ZORA(Zeroth-OrderRegularApproximationtotheDiracEquation)方法,其单电子方程为：[σ·p(c^2/2c^2-V~0)σ·p+V(r)]ψ=εψ。式中V~0为空间限域的势能函数：V~0(r=~A∑V~0^A(r~A),r~A=|r-R~A|,V~0^A(r~A)=V^A(r~A){1+exp[α(r~A-r~0^A]}^-^1。其中A表示分子的某个组成原子,R~A为A原子的位置矢量,V^A(r~A)为自由A原子的势函数,α和r~0^A为参数。改进的ZORA方法具有原来方法的所有优点,避免了原有ZORA方法因不满足标度变换不变性带来的缺陷,而且计算过程简单。具体计算表明,通过适当选择参数α和r~0^A,用本研究提出来的方法,在计算分子几何结构和键合能时,基本上消除了ZORA方法由于标度变换依赖性产生的误差。     

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.     

Bonding character of intermediates in on-surface Ullmann reactions revealed with energy decomposition analysis

On-surface synthesis has become a thriving topic in surface science. The Ullmann coupling reaction is the most applied synthetic route today, but the nature of the organometallic intermediate is still under discussion. We investigate the bonding nature of prototypical intermediate species (phenyl, naphthyl, anthracenyl, phenanthryl, and triphenylenyl) on the Cu(111) surface with a combination of plane wave and atomic orbital basis set methods using density functional theory calculations with periodic boundary conditions. The surface bonding is shown to be of covalent nature with a polarized shared-electron bond supported by π-back donation effects using energy decomposition analysis for extended systems (pEDA). The bond angle of the intermediates is determined by balancing dispersion attraction and Pauli repulsion between adsorbate and surface. The latter can be significantly reduced by adatoms on the surface. We furthermore investigate how to choose computational parameters for pEDA of organic adsorbates on metal surfaces efficiently and show that bonding interpretation requires consistent choice of the density functional.     

Quantum chemical calculations of N@Cn endofullerenes (n ≤ 60)

The geometric parameters and energy characteristics of small endofullerenes N@C_n (n = 20, 24, 30, 32, 40, 50) and N@C₆₀ in the quartet ground state were calculated by the B3LYP/6-31G* method. The N atom is located at the center of the carbon cage in all molecules except N@C₃₀, where it is bound to the cage wall. Encapsulation of nitrogen atom has little effect on the fullerene cage geometry for n = 40, 50, and 60. No significant charge transfer from the N endo-atom to the cage was revealed for all the N@C_n endofullerenes studied. The calculated spin density on the nitrogen endo-atom increases as the size (n) of the carbon cage increases. The relative stabilities of C_n fullerenes and corresponding endofullerenes N@C_n are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 15–20, January, 2006.     

Ab initio chemical kinetics for reactions of H atoms with SiHx (x = 1–3) radicals and related unimolecular decomposition processes

Hydrogen atoms and SiH_x (x = 1–3) radicals coexist during the chemical vapor deposition (CVD) of hydrogenated amorphous silicon (a‐Si:H) thin films for Si‐solar cell fabrication, a technology necessitated recently by the need for energy and material conservation. The kinetics and mechanisms for H‐atom reactions with SiH_x radicals and the thermal decomposition of their intermediates have been investigated by using a high high‐level ab initio molecular‐orbital CCSD (Coupled Cluster with Single and Double)(T)/CBS (complete basis set extrapolation) method. These reactions occurring primarily by association producing excited intermediates, ¹SiH₂, ³SiH₂, SiH₃, and SiH₄, with no intrinsic barriers were computed to have 75.6, 55.0, 68.5, and 90.2 kcal/mol association energies for x = 1–3, respectively, based on the computed heats of formation of these radicals. The excited intermediates can further fragment by H₂ elimination with 62.5, 44.3, 47.5, and 56.7 kcal/mol barriers giving ¹Si, ³Si, SiH, and ¹SiH₂ from the above respective intermediates. The predicted heats of reaction and enthalpies of formation of the radicals at 0 K, including the latter evaluated by the isodesmic reactions, SiH_x + CH₄ = SiH₄ + CH_x, are in good agreement with available experimental data within reported errors. Furthermore, the rate constants for the forward and unimolecular reactions have been predicted with tunneling corrections using transition state theory (for direct abstraction) and variational Rice–Ramsperger–Kassel–Marcus theory (for association/decomposition) by solving the master equation covering the P,T‐conditions commonly employed used in industrial CVD processes. The predicted results compare well experimental and/or computational data available in the literature. © 2013 Wiley Periodicals, Inc.     

Modeling the solvation shell of complexes in solution for quantum chemical calculations of electronic spectra

A procedure that allows for solvation effects is suggested; it is designed for quantum chemical calculations of the electronic spectra of complex compounds. Based on Monte Carlo (MC) simulation of the solvation shell one can calculate the electrostatic potential created by the solvation shell at the sites of all atoms of the complex; appropriate corrections are added to the diagonal elements of the Fock matrix and to the matrix elements of the Hamiltonian in the configuration interaction method. The method suggested has been implemented based on the semiempirical (CINDO) version of the CI (configuration interaction) technique and tested on the following compounds: [Ru(NH₃)₅(py)]²⁺, [Ru(NH₃)₅(pyz)]²⁺, [Ru(bpy)(CN)₄]^2?, [Ru(NO)(py)₄-NC-Ru(py)₄(CN)]³⁺.     

DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds

The (19)F NMR shieldings for 53 kinds of perfluoro compounds were calculated by the B3LYP-GIAO method using the 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311++G(d,p), 6-311G(2d,2p), 6-311++G(2d,2p), 6-311++G(2df,2p), 6-311++G(3d,2p), and 6-311++G(3df,2p) basis sets. The diffuse functions markedly reduce the difference between the calculated and experimental chemical shifts. The calculations using the 6-31++G(d,p) basis set give the chemical shifts within 10 ppm deviations from experimental values except for the fluorine nuclei attached to an oxygen atom, a four- and a six-coordinated sulfur atom, and FC(CF(3))(2) attached to a sulfur atom.     

Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals

We describe the implementation of a parallel, in-core, integral-direct Hartree-Fock and density functional theory code for the efficient calculation of Hartree-Fock wave functions and density functional theory. The algorithm is based on a parallel master-slave algorithm, and the two-electron integrals calculated by a slave are stored in available local memory. To ensure the greatest computational savings, the master node keeps track of all integral batches stored on the different slaves. The code can reuse undifferentiated two-electron integrals both in the wave function optimization and in the evaluation of second-, third-, and fourth-order molecular properties. Superlinear scaling is achieved in a series of test examples, with speedups of up to 55 achieved for calculations run on medium-sized molecules on 16 processors with respect to the time used on a single processor.     

Microscopic quantum mechanical Marcus theory for chemical reactions and its relationship to the Butler-Volmer equation used in redox flow battery analysis

The vanadium redox flow battery has been intensively examined since the 1970s. What is missing is a connection between the current-overpotential Butler-Volmer equation, which provides an extremely helpful starting point for analytical and numerical studies, and microscopic quantum mechanical behavior at the atomic level. Such a connection will allow further advancements beyond the macroscopic, though very useful and insightful, modeling already done in the literature. Here we show rigorously the connection between the Butler-Volmer transfer coefficients, and the Marcus Gibbs free energy quantum mechanical parameters, and develop the equation directly in terms of the quantum mechanical parameters.     

A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure

A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported. © 2015 Wiley Periodicals, Inc.     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.     

Nonaqueous capillary electrophoresis and quantum chemical calculations applied to investigation of acid–base and electromigration properties of azahelicenes

Nonaqueous capillary electrophoresis (NACE) using methanol (MeOH) as a solvent of the BGEs and quantum mechanical density functional theory (DFT) have been applied to determine the thermodynamic acidity (ionization) constants (pK_a) of mono- and diaza[5]helicenes, mono- and diaza[6]helicenes, and their dibenzo derivatives in MeOH and water. First, the mixed acidity constants, , of ionogenic pyridinium groups of azahelicenes and their derivatives in MeOH were obtained by nonlinear regression analysis of pH dependence of their effective electrophoretic mobilities. The effective mobilities were measured by NACE in a large series of methanolic BGEs within a wide conventional pH range (pH_MeOH 1.6–12.0) and at ambient temperature (21–26°C) in a home-made CE device. Prior to mixed acidity constant calculation, the effective mobilities were corrected to reference temperature (25°C) and constant ionic strength (25 mM). Then, the mixed acidity constants were recalculated to the thermodynamic acidity constants pK_a,MeOH by the Debye–Hückel theory of nonideality of electrolyte solutions. Finally, from the methanolic thermodynamic pK_a,MeOH values, the aqueous thermodynamic constants were estimated using the empirical relations between methanolic and aqueous acidity constants derived for structurally related pyridine derivatives. Depending on the number and position of the nitrogen atoms in their molecules, the analyzed azahelicenes were found to be weak to moderate bases with methanolic pK_a,MeOH in the range 2.01–8.75 and with aqueous in the range 1.67–8.28. The thermodynamic pK_a,MeOH obtained by the DFT calculations were in a good agreement with those determined experimentally by NACE.     

Molecular modeling of 3,4-pyridinedicarbonitrile dye sensitizer for solar cells using quantum chemical calculations

The geometries, electronic structures, polarizabilities, and hyperpolarizabilities of organic dye sensitizer 3,4-pyridinedicarbonitrile was studied based on Hartree–Fock (HF) and density functional theory (DFT) using the hybrid functional B3LYP. Ultraviolet–visible (UV–Vis) spectrum was investigated by time dependent DFT (TD-DFT). Features of the electronic absorption spectrum in the visible and near-UV regions were assigned based on TD-DFT calculations. The absorption bands are assigned to π → π1 transitions. Calculated results suggest that the three lowest energy excited states are due to photoinduced electron transfer processes. The interfacial electron transfer between semiconductor TiO₂ electrode and 3,4-pyridinedicarbonitrile is due to electron injection process from excited dye to the semiconductor’s conduction band. The role of cyanine in 3,4-pyridinedicarbonitrile in geometries, electronic structures, and spectral properties were analyzed.     

Latin American contributions to quantum chemical topology

We survey the contributions from Latin American theoretical chemists to the field of quantum chemical topology (QCT) over nearly the last 30 years with emphasis on the developments and applications of the quantum theory of atoms in molecules (QTAIM). Applications of QCT in the fields of excited states, electron delocalization, chemical bond, aromaticity, conformational analysis, spectroscopic properties, and chemical reactivity are presented. We also consider the coupling of QTAIM with time-dependent density functional theory, the virial theorem in the Kohn-Sham method and the inclusion of electron dynamical correlation in the interacting quantum atoms method using coupled cluster and multi-configurational densities. Additionally, we describe the development of efficient algorithms for the calculation of topological properties derived from the electron density. This review is aimed not only at providing an account of the contributions to QCT in Latin America but also at stimulating guides for further progress in the field.     

Theoretical calculations of the unimolecular canonical rate constants

Microcanonical rate constants k(E) and canonical rate constants k(T) for unimolecular reactions have been obtained through the calculations of cumulative reaction probabilities N(E) with the unsymmetrical Eckart potential tunneling correction. By way of example, the reactions HCN→CNH (I) and FNC→NCF (II) have been employed. For reaction (I), the calculated rate constants are in agreement with the experimental data; for reaction (II), the results are in accordance with the rate constants kCVT/MEPSAG(T) calculated by the common program POLYRATE.     

Bond dissociation energies for removal of the hydroxyl group in some alcohols from quantum chemical calculations

In this theoretical work, 22 alcohols and their geometric structure properties have been investigated employing quantum chemical methods to calculate the C? OH equilibrium bond distances and bond dissociation energies (BDEs). Since DFT methods have been researched to have low basis sets sensitivity for small and medium molecules in our previous work (Zhao et al., J Mol Struct, 2006, 766, 87), 22 title compounds have been studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE1PBE) in conjunction with the 6‐311G** basis set and the complete basis set (CBS–Q) method. Comparison with the available experimental data shows that CBS–Q and B3P86 methods calculated results agree very well with the experimental values, with the average absolute errors of 1.3 kcal/mol and 3.5 kcal/mol, respectively. So considering the expensive computational time, CBS–Q method can be chosen as a satisfactory method of predicting the accurate BDEs for removal of the OH group in small and medium size alcohols. And B3P86 method may give accurate BDEs for larger alcohols we haven't studied. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.