Molecular environment and temperature dependence of hyperfine interactions in sugar crystal radicals from first principles

The effect of the molecular environment and the temperature dependence of hyperfine parameters in first principles calculations in alpha-d-glucose and beta-d-fructose crystal radicals have been investigated. More specifically, we show how static (0 K) cluster in vacuo hyperfine calculations, commonly used today, deviate from more advanced molecular dynamics calculations at the experimental temperature using periodic boundary conditions. From the latter approach, more useful information can be extracted, allowing us to ascertain the validity of proposed molecular models.     

Relativistic pseudopotentional incorporating core/valence polarization and nonlocal effects

A relativistic pseudopotentional (RPP) for use in ab initio molecular electronic structure calculations is derived in the context of the relativistic effective core potential (REP) method of Lee et al. The resulting atom-specific RPP has salient features of the REP imbedded within it while retaining the form of a functional that is dynamically defined at runtime when used in calculations on molecules. The RPP is determined from Dirac-Fock wave functions for the isolated atom. Outer core two-electron interactions are incorporated into the RPP by means of variable coefficients that are defined in the context of the final molecular wave function. This form permits polarization of the outer core shells analogous to that occurring in all-electron molecular Hartree-Fock calculations while retaining these shells as part of the atomic pseudopotentional. Use of the RPP in post-Hartree-Fock molecular calculations permits the incorporation of core/valence correlation effects.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

单一组分分子基导体的研究进展

概述了单组分分子性金属的设计和实现过程,并对一些典型的单组分分子导体体系的结构和物理性质作了简单介绍.     

Standardized basis sets for high-level-correlated relativistic calculations of atomic and molecular electric properties in the spin-averaged Douglas-Kroll (no-pair) approximation I. Groups Ib and IIb

Summary The technique developed earlier for the generation of the so-called first-order polarized basis sets for accurate non-relativistic calculations of molecular electric properties is used to obtain similar basis sets suitable for calculations in the Douglas-Kroll no-pair approximation. The corresponding (relativistic) basis sets are devised for atoms of the Groups Ib and IIb of the periodic table and tested in calculations of atomic polarizabilities and dipole moments of the coinage metal hydrides. Excellent performance of these basis sets has been found in the case of molecular calculations.     

A non-local representation of the effective potential due to a molecular fragment

Summary A non-local representation of the effective potential due to a molecular fragment is proposed here. Using this technique one can reproduce both Coulomb and exchange operators with kernels made up by molecular orbitals localized on a given molecular fragment. Such an approach seems particularly effective for large molecules with well-defined chemical fragments since in this case the kernel orbitals can be prepared through separate calculations on each fragment. The performance of the method is illustrated through calculations on specific molecular examples.     

A reassignment of molecular orbital configurations of the electronic states of ScF

Ab initio molecular orbital calculations have been performed on low-lying electronic states of ScF. The calculations suggest a reassignment of the molecular orbital configurations of the lowest lying Φ states, and suggest also that some of the low-lying Π states may not be well described by single configuration wavefunctions.     

Six-dimensional quantum dynamics of H2 dissociative adsorption on the Pt(211) stepped surface

Results of experimental studies, and theoretical calculations utilizing classical trajectories, have shown that dissociation of H2 on the Pt(211) stepped surface is enhanced at low energies by a molecular trapping mechanism. Because quantum effects can play a large role at the low energies and long lifetimes that characterize molecular trapping, we have undertaken quantum dynamics calculations for this system, the first to treat all molecular degrees of freedom of a gas molecule reacting on a stepped metallic surface. The calculations show that molecular trapping persists in the quantum system, but only at much lower energies than experimentally seen, pointing to possible deficiencies in the potential energy surface. Classical and quasiclassical trajectory calculations on the same potential provide a reasonable picture of reaction overall, but many of the finer details are inaccurate, and certain classical reaction mechanisms are entirely invalid. We conclude that some skepticism should be shown toward any classical study for which long-lived trapping states play a role.     

Interpreting closed-loop learning control of molecular fragmentation in terms of wave-packet dynamics and enhanced molecular ionization

We interpret a molecular fragmentation experiment using shaped, ultrafast laser pulses in terms of enhanced molecular ionization during dissociation. A closed-loop learning control experiment was performed to maximize the CF3+CH3+ production ratio in the dissociative ionization of CH3COCF3. Using ab inito molecular structure calculations and quasistatic molecular ionization calculations along with data from pump-probe experiments, we identify the primary control mechanism which is quite general and should be applicable to a broad class of molecules.     

A quantitative analysis of the through-space and the through-bond interactions between lone-pairs in azines: pyridazine,pyrimidine and pyrazine

The INDO calculations were performed on the three azines: pyridazine, pyrimidine, and pyrazine. The cannonical molecular orbitais obtained by these calculations were then transformed into the localized molecular orbitals. With the use of the localized molecular orbitals, the variation in the lone-pair orbital energies of these molecules were pursued in the light of the through-space and/or the through-bond interactions between the specified localized molecular orbitals in a molecule selectively. The interactions were expressed by the summation of several terms: through-space, through-bond, through-virtuals and coupling terms.     

Comment on: “FTIR,FT-Raman,scaled quantum chemical studies of the structure and vibrational spectra of 1,5-dinitronaphthalene” by Arivazhaga et al. [Spectrochim. Acta A72 (2009) 941–946]

The title paper [1] reports ab initio calculations of the structure and molecular vibrations of 1,5-dinitronaphthalene. The calculations are unminimised, the molecular structure is wrong and the vibrational spectra are misinterpreted. These errors have been corrected and the vibrational spectra of 1,5-dinitronaphthalene have been reassigned in agreement with the optical and neutron spectroscopic data.     

Applications of molecular orbital theory to the interpretation of mass spectra. Prediction of primary fragmentation sites in organic molecules

Semi-empirical molecular orbital calculations have been carried out on the steroidal hormone estrone, both as a neutral molecule and the corresponding positively charge molecular ion. These calculations provide estimates of bond densities and net atomic charges, factors deemed important in past correlations of observed mass spectra with molecular structure. Calculated net charges appear to be unrelated to fragmentation processes. Calculated bond densities of the ground state molecular ion of estrone allow prediction of gross features of fragmentation. Bond densities of excited electronic states of the molecular ion may provide a basis for finer distinction among sites of initial bond cleavage, which is information crucial to rationalization of subsequent fragmentation of the molecular ion.     

Nanoscale Chemical Imaging of Interfacial Monolayers by Tip‐Enhanced Raman Spectroscopy

We report an investigation of interfacial fluorinated hydrocarbon (carboxylic‐fantrip) monolayers by nanoscale imaging using tip‐enhanced Raman spectroscopy (TERS) and density functional theory (DFT) calculations. By comparing TERS images of a sub‐monolayer prepared by spin‐coating and a π–π‐stacked monolayer on Au(111) in which the molecular orientation is confined, specific Raman peaks shift and line widths narrow in the transferred LB monolayer. Based on DFT calculations that take into account dispersion corrections and surface selection rules, these specific effects are proposed to originate from π–π stacking and molecular orientation restriction. TERS shows the possibility to distinguish between a random and locked orientation with a spatial resolution of less than 10 nm. This work combines experimental TERS imaging with theoretical DFT calculations and opens up the possibility of studying molecular orientations and intermolecular interaction at the nanoscale and molecular level.     

An improved program for molecular calculations with B functions

An improved version of a previously reported program for molecular calculations with B functions is presented. In this version, new algorithms for the three- and four-center electron repulsion integrals are used. The mathematical aspects of the algorithms are recognized and their performance analyzed. The results on full molecular calculations confirm the higher efficiency of the new algorithms in comparison with the old ones.     

Determination of the absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one by optical rotation computation

The absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one was determined by quantum chemical calculations of specific rotation angles with coupled–perturbed Hartree–Fock methods. The computation used molecular geometries obtained from ab initio calculations as well as from molecular mechanics and semi-empirical optimization. In addition to the dependence on geometry optimization strategies, the basis set dependence of the computed rotation angle was examined.     

Analytical calculations of molecular integrals for multielectron R-matrix methods

Closed-form analytical expressions for one- and two-electron integrals between Cartesian Gaussians over a finite spherical region of space are developed for use in ab initio molecular scattering calculations. In contrast with some previous approaches, the necessary integrals are formulated solely in terms of finite summations involving standard functions. The molecular integrals evaluated over the finite region of space are computed by subtracting the contributions outside the region from the integrals over all space. The latter integrals can be efficiently and accurately obtained from existing bound-state algorithms. Our approach incorporates molecular scattering calculations into current quantum chemistry programs and facilitates the unification of bound- and continuum-state calculations for both diatomic and polyatomic molecules. Multidimensional Monte Carlo numerical integrations validate the high accuracy of our closed form results for the two-electron integrals.     

Conformational dependence of the electrostatic potential-derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution

The electrostatic potential-derived charges for the catecholamine neurotransmitter dopamine were calculated at the STO-3G and 6-31G* basis sets for six different molecular conformations. The degree of variance of the charges with changing conformations was examined. The 6-31G* basis set produced charges that were more sensitive to changes in conformation than those derived from the STO-3G electrostatic potentials. The implication of the charge variations in molecular mechanics calculations was also investigated. The molecular mechanics results in the gas phase exhibited a variance depending upon the charge set used. The force field calculations varied much less when aqueous solvation was included in the calculations through a continuum model. © 1993 John Wiley & Sons, Inc.     

Ab initio calculations,using a small Gaussian basis set,of the electronic structure of the sulphate ion

Ab initio molecular orbital calculations of the electronic structure of the sulphate ion have been performed in which three Gaussian-type functions are used to simulate each member of a minimal basis of Slater-type orbitals. Comparative calculations on H₂S show that such a basis excellently reproduces the properties of the valence electrons given by calculations in a Slater basis. The expansion of the basis by the addition of sulphur 3d orbitals results in a large decrease in the molecular energy (1 a.u.) and has a pronounced effect on the ordering and energy of the molecular orbitals. The results of a number of semiempirical schemes are discussed in the light of these results.     

Calculations of molecular properties in hybrid coupled-cluster and molecular mechanics approach

We report benchmark calculations obtained with our new coupled-cluster singles and doubles (CCSD) code for calculating the first- and second-order molecular properties. This code can be easily incorporated into combined [Valiev, M.; Kowalski, K. J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) calculations using NWChem, enabling us to study molecular properties in a realistic environment. To test this methodology, we discuss the results of calculations of dipole moments and static polarizabilities for the Cl2O system in the CCl4 solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [Kowalski, K.; Valiev, M. J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of CCSD calculations.     

Testing the arbitrariness and limits of a pseudopotential technique through calculations on the series of diatoms HF,AlH, HCl,AlF, AlCl,F2, Cl2

The pseudopotential techniques present some degrees of freedom, the influence of which on molecular calculations must be tested to assess the stability and accuracy of the results. The present work uses a semi-local pseudopotential extracted from near Hartree-Fock atomic calculations; the shape of the inner part of the pseudoorbital, the analytic form of the pseudopotential are shown to have less influence than the choice of the valence basis set which must be optimized. The calculated molecular constants perfectly agree with the large basis set all-electron calculations, even for polar molecules.Equipe de Recherche Associée au CNRS No. 821.