Showing papers in "Journal of Molecular Structure-theochem in 1983"
TL;DR: The second-order Jahn-Teller effect as mentioned in this paper is an example of reactions proceeding by an interaction between the HOMO and the LUMO within the same molecule.
Abstract: The second-order Jahn-Teller effect is an example of reactions proceeding by an interaction between the HOMO and the LUMO within the same molecule. The consequences can be decomposition of the molecule or a structural change. First the general theory is given, and then a number of examples are presented.
243 citations
TL;DR: In this article, a new method for the solution of the coupled perturbed Hartree-Fock equations is outlined which avoids the four-index transformation of electron repulsion integrals.
Abstract: A new method for the solution of the coupled perturbed Hartree-Fock equations is outlined which avoids the four-index transformation of electron repulsion integrals. This allows the extension of analytic energy second derivative methods to large molecular systems. The new approach has been implemented for both closed- and open-shell molecules and a number of test cases considered, including as many as 96 contracted gaussian basis functions. The time required for the determination of all cartesian force constants varies from 8% to 65% of that required for analytic gradient techniques.
112 citations
TL;DR: The rotational conformations of BP*, 2,2′-DCBP, 2,3′-dcBP, DCBP, 3, 3′, 4,4, 5′5′-HCBP and TCBP were investigated by the GAUSSIAN-80 ab initio technique as mentioned in this paper.
Abstract: The rotational conformations of BP*, 2,2′-DCBP, 2,3′-DCBP, 3,3′-DCBP, 3,3′,4,4′-TCBP and 3,3′,4,4′,5′5′-HCBP are investigated by the GAUSSIAN-80 ab initio technique. All molecules that do not have ortho -substitution have an energy minimum at 42° and barriers of approx. 3.6 and 2.3 kcal mol −1 occur at 0° (and 180°) and 90°, respectively. Ortho -substitution results in an extremely high barrier at 0° (and 180°) and a shift of the energy minimum toward 90°. These results may account for the diminished physiological activity of ortho substituted PCB's; the planar (0° or 180°) rotamers are not energetically accessible.
63 citations
TL;DR: In this paper, the potential parameters for the non-bonded interaction terms Br, Br, C and H have been included for the first time within the Morse formulation and the effect of including excess charges on the atoms has been investigated.
Abstract: Molecular mechanics calculations of conformational structures, energies and barrier heights in substituted chloro- and bromoethanes and propanes are given which reproduce the available experimental data reasonably well. The effect of including excess charges on the atoms has been investigated. Potential parameters for the non-bonded interaction terms Br ⋯ Br, Br ⋯ C and Br ⋯ H have been included for the first time within the Morse formulation.
40 citations
TL;DR: In this paper, the optimal geometries, relative stabilities, dipole moments and ionization potentials of eight adenine and fifteen guanine tautomers have been calculated by the MNDO method.
Abstract: The optimal geometries, relative stabilities, dipole moments and ionization potentials of eight adenine and fifteen guanine tautomers have been calculated by the MNDO method. The calculated geometrical parameters agree well with crystallographic data and the dipole moments and ionization potentials are in accord with the available experimental results. The relative stabilities allow prediction of the most stable tautomers in the vapor phase and in non-polar solvents, in qualitative agreement with experiment. In addition, application of the simple continuous solvation model makes it possible to predict the most stable tautomers in aqueous solution.
39 citations
TL;DR: In this paper, the Applequist-Carl-Fung (ACF) method for calculating polarizabilities of polyatomic molecules was modified for treating planar aromatic molecules including chlorinated biphenyls (planar and rotated), dioxins and polyaromatic hydrocarbons.
Abstract: The Applequist—Carl—Fung (ACF) method for calculating polarizabilities of polyatomic molecules was modified for treating planar aromatic molecules including chlorinated biphenyls (planar and rotated), dioxins and polyaromatic hydrocarbons. The essential modification is to allow for anisotropic carbon atom polarizabilities; the resulting molecular anisotropies are much improved. In addition, a binding model is proposed which approximately accounts for the polarizability contributions (through dispersion) to the relative binding constants of similar molecules to a common receptor.
37 citations
TL;DR: In this article, the electronic and geometrical structures of 1,3-dipolar species are investigated by the semi-empirical and ab-initio molecular orbital methods and energy gradient techniques.
Abstract: The electronic and geometrical structures of 1,3-dipolar species are investigated by the semiempirical and ab-initio molecular orbital methods and energy gradient techniques. The diradical character (order parameter) is calculated to express quantitatively the symmetry and broken symmetry properties of their frontier orbitals. The clusterings of water to carbonyl oxide are investigated as an example for the stabilizations of unstable molecules by polar solvents. The present MO theoretical treatments indicate both nonradical and diradical behaviors of unstable 1,3-dipolar species such as carbonyl ylides, compatible with various experimental results reported by Huisgen and others.
35 citations
TL;DR: In this article, the Hartree-Fock gradient calculation with a 4-21 basis augmented by d functions on O and N was used to determine complete equilibrium geometries for all stable conformations.
Abstract: Complete equilibrium geometries have been determined for all stable conformations of cyclobutanol, C4H7OH, cyclobutylamine, C4H7NH2, and methyl cyclobutane C4H7CH3, by ab initio Hartree—Fock gradient calculation with a 4–21 basis augmented by d functions on O and N. Conformations differ in having the substituent equatorial (eq) or axial (ax) on the puckered ring and by gauche (g) or anti (a) orientation of the substituent hydrogen with respect to the ring hydrogen.
For C4H7NH2 four stable conformers exist, a—g—eq being the most stable with ΔE for the others being: g—g—eq, 3.2; g—g—ax, 4.2; and a—g—ax, 6.5 kJ mol−1. For C4H7OH only three conformers are found with a—eq most stable, ΔE for g—eq, 2.1, ΔE for g—ax, 8.1 kJ mol−1, and no minimum found for a—ax. For C4H7CH3, only two conformers can exist when the CH3 group staggers the adjacent CCH group. The eq form is 1.7 kJ mol−1 more stable than the ax. These results extend our earlier series and show that the equatorial position is most favored by the most electronegative substituent. The axial conformer becomes increasingly more stable in the series F < OH < NH2 < Cl < CH3 < Li.
Ring structural parameters show only small differences, but these vary quite systematically with substituent electronegativity. Trends are established for differences in adjacent vs. opposite CC bond lengths, ring puckering angle, distortions of the CH2 groups, ∠HCX and ∠XC2C1C4.
32 citations
TL;DR: The results obtained by ab initio SCF calculations both by the FOGO (floating orbital geometry optimization) and LCAO-MO methods indicate that open-chain N6 in C2 symmetry is more stable by more than 100 kJ mol−1 than the previously reported hexazine species (N6 in D6h symmetry) as mentioned in this paper.
Abstract: The results obtained by ab initio SCF calculations both by the FOGO (floating orbital geometry optimization) and LCAO—MO methods indicate that open-chain N6 in C2 symmetry is more stable by more than 100 kJ mol−1 than the previously reported hexazine species (N6 in D6h symmetry). The optimized geometries and changes in energies and in some physical properties due to the internal rotation along the central NN bond of N6 in the C2 species are reported in detail.
31 citations
TL;DR: In this paper, correlated calculations have been carried out for HeHHe + and HeH + 3, where correlation effects are unusually small and the correlation effects can be easily understood in terms of interacting molecular orbitals.
Abstract: Large basis set, correlated calculations have been carried out for HeHHe + and HeH + 3 . He is very slightly attractive towards H + 3 but forms a moderate bond to HHe + that can be easily understood in terms of interacting molecular orbitals. Correlation effects are unusually small.
31 citations
TL;DR: The fully optimized molecular structures of planar anisole, cis-guaiacol and trans-veratrole have been calculated on the STO-3G level of accuracy as discussed by the authors.
Abstract: The fully optimized molecular structures of planar anisole, cis -guaiacol and trans -veratrole have been calculated on the STO-3G level of accuracy. Comparisons with standard geometry structures indicate that the structural relaxation energy should be taken into account in e.g., internal rotation barrier or isodesmic reaction energy calculations. Superposition geometries constructed from fully optimized parent structures provide more advantageous reference geometries than the usual standard geometries, and may also serve as excellent initial geometries for further optimization.
TL;DR: In this article, the structures and conformations of cyclopentane and cyclohexene have been investigated using SCF gradient ab initio computation with a double zeta basis set, and the half-chair (C2) and the envelope (Cs) forms were found to be isoenergetic.
Abstract: The structures and conformations of cyclopentane, cyclopentene, and cyclopentadiene have been investigated by SCF gradient ab initio computation with a double zeta basis set. For cyclopentane the half-chair (C2) and the envelope (Cs) forms were found to be isoenergetic, consistent with the experimentally observed free pseudorotation. The barrier to coplanarity of the ring is 4.3 kcal mol−1. Cyclopentene has a puckered Cs equilibrium conformation with a very low barrier to planarity. Cyclopentadiene has a planar ring. The compounds with 5, 3 and 1 methylene groups, respectively, show a decreasing tendency to form puckered rings as interaction between adjacent methylene groups becomes of less significance compared with the influence of angle strain which favors ring planarity. A corrected geometrical optimization of the half-boat (Cs) form of cyclohexene is also presented.
TL;DR: In this article, the structures of ten conformations of glycerol have been refined without any geometrical constraints by ab initio gradient relaxation on the 4-21G level.
Abstract: The structures of ten conformations of glycerol have been refined without any geometrical constraints by ab initio gradient relaxation on the 4-21G level. The compound can exist in forms which possess a symmetry plane, and in forms in which asymmetry is induced by intramolecular interactions. The two most stable forms are of type αγ (Fig. 1) and γγ (Fig. 9). The latter is characterized by a chair-type six-membered ring closed by hydrogen bonding. The calculations make it possible to estimate the positions of the hydrogen atoms which are not known from experimental work. Intramolecular hydrogen bonds are approximately oriented along the directions conventionally defined for σ-,π-and sp 3 -type electron lone pairs on oxygen. The results also make it possible to describe the differences in local geometry which can cause the central carbon atom to be chiral. This is in contrast to presentations in which the chemical equivalence of the terminal CH 2 OH groups in glycerol is correlated with the assumption that the central carbon atom is symmetric. It is postulated that, rather, the chemical equivalence of the terminal groups can involve the rapidly interconverting equilibrium of asymmetric, enantiomeric forms. The results thus demonstrate that details of molecular local geometries can be important in interpretations of chemical reactivity.
TL;DR: In this article, it was shown that the tetrahedron can tolerate 2n or 2(n+2) skeletal electrons, but not 2n+1, and that the edge lengths of the tricapped trigonal prism and the 8-vertex D2d dodecahedron are not degenerate.
Abstract: Although most deltahedral (closo) boron clusters (e.g. anions BnHn2−) with n atoms are held together by 2(n+1) skeletal electrons, some closo deltahedra, like the 8-vertex D2d dodecahedron and the 9-vertex D3h tricapped trigonal prism, can tolerate 2n or 2(n+2) skeletal electrons. This is because their frontier orbitals are non-degenerate, a feature shared with B11H112− but not with other species BnHn2− (n = 5, 6, 7, 10 or 12). Closo 2n- or 2(n+2)-electron systems with these latter structures would have incomplete electron shells with unpaired electrons, and be prone to distortion to remove the degeneracy. The polyhedron edge-bonding or -antibonding characteristics of the HOMO and LUMO of BnHn2− (n = 8 or 9) can be used to rationalise the different edge lengths in Bn Cln and in Bi95+. The special situation that obtains for the tetrahedron - a deltahedron for which 2n or 2(n+2) skeletal electrons, but not 2(n+1), are appropriate - is noted.
TL;DR: In this paper, a projection method is described for elimination of spurious contributions to calculated cartesian force constants which give rise to non-zero frequencies for translational and rotational modes and which may cause errors in vibrational frequencies.
Abstract: A projection method is described for elimination of spurious contributions to calculated cartesian force constants which give rise to non-zero frequencies for translational and rotational modes and which may cause errors in vibrational frequencies. Illustrative calculations for water monomer (in STO-3G) and water dimer (in 4-31G) are discussed. The preference for deuterium-bonded versus hydrogen-bonded isotopomeric water-dimer structures is demonstrated by calculations which satisfy the Teller-Redlich product rule provided that projected force constants are employed.
TL;DR: In an attempt to characterize germanium doubly bonding, several properties of digermene were investigated with the ab initio SCF method in this article, and the thermodynamic and kinetic stabilities were discussed in comparison with data on ethylene, silene, disilene and germene.
Abstract: In an attempt to characterize germanium doubly bonding, several properties of digermene were investigated with the ab initio SCF method. The thermodynamic and kinetic stabilities are discussed in comparison with data on ethylene, silene, disilene, and germene.
TL;DR: In this paper, a relativistic molecular-orbital theory analogous to the non-relativistic one of Pople (1962) was formulated for the diamagnetic behaviour of electrons in the presence of an applied magnetic field.
Abstract: A relativistic molecular-orbital theory, analogous to the non-relativistic one of Pople (1962), has been formulated for the diamagnetic behaviour of electrons in the presence of an applied magnetic field. The molecular orbitals are written as linear combinations of gauge-invariant four spinors. A semi-empirical approach using Huckel-type approximations is employed. A similar treatment is developed for nuclear shielding tensors.
TL;DR: In this article, large-scale Gaussian orbital SCF-MO calculations for the title molecules are presented for the same class of molecules and the changes of electron distribution on complex formation are discussed in terms of Mulliken population analysis indices.
Abstract: Large-scale Gaussian orbital SCF—MO calculations are presented for the title molecules. Calculated equilibrium geometries, hydrogen-bond dissociation energies and one-electron properties are given to supplement available experimental data. Changes of electron distribution on complex formation are discussed in terms of Mulliken population analysis indices.
TL;DR: In this paper, a hydrogen-bond potential adjusted to the MM2 molecular mechanics force field is introduced, developed from MO calculations of 66 configurations of the water dimer, and the relative strengths of the well-known linear, cyclic and bifurcated forms of the dimer are satisfactorily reproduced.
Abstract: A hydrogen-bond potential adjusted to the MM2 molecular mechanics force field is introduced. It is developed from MO calculations of 66 configurations of the water dimer. Some modifications that were made to the MM2 force field and the addition of an extra potential are discussed. The rms deviation of the energies is 0.60 kcal mol−1. The relative strengths of the well-known linear, cyclic and bifurcated forms of the dimer are satisfactorily reproduced.
TL;DR: In this paper, the potential energy surfaces for bond rupture and hydrogen-migration pathways are presented for the ground and excited states of ethyl and vinyl radicals. And the relationship between the ground-and excited state surfaces is clearly delineated using orbital and state correlation diagrams.
Abstract: Ab initio SCF + CI calculations of the potential energy surfaces for bond rupture and hydrogen-migration pathways are presented for the ground and excited states of ethyl and vinyl radicals. For the ground state surfaces various methodological problems are discussed with regard to the use of single configuration RHF and UHF open-shell techniques. The relationship between the ground and excited state surfaces is clearly delineated using orbital and state correlation diagrams. The essentials of these qualitative diagrams are reproduced at the computational level. The main feature of the excited state migration pathway is that there exists a direct C2v adiabatic pathway taking the excited states of ethyl and vinyl radicals to the ground states of ethylene and acetylene + H, respectively. However, only in the case of the ethyl radical is this pathway energetically feasible. In the case of the vinyl radical, the presence of low lying excited states and subsequent high barriers indicates that excited vinyl radicals should be stable. However, the excited states of ethyl and other related alkyl radicals should be directly photodissociative or predissociative.
TL;DR: In this article, the authors present a discussion of the properties of molecular force fields expressed in dependent coordinates and stress is laid on the ambiguous definition of force fields in such coordinates and the resulting difficulties in the direct comparison of different force fields.
Abstract: The paper presents a discussion of the properties of molecular force fields expressed in dependent coordinates. Stress is laid on the ambiguous definition of force fields in such coordinates and the resulting difficulties in the direct comparison of different force fields. A method of unique definition of a force field in dependent coordinates is proposed. The properties of this force field, methods of its construction and possible applications are discussed.
TL;DR: In this article, the authors proposed two CEPA-VAR-based approximation methods for coupled-pair wave functions, which minimize the total energy expression with respect to the CI coefficients.
Abstract: The calculation of analytical gradients for coupled-pair wave functions is discussed. It is emphasized that gradients can only be efficiently evaluated if the CI coefficients minimize the total energy expression. Two CEPA versions are proposed which have this property. CEPA-F has fixed denominator shifts. CEPA-VAR is an approximation to CEPA-2: its denominator shifts are two-third of the pair correlation energies, and the energy formula is minimized with respect to the CI coefficients. Equations are presented for the derivatives of the localized orbitals which are needed in the localized form of CEPA-VAR.
TL;DR: In this paper, rational criteria for the choice of a chemically useful yet affordable basis set for ab initio molecular orbital calculations on systems of reasonable size involving sulphur atoms were developed.
Abstract: We have attempted to develop rational criteria for the choice of a chemically useful yet affordable basis set for ab initio molecular orbital calculations on systems of reasonable size involving sulphur atoms. The performance of many different bases has been assessed, regarding energies, molecular structures, force constants, bond energies and dipole moments for H2S2 and SO2. The optimum size was found to be 10s and 6p Gaussian primitives on S, contracted to 6s and 3p functions. d Polarization functions are found to be essential on sulphur.
TL;DR: In this paper, a general survey of the effect of bond length and bond angle optimisation on the conformational energies of various anomeric systems is made, and various contributions to the potential energy are analysed by decomposing the potential into three term Fourier components.
Abstract: Ab initio MO studies at the STO-3G and the 4-31G level are reported for aminomethanol (H2NCH2OH), aminesulfonic acid (H2NSO3H) and N-methylsulfamate (CH3NHSO3−). The potential energy surface of aminomethanol is compared with that of methanediol and the origin of “reverse anomeric effect” is discussed. The potential energy surface of aminesulfonic acid is compared with that of aminomethanol and sulfuric acid. The favored conformations are analysed in terms of the interaction of polar bonds and the dipoles on the atoms. Various contributions to the potential energy are analysed by decomposing the potential into three term Fourier components. A general survey is made of the effect of bond length and bond angle optimisation on the conformational energies of various anomeric systems.
TL;DR: In this paper, the dissociation energies of diatomic molecules have been computed by fitting an empirical potential function to the experimental potential energy curves for the electronic ground states of the molecules using the five parameter Hulburt-Hirschfelder function and Rao and Reddy's modified potential function.
Abstract: Experimental potential energy curves have been constructed for different electronic states of CaF, CaCl, CaI and CaH molecules by the method of Lakshman and Rao and of Morse. The dissociation energies of the diatomic molecules have been computed by fitting an empirical potential function to the experimental potential energy curves for the electronic ground states of the molecules. The five parameter Hulburt—Hirschfelder function and Rao and Reddy's modified potential function have been used. The estimated dissociation energies are 5.469 ± 0.012;4.085 ± 0.002;2.767 ± 0.022 and 1.679 ± 0.015 eV for CaF, CaCl, CaI and CaH respectively.
TL;DR: An empirical valence bond structure-resonance theory is applied to monocyclic oxocarbon dianions and neutral oxocarbons Graph theoretical techniques are used to carry out the calculations The resonance energies are partitioned among various types of resonance interactions Carbonyl group covalent-ionic resonance is the most prevalent type of stabilizing resonance term in every case as discussed by the authors.
Abstract: An empirical valence bond structure-resonance theory is applied to monocyclic oxocarbon dianions and neutral oxocarbons Graph theoretical techniques are used to carry out the calculations The resonance energies are partitioned among various types of resonance interactions Carbonyl group covalent-ionic resonance is the most prevalent type of stabilizing resonance term in every case (⩾50%) Resonance energies, charge distributions, and bond orders are compared with the results of MO calculations, and with relevant experimental data A qualitative valence bond interpretation of the concept of aromaticity is proposed based on cyclic terms that appear in the graph of the empirical structure-resonance theory Hamiltonian matrix On this basis, all oxocarbon dianions are found to be resonance stabilized and aromatic, whereas the neutral oxocarbons are nonaromatic but still stabilized by resonance
TL;DR: In this article, a simple model was proposed to predict the thermochemistry of free radical polymerizations in the gas phase by assuming that the heat of polymerization of a monomer A = B is equal to the enthalpy change of the process HABAH + A=B --> HABABAH.
Abstract: In this paper, we propose a simple model to predict the thermochemistry of free radical polymerizations in the gas phase. It consists of assuming that the heat of polymerization of a monomer A=B is equal to the enthalpy change of the process HABAH + A=B --> HABABAH. The heat of formation of species HABAH, A=B and HABABAH not yet experimentally determined are theoretically calculated using various ab initio methods of quantum chemistry. The enthalpies of polymerization of a series of monomers could be calculated in this way. They are generally in good agreement with the corresponding available experimental data. They could be also rationalized in terms of the stabilization energies of the monomers and the growing chains.
TL;DR: In this article, it is shown that the different dependence upon distance of these two related properties produces substantial differences in their spatial distribution, particularly prominent in the case of macromolecules such as the nucleic acids.
Abstract: The studies of the electrostatic properties of molecules and in particular of biomolecules and biopolymers have, till recently, been limited essentially to the exploration of their molecular electrostatic potential (MEP). We have extended these studies to the evaluation of the molecular electrostatic field (MEF). It is shown that the different dependence upon distance of these two related properties produces substantial differences in their spatial distribution, particularly prominent in the case of macromolecules, such as the nucleic acids. Thus, while the deepest potentials are found in the grooves of DNA, the highest fields are associated with its phosphate groups. This situation has important consequences for the exploration of the biochemical reactivity of these substances, MEP being particularly appropriate for the study of the interaction with ionic, electrophilic reactants and MEF for the study of the interaction with neutral dipolar species, prominent among which is water. Abundant evidence has been provided for the significance of MEP for the interaction of the nucleic acids and their constituents with cations. Recent evidence supports the preferential hydration of phosphates in these systems, in line with the results of MEF studies.
TL;DR: In this article, a conformational optimization for all isomers of bifurans and bipyrroles has been studied by performing a complete geometry optimization for each conformation.
Abstract: An INDO-SCF-LCAO-MO study has been performed for all isomers of bifurans and bipyrroles. The conformational problem for these molecules has been studied by performing a complete geometry optimization for each conformation. The trans conformers are the most stable for all isomers except for 2,3′-bifuran where the greater stability corresponds to the cis conformer. The torsional barrier about the interannular bond is also estimated for all isomers, together with total geometry optimization. The barriers are of relative significance but enable attainment of equilibria between both conformers. The particular case of 1,1′-bipyrrole, where an angular conformation presents the greater stability as a compromise between the contrary effects of nonbonded interactions and interannular conjugation, is discussed. The importance of performing geometry optimization on conformational problems is established.
TL;DR: In this paper, the 3-21G and double-zeta-plus-polarization (DZ plus polarisation) levels were used to optimise the geometry of RCN and RNC.
Abstract: Structures optimised at the 3-21G level are reported for RCN and RNC, where R is CH 2 − , CH 3 CH − , (CH 3 ) 2 C − , CH 3 , CH 3 CH 2 , (CH 3 ) 2 CH, CH 2 + , CH 3 CH + and (CH 3 ) 2 C + . Inclusion of diffuse functions does not change significantly the geometry of CH 2 CN − and CH 2 NC − . Geometries optimised at the double-zeta level are also reported for some of the smaller molecules. The cyano group is strongly stabilising in carbanions, with the effect being largest for primary anions and smallest for tertiary. In carbenium ions the α-cyano group is destabilising at all levels of calculation (3-21G, double-zeta and double-zeta plus polarisation) with the destabilisation increasing with the size of the basis set. The α-isocyano substituent is stabilising in both carbanions and carbenium ions, and is more effective at stabilising ions than the α-fluoro substituent.