On the use of pseudopotentials in molecular calculations

A series of tests was performed of the Kahn-Goddard-Melius-Topiol pseudopotentials in view of their utilization with small contracted basis sets in molecular computations. The effects of inner-shell separability and of basis set contraction are underlined. The utilizability of Topiol's valence least-squares fitted Gaussian basis sets is studied.     

Structure and properties of non-classical polymers II. Band structure and spin densities

Theoretical investigation of the band structure of three types of nonclassical polymers, namely alternant (one- and two-dimensional), nonalternant and heteroatomic, are carried out. Although polyradicals, these polymers have a considerable delocalization energy which may determine their relative stability.The spin-density distribution of the alternant type of non-classical polymers corresponds to a ferrimagnetic ground state at 0 K.The non-classical polymers represent a new class of organic systems as their band structure and magnetic properties essentially differ from those of common polymers.     

A theoretical study of electrophilic reactions

The electronic structures of protonated formyl and acetylium cations and their deprotonation paths leading to HCO⁺, COH⁺ and CH₃CO⁺have been studied by means of ab initio calculations. The results support Olah's theory that dipositive species can be the de facto reagents in electrophilic reactions.     

Configuration interaction methods for improving unrestricted Hartree-Fock spin densities

Limited Configuration Interaction wave functions based on Unrestricted Hartree-Fock natural orbitals are found to be easy to compute and to give much more satisfactory spin densities than are provided by techniques currently in use.     

Band structure of nonclassical polymers

It is shown that fully conjugated alternant nonclassical polymers are comparatively stable systems as a result of the considerable delocalisation energy.The energy characteristics of the polymers are strongly determined by the electron spin distribution of the degenerate nonbonding molecular orbitals; the full spin configuration,S>0, is favoured. The spin densities depend on the electron correlation and alternate; this corresponds to a ferrimagnetic state of the polymer at 0°K.     

A non-empirical molecular orbital study on the relative stabilities of adenine and guanine tautomers

The relative stabilities of a series of adenine and guanine tautomers have been calculated using anab initio Hartree-Fock-Roothaan SCF MO method. The calculated relative stabilities agree in general with the results of earlier semiempirical studies. According to the present study, tautomeric forms with regular Kekulé structure for the six-membered purine ring are the most stable. The amine-imine tautomerization of purine bases is not likely to be responsible for spontaneous mutations in DNA.     

On the configuration interaction method for singlet states

The direct CI method, which avoids explicit calculation of the Hamiltonian matrix, is presented in a new form. The method is linked with Davidson's algorithm for iterative evaluation of the ground state eigenvector. The viability of the method is indicated by the test calculations on water which are described.     

Theoretical studies on the conformation of saccharides

Conformations of 2-methoxytetrahydropyran as a model for the six-membered ring in aldopyranosides have been calculated by the PCILO method using the algorithm of the conjugated gradient to optimize the geometry. The calculated geometry of the fourteen basic forms of 2-methoxytetrahydropyran was found to be in agreement with the available data obtained by X-ray diffraction of pyranosides. The results indicate differences in the geometry of 2-methoxytetrahydropyran resulting from the change of the axial vs. equatorial position of the methoxyl group. These changes are particularly meaningful in the values of bond angles and they are in agreement with the anomeric and exoanomeric effects. The experimentally found differences in the energies of an axial (⁴ C ₁) and equatorial (¹ C ₄) conformer, G = 2.9–3.7 kJ/mol, and the dipole moment, = 1.20 ± 0.05 D (1D = 3.33 10^–30mAs) agree well with the calculated values E = 3.18 kJ/mol and <> = 1.18 D which, in turn, suggest that the axial conformer is preferred over the equatorial one by a ratio a:e = 78:22.     

Molecular orbital studies on the conformation of GABA (γ-aminobutyric acid)

In distinction to Extended Hückel Theory which predicts as the most stable conformation of free zwitterionic GABA a totally extended form, PCILO and SCF ab initio studies show that the intrinsically preferred conformation of the isolated molecule is a highly folded one, resulting from strong interactions between the two charged ends. Computations are also carried out for hydrated GABA in the supermolecule approach allowing moreover for the flexibility of binding of some of the water molecules of the first hydration shell. They predict the coexistence in solution of a large number of conformations showing different degrees of folding (or extension), a result confirmed by recent NMR studies. This and a number of similar results show that we have to adapt our thinking on the role of conformations in pharmacological activity to this situation, which was frequently obscured by the more abundant results of X-ray crystallography yielding a single conformation.     

Non-empirical molecular orbital theory of the electronic structure of molecular crystals

A non-empirical molecular orbital treatment of molecular crystals, based on SCF perturbation theory and matrix partitioning methods is presented.     

Cation binding to biomolecules

SCF ab initio computations are carried out on the binding of alkali and alkaline-earth cations to the phosphate monoanion. The effect of the binding on the conformational properties of the phosphodiester linkage and of the polar head of phospholipids is investigated. The results indicate that following the nature of the cation and the site of its binding, the interaction may have a profound influence on the conformation of the ligand. The consequences of this situation on the use of lanthanide probes in NMR studies are considered.     

Non-empirical calculations and basis set effects on the inversion geometry of the aniline molecule

The geometry of the amine group and the barrier to internal conversion in aniline have been studied by single-determinantab initio SCF calculations using several basis sets from minimal to double-zeta quality. The results obtained from different types and sizes of basis sets are discussed. Calculations performed with the two most flexible basis sets yield inversion barriers of 0.9–1.1 kcal/mole and angles of pyramidalization at the nitrogen atom of 38–39 ° which are in good agreement with the experimental results (1.3 kcal/ mole and 38 °). Orbital and overlap population analyses are performed and compared with the expected mesomeric and inductive effect. The calculated dipole moment 1.48–1.49 D also agrees with the experimental values (1.48–1.50 D).Dedicated to Professor O. E. Polansky, Mülheim/Ruhr, on the occasion of his 60th birthday.     

Evaluation of fourier transform of two-center charge distribution for arbitrary slater-type orbitals

Fourier transform of two-center charge distributions corresponding to arbitrary Slater-type orbitals are evaluated by a Gaussian quadrature procedure without any preliminary series expansion of the integrand. Convergence and accuracy of the method are discussed and illustrated.     

Theory of isomer shift in hemin

Using the self-consistent charge extended Hückel procedure, the charge density difference at Fe⁵⁷ nucleus, between hemin and Fe⁺³ ion is calculated. This is combined with the recent value of the calibration constant, –0.23±0.02a ₀ ³ mm/sec to obtain an isomer shift of –0.374 mm/sec between hemin and Fe⁺³ in good agreement with the value –0.392 mm/sec derived from experimental data and the calculated value of the isomer shift of Fe⁺³ with respect to K₃FeF₆ from first principle covalency investigations in the latter compound. is composed of contributions from core and valence electrons of the same order of magnitude, with the latter being more than one-half of the former. The core contribution is composed of a number of terms of comparable magnitude and differing signs, whose significance is discussed.Supported by grant HL 15196-02 from the Heart and Lung Institute of National Institute of Health.     

Band structure of even and ions of odd polyenes

The analysis of experimental data for singlet transitions (E _n) of even polyenes (I), cations (II) and anions (III) of odd polyenes show that for infinite chains E (I)/E (II)=E (I)/E (III) = 2:1. It is shown that the energy gap is equal for the three systems. In cases (II) and (III) there is a level (NBMO) in the gap which is vacant in (II) and occupied in (III). That is why the first optical transition in (II) and (III) depends on the semiwidth of the gap.     

Non-empirical SCF MO studies on the protonation of biopolymer constituents

Side-chain proton affinities for a series of peptide-forming amino acids have been calculated using ab initio Hartree-Fock-Roothaan SCF method; the order of proton affinities is Arg > His > Ser Tyr Lys. Protonation of some side-chains in a protein may introduce new energy levels in the band gaps thus fundamentally altering the conduction properties of the proteins.This paper is dedicated to Professor H. Hartmann for his 65th birthday.Guest at the Laboratory of the National Foundation for Cancer Research at the Chair of Theoretical Chemistry, University of Erlangen-Nürnberg.     

Clusters of hydrogen molecules: Ab initio SCF calculations corrected semiempirically for correlation energies

Stabilization energy of the (H₂) _n clusters (n = 2–8) was calculated as a sum of the SCF interaction energy and the semiempirical interaction correlation energy estimated according to Sinanolu and Pamuk. Optimum successive attachment of hydrogen molecules leads to the formation of a gas-phase solvation shell consisting of seven hydrogen molecules. Basis set effect has been found to be important with all clusters under study. The non-additivity effect was investigated with the (H₂)₄ cluster. Vertical ionization potentials of the clusters considered are predicted to be 0.4–0.6 eV lower than the ionization potential of the parent H₂ molecule.     

Non-additivity in water-ion-water interactions

The three-body system Li⁺(H₂O)₂ was analyzed to study that non-additive part of the interaction potential which can be obtained by the Hartree-Fock approximation.For long and intermediate distances the three-body correction was found to be well represented by the induction energy, where bond dipoles are induced on each water molecule by point charges located on the (unpolarizable) lithium ion and on the other molecule respectively: for shorter distances this approximation was corrected by means of an exponential repulsive term. Such a potential model for non-additive interactions was extended to the more general situation Li⁺(H₂O)_n, and Monte-Carlo calculations were carried out on clusters containing up to six water molecules; comparison with other simulation results and with available data showed a significantly improved agreement with experiment. Tentative values for H are presented for n =7, 8,..., 20, where experimental data are not available.     

Conformations of the thiathiophthenes and related molecules

A conformational ab initio MO study has been carried out for the thiathiophthene molecule (TTP) and two related model compounds, thiomalonaldehyde (TMA) and its conjugate base (TMA(-)). The conformational energy surfaces for TMA, TMA(-) and TTP were generated using a least squares fit to the calculated data and plotted on a CALCOMP plotter. The results of the calculations showed that the cis-cis planar conformation of TTP is the most stable in agreement with experimental findings. For TMA and TMA(-) the cis-cis planar conformation is not the most stable. Contour plots of the five occupied -MO's of TTP show great similarity to those of naphthalene.Less detailed calculations were carried out for 3-hydroxy-prop-2-en-1-thione (HPT) and 3-mercapto-prop-2-en-1-thione (MPT). HPT was shown to be most stable in the cis planar hydrogen bonded conformation in agreement with the experimentally obtained results. For MPT the non-hydrogen bonded planar structure was found to be the most stable.     

Comments on the electronic properties of cyclopropane,cyclobutane, and cyclohexane

Spectral quantities of cyclopropane, cyclobutane, cyclohexane, and of several derivatives, have been calculated by a semiempirical all-valence electron SCF-CI MO method. In cyclopropane, HOMO is practically localized in the carbon-frame, and LVMO is purely so. In cyclobutane, these two MO's are based on C-H bonds, while cyclohexane holds an intermediate position. Despite the overall similarity-experimental and computed-of the spectra of these molecules, assignments are non-parallel. Like cyclopropane, cyclobutane can extend conjugation, but to a diminished degree; cyclohexane behaves in this respect like an acyclic alkane. An interpretation of this gradation, in terms of the nature of high-lying MO's, is proposed.