A quantum-mechanical study of the interaction of methylglyoxal with guanine

Ab initio self-consistent field molecular orbital computations on the relative stabilities of the different possible intermediate adducts for the reactions between methylglyoxal and guanine, as well as the evaluation of the relative stabilities of the two different possible final cyclic products (IIIb and IIIc) point all to the conclusion that it is the addition product in which the methyl group is close to the amino nitrogen which is the most stable one.     

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.     

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.     

Quantum mechanical studies of environmental effects on biomolecules

LCAO SCF calculations with a (7s, 3p/3s) atomic basis are performed on urea and hydrated urea in order to determine the preferred sites of water fixation using the supermolecule approach. It appears that up to five water molecules can be directly bound to urea in the first hydration shell.     

Electronic structure of unstable intermediates

The geometry of the linear molecule HBO, has been investigated within the restricted Hartree-Fock LCAO-MO-SCF approximation. The calculated bond lengths for the near Hartree-Fock calculation were R(H-B)=2.1913 bohr, R(B-O)=2.2284 bohr. Several one electron properties have been calculated for the minimum energy configuration.     

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.     

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.     

Studies of the energy spectrum of α, ω- substituted polymethine chains. II. Polymethine chains with odd number of methine groups

The analysis of the experimental data for the energy of the longest wavelength optical transitions _n,opt of substituted polymethines X (CH)_2n+1 X shows that in the asymptotic case (n) _,opt does not tend to zero, as it follows from the empirically established correlations, but has a finite, non-zero value. It is shown that the energy gap of odd polymethines is the same as that of the even polymethines - the polyenes (E 2 eV). The substituents (X N, O, B) are responsible for the appearance of levels in the gap. These, depending on the substituent character, are vacant (X B) or occupied (X N, O). The transition from or to such a level determines the longest wavelength optical transition energy of polymethines.     

A simulation of the exchange potential in unrestricted and restricted Hartree-Fock calculations studied on atoms

The spherical average of the Hartree-Fock exchange potential depending on each spin orbital is compared with Slater's exchange potential, V _xs, as demonstrated for the phosphorus atom. It is shown that the former potential can be simulated by (a + br)V _xs, where r is the radius and the constants a and b are calculated for each spin orbital. This simulation is tested for the iron atom and it is found that the results agree well with those obtained from unrestricted and restricted Hartree-Fock calculations, respectively. The applicability of this new method in energy band structure calculations is briefly discussed.Dedicated to Professor H. Hartmann on the occasion of his 65th birthday.     

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.     

Theoretical study of the potential energy curves of the series of diatomic radicals MeIIX

The potential energy curves of some low lying electronic states of the diatomic radicals BeCl and MgF have been calculated. The calculation has been performed according to a stepwise procedure, outlined in a previous work. The potential energy curves are very similar to those of the mercury halide radicals, the electronic transitions of which can be employed for efficient laser apparatus.     

Ab initio study of hydrazoic acid

SCF and CI calculations were carried out on the ground^1A state of HN₃. The equilibrium geometry and vibration frequencies were computed. The results point to a planar structure (groupC _s) but to a non-linear (170 °) N-N-N conformation. The calculated vibration frequencies are in fair agreement with experimental assignments.The dissociation path of the molecule to NH and N₂ products was investigated and compared to the isoelectronic reaction of diazomethane. The dissociation energy of hydrazoic acid is estimated to be about –8 kcal/mole, with a potential barrier to dissociation of about 30 kcal/mole.Boursier IRSIA     

Conformational analysis of dimethylphosphate with quantum-mechanical and classical methods

In order to shed light on the conformational behavior of polynucleotide chains, and in particular to clarify the origins of the barriers to internal rotation in the phosphodiester linkage, we computed, with a quantum-mechanical ab initio procedure, the energies associated to 86 combinations of the two torsion angles in the dimethylphosphate anion (CH₃O)₂PO₂ ^–, and then we sought for an analytical expression apt to reproduce these energies with the highest possible accuracy. An excellent agreement (standard deviation of the fitted energies from the ab initio energies 0.28 kcal/mole) with the quantum-mechanical calculations was reached with a potential consisting of four terms: 1) a 6–12 Lennard-Jones contribution, in which different parameters are used to describe the interactions of methyls with the ester oxygens and with the anionic oxygens; 2) a contribution with twofold periodicity, accounting for the anomeric effects connected to the interactions between the lone pair electrons and the polar bonds of phosphorus with the anionic oxygens; 3) a contribution with threefold periodicity, representing the usual bond-staggering term; and 4) a Coulombic contribution, arising from electrostatic interactions between partially charged atoms.     

The combinatorics of graphical unitary group approach to many electron correlation

The combinatorics of Gel'fand states which are useful in the graphical unitary group approach to many electron correlation problem and spin free quantum chemistry is considered. Using operator theoretic methods it is shown that the generators of Gel'fand states are S-functions.     

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.     

Application of intermolecular SCF-perturbation theory to the regioselectivity in the Diels-Alder reaction

Intermolecular perturbation theory in the density matrix formalism is applied to investigate the directional behaviour of an electron-donating (-CH₃) or an electron-accepting (-CN) group in 1- or 2-substituted butadienes in the Diels-Alder reaction with acrylonitrile. The calculated CNDO/2 perturbation energies are analysed in three different ways by considering: a) the different perturbation energies, b) the diatomic parts of the interaction energy and c) the HOMO-LUMO contribution to the second-order energy. The regioselectivity is due to a subtle balance of charge-transfer interactions and steric effects of the substituents on the diene and the dienophile. The changes of intra- and intermolecular diatomic energy contributions are correlated with the process of bond formation and bond weakening. The intermolecular perturbation energies are dominated by pairwise interactions between the terminal C-atoms and by the secondary Woodward-Hoffmann interaction. These three localized interactions determine the endo addition and reflect the orienting power of the substituents.     

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.     

SCF-CI studies on the electronic ground state of water: Potential energy hypersurface and spectroscopic constants

Large-scale Hartree-Fock self-consistent field calculations, employing extended Gaussian basis sets, and configuration interaction studies are performed to calculate the energy hypersurface of the electronic ground state of the water molecule and to investigate the accuracy requirements in view of the determination of molecular spectroscopic constants. From the calculated points on the hypersurface the theoretical equilibrium geometry, the force field through fourth order, the spectroscopic constants _i, x_ij, _i as well as the Darling-Dennison and Fermi resonance constants are evaluated. The CI surface yields an equilibrium structure for H₂O withr _e = 0.9501 Å and _e=105.33 ° (r _exp = 0.9572 Å and _exp = 104.52 °). The vibrational levels are obtained with a systematic error of about 2 percent and the rotational constants to about 1 percent compared to spectroscopic data. The relative energy maximum corresponding to the linear structure with = is calculated to be 11890cm^–1, within the error limits of the values deduced from experimental measurements.     

Ab initio SCF and CI study of the electronic spectrum of pyridine N-oxide

Configuration interaction (CI) studies of ground, n *, * * electronically excited states are reported for pyridine N-oxide. The transition energy to the lowest * excited ¹ B ₂ state is calculated at 4.35 eV, compared to the experimental spectrum range of 3.67–4.0 eV. This state lies below the lowest n * excited ¹ A ₂ state calculated at 4.81 eV above the ground state. The only experimentally reported triplet state at 2.92 eV above the ground state is predicted to be the ³ A ₁ (*) state. The calculated energy lies at 3.27 eV. Numerous other high-lying singlet states as well as the triplet states have also been calculated. The intramolecular charge transfer character of the ground and the excited states have been studied in terms of the calculated dipole moment and other physical properties.