Ab Initio STO-3G Research Articles

Need for electronic correlation calculations in polymers

The presence of nonsinglet instabilities of the restricted Hartree-Fock ground-state wavefunction may be an indication of strong correlation effects. We have recently observed that such instabilities persist in some conjugated polymers even with localizable electronic structure, like strongly alternating polyene [(CH)x] or its isoelectronic analog (polymethineimine) by performing ab initio STO-3G unrestricted Hartree-Fock (UHF) calculations for these chain systems, using different geometrical arrangements. We suggest that coupled-cluster calculations might give a resolution to this problem.

Ab-initio sto-3G energy of tautomerism for uracil

Ab-initio sto-3G energies for uracil (U) and the tautomer 4-hydroxyuracil (U*) are reported. The four highest occupied molecular orbital energies for uracil correlate with experimental photoelectron ionization potentials with a least-squares linear correlation coefficient of 0.999. The energy ΔEt for U ⇋ U* using the best available geometries is 25.5 kcal/mole. The reaction field continuum model for the solvent effect indicates that ΔEt may be lowered by approximately 3 kcal/mole. Therefore the diketo form of uracil is theoretically determined to be the most stable form in solution as well as in the gas phase, in complete agreement with experiment.

The exploration of the conformational properties of biological phenethylamines by molecular orbital techniques

PCILO computations using x-ray determined crystal geometry as input data indicate that the gauche and trans conformers have practically identical energies in the majority of fundamental biological phenethylamines and phenethanolamines. Ab initio sto 3G computations indicate a small but definite preference of the isolated molecule for a gauche conformation. This result is confirmed for phenethylamine by an ab initio 4-31 G computation and by a computation using Clementi's 7s, 3p/3s basis contracted to 2s 1p/1s set. The exclusive occurrence of trans conformers in the crystal and their preponderance in solution is attributed to the effect of environmental forces. Explicit computations on the effect of water, using the supermolecule approach, confirm the tendency of the solvent to favor the trans conformer.

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. II. Isomeric aza-deazaanalogues of adenosine

Isomeric aza-deazaanalogues of adenosine and their N1-protonated forms (except for that of 8-aza-1-deazaadenosine) were studied by computer modeling to find a relationship between their molecular structures and the properties as substrates for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The previously proposed mechanism of the substrate acceptance in the active site of mammalian adenosine deaminase was refined, and the potential substrate properties were predicted for two previously unstudied adenosine analogues, 5-aza-9-deazaadenosine and 8-aza-3-deazaadenosine.

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. I. Adenosine and its aza- and deaza-analogs

Aza- and deazaanalogues of adenosine, including their 1-protonated forms (except for that of 1-deazaadenosine), were studied by computer computation to find a relationship between their molecular structures and substrate properties for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated for these compounds using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The mechanism that determines the substrate selectivity of mammalian adenosine deaminase is discussed. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.

Quantum chemical studies on intercalation of lithium into polyacene

The structure and properties of Li-doped polyacenic semiconductor (PAS) material have been investigated, Quantum Chemical methods ab initio STO-3G were used to calculate electronic properties of PAS doped with lithium. The semiempirical MO method AM1 was used to optimize the geometric parameters of PAS. The theoretical results showed that the doped lithium was neither in metallic nor ionic state in deeply doped PAS (C 2 Li). The intercalated lithium formed polycenter bonds with carbon atoms, and made the interlayer distance of two parallel polyacenic rings decrease. On the other hand, the total energy of Li-doped PAS system decreased, and made the doped state stable. The theoretical results are in good agreements with the experiment.

Potential Energy Surfaces for Liquid Ammonia: An Estimation of ab initio Calculations for Molecular Simulations

Abstract Hydrogen-bond-enhanced interactions were generated for ammonia pairs by ab initio calculations using tempered basis sets. The potential function obtained by the generation of interaction energies was applied to a Monte Carlo simulation for the liquid state of ammonia. The simulated bulk properties were considered compared with a previous ab initio STO-3G based simulation. The thermodynamic properties were obtained in the simulation and compared with those of a liquid water system to which the same manner of enhancement for the hydrogen bond was applied. The qualitative difference between the two liquids was reproduced.

Green's function calculation of through-bond electronic coupling in donor–bridge–acceptor model systems

The Green's function formalism is applied for the calculation of the effective through-bond donor–acceptor coupling in model molecular systems. The calculation is performed at a Hartree–Fock (self-consistent) level, by using semiempirical AM1 and CNDO/S, and ab initio STO-3G methods. The results are compared with that obtained from the splitting of the appropriate levels, by using the Koopmans' theorem, within each one of the selected quantum chemical methods.

Semi-empirical and ab initio study of pericyclized naphthalene systems containing an eight-membered ring

The conformational properties of peri-bridged naphthalenes in which the C-1 and C-8 atoms of the naphthalene ring are bonded by five atoms in a bridging chain Z [Z=(CH2)5, 1a; (CH2)2O(CH2)2, 1b; (CH2)2S(CH2)2, 1c; CH2OCH2OCH2, 1d; CH2SCH2SCH2, 1e; O(CH2)3O, 1f; S(CH2)3S, 1g] were studied by the Modified Neglect of Diatomic Overlap (MNDO) semi-empirical SCF MO method. Two minimum-energy conformations, namely chair and boat, with similar energies were found for 1a–c and 1e–g, which are separated by fairly low (3.5–6.2kcalmol−1) energy barriers. The barriers for chair-to-chair ring inversion in these compounds are 9.7–12.4kcalmol−1. For compound 1d, only the chair conformation was found to have the lowest energy; the twist and boat conformations are less stable by 1.1 and 1.4kcalmol−1, respectively. Ab initio STO-3G calculations were carried out for 1a.

Molecular electrostatic potential in differential inhibition of prostaglandin endoperoxide synthase (cyclooxygenase) by non-steroidal antiinflammatory drugs

Molecular electrostatic potentials (MEPs) calculated from MNDO wavefunctions were compared with ab initio STO-3G, 3-21G and 6-31G ∗∗ values and qualitative agreement was found for diverse classes of nonsteroidal antiinflammatory agents (NSAIDs). The MNDO MEPs present some differences with ab initio potentials in describing the electrostatic features of the aromatic molecules examined (meclofenamic, indomethacin, pirprofen, and cycloprofen). All compounds showed an extended region with positive MEP values and negative potential zones in the neighbourhood of the carboxyl group. The differences between the central and upper regions of the MEP distribution obtained for these NSAIDs might explain the time-dependent cyclooxygenase inhibition.

Quantum molecular modeling of hyaluronan

Molecular modeling of the secondary structure of hyaluronan is presented on the basis of the following molecular models: GlcA, GlcNAc, GlcA 1 → 3 GlcNAc, GlcNAc 1 → 4 GlcA, GlcNAc 1 → 4 GlcA 1 → 3 GlcNAc and GlcA 1 → 3 GlcNAc 1 → 4 GlcA. The optimized geometries of the monosaccharides obtained using AM1 and ab initio STO-3G methods are in good agreement with the crystallographic data. The flexibility of the β1 → 3 and β1 → 4 linkages was studied using AM1 and ab initio HF/3-21G methods. Our study shows that in all cases the β1 → 3 linkage is more flexible than the β1 → 4 linkage. The minimal energy conformations of the di- and trisaccharides studied correspond to a compact conformation for the β1 → 3 linkage and to standard conformations in agreement with the left-handed helices of sodium hyaluronate or calcium hyaluronate. The electrostatic properties and the frontier orbital characteristics obtained at the HF/3-21G level are discussed.

The generalized parameterization procedure for the semiempirical MO method and calculation of ionization potentials for the third row element molecules

The valence electron ionization potentials ( I l ) were collected from a unique resource for the elements from H to Xe. The electron affinities ( A 1) of halogen atoms in each period were obtained from the same resource of I l . The A l values of the remaining elements were obtained by a combined formulation of Slater-Condon integrals and Pariser-Parr approximation. The generalized bond parameter proportionality constant K nl of each period was also evaluated. Using these parameters, twenty-four molecules consisting of only third row elements were selected for the s-p-d INDO-MO calculations. In order to check the reliability of the energy calculations, similar calculations of ab initio type STO-3G ∗, along with semiempirical-type PM3 and AM1 methods were also carried out for comparison. The Koopmans' theorem was applied to compare the experimentally measurement and calculation of the first ionization potentials in all the cases. The results of the present study indicated that the s-p-d INDO MO computed with the new parameterization procedure which given here is the best method among all the methods used in the present work.

Electronic structure of testosterone: A semiempirical and ab initio assessment

Testosterone (17β-hydroxy-4-androsten-3-one) was studied by the semiempirical AM1 and PM3 and ab initio STO-3G*, 3–21G*, and 6–31G* methods. The goals were to compare those methods and to know the electronic structure of the hormone. Full geometry optimization was performed, and two crystal conformers (T1 and T2), and experimental dipole moment in solution were used for comparison. One conformer with a dipole moment similar to the solvated conditions was generated. Total energy, entalphies, dipole moments, charges, electrostatic potentials, and highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbital (LUMO) were calculated. Root-mean-square (RMS) index of the theoretical molecules against T1 and T2 showed best results with the 3–21G* and 6–31G* methods, while AM1 gave better energies than PM3. Dipole moments were directed toward the OH group and the botton face of the A ring. The frontier orbitals were located along the C4–C5 π bond, particularly the LUMO was split between C4 and C5, predicting the action of enzymes at C5 yielding to 5α and 5β-reduced androgens. Electrostatic potentials might be also of biological importance since they are coincidental with the dipole-moment orientation. Finally, it is interesting that the solvatedlike conformer, its properties, and the OH group laid between the same group of T1 and T2 and with a total energy between the crystals and the gas phase or in vacuo conditions. This results might also explain the biology of testosterone and use them to model the hormone-receptor interaction. © 1997 John Wiley & Sons, Inc.

Electronic structure of testosterone: A semiempirical and ab initio assessment

Testosterone (17β-hydroxy-4-androsten-3-one) was studied by the semiempirical AM1 and PM3 and ab initio STO-3G*, 3–21G*, and 6–31G* methods. The goals were to compare those methods and to know the electronic structure of the hormone. Full geometry optimization was performed, and two crystal conformers (T1 and T2), and experimental dipole moment in solution were used for comparison. One conformer with a dipole moment similar to the solvated conditions was generated. Total energy, entalphies, dipole moments, charges, electrostatic potentials, and highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbital (LUMO) were calculated. Root-mean-square (RMS) index of the theoretical molecules against T1 and T2 showed best results with the 3–21G* and 6–31G* methods, while AM1 gave better energies than PM3. Dipole moments were directed toward the OH group and the botton face of the A ring. The frontier orbitals were located along the C4–C5 π bond, particularly the LUMO was split between C4 and C5, predicting the action of enzymes at C5 yielding to 5α and 5β-reduced androgens. Electrostatic potentials might be also of biological importance since they are coincidental with the dipole-moment orientation. Finally, it is interesting that the solvatedlike conformer, its properties, and the OH group laid between the same group of T1 and T2 and with a total energy between the crystals and the gas phase or in vacuo conditions. This results might also explain the biology of testosterone and use them to model the hormone-receptor interaction. © 1997 John Wiley & Sons, Inc.

Semiempirical and Ab inito MO-Calculations on Phenol: Geometry, Vibrational Frequencies, MO-Energies and Thermodynamic Properties

The geometry, ionization potentials, vibrational frequencies and intensities of phenol have been calculated using the semiempirical MNDO/PM3 and the ab initio minimum basis STO-3G methods. The values were used to calculate the ideal gas state thermodynamic properties for the temperature range 300-900^{\circ}K. The previous MNDO and AM1 calculations were repeated for lack of reported data. Comparison of the PM3 values with available experimental and other theoretical data indicates that PM3 gives satisfactory results.

Nonempirical wave functions for very large molecules. II. The PRDDO/M/FCP method

The authors describe enhancements to the method of partial retention of diatomic differential overlap (PRDDO). The new method, denoted PRDDO/M, employs a basis set of not quite orthogonal atomic orbitals (NQOAOS) and utilizes sparse matrix techniques to greatly increase the computational efficiency for large molecules. Other modifications, including a complete reparametrization of the method against ab initio STO-3G calculations and implementation of integral screening/damping algorithms, are described. The method is an order of magnitude or more faster than are STO 3G single-point calculations using modern ab initio codes, with little loss in accuracy. 15 refs., 5 figs., 6 tabs.

Calculation of the electronic structure and nonlinear optical properties of three blue dyes

The structure of three important dyes, based on a donor-acceptor anthraquinone ( I), azobenzene ( II), and a dicyanovinyl benzothiophene-1,1-dioxide ( III), have been calculated at both the AM1 and the ab initio STO-3G level and the results compared with experimental data where available. Good correlations are obtained between their calculated transition energies and oscillator strengths and experimental spectra. The hyperpolarisability of each structure, calculated using a sum-over-states approach at an applied field of 1.49 eV (830 nm), is predicted to be poor for the anthraquinone ( I), but large for the azobenzene ( II) and dicyanovinyl arylsulphone ( III) suggesting that these materials may have potential application in nonlinear optics as second harmonic generators.

Theoretical study of C 24N 4 molecule

Both ab initio 6-31G, 3-21G and STO-3G basis sets and semiempirical PM3 and AM1 molecular orbital calculations are carried out on the C 24N 4 molecule of the T d symmetry group. Results on the fully optimized structure which constrained T d symmetry, molecular orbitals and vibrational frequency were obtained by both ab initio and semiempirical methods. The binding energy and various thermodynamic properties were also calculated via the PM3 and AM1 semiempirical methods. All the evidence of this work proves that the C 24N 4 molecule is stable and that its four six-membered rings with a remarkable delocalized C…C bond are similar to the related rings in the C 60 buckminsterfullerene structure.

A quantum-chemical study of para/ortho-toluene alkylation by adsorbed methoxy species on zeolites

MNDO and PM3 semiempirical methods have been employed to study the mechanism of toluene alkylation by methanol on zeolites, by means of the cluster (H) 3SiO(CH 3)T(H) 2OSi(H) 3 in were T  Al, B, Ga. Two possible reaction mechanisms have been found. The first one corresponds to the classical process of aromatic electrophilic substitution, in which the transition state of the reaction shows distances and angles according to the precursor of the Wheland intermediate. The second mechanism proceeds in one concerted step, in which the transfer of the proton from the toluene to the basic oxygen of the zeolite is simultaneous to the transfer of the methyl cation from the zeolite to the toluene. The effect of chemical composition of the cluster on regioselectivity has been studied, and perturbed molecular orbital (PMO) analysis of the system at the ab initio HF STO-3G level has shown that covalent interactions are important. The energy of the covalent interaction between the molecular orbitals of the toluene and the cluster mainly HOMO-LUMO, are more important in para than in ortho positions.

Theoretical Evaluation of Hyperpolarizability of l-2-Pyrrolidone-5-carboxylic Acid (l-PCA)

Abstract l-2-Pyrrolidone-5-carboxylic acid (l-PCA) is a novel nonlinear optical material with the optical transparent range down to the UV region. l-PCA molecules are hydrogen-bonded to form the three-dimensional network in a crystal. It has been thought that the network of hydrogen bonds influences on the stability of the crystal structure as well as the second-order optical nonlinearity. We have performed the theoretical evaluation of the contributions of the intermolecular hydrogen bonds to structural stability and second-order nonlinearity in the l-PCA crystals by use of the molecular orbital calculation methods. In the calculation of CNDO/S-SECI (singly excited configuration interaction) method, it is shown that the primary contributor to the molecular hyperpolarizability (β) is an nπ → π* transition in the amide moiety of l-PCA molecule. The calculation of intermolecular interaction energies for l-PCA clusters by the ab initio STO-3G method indicates that the hydrogen bonds in the crystal contribute to the stabilization of the crystal structure by −7.8 to −9.1 kcal mol−1 for one hydrogen-bond formation. Furthermore, it is also confirmed by CNDO/S-CHF (coupled Hartree–Fock) calculation that the hydrogen-bonding interactions induce the enhancement of the βXyz value, a unique β component contributing to the nonlinear optical coefficient (d14). On the basis of the calculated β components, d14 can be estimated to be d14 = 0.30 pm V−1 by the oriented-gas model. This value is in good agreement with the experimental result. Therefore, these results verify that the hydrogen bonds between l-PCA molecules contribute not only to the physical and chemical stability of l-PCA crystals but also to the enhancement of β values. This theoretical estimation shows the effectiveness of the hydrogen bonds in second-order nonlinear optical crystals.