Comparison of experimental and ab initio HF and DFT vibrational spectra of benzimidazole

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of benzimidazole. The laser Raman and Fourier transform infrared spectra of benzimidazole were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by HF and density functional B3LYP method with the 6-311G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311G(d,p) and B3LYP/6-31G(d,p)/6-311G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of benzimidazole is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques

Summary The conformational preferences of 12 molecular substructures in the crystalline state have been determined and compared with those predicted for relevant model compounds by ab initio molecular orbital calculations. Least-squares regression shows that there is a statistically significant correlation between the crystal-structure conformer distributions and the calculated potential-energy differences, even though the calculations relate to a gas-phase environment. Torsion angles associated with high strain energy (>1 kcal mol^-1) appear to be very unusual in crystal structures and, in general, high-energy conformers are underrepresented in crystal structures compared with a gas-phase, room-temperature Boltzmann distribution. It is concluded that crystal packing effects rarely have a strong systematic effect on molecular conformations. Therefore, the conformational distribution of a molecular substructure in a series of related crystal structures is likely to be a good guide to the corresponding gas-phase potential energy surface.     

Electric dipole moments of thietane in excited states of the ring puckering vibration: an experimental and ab initio study

The electric dipole moment in the ground state (v_p = 0) and the first five excited states (v_p = 1 … 5) of the ring puckering vibration of thietane have been determined from Stark shifts of rotational transitions. The results are: 0|μ_a|0 = 1.87583(16) D, 1|μ_a|1 = 1.87341(18) D, 2|μ_a|2 = 1.89759(28) D, 3|μ_a|3 = 1.88688(29) D, 4|μ_a|4 = 1.90036(18) D, 5|μ_a|5 = 1.88596(59) D. The dependence of these values on v_p shows the zig-zagging behaviour typical of modes with double minimum potentials. A combined analysis of the ground and first excited states yielded also a precise value for the transition moment, 0|μ_c|1 = 0.24023(49) D.

A potential and electric dipole moment function has been derived from ab initio calculations, using MP2 and the 6–31G** basis set. Expectation values of the dipole and transition moments were determined from these data. Absolute values are about 5% in error, but the variation with vibrational state is reproduced excellently by the theoretical values.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters

In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.     

The ab initio calculated molecular structures,force fields and vibrational frequencies of some organic azides

Double zeta basis molecular calculations were carried out on the hydrazoic acid and azidomethane molecules. The molecular structures were optimized by the gradient method and the force fields were obtained by numerical differentiation of the gradient vector. The computed harmonic force fields and vibrational frequencies were compared with experimental values.     

Molecular electrostatic potentials: Comparison of ab initio and CNDO results

The possibilities of utilization of CNDO wave functions for computing molecular electrostatic potentials are studied by comparison with ab initio results for H₂O and H₂CO.

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Zusammenfassung Die Möglichkeiten der Verwendung von CNDO-Wellenfunktionen zur Berechnung molekularer elektrostatischer Potentiale werden durch Vergleich mit ab initio Rechnungen für H₂O und H₂CO untersucht.

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Résumé Les possibilités d'utilisation de fonctions d'onde CNDO pour le calcul des potentiels électrostatiques moléculaires sont étudiées par comparaison avec des résultats ab initio pour H₂O et H₂CO.

     

Infrared experimental and ab initio quantum mechanical studies of 2-mercaptopyrimidine tautomers

Results are presented from ab initio SCF(3-21G*) calculations for the geometries and vibrational spectra (wavenumbers and absolute intensifies) of the thiol and thione tautomers of 2-mercaptopyrimidine. The results of calculations are compared with available experimental data, particularly with the reported vibrational spectra of the molecule isolated in inert gas matrices (Ar, N₂) and in crystalline state. The calculations of the normal modes predicted the experimental spectrum close enough to allow reliable assignment of most of the bands. The thiol⇌⇌thione tautomerism of the molecule is discussed. Matrix isolated monomers were observed in the thiol form only. That agrees with the results of ab initio calculations of internal energies of the tautomers [SCF(6-31Gu*) + MBPT(2)(6-31G*) + vib(0)(3-21G*); at the SCF(3-21G*) geometries] which predict the energy of thiol form to be ≈33 kJ mol⁻¹ lower than that of thione form. In the crystalline state the hydrogen-bonded associations in the thione form dominate while in disordered amorphous layers, in matrices with a high guest-to-host ratio and in annealed matrices the associations both in thiol and thione form were observed.     

A density functional treatment of organolithium compounds: Comparison to ab initio,semiempirical, and experimental results

Density functional calculations on several classes of organolithium compounds are described. The compounds studied include lithium bonds to carbon, oxygen, and nitrogen and are representative of most types of organolithium compounds that have appeared in the recent literature. The computational results are compared to those using MNDO, which has been shown to have some serious deficiencies in compounds involving carbon–lithium bonds, and to PM3 results, which offer some improvement over MNDO for many organolithium compounds. Most of the density functional calculations with a large basis set are in good agreement with available ab initio and experimental data. Calculated carbon–lithium bond lengths were slightly shorter than those calculated by other ab initio methods and were substantially longer than those calculated by MNDO, which is known to underestimate carbon–lithium bond lengths severely. Dimerization energies of methyllithium, calculated by DMol, were also in good agreement with those of other ab initio calculations. Lithium–nitrogen bonds in lithium amides were calculated to be slightly shorter by DMol than by MNDO, although the two methods were in qualitative agreement for this type of compound. © 1995 by John Wiley & Sons, Inc.     

Intermolecular and intramolecular interactions calculated with ab initio perturbative configuration interaction method using strongly localized orbitals

We have applied the ab initio formulation of the perturbative configuration interaction using localized orbitals (PCILO ) method up to third order to calculate intermolecular and intramolecular interaction energies going beyond the ab initio Hartree–Fock calculation. For the rotational barrier in ethane our results agree well with the experimental value and the cis- and even the trans-barriers in HOOH are at least qualitatively reproduced with the aid of the STO -3G basis set. In the case of the water dimer we obtain an equilibrium intermolecular distance and interaction energy which are confirmed by other calculations. We can further conclude from our studies that one has to include higher orders in the perturbation expansion as the system becomes more complicated. It is especially the last aspect which hinders the application of the ab initio PCILO to estimate the major part of the electron correlation energy for large molecules.     

Comparison of nitroaldol reaction mechanisms using accurate ab initio calculations

In the nitroaldol reaction, condensation between a nitroalkane and an aldehyde yields a nitroalcohol that can undergo dehydration to yield a nitroalkene. Amine-functionalized, MCM-41-type mesoporous silica nanosphere (MSN) materials have been shown to selectively catalyze this reaction. Gas-phase reaction paths for the several competing mechanisms for the nitroaldol reaction have been mapped out using second-order perturbation theory (MP2). Improved relative energies were determined using singles and doubles coupled cluster theory with perturbative triples, CCSD(T). The mechanism in the absence of a catalyst was used to provide a baseline against which to assess the impact of the catalyst on both the mechanism and the related energetics. Catalyzed mechanisms can either pass through a nitroalcohol intermediate as in the classical mechanism or an imine intermediate.     

Heats of formation of organic molecules calculated from ab initio theory and a group equivalent scheme: Alkenes

A bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6-31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.     

Acido-base behavior of hydroxamic acids: experimental and ab initio studies on hydroxyureas

The values of Ka, DeltaSa, and DeltaHa for deprotonation of hydroxyurea (HU) and N-methylhydroxyurea (NMHU), as targeted compounds, and for betainohydroxamic acid, were potentiometrically determined. Although NMHU has two and HU even three deprotonation sites, the measurements confirm that they behave as weak acids with a single pK a approximately 10. Comparison with analogous thermodynamic parameters previously determined for series of monohydroxamic acids reveals deviations from a DeltaSa, vs DeltaHa plot for HU and NMHU, raising the question of the dissociation site of hydroxureas in water. In addition to the deprotonation of the hydroxyl oxygen, ab initio calculations performed at the MP2/6-311++G(d,p) level of theory for these two compounds indicate a notable participation of the nitrogen deprotonation site in HU. The calculations for the isolated, monohydrate, trihydrate, and decahydrate molecular and anionic forms of hydroxyureas support the importance of hydrogen bonding in the gas and aqueous phases. The hydroxylamino nitrogen in HU is the most acidic site in water, contributing approximately 94% to the overall deprotonation process at 25 degrees C. On the contrary, the hydroxylamino oxygen is by far the most favored deprotonation site in NMHU, contributing almost 100% in aqueous medium. The predicted participations of two deprotonation sites in HU, calculated at the MP2/6-311++G(d,p) level of theory, combined with the calculated relative reaction enthalpy and entropy for the deprotonation, satisfactorily explain the observed deviation from linearity of DeltaHa vs DeltaSa, plot. There is no such a simple explanation for acid-base behavior of NMHU.     

The use of scaled moments of inertia in experimental structure determinations of polyatomic molecules

Recently developed procedures for determining near-r _e structures (r _m ^p )from scaled ground-state moment of inertia data have been extended to general polyatomic molecules. A simple and general empirical method for correctingl _m ^p moments for the large vibration-rotation effects of deuterium substitution has been proposed and illustrated for a variety of polyatomic molecules. The correction requires utilization of a bond elongation parameter,δr _D ,whose experimental value is found to be approximately 0.003 Å. A theoretical justification of the approximation has been provided for linear triatomic molecules.     

Solvent-dependent stereoselectivity in a Still-Wittig rearrangement: an experimental and ab initio study

[see reaction]. The Still-Wittig rearrangement gave opposite selectivities for (Z:E)-alkenes in THF (3:1) vs toluene (1:3) in the synthesis of serine-proline dipeptide amide isosteres. Four transition states leading to (Z)-and (E)-alkenes with THF and without (representing toluene) were identified by ab initio calculations at the 3-21G* level. The calculated (Z:E)-ratios with THF (4.7:1) and without THF (1:3.2) suggested that the transition state geometries and energies were well-represented by the calculations.     

Comparison of classical mechanics and the coupled states approximation for Li+-CO scattering on an ab initio calculated CI potential energy surface

The dynamics of rotational excitation on an ab initio calculated CI rigid rotor potential energy surface for Li⁺-CO are investigated using classical mechanics and the quantum mechanical coupled-states (CS) approximation. Transition probabilities out of the j = 0 initial level are calculated for various impact parameters between b = 0 and 40a_o for 1 eV collisions. The classical results agree well with the average of Δj-even and Δj-odd quantum transition probabilities except for a few lower impact parameters where CS seems to underestimate the large Δ transitions. No propensity rule is observed for the preference of the Δj-even versus Δj-odd transitions as might have been expected.     

Potential function of internal rotation for isoprene from ab initio calculations and experimental data

Ab initio computations of the potential energy curve of internal rotation around the central single C---C bond of isoprene have been performed at the Hartree—Fock level with a 3·21G basis set. The similarity of the slope of the curve obtained and the potential energy curve calculated for a more complete basis set (7s3p/4s2p) [Kavana-S2ebø, J. Mol. Struct. 106 (1984) 259] is discussed. The values of the Pitzer function F(φ), its Fourier expansion coefficients, and coefficients of the potential energy expansion were calculated from data given in the above reference. The correction of the potential energy expansion coefficients was carried out from frequencies of torsional “hot” bands of isoprene and torsional overtone of its second rotational isometric form. It was shown that the isoprene second isomer is realized as a gauche-form. The potential energy expansion coefficients were obtained as follows: V₁ = 399.9, V₂ = 1330.22, V₃ = 781.8 and V₄ = −175.8 cm⁻¹.