Hydrogen bonds: a comparison of semiempirical and ab initio treatments

H-bonding interactions calculated using the AM1, PM3 and SAM1 semiempirical molecular orbital methods are compared with the best available ab initio calculations for several intermolecular interactions of interest: acetic acid dimers, water/ acetylene, water/HCN, formaldehyde/acetylene, formaldehyde/HCN, ozone/acetylene, ozone/HCN, acetylacetone, melamine/ cyanuric acid, and nitromethane/ammonia. Experimental values are also presented where available. The energetic comparisons are based upon enthalpies of interaction from the ab initio calculations after counterpoise and vibrational corrections have been applied. Overall, AM1 seems to do best, except for O---H…O interactions, where none of the three methods excel.     

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.     

Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions

A quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO-3G, 3-21G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3-D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions). © 1993 John Wiley & Sons, Inc.     

Dynamical dimer method for the determination of transition states with ab initio molecular dynamics

A dynamical formulation of the dimer method for the determination of transition states is presented. The method is suited for ab initio molecular dynamics using the fictitious Lagrangian formulation. The method has been applied to the conrotatory ring opening of chlorocyclobutadiene, an example, where the application of the drag method is problematic.     

Systematic characterization of transition states for radical decompositions

A one-parameter analytical potential energy function for β-bonds in free radicals is described, which accounts quantitatively for their observed stretching frequencies and the position and size of the activation barriers for their fission. It is shown that such a function can be used to characterize a priori the corresponding transition states by assuming that the structural and spectroscopic changes taking place along the minimum energy path track the development of pi bonding rather than following a simple exponential dependence on the reaction coordinate. This procedure, tested by comparing predicted A-factors and isotope effects with experimental data for alkyl radicals and ab-initio calculations on C₂H₅, fully encodes the basic features of radical decomposition reactions and provides a simple, realistic, and self-consistent technique for the estimation of their kinetic parameters.     

Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

The torsional levels of (H2O)3 and (D2O)3 were calculated in a restricted dimensionality (three-dimensional) model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very accurate water dimer levels, also reproduce the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT(ASP-W)III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.     

Asymmetric transition states of allylation reaction: an ab initio molecular orbital study

An ab initio MO study of the allylation of α-methoxypropanal by allylboronic acid has been carried out. The calculated most stable transition state arrangement was found to be similar to that proposed by Cornforth. The Felkin–Anh orientation was found to be less stable than the Cornforth-like arrangement at the B3LYP/6-31G* level of theory in the six-membered cyclic transition state.     

Radical stabilizing effects : A comparison of transition state effects (rates of azoalkane decompositions) with calculated (ab initio) pi spin densities

Rate studies on five azoalkanes (4a-e) have been studied to assess important radical stabilizing effects. MO calculations of spin densities for three radicals with pi systems are correlated with kinetic rates of radical formation.     

An ab initio calculation of K-spectra in molecules HCl and HF

An ab initio calculation of energies and intensities of K-emission and K-absorption spectra in molecules HCl and HF are carried out. An electronic readjustment due to a hole in a molecular core is taken into account. A vibrational structure of K-emission and K-absorption spectra is also calculated. The calculation shows that it is possible to detect a vibrational structure of valence bonding levels in X-ray emission spectra. A good agreement with experiment is obtained.     

Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.     

A theoretical study of malonate ion and its metal binding by ab initio and semiempirical techniques

STO-3G and CNDO calculations have been performed on malonate ion and its Mg²⁺ complexes. The parallel carboxyl group arrangement is found to be the single minimum energy conformation with both techniques. In the metal binding studies, the binding of a Mg²⁺ to a single carboxyl is preferred over binding symmetrically to both carboxyls in their parallel conformation. These results are consistent with X-ray structure results on calcium malonate.     

The structure of potassium hydrogentartrate: A combined X-ray,semiempirical, and ab initio study

Single crystals of potassium hydrogentartrate, (2R,2R)-KO₂C(CHOH)₂CO₂H, were taken from a three-year-old wine bottle. The structure was determined by low-temperature single-crystal X-ray diffraction analysis using a Siemens SMART diffractometer. (2R,2R)-KO₂C(CHOH)₂CO₂H crystallizes in the orthorhombic space group P2₁2₁2₁ with Z = 4 and unit cell dimensions a = 7.6065(5), b = 7.7599(5), and c = 10.6054(7) Å. The structure of an isolatedhydrogentartrate anion, (2R,2R)-[O₂C(CHOH)₂-CO₂H]⁻, was calculated at the semiempirical AM1 and PM3 levels of theory with a VSTO-3G* basis set and in addition ab initio at the self-consistent level of theory using a standard 6-31G(d, p) basis set (Non-SI units employed: kcal ≈ 4.184 kJ, Å = 10⁻¹⁰ m).© 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:307–310, 1998     

A semiempirical and ab initio MO study of the tautomers ofN-unsubstituted pyrazolones [hydroxy pyrazoles]

Semiempirical (MNDOC, MINDO/3, AM1, and MNDO) and ab initio (STO-3G and 4-31G basis sets) calculations on the relative stabilities, structures, and dipole moments of the 8 theoretically possible tautomeric forms of pyrazolone are reported. It is shown that MNDO + CI and MINDO/3 predict that 5-hydroxy pyrazole, 3-hydroxy pyrazole, and 2-pyrazolin-5-on are the most stable. These results correspond to the known experimental data. Of all used quantum chemical methods, the MINDO/3 results for the dipole moments of the investigated tautomers are in best agreement with the known experimental data. The electronic excitation energies were calculated using the CNDO/S-CI method. The results are in good agreement with the experimental UV spectra.     

Nuclear momentum distribution in solid and liquid HF from ab initio calculation

A calculation of nuclear momentum distribution of liquid and solid hydrogen fluoride was performed. In both systems, density functional theory generalized gradient approximation functional of Perdew, Burke, and Ernzerhof was used for the calculation: for liquid hydrogen fluoride, using an atom centered basis set for an isolated molecule with optimized geometry, and for solid hydrogen fluoride using plane-wave basis sets on optimized orthorhombic crystal cell. For liquid hydrogen fluoride, a semiclassical approach was adopted with the vibrational contribution to momentum distribution obtained from the density functional theory calculation and translational and rotational contributions calculated classically. Nuclear momentum distribution in the solid hydrogen fluoride was calculated entirely quantum mechanically using phonon dispersion and vibrational density of states calculated in the framework of plane-wave density functional theory. Theoretical results were contrasted with recently obtained results of Compton (deep inelastic) neutron scattering on liquid and solid hydrogen fluoride. In case of liquid hydrogen fluoride, almost a perfect agreement between theory and experiment was achieved within the harmonic Born-Oppenheimer approximation. For the solid system under investigation, the harmonic approximation leads to small (4%) overestimation of the square root of the second moment indicating that neutron Compton scattering technique is sensitive to proton delocalization due to hydrogen bonding in solid hydrogen fluoride.     

High-level ab initio studies of unimolecular dissociation of the ground-state N3 radical

A comprehensive study of the unimolecular dissociation of the N(3) radical on the ground doublet and excited quartet potential energy surfaces has been carried out with multireference single and double excitation configuration interaction and second-order multireference perturbation methods. Two forms of the N(3) radical have been located in the linear and cyclic region of the lowest doublet potential energy surface with an isomerization barrier of 62.2 kcal/mol above the linear N(3). Three equivalent C(2v) minima of cyclic N(3) are connected by low barrier, meaning the molecule is free to undergo pseudorotation. The cyclic N(3) is metastable with respect to ground state products, N((4)S)+N(2), and dissociation must occur via intersystem crossing to a quartet potential energy surface. Minima on the seams of crossing between the doublet and quartet potential surfaces are found to lie substantially higher in energy than the cyclic N(3) minima. This strongly suggests that cyclic N(3) possesses a long collision-free lifetime even if formed with substantial internal excitation.     

An ab initio comparison of dichalcogen hydrides

A theoretical study of HSH, HSeH, HTeH, HSSH, HSeSH, HSeSeH, HTeSH, HTeSeH, and HTeTeH was carried out by ab initio molecular orbital methods employing minimal Gaussian basis sets MINI-1 and MINI-1* of Huzinaga and his group. Both basis sets yield accurate estimates on the equilibrium geometries of monochalcogen hydrides. In the case of dichalcogen hydrides, however, the inclusion of d-polarization functions for sulfur, selenium, and tellurium greatly improve the accuracy of the geometry prediction. The unpolarized MINI-1 basis sets yield essentially correct orbital energies and therefore suffice for the comparative study on the electronic structures in similar molecules. The results with both basis sets imply close similarities in the electronic structures of SS, SeS, and SeSe bonds with more marked differences in bonds containing tellurium as a consequence of notably smaller orbital energy of the 5s- orbital of tellurium as compared to the corresponding orbitals in sulfur and selenium. The barriers to internal rotation about the chalcogen—chalcogen bond in all dichalcogen hydrides are similar. The cis- and trans-barrier heights are ca. 23 and 14 kJ mol⁻¹, respectively. The relative stabilities of different hydrides are discussed.     

Vibrational study of dialkylphosphonates: di-n-propyl- and di-i-propylphosphonates by semiempirical and ab initio methods

Fourier transform infrared and Fourier transform Raman spectra of n-C(3)H(7) and i-C(3)H(7) dialkylphosphonates have been obtained. Semiempirical AM1 and the ab initio orbital molecular RHF/6-31G* theories have been used to study the molecular geometry, and the harmonic vibrational spectra with the purpose to assist the experimental assignments of these compounds. An extensive discussion on the assignment of the C-C, C-O, P-O and P=O stretching is carried out based on experimental data of compounds which have the propyl and isopropyl groups, as well as comparing the vibrational spectra of propane. Most of the RHF/6-31G* and AM1 results, once applied the appropriate scaling factor, showed an excellent agreement with the experimental wavenumbers. A few calculated frequencies related to CC and CO stretching do not agree well with the experimental trends.     

Quantum chemical ab initio calculations for excited states of F IV

Quantum chemical ab initio calculations have been performed for the ground state and for several excited states of the F³⁺ ion (F IV). Three levels of accuracy have been used: Frozen-core SCF calculations (FRC-SCF) to determine orbital energies ε _nl and quantum defects δ _l for excited Rydberg orbitalsnl; frozen-core SCF followed by CI calculations (FRC-CI) which account for multiplet splittings and configuration mixings, and multi-configuration coupled-electron-pair approximation (MC-CEPA) calculations which include dynamic correlation effects. The accuracy of the calculated excitation energies is in the order of 5000 cm^?1 at the FRC-CI level and in the order of 500 cm^?1 at the MC-CEPA level. This latter error amounts to about 0.1% for excitation energies in the range of 400000 to 600000 cm^?1. The MC-CEPA calculations have been performed for 17 experimentally known states and for 14 experimentally unknown states, in particular for the configurations 2s2p ² (² D)3s, 2s 2p ²(² S)3s, 2s ² 2p 4p, and 2s ² 2p 5p.     

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.