Excited-state structure and vibrations of p-diaminobenzene studied by ab initio calculations

The structures and vibrations of p-diaminobenzene (PDAB) in the S₀ and S₁ states have been studied by ab initio quantum-chemical calculations. Results from geometry optimization show that the two stable cis and trans conformers of PDAB are non-planar in the S₀ state. Upon electronic excitation to the S₁ state, enhanced interaction between the ring and the amino substituent causes the molecule to become planar and contract along the long in-plane axis. A detailed analysis of the normal vibrations of PDAB in both states has been done on the basis of the motions of individual atoms as well as reduced masses, force constants and frequencies. The computed frequencies are in reasonably good agreement with the available experimental data.     

Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method

 Hybrid potentials have become a common tool in the study of many condensed-phase processes and are the subject of much active research. An important aspect of the formulation of a hybrid potential concerns how to handle covalent bonds between atoms that are described with different potentials and, most notably, those at the interface of the quantum mechanical (QM) and molecular mechanical (MM) regions. Several methods have been proposed to deal with this problem, ranging from the simple link-atom method to more sophisticated hybrid-orbital techniques. Although it has been heavily criticized, the link-atom method has probably been the most widely used in applications, especially with hybrid potentials that use semiempirical QM methods. Our aim in this paper has been to evaluate the link-atom method for ab initio QM/MM hybrid potentials and to compare the results it gives with those of previously published studies. Given its simplicity and robustness, we find that the link-atom method can produce results of comparable accuracy to other methods as long as the charge distribution on the MM atoms at the interface is treated appropriately. Received: 27 September 2002 / Accepted: 21 October 2002 / Published online: 8 January 2003 Correspondence to: M. J. Field e-mail: mjfield@ibs.fr Acknowledgements. The authors thank the Institut de Biologie Structurale – Jean-Pierre Ebel, the Commissariat à l'Energie Atomique and the Centre National de la Recherche Scientifique for support of this work.     

Adsorption of polyacrylic acid on aluminium oxide: DRIFT spectroscopy and ab initio calculations

Diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy was used to study the adsorption process of the water-soluble polyacrylic acid (PAA) polymer on hydrous δ-Al₂O₃. Vibrational assignment of PAA, sodium polyacrylate, (Na–PA) and the PA-oxide surface complex was achieved by comparison of observed band position and intensity in the DRIFT spectra with wavenumbers and intensities from ab initio quantum mechanical calculations. The presented data of polyacrylic acid suggest that IR data calculated ab initio on relatively short oligomers (quantum-mechanical oligomer approach) may provide valuable information regarding the interpretation of polyelectrolyte infrared spectra. Batch adsorption experiments were performed to sorb PAA onto the δ-Al₂O₃ surface. The results obtained from DRIFT studies were compared with adsorption isotherm experiments in order to relate the level of PAA coverage to the nature of the surface complex. Ab initio molecular orbital calculations on PAA/Al₂O₃ clusters were used to model possible surface complexes. Strong correlation were found between theoretical and observed DRIFT frequencies of the antisymmetric R-COO⁻ vibration. A number of possible configurations of the polyacrylic acid/aluminate surface complex were tested via ab initio calculations. These possible configurations included different di-aluminium octahedral Al³⁺ surface models. Results obtained from adsorption isotherm experiments, DRIFT spectra and ab initio calculations indicate that the carboxylate oxygens bridge an Al³⁺-octahedral dimer [Al₂(OH)₂4(H₂O)2(OH)] in a ligand-exchange inner sphere complex.     

A study of the excited state structure and vibrations of hydroquinone by ab initio calculations and resonant two-photon ionization spectroscopy

Hydroquinone (HYQ) in the lowest electronically excited state has been studied by ab initio quantum chemical calculations and resonant two-photon ionization (R2PI) spectroscopy. Calculations at the MP2/6-31G* and CIS/6-31G* levels yield satisfactory results on structures and vibrational frequencies of the cis-HYQ and trans-HYQ in both the S₀ and S₁ states. Only transitions involving in-plane modes are observed in the R2PI spectrum of HYQ. All spectral bands including some newly observed ones have been successfully assigned with the help of our computed results and analogy with the reported spectra for similar molecules.     

Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol⁻¹, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: <r_g(C–C)>=1.403±0.003 Å, r_g(Si–C)=1.870±0.004 Å, and r_g(Si–H)=1.497±0.007 Å. The calculations indicate that the C_ipso–C_ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.     

Infrared and Raman spectra, ab initio calculations and vibrational assignment for 3-fluoro-1-butyne

The infrared (3500-80 cm⁻¹) and Raman (3500-20 cm⁻¹) spectra of 3-fluoro-1-butyne, CH₃CHFCCH, have been recorded for the gas and solid. Additionally, the Raman spectrum of the liquid has also been recorded to aid in the vibrational assignment. Ab initio electronic structure calculations of energies, geometrical structures, vibrational frequencies, infrared intensities, Raman activities and the potential energy function for the methyl torsion have been calculated to assist in the interpretation of the spectra. The fundamental torsional mode is observed at 251 cm⁻¹ with a series of sequence peaks falling to lower frequency. The three-fold methyl torsional barrier is calculated to be 1441 ± 20 cm⁻¹ (4.12 ± 0.06 kcal mol⁻¹) where the uncertainty is partly due to the uncertainty in values of the V₆ term. A complete vibrational assignment is proposed based on band contours, relative intensities, and ab initio predicted frequencies. Several fundamentals are significantly shifted in the condensed phases compared to values in the vapor state.     

A theoretical analysis of the explanation of the significant differences in antiferromagnetic interactions between homologous μ-alkoxo and acetate bridged dicopper(II) complexes: ab initio and semi-empirical calculations

A magnetostructural classification of dimmers, containing the Cu (μ-alkoxo) Cu core, based on data obtained from X-ray diffraction analysis reported in the literature has been performed. In these complexes, the local geometry around the copper ions is generally a square planar and each copper ion is surrounded by one N atom and three O atoms. The influence of the overlap interactions between the bridging ligands and the metal (Cu) d orbitals on the super-exchange coupling constant has been studied by means of ab initio Restricted Hatree–Fock molecular orbital calculations. The interaction between the magnetic d orbitals and highest occupied molecular orbitals of the acetate oxygens has been investigated in homologous μ-acetato-bridged dicopper(II) complexes which have significantly different −2J values (the energy separation between the spin-triplet and spin-singlet states). In order to determine the nature of the fronter orbitals, Extended Hückel molecular Orbital calculations are also reported. Ab initio restricted Hartree–Fock calculations have shown that the acetato bridge and the alkoxide bridge contribute to the magnetic interaction countercomplementarily to reduce antiferromagnetic interaction.     

Gas-phase enthalpies of formation of the fluorobenzenes family and their dewar isomers from ab initio calculations

The standard gas-phase enthalpies of formation, at T = 298.15 K, of the complete series of fluorobenzene and their corresponding dewar isomers have been determined by means of the CBS-QB3 and G3MP2B3 composite approaches. These values have been estimated by using appropriate supporting reactions, such as, reactions of atomization or of atom substitution. The results show that there is a linear dependence between the enthalpy of the most stable n-fluorobenzene and the corresponding n-fluorodewar benzene (n = 0, 1, …, 6). Further, the estimates are always more negative than the experimental results and so, suggested enthalpies of formation for 1,2,3-, 1,2,4- and 1,3,5-trifluorobenzenes and for 1,2,3,4- and 1,2,3,5-tetrafluorobenzenes are those retrieved from G3MP2B3 calculations added by 8 kJ/mol. The interaction of four different M⁺ ions with fluorobenzene and the three difluorobenzenes shows that the σ-interaction with 1,2-difluorobenzene is stronger than π-interaction on these fluorobenzenes.     

Unimolecular rearrangement of α-silylcarbenium ions. An ab initio study

The unimolecular rearrangements of hydrogen, methyl and phenyl groups at the Si atom in α-silylcarbenium ions have been investigated using an ab initio molecular orbital method. MP2/6–31 + G^*//HF/6–31G^* calculations predict that all three groups migrate from the Si to an adjacent C_α with no energy barrier. Thus, the silicenium ion is the only stable species in each potential energy surface. The conformation of the benzylsilicenium ion, (C₆H₅)CH₂−SiH₂⁺, indicates that the phenyl ring is significantly bent toward the silyl cationic center in order to interact with the vacant 3p(Si⁺) orbital. In contrast to MP2 results, Hartree-Fuck calculations (both HF/3–21G^* and HF/6–31G^* levels) predict small energy barriers for 1,2-migrations of H and Me (1.4 kcal mol⁻¹ for H migration, and 1.5 kcal mol⁻¹ for Me migration, respectively, at the HF/6–31G^* level). This difference provides convincing evidence that the incorporation of electron correlation is of particular importance in describing the potential energy surface for the rearrangement of α-silylcarbenium ions to silicenium ions. The results of the calculations have also been applied to the possible rearrangement mechanism of α-chlorosilanes to chlorosilanes, assuming that the experimental conditions are favorable toward the generation of ionic species. Various factors which may govern the migratory aptitudes of various R groups, i.e. (1) activation energies, (2) overall reaction energies and (3) the conformational preference of reactants have been investigated. The calculated activation energy obtained, namely the energy for the generation of the silicenium ion and the C⁻¹ ion from an α-chlorosilane, is consistent with the experimental migratory aptitude in the gas phase observed in mass spectrometers.     

An ab initio study of pyruvic acid

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Möller-Plesset level of theory using the 6-311++G^** basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.     

Infrared and Raman spectra, conformational stability, ab initio calculations of structure, and vibrational assignment of 2-hexyne

The infrared spectra (3500–50 cm⁻¹) of the gas and solid and the Raman spectra (3500–50 cm⁻¹) of the liquid and solid have been recorded for 2-hexyne, CH₃–CC–CH₂CH₂CH₃. Variable temperature studies of the infrared spectrum (3500–400 cm⁻¹) of 2-hexyne dissolved in liquid krypton have also been recorded. Utilizing four anti/gauche conformer pairs, the anti(trans) conformer is found to be the lower energy form with an enthalpy difference of 74±8 cm⁻¹ (0.88±0.10 kJ/mol) determined from krypton solutions over the temperature range −105 to −150 °C. At room temperature it is estimated that there is 42% of the anti conformer present. Equilibrium geometries and energies of the two conformers have been determined by ab initio (HF and MP2) and hybrid DFT (B3LYP) methods using a number of basis sets. Only the HF and DFT methods predict the anti conformer as the more stable form as found experimentally. A vibrational assignment is proposed based on the force constants, relative intensities, depolarization ratios from the ab initio and DFT calculations and on rotational band contours obtained using the calculated equilibrium geometries. From calculated energies it is shown that the CH₃ group exhibits almost completely free rotation which is in agreement with the observation of sub-band structure for the degenerate methyl vibrations from which values of the Coriolis coupling constants, ζ, have been determined. The results are compared to similar properties of some corresponding molecules.     

MP2, DFT and ab initio calculations on thioxanthone

Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. ¹³C and ¹H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties.     

Vibrational spectra, conformations, ab initio calculations and vibrational assignments of 3-pentyn-2-ol

The infrared spectra of 3-pentyn-2-ol, CH₃CCCH(OH)CH₃, have been recorded as a vapour and liquid at ambient temperature, as a solid at 78 K in the 4000–50 cm⁻¹ range and isolated in an argon matrix at ca. 5 K. Infrared spectra of the solid phase at 78 K were obtained before and after annealing to temperatures of 120 and 130 K. The IR spectra of the solid were quite similar to that of the liquid.

Raman spectra of the liquid were recorded at room temperature and at various temperatures between 295 and 153 K. Spectra of an amorphous and annealed solid were recorded at 78 K. In the variable temperature Raman spectra, some bands changed in relative intensity and were interpreted in terms of conformational equilibria between the three possible conformers. Complete assignments were made for all the bands of the most stable conformer in which OH is oriented anti to C₁(a_Me). From various bands assigned to a second conformer in which OH is oriented anti to H_gem(a_H), the conformational enthalpy differences was found to be between 0.4 and 0.8 kJ mol⁻¹. The highest energy conformer with OH anti to C₃(a_C) was not detected.

Quantum-chemical calculations have been carried out at the MP2 and B3LYP levels with a variety of basis sets. Except for small basis set calculations for which the a_H conformer had slightly lower energy, all the calculations revealed that a_Me was the low energy conformer. The B3LYP/cc-pVTZ calculations suggested the a_Me conformer as more stable by 0.8 and 8.3 kJ mol⁻¹ relative to a_H an a_C, respectively. Vibrational wavenumbers and infrared and Raman band intensities for two of the three conformers are reported from B3LYP/cc-pVTZ calculations.     

Propionaldehyde: ab initio and semi-empirical calculations

The internal rotation of propionaldehyde about the 1–2 bond has been studied by means of ab initio calculations. The most stable conformer has methyl and carbonyl eclipsed. Increasing the 1–2 dihedral angle to 60°, 120°, and 180° gives energies of 1.7, 0.4, and 0.7 Kcal/mol, respectively. The agreement with force field calculations and with experiment is reasonable.     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Far infrared spectra, conformational equilibria, vibrational assignments, ab initio calculations and structural parameters for 2-bromoethanol

The far infrared spectrum from 370 to 50 cm⁻¹ of gaseous 2-bromoethanol, BrCH₂CH₂OH, was recorded at a resolution of 0.10 cm⁻¹. The fundamental O–H torsion of the more stable gauche (Gg′) conformer, where the capital G refers to internal rotation around the C–C bond and the lower case g to the internal rotation around the C–O bond, was observed as a series of Q-branch transitions beginning at 340 cm⁻¹. The corresponding O–H torsional modes were observed for two of the other high energy conformers, Tg (285 cm⁻¹) and Tt (234 cm⁻¹). The heavy atom asymmetric torsion (rotation around C–C bond) for the Gg′ conformer has been observed at 140 cm⁻¹. Variable temperature (−63 to −100°C) studies of the infrared spectra (4000–400 cm⁻¹) of the sample dissolved in liquid xenon have been recorded. From these data the enthalpy differences have been determined to be 411±40 cm⁻¹ (4.92±0.48 kJ/mol) for the Gg′/Tt and 315±40 cm⁻¹ (3.76±0.48 kJ/mol) for the Gg′/Tg, with the Gg′ conformer the most stable form. Additionally, the infrared spectrum of the gas, and Raman spectrum of the liquid phase are reported. The structural parameters, conformational stabilities, barriers to internal rotation and fundamental frequencies have been obtained from ab initio calculations utilizing different basis sets at the restricted Hartree–Fock or with full electron correlation by the perturbation method to second order. The theoretical results are compared to the experimental results when appropriate. Combining the ab initio calculations with the microwave rotational constants, r₀ adjusted parameters have been obtained for the three 2-haloethanols (F, Cl and Br) for the Gg′ conformers.     

Ab initio calculations on the molecular structure of fluorocyanopolyynes

The molecular structure of the first three members of the fluorocyanopolyynes was studied by ab initio Hartree-Fock calculations with a polarized double zeta basis set and at MP2 level with the same basis set. Alternating triple and single bonds were found; a theoretical estimate of rotational constants and dipole moments was performed and a comparison with the available experimental data was made. An analysis of the theoretical vibrational frequencies of the title compounds was carried out.     

Conformational studies of cyclopropylmethyl isocyanate from temperature dependent FT-IR spectra of xenon solutions and ab initio calculations

Variable temperature (−55 to −100 °C) studies of the infrared spectra (3200 to 100 cm⁻¹) of cyclopropylmethyl isocyanate, c-C₃H₅CH₂NCO, dissolved in liquefied xenon, have been carried out. The infrared spectra (gas and solid) as well as the Raman spectrum of the liquid have been recorded from 3200 to 100 cm⁻¹. By analyzing six conformer pairs in xenon solutions, an enthalpy difference of 193 ± 19 cm⁻¹ (2.31 ± 0.23 kJ/mol) was obtained with the gauche–cis rotamer (the first designation indicates the orientation of the CNCO group with respect to the three-membered ring, the second designation indicates the relative orientation of the NCO group with respect to the bridging CC bond) the more stable form and the only form present in polycrystalline solid. The abundance of the cis–trans conformer present at ambient temperature is 16 ± 1%. The potential function governing the conformational interchange has been obtained from B3LYP/6-31G(d) calculations and the two-dimensional potential has been obtained. From MP2 ab initio calculations utilizing various basis sets with diffuse functions, the gauche–cis conformer is predicted to be more stable by 223 to 269 cm⁻¹, which is consistent with the experimental results. However, without diffuse functions the predicted conformational energy differences are much smaller (77–166 cm⁻¹). Similar diffuse function dependency affects density functional theory calculations by the B3LYP method to a lesser extent. A complete vibrational assignment for the gauche–cis conformer is proposed and several fundamentals for the cis–trans conformer have been identified. The structural parameters, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and r₀ structural parameters are estimated. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.     

Conformational and structural studies of 1-fluorosilacyclobutane from temperature dependent FT-IR spectra of krypton solutions and ab initio calculations

The infrared spectra (3500 to 40 cm⁻¹) of gaseous and solid and the Raman spectra (3500 to 30 cm⁻¹) of liquid and solid 1-fluorosilacyclobutane, c-C₃H₆SiFH, have been obtained. Both the axial and equatorial conformers with respect to the fluorine atom have been identified in the fluid phases. Variable temperature (−105 to −150 °C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 282 ± 27 cm⁻¹ (3.37 ± 0.32 kJ/mol), with the equatorial conformer the more stable form and the only conformer remaining in the annealed solid. At ambient temperature there is approximately 21 ± 2% of the axial conformer present in the vapor phase. From isolated Si–H stretching frequencies the Si–H (r₀) distances are calculated to be 1.484 and 1.485 Å for the equatorial and axial conformers, respectively. Structural parameters have been predicted from MP2/6-311 + G(d,p) ab initio calculations and the adjusted r₀ parameters for both conformers were obtained from a combination of the ab initio predicted values and the six previously reported microwave rotational constants. Along with the Si–H bond distance, the Si–C, and C–C distances of 1.865(5), and 1.571(5) Å, respectively, for the equatorial conformer are significantly different from the values for these parameters previously reported from an election diffraction study. Both the SiC and CC distances and the SiF distance are longer by 0.002 and 0.004 Å, respectively, for the axial conformer. Structural parameters have also been obtained for silacyclobutane, c-C₃H₆SiH₂ and ethylsilylfluoride, CH₃CH₂SiH₂F, from combined ab initio predicted values and previously reported rotational constants. Several of these newly determined parameters are significantly different from those previously reported for both molecules. Complete equilibrium geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, and depolarization ratios have been determined for both rotamers by ab initio calculations employing the 6-31G(d) basis set at the level of Moller–Plesset (MP) to second order. A complete vibrational assignment supported by normal coordinate calculations is proposed for the equatorial conformer, and several of the fundamentals of the axial conformer have also been identified. The results are discussed and compared to corresponding quantities for some similar molecules.