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.     

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.     

β‐Aminoacrolein: An ab initio,AIM and NBO study

The molecular structure and the intramolecular hydrogen bonding of β‐aminoacrolein and its simple derivatives were investigated at the MP2 and B3LYP levels of theory using the standard 6‐311++G(d, p) basis set. The “atoms in molecules” or AIM theory of Bader which is based on topological properties of the electron density (ρ), was used. Additionally, an analysis of the critical points was performed to study the nature hydrogen bonding in these systems. Natural bond orbital (NBO) analysis was also carried out for to better comprehend the nature of the intramolecular interactions in β‐aminoacrolein and its derivatives. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A Conformational Study on Silacyclohexane. Comparison of ab initio (HF,MP2), DFT,and Molecular Mechanics Calculations. Conformational Energy Surface of Silacyclohexane

The structures and relative energies for the basic conformations of silacyclohexane 1 have been calculated using HF, RI‐MP2, RI‐DFT and MM3 methods. All methods predict the chair form to be the dominant conformation and all of them predict structures which are in good agreement with experimental data. The conformational energy surface of 1 has been calculated using MM3. It is found that there are two symmetric lowest energy pathways for the chair‐to‐chair inversion. Each of them consists of two sofa‐like transition states, two twist forms with C₁ symmetry (twist‐C₁), two boat forms with Si in a gunnel position (C₁ symmetry), and one twist form with C₂ symmetry (twist‐C₂). All methods calculate the relative energy to increase in the order chair < twist‐C₂ < twist‐C₁ < boat. At the MP2 level of theory and using TZVP and TZVPP (Si atoms) basis sets the relative energies are calculated to be 3.76, 4.80, and 5.47 kcal mol^–1 for the twist‐C₂, twist‐C₁, and boat conformations, respectively. The energy barrier from the chair to the twisted conformations of 1 is found to be 6.6 and 5.7 kcal mol^–1 from MM3 and RI‐DFT calculations, respectively. The boat form with Si at the prow (C_s symmetry) does not correspond to a local minimum nor a saddle point on the MM3 energy surface, whereas a RI‐DFT optimization under C_s symmetry constraint resulted in a local minimum. In both cases its energy is above that of the chair‐to‐twist‐C₁ transition state, however, and it is clearly not a part of the chair‐to‐chair inversion.     

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

Ab initio HF and MP2 calculations on prototype model linkages of phosphorothioate DNA backbones illuminate the effects of phosphorothioation on electronic and structural properties of DNA backbone. The replacement of a bridging oxygen atom by sulfur in the phosphodiester linkage is energetically favored over that of replacement of a non-bridging oxygen atom. In phosphorothioate derivatives containing the P(OS)_nb moiety, the non-bridging oxygen atom always bears a higher negative charge than the non-bridging sulfur. Additional calculations on protonated (neutral) adducts suggest that phosphorothioation of the phosphodiester linkage lowers its proton affinity. Moreover, protonation of the non-bridging oxygen atom at phosphorous is favored over the protonation of the non-bridging sulfur atom for linkages containing the P(OS)_nb moiety. The ab initio calculated structural parameters are compared to the available crystallographic data of small phosphorothioate molecules and phosphorothioate oligodeoxynucleotides. These results have implications upon the biological activity of phosphorothioate DNA analogs.     

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.     

IR, Raman and theoretical ab initio RHF study of aminoglutethimide — an anticancer drug

A comparative analysis of the IR and Raman spectra of aminoglutethimide (AG) dissolved in CCl₄, CHCl₃ and CH₃CN was performed. Most of the absorption bands were assigned to characteristic group vibrations with the use of the IR and Raman spectra of deuterated AG, glutethimide, N-methyl glutethimide and glutarimide. The AG samples very weakly interacting with the environment were studied with the use of the Ar matrix isolation IR spectra. For comparison, the IR and Raman spectra of the crystalline samples formed by hydrogen-bonded AG molecules were recorded. The spectra were analyzed also in terms of normal modes and the harmonic approximation with the use of the ab initio restricted Hartree-Fock theory. It was found that increasing the solute concentration in CCl₄ and CHCl₃ leads to formation of the autoassociates. In CH₃CN the solute–solvent AG–CH₃CN dimers occur. Possible structures of the associates were theoretically studied on the model systems: the centrosymmetric glutarimide dimer and the linear AG–CH₃CN dimer. By a comparison of the theoretical and experimental spectra we were able to identify several peaks originating from the solute–solvent interactions.     

An ab initio and matrix isolation infrared study of the 1:1 C2H2–CHCl3 adduct

The details of weak C–Hπ interactions that control several inter and intramolecular structures have been studied experimentally and theoretically for the 1:1 C₂H₂–CHCl₃ adduct. The adduct was generated by depositing acetylene and chloroform in an argon matrix and a 1:1 complex of these species was identified using infrared spectroscopy. Formation of the adduct was evidenced by shifts in the vibrational frequencies compared to C₂H₂ and CHCl₃ species. The molecular structure, vibrational frequencies and stabilization energies of the complex were predicted at the MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels. Both the computational and experimental data indicate that the C₂H₂–CHCl₃ complex has a weak hydrogen bond involving a C–Hπ interaction, where the C₂H₂ acts as a proton acceptor and the CHCl₃ as the proton donor. In addition, there also appears to be a secondary interaction between one of the chlorine atoms of CHCl₃ and a hydrogen in C₂H₂. The combination of the C–Hπ interaction and the secondary ClH interaction determines the structure and the energetics of the C₂H₂–CHCl₃ complex. In addition to the vibrational assignments for the C₂H₂–CHCl₃ complex we have also observed and assigned features owing to the proton accepting C₂H₂ submolecule in the acetylene dimer.     

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 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.     

Defective α‐Fe2O3(0001): An ab Initio Study

By using density functional theory calculations at the PBE+U level, we investigated the properties of hematite (0001) surfaces decorated with adatoms/vacancies/substituents. For the most stable surface termination over a large range of oxygen chemical potentials (${\mu _{\rm{O}} }$ ), the vacancy formation and adsorption energies were determined as a function of ${\mu _{\rm{O}} }$ . Under oxygen‐rich conditions, all defects are metastable with respect to the ideal surface. Under oxygen‐poor conditions, O vacancies and Fe adatoms become stable. Under ambient conditions, all defects are metastable; in the bulk, O vacancies form more easily than Fe vacancies, whereas at the surface the opposite is true. All defects, that is, O and Fe vacancies, Fe and Al adatoms, and Al substituents, induce important modifications to the geometry of the surface in their vicinity. Dissociative adsorption of molecular oxygen is likely to be exothermic on surfaces with Fe/Al adatoms or O vacancies.     

Complete basis set ab initio computational study of three-dimensional aromaticity in highly symmetric hydrogen clusters

The aromaticity of planar and highly symmetric three-dimensional hydrogen clusters were evaluated with the complete basis set ab initio computational method. The energy of formation of the hydrogen clusters from the hydrogen molecule and hydrogen molecular ions were used in comparison to their relative stabilities. The aromaticity of planar hydrogen clusters, as well as hydrogen clusters in the three dimensions, arranged as highly symmetric regular polyhedra (Plato's polyhedras), were discussed with respect to the Hückel and Möbius aromatic rules.     

Electron-spin magnetic moments of the 2Σ+ ions Li2+, Li2−, and Be2+: An ab initio ROHF study

For the ²Σ⁺ ground states of the ions Li₂⁺, Li₂⁻, and Be₂⁺, the dependence of the magnetic moment (parametrized by g-shifts) on the bond length R was studied at the ROHF level. The Δ g-values were calculated via a perturbative approach (complete to second order in Breit-Pauli interactions) using quadruple-zeta AO basis sets augmented by semidiffuse and polarization functions. All Δ g-values in these systems are negative. The parallel component Δ g_∥ generally changes little with R, remaining close to the g-shift of the corresponding ²S atomic dissociation product. For Li₂⁺ and Be₂⁺, the perpendicular component Δ g _⟂ is more sensitive to geometry than is Δ g_∥, mainly because of the second-order magnetic coupling with excited ²Π states. For Li₂⁻, Δ g _⟂ and Δ g_∥ are similar due to the large size of the 2σ_u, SOMO, resulting in g-values close to that of a free electron. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 511–521, 1997     

Unimolecular isomerization/decomposition of cyclopentadienyl and related bimolecular reverse process: ab initio MO/statistical theory study

The cyclopentadienyl radical decomposition has been studied in detail by high‐level correlation MO methods combined with multichannel RRKM rate constant calculations. The product channels of the reaction were examined by calculating their pressure‐dependent branching rate constants. The overall reaction rate has been shown to be controlled by the first transition state corresponding to 1,2‐hydrogen atom migration. Also, the reverse bimolecular reactions (C₃H₃ + C₂H₂ → products) have been included in the study. We provide a summary of pressure dependent rate constant expressions for the 1000–3000 K temperature range that may be useful for kinetic modeling of relevant combustion systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 415–425, 2000     

C D : a computer program to generate 1D, 2D and 3D grids of functions dependent on the molecular ab initio electron density

A program to compute many functions dependent on the electron density ρ(r) from the results of ab initio molecular calculations is presented. The program allows the generation of different one-, two-, and three-dimensional grids for further graphical representation or numerical analysis. Other options like extracting separate atom contributions to the function computed or locating maximum and minimum values are also implemented. A number of illustrative applications regarding different ρ(r)-dependent functions are presented and the performance and portability of the program is discussed.     

Chemisorption of HSi(OH)3 on silica surfaces: an ab initio periodic study

The study of the grafting of trialkoxysilane R′Si(OR)₃ molecules on amorphous silica has been undertaken at the Hartree–Fock level using a biperiodic model for the surface. Different types of slab cut out from the model system Edingtonite (a tetragonal silica structure with five SiO₂ groups per unit cell) have been used to simulate isolated and interacting silanol sites at the amorphous silica surface, while only the simple case of HSi(OH)₃ has been considered for the interacting molecule. In a first step, for each type of surface the geometrical parameters have been optimised and the surface formation energy determined. The geometrical structure of the grafted molecule is compared with that of the isolated one. The geometrical strains of the surfaces with either isolated or interacting silanols are also compared before and after the grafting reactions. The calculated values of the chemisorption energies show that the grafting process is favored on isolated silanols only if correlation effects are included.     

Preferred Binding of Carboxylates by Chiral Urea Derivatives Containing α‐Phenylethyl Group

An efficient, simple protocol for the synthesis of a new family of chiral ureas 1 – 4 is described. The binding properties of 1 – 4 toward different anion (acetate, benzoate, fluoride, and chloride) have been studied by ¹H‐NMR titration and have been observed in the case of 4 is a selective receptor for acetate. The theoretical calculation M06/6‐311+G(d,p) helped us explain the binding properties observed. The most interesting observation is that this calculated structure is consistent with expected, based on the concept of allylic 1,3‐strain (A^1,3 strain). When chiral caboxylates were studied, urea 1 was the best in discriminating between enantiomers.     

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.