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.     

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.     

A comparative study by AM1, PM3 and ab initio HF/3-21G methods on the structure and reactivity of monosubstituted carbanion 1,2,4-triazolium ylides

A full conformational analysis of six 1,2,4-monosubstituted carbanion 1,2,4-triazolium ylides 4 a–f was performed using AM1, PM3 and HF/3-21G methods. The C-type conformers were found as the most stable structures by these different methods. This study also includes a qualitative estimation of the chemical behavior of triazolium ylides 4 a–f as nucleophilic agents on the level of ylide carbon atoms. The ab initio 3-21G method seems to be the most suitable in the characterization of these molecular systems.     

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.     

Molecular structures and ab initio molecular orbital calculations of the optically active derivatives of 1-aminocyclopropane-1-carboxylic acid

The novel optically active derivatives of 2,2′-disubstituted-1-aminocyclopropane-1-carboxylic acid (−)-2 and (+)-3 were synthesised from the spiro-azlactone (+)-1. Oxidation of the diol moiety of (+)-3 gave by ring enlargement the racemic mixture of 2,3-dihydrofuran derivative (±)-6. This conversion is explained by stepwise rearrangement of the initially formed tetrasubstituted cyclopropanecarbaldehyde 4 through zwitterionic's reactive intermediate 5. The formation of (±)-6 is preferred energetically as established by ab initio calculations of the ground states and possible intermediates for that rearrangement. The crystal structure and absolute configuration of the compounds (+)-1, (−)-2, (+)-3 and (−)-7 were determined by single-crystal X-ray diffraction method. All four compounds possess Z-configuration of the cyclopropane ring. The dioxolane ring in the structures (+)-1 and (−)-2 adopts half-chair conformation, while the cyclopropane ring and geminally substituted groups in the structures (−)-2, (+)-3 and (−)-7 possess the anticlinal conformation. The molecules of the compound (+)-1 are connected by very weak intermolecular hydrogen bond of C-H?O type. In the compounds (−)-2, (+)-3 and (−)-7inter- and intramolecular hydrogen bonds of N-H?O type were observed. The spiro-compound (+)-1 exhibited a more pronounced inhibitory activity against the proliferation of murine leukemia and human T-lymphocytes cells than other type of tumor cell lines and normal human fibroblast cells.     

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.     

A further study on closo boron hydrides B_(16)H_(16)~(2-)(D_2) and B_(16)H_(16)(Td) using ab initio molecular orbital theory

Ab initio molecular orbital calculations of doubly negative charged B16H162-(D2) and neutral B16H16(Td) have been done at the HF/6-31G level.They are predicted to be chemically and kinetically stable by vibrational analyses on their respective energy hypersurface of the HF/6-31G level.The geometrical structure of the species B16H1622-(D2) was discussed.     

A further study on closo boron hydrides B16H2−16 (D2) and B16H16Td) using ab initio molecular orbital theory

Ab initio molecular orbital calculations of doubly negative charged B₁₆H^2?₁₆(D₂) and neutral B₁₆H₁₆(Td) have been done at the HF/6-31G level. They are predicted to be chemically and kinetically stable by vibrational analyses on their respective energy hypersurface of the HF/6-31G level. The geometrical structure of the species B₁₆H²₁₆ (D₂) was discussed.     

Ab initio molecular orbital study of potential energy surface for the H2NO(B1)→NO(Π)+H2 reaction

The mechanism of the H₂NO(²B₁)→NO(²Π)+H₂ reaction has been examined using ab initio molecular orbital methods. Ground-state and first-excited-state potential surfaces were plotted at the FOCI/cc-pVTZ level of theory as functions of two appropriate internal degrees of freedom. A conical intersection was found on the C_s pathway that is symmetric with respect to the plane perpendicular to the molecular plane of C_2v H₂NO(²B₁). It is therefore considered that trajectories that start from H₂NO(²B₁) towards the product region detour around the conical intersection, pass through the neighborhood of the transition state that is located at the saddle point on the C_s pathway, and finally reach the products, NO(²Π)+H₂. Thus we can explain the mechanism of the H₂NO(²B₁)→NO(²Π)+H₂ reaction, which has remained unclear to date.     

An ab initio molecular orbital study of the trimethylgallium-arsine adduct: (CH3)3Ga:AsH3

The structure, harmonic frequencies, and binding energy of the trimethylgallium-arsine adduct, (CH₃)₃Ga: AsH₃, have been computed using ab initio molecular orbital methods, and, where possible, compared with experimental results. The structures and frequencies of the precursors trimethylgallium and arsine are perturbed to only a small extent upon adduct formation. The binding energy of (CH₃)₃Ga: AsH₃ is found to be 5.2 kcal/mol lower than that for H₃Ga:AsH₃ at the MP2/HUZSP^*//RHF/HUZSP^* level of computation.     

Unusual conformational properties of 1,3-dimethyl-1,1,3,3-tetrakis(trimethylsilyl)trisilane: A preparative, X-ray, Raman spectroscopic and ab initio study

The heptasilane Me(SiMe₃)₂SiSiH₂SiMe(SiMe₃)₂ was synthesized from Me(SiMe₃)₂SiK and H₂Si(OSO₂CF₃)₂. Crystals suitable for a X-ray single crystal analysis could be grown, with the somewhat surprising result that the two dihedral angles (H₃)CSiSi(H₂)Si are different in the crystal (24.58(10)° and 31.67(11)°). SiSiSi-bonds angles are widened, with values up to 117°. Ab initio calculations at the density functional B3LYP level employing 6-311G(d) basis sets predict minima for five conformers 1-5 with relative energies 0.0, 3.1, 8.2, 10.8 and 18.1 kJ/mol, respectively. Moreover, SiSiSiSi dihedral angles spanning the range 43.5-172.3° are predicted, reflecting the small forces which are required for distorting these angles.In the Raman spectrum of a solution in toluene, three lines at 350, 340 and 330 cm⁻¹ are observed in a wavenumber range which is typical for the SiSi-pulsation of methylated oligosilanes. The relative intensity ratio of the bands is temperature dependent, reflecting the changes in conformer concentrations that occur according to Boltzman’s law. Supported by the ab initio calculations, the Raman band at 350 cm⁻¹ is assigned to an ‘averaged’ conformer 1 and 2, because a rapid interconversion between 1 and 2 has to be assumed due to a small barrier separating them. The bands with wavenumbers 340 and 330 cm⁻¹ originate from conformers 3 and 4. From the Raman spectra, relative energies 0.0 (1 + 2), 2.2 (3) and 6.3 (4) kJ/mol are deduced, the presence of 5 is not observed. Caused by solvent effects, these values differ somewhat from the ab initio results.     

1,5-Diamino-1H-1,2,3,4-tetrazolium picrate: X-ray molecular and crystal structures and ab initio MO calculations

The crystal and molecular structures of 1,5-diamino-1H-1,2,3,4-tetrazolium picrate (DATP) were determined by X-ray diffraction analysis. The tetrazolium cation in DATP has a structure with protonated N4 atom of the ring. Two amino groups in the cation are found to be rather different. The 5-amino group lies in the plane of the tetrazole ring and valence angles around the N atom are close to 120°, which indicates sp² hybridization of atomic orbital of the nitrogen atom. In contrast, valence angles around the N atom of the 1-amino group are close to tetrahedral angle, which suggests sp³ hybridization. The exocyclic C-N bond in the cation is substantially shorter than that in 1,5-diaminotetrazole. The obtained results indicate a conjugation between the π-system of the tetrazole ring and the 5-amino group. The results of ab initio calculations of electronic structure and relative stability for various tautomeric forms of protonated 1,5-diaminotetrazole using MP2/6-31G* and B3LYP/6-31G* levels of theory are in a good agreement with X-ray data and show that there are differences in σ-electron overlap populations for the C-N bonds in the cation in DATP, while π-electrons are delocalized.     

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.     

Infrared, and Raman spectra, conformational stability, normal coordinate analysis, ab initio calculations, and vibrational assignment of 1-chlorosilacyclobutane

The infrared spectra (3500–40 cm⁻¹) of gaseous and solid and the Raman spectra (3500–30 cm⁻¹) of liquid and solid 1-chlorosilacyclobutane, c-C₃H₆SiClH, have been obtained. Both the axial and equatorial conformers with respect to the chlorine 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 211±17 cm⁻¹ (2.53±0.21 kJ/mol), with the equatorial conformer being the more stable form and the only conformer remaining in the annealed solid. At ambient temperatures, approximately 26% of the axial conformers are present in the vapor phase. A complete vibrational assignment is proposed for the equatorial conformer, and many of the fundamentals of the axial conformers have also been identified. The vibrational assignments are supported by normal coordinate calculations utilizing ab initio force constants. 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 levels of restricted Hartree–Fock (RHF) and/or Moller–Plesset (MP) to second order. Structural parameters have also been obtained using MP2/6-311+G(d,p) ab initio calculations. The r₀ parameters for both conformers are obtained from a combination of the ab initio predicted values and the twelve previously reported microwave rotational constants. The results are discussed and compared to those obtained for some similar molecules.     

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.     

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.     

Structure and spectra of 1,3-dioxanes. II. Microwave spectrum, structural parameters, and ab initio calculations of 2-methyl-1,3-dioxane

The microwave spectra of five isotopomers with the ¹³C and ¹⁸O natural abundance isotopes of the 2-methyl-1,3-dioxane molecule (22–50 GHz) were studied. Rotational transitions of a and c types with 4 ≤ J ≤ 12 were identified. The rotational constants and the substitution r _s and effective r _o structural parameters of the molecule were determined. Ab initio calculations on 2-methyl-1,3-dioxane were performed with molecular structure optimization. The results of quantum-chemical calculations at different levels are compared with experimental data.     

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.     

Modelling of interactions between volatile anaesthetics (halothane,enflurane) and aromatic compounds,ab initio study

For many years halothane and enflurane have been used clinically as volatile anaesthetics, however, their mechanism of action is still not fully understood. Recently, it has been suggested that they can act by a direct bonding to neuroreceptors containing the aromatic groups. In this work, the halothane?benzene and enflurane?benzene complexes were studied by the ab initio MP2 and CCSD(T) methods. All possible structures of the complexes were calculated by means of the counterpoise CP-corrected gradient optimization technique. It has been found that among these species, the C–H?π hydrogen bonded complexes are the most stable. The CCSD(T)/CBS calculated stabilization energies for halothane and enflurane complexes are: −10.56 and −9.72 kcal mol⁻¹, respectively. The interaction energy is mainly dominated by the dispersion attraction. In the case of enflurane, the C–H bond shows a very small contraction (by −0.0008 Å) upon complexation. This change is accompanied by the blue-shift (20 cm⁻¹) of the C–H stretching frequency and an increase of the infrared intensity of the corresponding mode by 7 km mol⁻¹. Similar results were obtained for the halothane complex: a small contraction of the C–H bond; an increase of the C–H stretching frequency by 11 cm⁻¹ (blue-shift); and an increase of the infrared intensity by 37 km mol⁻¹. In order to explain the nature of these effects, the halothane and enflurane molecules were studied in the electric field generated by benzene atoms, and Natural Bond Orbital (NBO) analyses were performed. The molecular dipole moments of these molecules were calculated with respect to the C–H bond changes. The positive dipole moment derivative obtained for halothane is in agreement with the literature data, while, in the case of enflurane, an unusual effect is observed, the blue-shift of the C–H stretching frequency is accompanied by the positive dipole moment derivative for one C–H bond and the negative for the other C–H bond. The mechanisms responsible for contraction and strengthening of the C–H bonds are discussed.