Structural stability, S-O rotational barrier and vibrational analyses of monomeric non-planar halosulfonic acids X-SO2-OH (X=F, Cl and Br)

The structural stability of halosulfonic acids X-SO2-OH (X=F, Cl and Br) were investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The potential energy curve for the XSOH internal rotation around S-O bond was consistent with one minimum that corresponds to non-linear structure with XSOH torsional angle of about 80 degrees . The vibrational frequencies were computed at DFT-B3LYP level for the stable non-planar structure of the three molecules. Normal coordinate calculations were then carried out and the potential energy distributions (PED) were calculated for the molecules. On the basis of PED values and comparison with experimental data reliable assignments were provided for normal modes of fluoro-, chloro- and bromosulfonic acids.     

Theoretical evidence for a NH...XC blue-shifting hydrogen bond: complexes pairing monohalomethanes with HNO

Correlated ab initio calculations are used to analyze the interaction between nitrosyl hydride (HNO) and CH3X (X = F, Cl, Br). Three minima are located on the potential energy surface of each complex. The more strongly bound contains a NH...X bond, along with CH...O; CH...O and CH...N bonds occur in the less stable minimum. Binding energies of the global minimum lie in the range of 11-13 kJ/mol, and there is little sensitivity to the identity of the halogen atom. Unlike most other such hydrogen bonds, the NH covalent bond in this set of complexes becomes shorter, and its stretching frequency shifts to the blue, upon forming the NH...X hydrogen bond. The amount of this blue shift varies in the order F > Cl > Br.     

Conformation and intramolecular hydrogen bonding of 2-chloroacetamide as studied by microwave spectroscopy and quantum chemical calculations

The microwave spectrum of 2-chloroacetamide (ClCH2CONH2) has been investigated at room temperature in the 19-80 spectral range. Spectra of the 35ClCH2CONH2 and 37ClCH2CONH2 isotopomers of one conformer, which has a symmetry plane (Cs symmetry), were assigned. The amide group is planar, and an intramolecular hydrogen bond is formed between the chlorine atom and the nearest hydrogen atom of the amide group. The ground vibrational state, six vibrationally excited states of the torsional vibration about the CC bond, as well as the first excited state of the lowest bending mode were assigned for the 35ClCH2CONH2 isotopomer, whereas the ground vibrational state of 37ClCH2CONH2 was assigned. The CC torsional fundamental vibration has a frequency of 62(10) cm(-1), and the bending vibration has a frequency of 204(30) cm(-1). The rotational constants of the ground and of the six excited states of the CC torsion were fitted to the potential function Vz = 16.1( + 2.3) cm(-1), where z is a dimensionless parameter. This function indicates that the equilibrium conformation has Cs symmetry. Rough values of the chlorine nuclear quadrupole coupling constants were derived as chi(aa) = -47.62(52) and chi(bb) = 8.22(66) MHz for the 35Cl nucleus and chi(aa) = -34.6(10) and chi(bb) = 6.2(11) MHz for the 37Cl nucleus. Ab initio and density functional theory quantum chemical calculations have been performed at several levels of theory to evaluate the equilibrium geometry of this compound. The density functional theory calculations at the B3LYP/6-311++G(3df,2pd) and B3LYP/cc-pVTZ levels of theory as well as ab initio calculations at the MP2(F)/cc-pVTZ level predict correct lowest-energy conformation for the molecule, whereas the ab initio calculations at the QCISD(FC)/6-311G(d) and MP2(F)/6-311++G(d,p) levels predict an incorrect equilibrium conformation.     

Structural relaxation upon internal rotation in cis-methyl nitrite,CH3 ONO

The ab initio SCF gradient method has been used to obtain changes of bond lengths and valence angles upon internal rotation of CH₃ and NO groups in cis-methyl nitrite. The data for methyl torsion are confirmed by comparison of calculated and observed shifts of rotational constants in the first methyl torsional state.     

Semiempirical (AM1) and ab initio calculations of 2-X-adenine (X = H, F, Cl) and β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribofuranose

We performed semiempirical (AM1) and ab initio (3-21G and 4-31G^**) calculations, with complete optimization of geometry, for 2-X-adenine (X = H, F, Cl) and selected conformers of β-D-1-amino-2,3-didehydro-1,2,3-trideoxyribo-furanose. Together (as 2-X-2',3'-didehydro-2',3'-dideoxyadenosine), or in separate conjunction with similar fragments, these structures belong to a group of 2',3'-dideoxynucleosides with potential anti-HIV activity.

The 2-X-adenine molecules are basically flat. For the halogenated species, especially the chlorine derivative, the results of the semiempirical method differ from the ab initio findings more widely than for adenine.

The results for the ribose derivative show the existence of conformers differing very little in energy. Ring puckering does not appear to depend on exocyclic torsion angles, structures with different conformations around the exocyclic C-C bond having similar ring conformations in all the cases analysed. The AMI method yielded geometries similar to those obtained ab initio with 3-21G.     

Photoinduced isomerization of the photoactive yellow protein (PYP) chromophore: interplay of two torsions, a HOOP mode and hydrogen bonding

We report on a detailed theoretical analysis, based on extensive ab initio calculations at the CC2 level, of the S(1) potential energy surface (PES) of the photoactive yellow protein (PYP) chromophore. The chromophore's photoisomerization pathway is shown to be fairly complex, involving an intimate coupling between single-bond and double-bond torsions. Furthermore, these torsional modes are shown to couple to a third coordinate of hydrogen out-of-plane (HOOP) type whose role in the isomerization is here identified for the first time. In addition, it is demonstrated that hydrogen bonding at the phenolate moiety of the chromophore can hinder the single-bond torsion and thus facilitates double-bond isomerization. These results suggest that the interplay between intramolecular factors and H-bonding determines the isomerization in native PYP.     

A conformational analysis of 4,4'-bipyridinium dication

A conformational analysis of the 4,4'-bipyridinium dication has been investigated using the results from 10 ab initio STO-3G calculations in which the inter-ring bond length was optimized at each torsion angle. The most reliable calculation yields: a lowest energy conformer with an equilibrium torsional angle of 45.3° and inter-ring (R_c-c) bond length of 0.152 nm; a barrier height of 5.86 kJ mol⁻¹. An examination of the fitted Fourier series indicates that half of the theoretical data points effectively reproduced the more extensive surface. Furthermore, a comparison of the calculations and fitted surfaces indicate that a rigid rotor is an excellent approximation for this molecule.     

Ab initio calculation of the potential functions for internal rotation around the CS bonds in simple ethene thiols

Ab initio calculations with complete geometry optimisation have been used to study internal rotation in compounds of the type XCH = CHSH, X = CN, H, CH₃ and F, with X located trans to the sulphur atom. Potential functions for the CS torsion have been obtained for each case and it has been established that the dominant framework changes accompanying internal rotation in these molecules involve the CCS angle and CS bond length. Furthermore, it has been shown that the nature of the substituent X significantly affects the molecular conformation of the SH group. The observed trends are discussed in terms of a simple model.     

An empirical potential for the O-H·O Hydrogen bond: Part I. Comparison with ab initio molecular orbital results

An empirical potential energy function has been devised for the O-H·O hydrogen bond, for use with the MMI force field. The energy of the hydrogen bond is described as the sum of van der Waals, electrostatic and Morse components. The function has been used to calculate the potential energy hypersurface of the water dimer, and the results are compared with published ab initio molecular orbital studies. Satisfactory agreement is obtained except for orientations involving very short H·H contacts. The geometry and hydrogen bond energy of the equilibrium linear form of (H₂O)₂ are calculated to be r(O·O) = 2.84 Å, θ = 36°, ΔE = ?5.35 kcal mol^?1, which are close to the values obtained by experiment, and from molecular orbital calculations. The relative importance of the electrostatic component of the empirical hydrogen bond energy is consistent with molecular orbital energy decomposition studies. The empirical function has also been used to calculate the energy of the water trimer in orientations which serve as models for the crystallographic bifurcated hydrogen bond. The results indicate that, in these orientations, the trimer is typically 0–3 kcal mol^?1 more stable than the dimer, a result which is consistent with ab initio calculations.     

Analysis of the HOOO torsional potential

Torsional levels of cis and trans HOOO and DOOO, observed previously via infrared action spectroscopy [E. L. Derro, T. D. Sechler, C. Murray, and M. I. Lester, J. Chem. Phys. 128, 244313 (2008)], have been used in conjunction with ab initio theory to obtain a torsional potential energy surface for the hydrotrioxy radical. High level electronic structure calculations based on the equation-of-motion coupled-cluster method for ionized states (EOMIP-CCSD) are utilized to produce a torsional potential. Eigenvalues of the potential are computed by diagonalizing the torsional hamiltonian in a free-rotor basis. Uniform scaling of the theoretical potential by a factor of 1.35 yields vibrational frequencies in good agreement with the experiment, and allows prediction of the barrier height to isomerization of ～340 cm(-1) and relative stability of trans-HOOO with respect to cis-HOOO of ～70 cm(-1). Examination of the optimized nuclear coordinates with respect to the torsional angle, suggests that the central O-O bond length is strongly coupled to the torsion and is important in determining the relative stabilities of the two conformers. The scaled potential is then used to determine the torsional contribution to the partition function for atmospheric modeling of HOOO.     

High resolution millimeter-wave spectroscopy of vinyltellurol

The millimeter-wave rotational spectrum of vinyltellurol has been recorded and assigned for the first time. To support the spectrum assignment, high level ab initio calculations have been carried out. Geometries, total electronic energies, and harmonic vibrational frequencies have been determined at the MP2 level. A small-core relativistic pseudopotential basis set (cc-pVTZ-PP) was employed to describe the tellurium atom. Two stable conformers, synperiplanar (sp) and anticlinal (ac), have been identified. The sp conformer is planar with a small negative inertia defect of -0.025 u ?(2). The ac conformer was found to be nonplanar with a C-C-Te-H dihedral angle of about 140° from sp. This conformer exhibits a large amplitude motion associated with the torsion about the C-Te bond. The barrier to internal rotation is about 1 kJ/mol, according to the theoretical calculations. For the ac conformation, a torsional potential function consisting of quartic and quadratic terms of the torsional angle has been partially determined from the observed rotational constants.     

Sensitivity of the H + CH3 → CH4 recombination rate constant to the shape of the CH stretching potential

Using a potential-energy surface obtained in part from ab initio calculations, the H + CH₃ → CH₄ bimolecular rate constant at T = 300 K is determined from a Monte Carlo classical trajectory study. Representing the CH stretching potential with a standard Morse function instead ofthe ab initio curve increases the calculated rate constant by an order of magnitude. The experimental recombination rate constant is intermediate of the rate constants calculated with the Morse and ab initio stretching potentials.Two properties of the H + CH₃ α CH₄ potential-energy surface which significantly affect the recombination rate constant are the shape of the CH stretching potential and the attenuation of the H₃CH bending frequencies. Ab initio calculations with a hierarchy of basis sets and treatment of electron correlation indicate the latter is properly described [13]. The exact shape of the CH stretching potential is not delineated by the ab initio calculations, since the ab initio calculations are not converged for bond lengths of 2.0–3.0 Å [12]. However, the form of this stretching potential deduced from the highest-level ab initio calculations, and fit analytically by eq. (2), is significantly different from a Morse function. The experimental recombination rate constant is intermediate of the rate constants calculated with the Morse and ab initio CH stretching potentials. This indicates that the actual CH potential energy curve lies between the Morse and ab initio curves. This is consistent with the finding that potential energy curves for diatomics are not well described by a Morse function [12].     

Classical and quantum studies of the photodissociation of a HX (X=Cl,F) molecule adsorbed on ice

The photodissociation dynamics of a HX (X = Cl,F) molecule adsorbed on a hexagonal ice surface at T = 0 K is studied using time-dependent quantum wave packets and quasiclassical trajectories. The relevant potential energy surfaces are calculated using high-level ab initio methods. We present here two dimensional calculations for the dynamics of the hydrogen photofragment for both HCl and HF molecules. The purpose of this paper is to compare the photodissociation dynamics of the two molecules which are adsorbed on the ice surface with different equilibrium geometries. The total photodissociation cross section and the angular distribution are calculated. The comparison with classical trajectory calculations provides evidence for typical quantum effects and reveals rainbow structures.     

Raman and infrared spectra,conformational stability,barriers to internal rotation,r 0 structural parameters,ab initio calculations,and vibrational assignment for vinyl chloroformate

The Raman (3200 to 10 cm^–1) and infrared (3500 to 50 cm^–1) spectra of vinyl chloroformate, H₂C=CHOC(O)Cl, have been recorded for both the gas and solid. Additionally, the Raman spectrum of the liquid has been recorded, and depolarization ratios have been obtained. These data have been interpreted on the basis that the only stable conformation present at ambient temperature is thetrans-trans rotamer, where the firsttrans refers to the vinyl moiety relative to the O—CCl bond and the second to the C—Cl bond relative to the=C—O bond. Using harmonic rigid asymmetric top calculations, the infrared vapor phase contours for the C=O and the C=C stretch were predicted for thetrans-trans and for thecis-trans conformer, and were compared with experiment. For both fundamentals thetrans-trans hybrid reproduces the experimental contour, whereas thecis-trans contours fail to do so for both fundamentals. From far-infrared spectrum of the vapor obtained at 0.1 cm^–1 resolution, the C(O)Cl andO-vinyl torsional fundamentals have been observed at 132 and 61 cm^–1, respectively. Ther ₀ structural parameters have been obtained from a combination of ab initio calculated parameters with appropriate offset values and the fit of the microwave rotational constants for the two naturally occurring chlorine isotopes. The structure, barrier to internal rotation, and vibrational frequencies have been determined from ab initio Hartree-Fock gradient calculations, using the 3-21G^* and 6-31G^* basis sets. These results are compared to those obtained experimentally and to similar quantities for some related molecules.     

Valence bond calculations of hydrogen transfer reactions: a general predictive pattern derived from theory

Hydrogen abstraction reactions of the type X(*) + H-H' --> X-H + H'(*) (X = F, Cl, Br, I) are studied by ab initio valence bond methods and the VB state correlation diagram (VBSCD) model. The reaction barriers and VB parameters of the VBSCD are computed by using the breathing orbital valence bond and valence bond configuration interaction methods. The combination of the VBSCD model and semiempirical VB theory leads to analytical expressions for the barriers and other VB quantities that match the ab initio VB calculations fairly well. The barriers are influenced by the endo- or exothermicity of the reaction, but the fundamental factor of the barrier is the average singlet-triplet gap of the bonds that are broken or formed in the reactions. Some further approximations lead to a simple formula that expresses the barrier for nonidentity and identity hydrogen abstraction reactions as a function of the bond strengths of reactants and products. The semiempirical expressions are shown to be useful not only for the model reactions that are studied in this work, but also for other nonidentity and identity hydrogen abstraction reactions that have been studied in previous articles.     

Low energy electron energy-loss spectroscopy of CF3X (X=Cl,Br)

We report threshold electron energy-loss spectra for the fluorohalomethanes CF3X (X=Cl,Br). Measurements were made at incident electron energies of 30 and 100 eV in energy-loss range of 4-14 eV, and at scattering angles of 4 degrees and 15 degrees. Several new electronic transitions are observed which are ascribable to excitation of low-lying states as well as are intrinsically overlapped in the molecules themselves. Assignments of these electronic transitions are suggested. These assignments are based on present spectroscopic and cross-section measurements, high-energy scattering spectra, and ab initio molecular orbital calculations. The calculated potential curves along the C-X bond show repulsive nature, suggesting that these transitions may lead to dissociation of the C-X bond. The present results are also compared with the previous ones for CF3H, CF4, and CF3I.     

How phonons govern the behavior of short, strong hydrogen bonds in urea-phosphoric acid

Recent neutron diffraction data have shown that the hydrogen atom involved in the short, strong hydrogen bond in urea-phosphoric acid migrates toward the midpoint of the hydrogen bond as the temperature increases. With the help of solid state ab initio calculations and inelastic neutron scattering, we have investigated the temperature dependence of the structural and vibrational properties of the system. The potential energy surface of the proton in the short, strong hydrogen bond and the thermal population of the energy levels therein cannot account for the observed proton migration. Ab initio molecular dynamics simulations clearly reveal the migration of the proton. This molecular dynamics result was reported recently by other authors, but they only offered a tentative explanation in terms of a resonance between high-frequency vibrations, which is not supported by the calculations presented here. We explain the proton migration in terms of phonon-driven structural fluctuations and their impact on the temperature-dependent evolution of the potential energy surface of the short hydrogen-bond proton.     

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.     

Rotational isomemsm in difluoroacetyl fluoride: Part II. AB initio calculations

The potential energy function for internal rotation of difluoroacetylfluoride around the C-C axis has been obtained by ab initio SCF calculations in a Gaussian basis set. Two minima are predicted with H and F atoms trans (α = O²) and gauche (α = 107–108°), respectively. Gauche- DFAF is incorrectly predicted to have the lower energy, but the addition or bond functions to the basis reduces the gauche-trans energy difference to ?0.1 kcal mole^?1. Dipole moments and torsional excitation energies are reported for both conformations and the significance of the computed potential function is critically analyzed. No support has been found for the suggestion that the C-F bonds in the CHF₂-group of gauche-DFAF are significantly different.     

An ab initio potential energy surface for the υ4 vibrational mode of hydrogen peroxide

In this paper, the levels and the torsional microstates of hydrogen peroxide are determined from fully optimized ab initio calculations using a nuclear model in one dimension. Calculations have been performed at the MP2 level with the 6-311 G(2df,2pd), 6-31 1+G(2df,2pd), cc-pVTZ and AUG-cc-pVTZ basis sets including polarization orbitals and diffuse functions. The most stable conformation, calculated with the MP2/AUG-cc-pVTZ approach, is a trans–gauche conformer lying at 67.5° from the trans structure. By using the same level of calculations, the heights of the trans and cis barriers have been determined to be 386.5 and 2643.8 cm⁻¹ in a good agreement with the experimental data. The variational torsional levels split into four components by the tunnelling effect of the barriers. The splitting of the fundamental level caused by the trans barrier has been found to be 11.8683 cm⁻¹, whereas the splitting caused by the cis barrier is insignificant under n=2. Current ab initio energies confirm the experimental assignments and verify the separability of the torsion from the rest of the vibrations. However, the experimental relation of dependence on the torsion of the rotational constants cannot be reproduced in one-dimension and depends on several additional vibrational effects.