Computational thermochemistry of glycolaldehyde

We use a variant of the focal point analysis to refine estimates of the relative energies of the four low‐energy torsional conformers of glycolaldehyde. The most stable form is the cis‐cis structure which enjoys a degree of H‐bonding from hydroxyl H to carbonyl O; here dihedral angles τ₁ (O?C? C? O) and τ₂ (C? C? O? H) both are zero. We optimized structures in both CCSD(T)/aug‐cc‐pVDZ and aug‐cc‐pVTZ; the structures agree within 0.01 Å for bond lengths and 1.0 degrees for valence angles, but the larger basis brings the rotational constants closer to experimental values. According to our extrapolation of CCSD(T) energies evaluated in basis sets ranging to aug‐cc‐pVQZ the trans‐trans form (180°, 180°) has a relative energy of 12.6 kJ/mol. The trans‐gauche conformer (160°, ±75°) is situated at 13.9 kJ/mol and the cis‐trans form (0°, 180°) at 18.9 kJ/mol. Values are corrected for zero point vibrational energy by MP2/aug‐cc‐pVTZ frequencies. Modeling the vibrational spectra is best accomplished by MP2/aug‐cc‐pVTZ with anharmonic corrections. We compute the Watsonian parameters that define the theoretical vibrational‐rotational spectra for the four stable conformers, to assist the search for these species in the interstellar medium. Six transition states are located by G4 and CBS‐QB3 methods as well as extrapolation using energies for structures optimized in CCSD(T)/aug‐cc‐pVDZ structures. We use two isodesmic reactions with two well‐established thermochemical computational schemes G4 and CBS‐QB3 to estimate energy enthalpy and Gibbs energy of formation as well as the entropy of the gas phase system. Our extrapolated electronic energies of species appearing in the isodesmic reactions produce independent values of thermodynamic quantities consistent with G4 and CBS‐QB3. © 2013 Wiley Periodicals, Inc.     

Vibrational and electronic absorption spectroscopy of dibenzo[b,def]chrysene and its ions

The vibrational and electronic absorption spectra of dibenzo[b,def]chrysene (DBC) and its ions in argon matrixes have been recorded. Assignment of the observed infrared (IR) bands has been made by comparison with the density functional theory (DFT) computations of harmonic vibrational frequencies (with 6-31G(d,p) or 6-311+G(d,p) basis sets). Extensive time-dependent (TD) DFT calculations of vertical excitation energies have aided in the assignment of the experimental electronic absorption transitions. In general, the theoretical predictions are in good agreement with the observed ultraviolet and visible bands. By correlating IR and UV-visible band intensities (after UV photolysis), it has been shown that both DBC cations and anions are formed. The IR band intensity distributions of the DBC ions differ markedly from neutral DBC. A synthetic spectrum composed of neutral, cationic, and anionic DBC contributions compares reasonably well with the interstellar features of the "unidentified infrared" (UIR) bands from the reflection nebula NGC 7023. Finally, it is shown that the electronic absorption bands of the DBC ions lie in close proximity to several of the diffuse interstellar visible absorption bands (DIBs).     

Vibrational analysis of n-butyl, isobutyl, sec-butyl and tert-butyl nitrite

Raman and infrared spectra of n-butyl, isobutyl, sec-butyl and tert-butyl nitrite are reported. Density functional theory and M?eller-Plesset calculations with 6-31G* and 6-311G* basis sets were used to determine ground state molecular geometries and vibrational frequencies of these compounds. Calculations and spectral data of these molecules were used to perform partial vibrational mode assignments for the observed transitions. In agreement with previous investigations of alkyl nitrites, cis and trans rotational conformers of n-butyl, isobutyl and sec-butyl nitrite were observed in the gas phase infrared spectra and the condensed phase Raman and infrared spectra. Among the several predicted geometries of these compounds, the cis-trans geometry (cis with respect to the C-O-N=O dihedral angle and trans with respect to the C-C-O-N dihedral) was calculated to be the most stable conformer of n-butyl and isobutyl nitrite, while the cis-gauche conformer was found to be the most stable geometry of sec-butyl nitrite. The cis-type structures of these three molecules are favored due to formation of a pseudo hydrogen bond between the nitrite group and the alpha-carbon hydrogen atoms. Hindrance with the alkyl moiety, however, causes the trans conformer (trans with respect to the C-O-N=O dihedral) of tert-butyl nitrite to lie lower than its cis conformer, a result that was supported by our spectroscopic measurements. The characteristic N=O stretch frequency for the trans conformers of all the compounds examined was observed to decrease with increasing branching at the alpha-carbon, while the same mode for the cis conformers shows no change among the primary and secondary nitrites. Evidence is also provided that suggests that the relative number of cis conformers to trans conformers decreases as the alpha-carbon branching increases.     

Infrared spectrum of solid isocyanic acid (HNCO): vibrational assignments and integrated band intensities

Infrared spectra of thin films of solid HNCO condensed from the gas phase are characterized in terms of their vibrational frequencies, mode assignments, and integrated band intensities at low temperatures ( approximately 20-145 K). Isocyanic acid is shown to react with water (H2O) and ammonia (NH3) even at low temperatures; consequently, it may be an important species in the chemistry of interstellar ices and comets.     

Mono,di, tri and tetraethylene glycol: Spectroscopic characterization using density functional method and experiment

We report infrared and electronic absorption spectra of mono, di, tri and tetra ethylene glycol (EG) in gas phase, their cation and anion and in water solvent using density functional theory calculations at B3LYP/TZVP level. Structural paramaters, rotational and centrifugal distortional constants and dipole moments are also reported. A siginificant shifts in vibrational frequencies and peaks in electronic absorption spectra have been observed upon ionization of mono, di, tri and tetra ethylene glycols. We have also obtained experimental vibrational spectrum of monoethylene glycol. Vibrational frequencies of mono ethylene glycol from theory and experiment are compared. We have used integral equation formalism polarizable continuum model (IEFPCM) model to study the influence of water solvent on vibrational frequencies of neutral mono, di, tri and tetra ethylene glycol. Electronic absorption spectra for these molecules have been obtained using Time dependent density functional theory (TDDFT).     

Experimental IR and Raman spectra and quantum chemical studies of molecular structures, conformers and vibrational characteristics of nicotinic acid and its N-oxide

FTIR and Raman spectra of nicotinic acid and its N-oxide have been recorded and analyzed. The stabilities, optimized molecular geometries, APT charges and vibrational characteristics for the two possible conformers of nicotinic acid and its N-oxide have been computed using DFT method. The E (trans) conformers of both the molecules are found to be more stable and less polar than their respective Z (cis) conformers. Due to addition of an O atom at the N1 site in nicotinic acid the magnitudes of atomic charges on all the H atomic sites of the nicotinic acid N-oxide molecule are found to increase. Most of the vibrational frequencies have nearly the same magnitude for the two conformers of both the molecules. However, significant changes are noticed in their IR intensities, Raman activities and depolarization ratios of the Raman bands. The calculated frequencies have been correlated with the experimental frequencies.     

Charge and temperature effects on hydrated tryptamine cluster ions

Infrared photodissociation spectra of M(+)(tryptamine)(H(2)O)(0-3)Ar(0-1) (M = Na, K) are presented here to demonstrate the role of charge and temperature in directing the conformation of tryptamine, a derivative of the amino acid tryptophan. All of the cluster ions discussed here are built from the two high-energy tryptamine conformers that have never been previously observed in neutral gas-phase studies. The Na(+) or K(+) provides a positive charge that stabilizes the Gpy(in) and Gph(in) conformers. DFT calculations are used to identify stable conformers and their corresponding harmonic vibrational frequencies in the CH, NH, and OH stretching regions, which aid in the interpretation of the experimental spectra. In some cases this interpretation is fairly straightforward by using the global minimum-energy structures. The more complex spectra associated with the argonated cluster ions suggest that high-energy isomers, trapped during the cluster ion formation process, are also present.     

Molecular conformers in gas-phase ethanol: A temperature study of vibrational overtones

Overtone absorption spectra are reported for ethanol vapor (10150–19900 cm^?1) measured by intracavity photoacoustic spectroscopy. The OH overtones are composed of two sub-bands which are assigned as the transitions of two conformers of the OH bond in the trans or gauche position with respect to the methyl group. From the temperature dependence of the OH overtone intensity we determine the enthalpy difference between the conformers to be 0.7 ± 0.1 kcal/mole.     

Vibrational spectroscopy (FT-IR and FT-Raman) investigation, and hybrid computational (HF and DFT) analysis on the structure of 2,3-naphthalenediol

The FT-IR and FT-Raman vibrational spectra of 2,3-naphthalenediol (C(10)H(8)O(2)) have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1) in solid phase. A detailed vibrational spectral analysis has been carried out and the assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-Fock (HF) and DFT (LSDA and B3LYP) methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. There are three conformers, C1, C2 and C3 for this molecule. The computational results diagnose the most stable conformer of title molecule as the C1 form. The isotropic computational analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and DFT methods. Comparison of the simulated spectra provides important information about the capability of computational method to describe the vibrational modes. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and Frontier molecular orbital energies, are performed by time dependent DFT approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds are discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated. The statistical thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) and their correlations with temperature have been obtained from the theoretical vibrations.     

Investigation of ethyl peroxy radical conformers via cavity ringdown spectroscopy of the A-X electronic transition

Both stable conformers, trans (T) and gauche (G), of the ethyl peroxy radical and its perdeutero analogue have been observed via cavity ringdown spectroscopy (CRDS) of the A2A'-X2A' ' electronic transition in the near-IR. Assignments of specific spectral lines to the electronic transition origin (T00), to observed vibrational hot bands, and to the COO bend and the O-O stretch vibrations are given with the help of equation of motion (EOMIP) quantum chemical calculations. In particular, spectral information for the previously unknown/unassigned T conformer of ethyl peroxy is given in this study for the first time and compared to the data for the previously observed G conformer. The conformer assignment is confirmed by an analysis of the partially resolved rotational structures. The electronic origins for the T and G conformers of C2H5O2 are located at 7362(1) and 7592(1) cm-1, respectively.     

Spatial distributions and interstellar reaction processes

Methyl formate presents a challenge for the conventional chemical mechanisms assumed to guide interstellar organic chemistry. Previous studies of potential formation pathways for methyl formate in interstellar clouds ruled out gas-phase chemistry as a major production route, and more recent chemical kinetics models indicate that it may form efficiently from radical-radical chemistry on ice surfaces. Yet, recent chemical imaging studies of methyl formate and molecules potentially related to its formation suggest that it may form through previously unexplored gas-phase chemistry. Motivated by these findings, two new gas-phase ion-molecule formation routes are proposed and characterized using electronic structure theory with conformational specificity. The proposed reactions, acid-catalyzed Fisher esterification and methyl cation transfer, both produce the less stable trans-conformational isomer of protonated methyl formate in relatively high abundance under the kinetically controlled conditions relevant to interstellar chemistry. Gas-phase neutral methyl formate can be produced from its protonated counterpart through either a dissociative electron recombination reaction or a proton transfer reaction to a molecule with larger proton affinity. Retention (or partial retention) of the conformation in these neutralization reactions would yield trans-methyl formate in an abundance that exceeds predictions under thermodynamic equilibrium at typical interstellar temperatures of ≤100 K. For this reason, this conformer may prove to be an excellent probe of gas-phase chemistry in interstellar clouds. Motivated by new theoretical predictions, the rotational spectrum of trans-methyl formate has been measured for the first time in the laboratory, and seven lines have now been detected in the interstellar medium using the publicly available PRIMOS survey from the NRAO Green Bank Telescope.     

E/Z conformation and the vibrational spectroscopy of Me2NN(O)=NOMe

The simple neutral diazenium diolate, O2-methyl-1-(N, N-dimethylamino)diazen-1-ium-1,2-diolate, [Me2NN(O)=NOMe], was experimentally examined by vibrational spectroscopy and the results compared to the theoretically calculated values in an effort to detect both Z and E conformers which result from the stereochemistry of the N=N multiple bond. Room-temperature Raman and infrared spectra were measured and the results compared with the values calculated theoretically with MP2 and density functional techniques (B3LYP). An analysis of the observed frequencies suggests that, down to a detection limit of about 1/1000, only a small quantity of trans (E) diazeniumdiolate, <0.05%, may be present at room temperature.     

Conformer assignment of OH stretches in ethanol and isopropanol

Rigid harmonic asymetric top contour simulation is applied to assign the OH stretch transitions observed in the vapour phase infrared spectra of ethanol and isopropanol to gauche and trans conformers. For hetanol, the high frequency ν(OH) absorption must be assigned to the trans, for isopropanol the high frequency absorption is found to be due to the gauche conformer.     

Vibrational and conformational analysis of chloromethyldifluorophosphine,ClCH2PF2

The vibrational spectra of chloromethyldifluorophosphine have been recorded in the different physical states. Both gauche and trans conformers are identified in the spectra. Temperature dependent studies and calculated dipole moments (CNDO/2) indicate that the gauche conformer is more stable in the gas-phase while the trans is more stable in the liquid phase. In the solid phase, both conformers are present, although the trans strongly dominates.     

Triplet electronic states in d(2) and d(8) complexes probed by absorption spectroscopy: a CASSCF/CASPT2 analysis of [V(H2O)6]3+ and [Ni(H2O)6]2+

Octahedral complexes of transition metal ions with d(2) and d(8) electron configurations have triplet electronic states with identical T(2g), A(2g), T(1g)((3)F), and T(1g)((3)P) symmetry labels. CASSCF and CASPT2 calculations indicate the predominant electronic configurations for each triplet state. The two (3)T(1g) states show strong configuration mixing in the d(8) complex [Ni(H(2)O)(6)](2+), but much weaker mixing occurs between these states in the d(2) compound [V(H(2)O)(6)](3+). Calculated vibrational frequencies and equilibrium geometries for the triplet states are used to obtain theoretical absorption spectra that are in agreement with the experimental data.     

ZEKE spectroscopy and theoretical calculations of copper-methylamine complexes

The copper-monomethylamine and -dimethylamine complexes were produced in a supersonic jet and examined using single-photon zero kinetic energy (ZEKE) photoelectron spectroscopy and theoretical calculations. The adiabatic ionization potentials (I.P.) of the complexes and vibrational frequencies of the corresponding ions were measured from their ZEKE spectra. The equilibrium geometries, binding energies, and vibrational frequencies of the neutral and ionized complexes were obtained from MP2 and B3LYP calculations. The observed vibrational frequencies of the ionic complexes were well-reproduced by both calculations, whereas the Franck-Condon intensity patterns of the spectra were simulated better by MP2 than B3LYP. The observed I.P. and vibrational frequencies of the Cu-NH(n)(CH3)(3-n) (n = 0-3) complexes were compared, and methyl substitution effects on their ZEKE spectra were discussed.     

Structure of proton disolvates formed in the acid hydrolysis of ethyl formate and methyl acetate

By the density functional method (B3LYP/6-31++G(d,p)) optimal structures of proton hetero and homo disolvates involving water molecules, ethyl formate, methyl acetate and products of their hydrolysis are calculated. The data on the structure of these ions and the strength of their H bonds are analyzed together with the results of a similar calculation previously performed for methyl formate. It is shown that in proton solvation by two molecules present in the solution during the hydrolysis of ethyl formate, methyl acetate, and methyl formate stable (X…H…X)⁺ or (X…H…Y)⁺ particles form. Structural and energy parameters of their O…H…O bridges obey the same regularities and are mainly determined by a difference in the proton affinity of X and Y molecules. Calculation results are compared to the data of a number of experimental studies of the acid hydrolysis of esters.     

Vibrational spectrum of glycine molecule

The infrared and Raman spectra of glycine molecule has been studied in spectral region 400-4000 cm(-1) in solid form as well as in water. The vibrational frequencies for the fundamental modes of the glycine in neutral and its zwitterionic form have also been calculated using AM1 semiempirical method as well as ab initio method with minimal basis set. The reliability of the minimal basis set and AM1 method with higher basis sets, for IR spectra of the neutral glycine conformers were examined. We find that the 6-21G basis set calculation yields structural parameters, rotational constant and dipole moment of glycine conformers, which are very similar to those obtained from extended basis set calculation as well as experimental values. IR frequencies for glycine conformer I are also calculated in water using SCRF=PCM model and compared with experimental values. A comparison between calculated frequencies for neutral glycine, and its zwitterionic form with observed IR and Raman bands have been made. The total energies for gas phase glycine and its zwitterionic form along with those of hydrated forms were also calculated. It is found from the calculations that in the gas phase neutral glycine is more stable as compared to its zwitterionic form.     

Electronic spectra of 1-methyl and 2-methyl phenanthrenes and their radical cations

Electronic spectra of phenanthrene (P), 1-methyl phenanthrene (1-MeP), 2-methyl phenanthrene (2-MeP) and their monopositive ions are investigated experimentally as well as theoretically. The ions were produced by photo-oxidation of the hydrocarbons in boric acid matrix. The electronic absorption spectrum of 2-methyl phenanthrene cation (2-MeP+) is entirely new. For the interpretation of the electronic spectra of neutral and ionized MePs, semi-empirical AM1 (Austin Model 1) calculations are carried out for the first time. The bathochromic shifts in the spectral bands of the neutral and ionized MePs are attributed to 'conjugative' effect. The present experiments reveal that the 448 nm band of 1-methyl phenanthrene cation (1-MeP+) and the 486 nm band of 2-MeP+ show close matching with the respective 450 nm and 488 nm 'diffuse interstellar bands'. This suggests the possibility of the existence of such ionic species in the interstellar matter.     

Theoretical and experimental study of the vibrational spectrum of N-acetyl-L-alanine

The energies, vibrational frequencies and IR intensities of cis- and trans-N-acetyl-L-alanine (NAAL) are computed using the density functional theory (B3LYP) combined with the 6-311G(d, p) basis set. The trans conformer is characterized by an intramolecular NH ... O hydrogen bond leading to the formation of a five-membered ring and is by 23 kJ mol(-1) more stable than the cis conformer. The difference between the vibrational frequencies and IR intensities computed for the two conformers is discussed. The IR spectra at different temperatures and the Raman spectra of solid NAAL and its deuterated counterpart are investigated and discussed. The frequencies of the v(OH) vibration and the isotopic ratio suggest the formation of short OH ... O hydrogen bonds in the solid state. The NH group seems also to be involved in a weak hydrogen bond.