Adsorption and vibrational spectroscopy of ammonia at mordenite: ab initio study

The adsorption of ammonia at various active centers at the outer and inner surfaces of mordenite, involving Br?nsted acid (BA) sites, terminal silanol groups, and Lewis sites has been investigated using periodic ab initio density-functional theory. It is shown that ammonia forms an ammonium ion when adsorbed at strong BA sites. The calculated adsorption energies for different BA sites vary in the interval from 111.5 to 174.7 kJ/mol depending on the local environment of the adduct. The lowest adsorption energy is found for a monodentate complex in the main channel, the highest for a tetradentate configuration in the side pocket. At weak BA sites such as terminal silanol groups or a defect with a BA site in a two-membered ring ammonia is H bonded via the N atom. Additional weak H bonds are formed between H atoms of ammonia and O atoms of neighboring terminal silanol groups. The calculated adsorption energies for such adducts range between 61.7 and 70.9 kJ/mol. The interaction of ammonia with different Lewis sites is shown to range between weak (DeltaE(ads)=17.8 kJ/mol) and very strong (DeltaE(ads)=161.7 kJ/mol), the strongest Lewis site being a tricoordinated Al atom at the outer surface. Our results are in very good agreement with the distribution of desorption energies estimated from temperature-programmed desorption (TPD) and microcalorimetry experiments, the multipeaked structure of the TPD spectra is shown to arise from strong and weak Br?nsted and Lewis sites. The vibrational properties of the adsorption complexes are investigated using a force-constant approach. The stretching and bending modes of NH(4) (+) adsorbed to the zeolite are strongly influenced by the local environment. The strongest redshift is calculated for the asymmetric stretching mode involving the NH group hydrogen bonded to the bridging O atom of the BA site, the shift is largest for a monodentate and smallest for a tetradentate adsorption complex. The reduced symmetry of the adsorbate also leads to a substantial splitting of the stretching and bending modes. In agreement with experiment we show that the main vibrational feature which differentiates coordinatively bonded ammonia from a hydrogen-bonded ammonium ion is the absence of bending modes above 1630 cm(-1) and in the region between 1260 and 1600 cm(-1), and a low-frequency bending band in the range from 1130 to 1260 cm(-1). The calculated distribution of vibrational frequencies agrees very well with the measured infrared adsorption spectra. From the comparison of the adsorption data and the vibrational spectra we conclude that due to the complex adsorption geometry the redshift of the asymmetric stretching is a better measure of the acidity of an active sites than the adsorption energy.     

Force fields of allylamine conformers as studied by an ab initio calculation and infrared spectroscopy

The quadratic force constants of the five possible conformers of allylamine were calculated by an ab initio MC method. The infrared spectra of this molecule in the gas phase were remeasured and analyzed on the basis of the calculated vibrational frequencies. A potential energy surface with respect to the skeletal torsions was also calculated. The relative abundances of the S⁺G⁺, ST, CT, CG, and S⁺G^? conformers, predicted to be 44:32:16:7:1 at room temperature, are consistent with the experimental data.     

Ab initio structures and vibrational analysis of the isoprene conformers

Complete gradient optimizations of the structures and the calculation of the harmonic force fields of the s-trans(anti) and gauche conformers of isoprene (2-methylbuta-1,3-diene) are reported at the RHF/6-31G level. The dihedral angle of the gauche conformer is found to be 41.0° from the planar s-cis(syn) form. The force fields obtained are refined using scale factors transferred from analogous calculations for trans-butadiene-1,3 and ethane. The direct vibrational problems are solved for both conformers of isoprene. A complete assignment of the experimental vibrational frequencies is given.     

An ab initio and DFT study of structure and vibrational spectra of disiloxane H3SiOSiH3 conformers. Comparison to experimental data

The structural and vibrational properties of siloxane monomers may account in the physical and chemical properties of silicone polymers. Because disiloxane (H(3)SiOSiH(3)) is the smallest molecule in the set which runs through small siloxanes like hexamethyldisiloxane (CH(3))3SiOSi(CH(3))3 to silicone polymers, its energetic, structural and vibrational features have been investigated in detail using density functional theory (B3LYP), post Hartree-Fock methods (MP2 and CCSD(T)) and basis sets up to spdfg quality. Five conformations were considered: three bent structures with C2v (double staggered, SS, and double eclipsed, EE, conformations) and Cs symmetries, and two linear forms with D3d and D3h symmetries. At all levels of theory, the relative stability was C2v(SS) approximately C2v(EE)>Cs>D3h>D3d. The difference of energy between the two C2v conformers is lower than 0.04 kcal/mol. At the highest level of theory (CCSD(T)/cc-pVQZ), the barrier to linearisation from C(2v) to D(3h) conformers was calculated at 0.43 kcal/mol, which is extremely low. Most of the structural and vibrational features of the disiloxane do not depend on the conformation of the molecule but are strongly influenced by the SiOSi angle. Anharmonic calculations allowed, without any scaling factor, an exhaustive reinvestigation of the assignments of observed wavenumbers in the infrared and Raman spectra of gaseous disiloxane. Particularly, in the gas phase spectrum, the SiOSi symmetric and antisymmetric stretches have been assigned at 599 and 1105, 596 and 1060, 527 and 1093 cm(-1) for H(3)SiOSiH(3), H(3)Si(18)OSiH(3) and D(3)SiOSiD(3), respectively. The experimental wavenumber splitting of SiOSi symmetric and antisymmetric stretches of H(3)SiOSiH(3) gave an estimation of the SiOSi angle at around 145 degrees . Ab initio methods were revealed more accurate for structural parameters, when DFT/B3LYP was enough for spectral assignments, even at the harmonic level using a single scaling factor.     

方酸构象和振动光谱的从头算研究

在6-31G^*^*水平上对方酸(3, 4-二羟基-3-环丁烯-1, 2-二酮)三种构象异构体进行了SCF计算。结果表明ZZ型异构体最稳定, ZE型次之。用等键反应能量分析方酸的稳定性, 并与苯作比较, 讨论方酸的芳香性。在6-31G水平上计算了方酸三种构象的振动频率。     

Addition of anions to carbonyl compounds: an ab initio study

Energies for the addition of anionic nucleophiles, Z(-), to carbonyl compounds, XYCO, are calculated at the G2(MP2) level of theory. The substituents X, Y, and Z are taken from the set {H, CH3, NH2, OH, F, CF3, CHCH2, CHO, CCH, and CN}. The basicity and, to a lesser extent, ionization potential of Z(-) were found to correlate with the enthalpy of addition of Z(-) to H2CO. The enthalpy of addition of Z(-) to XYCO relative to H2CO is largely independent of Z. The ordering of the enthalpies of addition for the series of XYCO's is rationalized. By using a thermodynamic cycle, the independence of this ordering from Z is attributed to the additivity of the inductive stabilization of XYZCO(-) by X and Y versus H2ZCO(-). A method for estimating the enthalpy of addition for nucleophile/carbonyl combinations not studied above is described and shown to give good results on a model system.     

l-Cysteine: Neutron spectroscopy, Raman, IR and ab initio study

Inelastic incoherent neutron scattering (IINS) spectra were obtained at 10K for normal and deuterated l-cysteine. Raman and infrared spectra were also recorded. Geometry of l-cysteine molecule was optimized for the zwitterion form using ab initio HF/6-31G* level. The theoretical frequencies of normal and d(4)-l-cysteine were compared with INS, Raman and IR spectra. Normal coordinate analysis and band assignments based on ab initio calculations and experimental data are presented.     

Relative Stability ofcis andtrans conformers of 2- and 3-fluorostyrene: An ab initio SCF-MO study

Ab initio SCF-MO calculations, mainly at the 6-31G F^* level with 3-21G F^* fully optimized geometries, were performed for 2- and 3-fluorostyrene in different comformations.Structures and conformational preferences of these molecules are compared with available data and discussed. It was found that the 2-fluorostyrene molecule has acis-trans energy difference of ca. 2.4 kJ mol^–1, showing a small barrier to planarity of 0.26 kJ mol^–1 in thetrans form. While the reduced stability of thecis form is mainly ascribed to a repulsive F ... vinyl group interaction, the partial loss of resonance stabilization between the ring and the vinyl group in the trans form and the H₆ ... H_c repulsive interaction in this form are taken to explain the local maximum at=180. In the 3-fluorostyrene molecule, thecis form is favored over thetrans by ca. 0.5 kJ mol^–1. An appreciable asymmetry of charge distribution found for thetrans form is assumed to slightly overweigh the difference in nuclear repulsion energy favorable to this conformation, thus explaining the observed relative stability.     

Matrix isolation infrared and ab initio studies on conformers of 3-fluoropropene

The infrared spectra of the cis and gauche conformers of 3-fluoropropene, CH₂CHCH₂F, were studied in Ne, Ar, Kr and Xe matrices. An infrared-induced cis to gauche rotamerization was found in Ar, Kr and Xe matrices. A thermal interconversion process was also found. Its direction was dependent upon the host, being the same as that of the IR process in Kr but reverse in Ar and Xe. In Ar and Xe matrices considerable site-splitting occurs in the IR spectra and a detailed analysis of the processes in different sites is given. An energy difference of 2.5±0.3 kJ mol⁻¹ between the cis and gauche species was obtained on assuming that the gas phase equilibrium between the conformers is trapped upon deposition. A slow dark process from cis to gauche conformer was observed in Kr matrices at temperatures above 15 K, possibly due to tunnelling. Ab initio calculations were carried out on 3-fluoropropene. The torsional potential energy curve and spectra of the conformers were calculated at the MP2(full)16-31G** level and were compared with the experimental results.     

The structure of linear SiCC: An ab initio SCF CI study including vibrational effects

Large-scale SCF CI calculations have been performed for the ground ¹Σ⁺ state of linear SiCC. The calculation includes up to quadruple excitations in the valence space plus all single and double excitations from the valence localized orbitals of the single HF configuration. Vibrational wavefunctions have been derived from the CI potential surface. Vibrational frequencies including anharmonicity corrections are calculated together with the zero-point vibrational correction to the rotational constant. The large dipole moment, 4.62 D, should make this molecule suitable for radioastronomic searches.     

Structural, vibrational and ab initio studies of L-histidine oxalate

Single crystals of L-histidine oxalate were obtained by slow evaporation of an aqueous solution at room temperature. The grown crystals have been subjected to X-ray diffraction (XRD), Infrared, and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2(1)2(1)2(1,) the crystal cohesion is achieved by relatively strong hydrogen bonds, so that the NH3 groups show significant distortion with respect to the tetrahedral symmetry. Raman and infrared spectra of the title compound were recorded in the frequency range 300-3200 and 400-4000 cm-1, respectively. To obtain a reliable assignment of the observed spectral lines, we have calculated the geometry and the frequencies of the vibrational modes of histidine cation and the oxalate anion using the semi empirical PM3 method.     

Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine

A full structural assignment of the conformers of gaseous tyrosine is presented. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and optimized at the B3LYP6-311G* level of theory and then subjected to further optimization at the B3LYP6-311++G** level. A total of 76 conformers are found and their dipole moments, rotational constants, and harmonic frequencies are determined. Accurate relative energies are given at the MP26-311G(2df,p)B3LYP6-311++G** level of theory. Characteristic H-bonding types are classified and listed for all the conformers. The four most stable conformers display an intramolecular H bond, COOH...NH(2), and an additional H-bonding interaction between the amino group and pi electron of the aromatic ring. The results further confirm that the global minimum conformations of the aromatic amino acids have the same H-bonding type. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperatures with which the theoretical results match that of experiments are indicated.     

The vibrational structure of the oxygen K-shell spectra in acenaphthenequinones: an ab initio study

The vibrational structure of the K-shell O1s → π? of acenaphthenequinone C(12)H(6)O(2) and its halogenated compound C(12)H(2)Br(2)Cl(2)O(2) has been simulated using an entirely ab initio approach. For both molecules, analysis of the calculated Franck-Condon factors confirm without ambiguity that, contrary to initial claims, the C-H stretching modes are not modified in the core states and are not excited. For C(12)H(6)O(2), the vibrational fine structure appears to be mainly due to three modes, involving C=O? asymmetric stretch and in-plane ring deformation modes, due to the symmetry breaking of the core state. For C(12)H(2)Br(2)Cl(2)O(2), the vibrational excitation arises essentially from the C=O? asymmetric stretch, with numerous secondary peaks arising from hot and combination bands. For both molecules, these bands are probably responsible for the asymmetry deduced in the experimental fits using a unique Morse potential and initially assigned to anharmonic effects.     

The vibrational spectrum of alpha-AlOOH diaspore: an ab initio study with the CRYSTAL code

The vibrational spectrum of alpha-AlOOH diaspore has been calculated at the B3LYP level of theory with a double-zeta quality Gaussian-type basis set by using the periodic ab initio CRYSTAL code. Harmonic frequencies at the Gamma point and the corresponding 48 normal modes are analyzed and classified in terms of simple models (octahedra modes, hydrogen stretching, bending, rotations) by direct inspection of eigenvectors, graphical representation, and isotopic substitution. Hydrogen modes are fully separated from the octahedra modes appearing under 800 cm(-1); bending modes are located in the range of 1040-1290 cm(-1), whereas stretching modes appear at 3130-3170 cm(-1). The available experimental IR and Raman spectra are characterized by broad bands, in some cases as large as 800 cm(-1), and individual peaks are obtained by decomposing these bands in terms of Lorentz-Gauss product functions; such a fitting procedure is affected by a relatively large degree of arbitrariness. The comparison of our calculated data with the most complete sets of experimental data shows, nevertheless, a relatively good agreement for all but the H modes; the mean absolute differences for modes not involving H are 10.9 and 7.2 cm(-1) for the IR and the Raman spectra, respectively, the maximum differences being 15.5 and 18.2 cm(-1). For the H bending modes, differences increase to 30 and 37 cm(-1), and for the stretching modes, the calculated frequencies are about 200 cm(-1) higher than the experimental ones; this is not surprising, as anharmonicity is expected to red shift the OH stretching by about 150 cm(-1) in isolated OH groups and even more when the latter is involved in strong hydrogen bonds, as is the case here.     

Detailed ab initio studies of the conformers and conformational distributions of gaseous tryptophan

A systematic and extensive conformational search has been performed to characterize the gas-phase tryptophan structures. A total of 648 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and were optimized at the DFT/B3LYP/6-311G* level of theory. A total of 45 local minima conformers were found. Further optimization of the 45 conformers with B3LYP and MP2/6-311++G** did not produce meaningful structural change, and accurate geometries, dipole moments, rotational constants, harmonic frequencies, and relative energies were then determined. Combined with statistical mechanics principles, the conformational distributions of gas-phase tryptophan at different temperatures are shown. The results clearly support the conclusion drawn by Compagnon et al. that only one dominant isomer existed in the molecular beam at 85 K and add further evidence that the supersonic jet expansion or embedding helium droplets did not produce an equilibrium distribution.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.     

Axial and equatorial hydrogen-bond conformers between (CH2)3S and H(D)F: Fourier transform infrared spectroscopy and ab initio calculations

The coexistence of axial and equatorial hydrogen-bonded conformers of 1?:?1 (CH(2))(3)S-HF (and -DF) has been observed in the same adiabatic expansion of a supersonic jet seeded with argon and in a static absorption cell at room temperature. High level calculations computed the axial conformer to be the most stable one with a small energy difference with respect to the equatorial one, in full agreement with previous microwave experiments. On the grounds of band contour simulations of FTIR spectra and ab initio energetic and anharmonic vibrational calculations, two pairs of ν(s) HF donor stretching bands, observed in a series of jet-FTIR spectra at 3457.9 and 3480.5 cm(-1) have been respectively assigned to the axial and equatorial forms of the 1?:?1 complex. In the jet-FTIR spectra series with HF, the assignment of an additional broad band (about 200 cm(-1) higher in frequency with respect to ν(s)) to a 1?:?2 complex has been supported by theoretical investigations. Experimental detection of both axial and equatorial forms of a cyclic trimer has been confirmed by calculated energetic and vibrational properties. The nature of hydrogen bonding has been examined within topological frameworks. The energetic partitioning within the 1?:?1 dimers has been elucidated with SAPT techniques. Interestingly, the interconversion pathway between two 1?:?1 structures has been explored and it was seen that the formation of the 1?:?1 complex affects the interconversion barrier on the ring puckering motion. The band contour analysis of gas phase FTIR experiments provided a consistent set of vibrational frequencies and anharmonic coupling constants, in good agreement with ab initio anharmonic vibrational calculations. Finally, from a series of cell-FTIR spectra recorded at different partial pressures of (CH(2))(3)S and HF monomers, the absorption signal of the 1?:?1 complex could be isolated which enabled to estimate the equilibrium constant K(p) = 0.023 at 298 K for the dimerization.     

IR-induced conformer interconversion processes of glycolaldehyde in low-temperature matrices,and ab initio calculations on the energetics and vibrational frequencies of the conformers

Both IR-induced and thermal conformer interconversion processes of glycolaldehyde (CHOCH₂OH) were studied in low-temperature Ar, Kr and Xe matrices. The observed photochemical reaction induced by broad-band IR irradiation is interpreted to proceed from the lowest-energy conformer Cc which prevails after deposition to conformer Tt. In Xe and Kr the photochemical steady state (ratio [Tt]/[Cc]) depends on the matrix temperature; two conformers, Tg and Tt, seem to be in thermal equilibrium, and at elevated temperatures species Tg is enriched, and then the reverse photoprocess Tg → Cc occurs more rapidly than the competing reverse process, Tt → Cc which prevails at 13 K. Because of the thermal equilibrium the routes of the forward and reverse photoprocesses are considered to be different. A thermal reverse process, Tt → Tg → Cc, is observed at temperatures above 30 K in Xe and Kr. The role of the torsional barrier heights in determining the rates of the photoprocesses is emphasized. To aid in the interpretation of the experimental results, ab initio calculations were carried out. Geometries and energies of all conformers of glycoaldehyde as well as the geometries of the most important saddle points were fully optimized at the HF/6-31G** level, and vibrational spectra were calculated on the HF/4-31G level; the latter conformed to the experimental conformer assignment.