Matrix-isolation FT-IR study and theoretical calculations of the vibrational, tautomeric and H-bonding properties of hypoxanthine

The neutral compound hypoxanthine is investigated using the technique of matrix-isolation FT-IR spectroscopy combined with density functional theory (DFT) and ab initio methods. Two theoretical methods (RHF and DFT/B3-LYP) are compared for vibrational frequency prediction, and four methods (RHF//RHF, MP2//RHF, DFT//DFT and MP2//DFT) for prediction of the relative energies of the tautomers and the interaction energies of the complexes. All the possible tautomeric forms have been considered theoretically, and the results indicate that two oxo forms (O17 and O19) and one hydroxy form (H9-r1) are the three most stable forms. The experimental FT-IR spectra are consistent with this prediction, and nearly all the characteristic spectral features of these forms have been identified in the spectrum. A theoretical study of the H-bonded complexes of these three tautomers with water is also performed. Several structures have been found for each form and the results demonstrate that the closed complexes with two H-bonds are the most stable systems due to the H-bond cooperative effect.     

Matrix-isolation FT-IR and DFT theoretical studies of the intramolecular hydrogen bonding in Mannich bases

FT-IR Ar-matrix isolated spectra were studied for dichloro- (Cl₂-MB) and tetrachloroderivatives (Cl₄-MB) of the ortho Mannich base. The spectra were analyzed based on the DFT calculated frequencies and intensities and compared with those recorded in CCl₄ solution in the region of the ν(OH) and ν(OD) vibrations. The matrix-isolated spectra are characterized by narrower ν(OH) and ν(OD) bands with much better resolved fine structure than in solution. The fine structure originates from the anharmonic coupling with the low frequency modes as well as from Fermi resonance. The ν(OD) band shapes can be reproduced exclusively by assuming the Fermi resonance with overtones and summation of the frequencies of modes into which the bridge atoms are involved. The frequency isotopic ratio (ISR) is for both compounds 1.33 while the half-width ratios are equal to 1.82 and 1.94, for Cl₂-MB and Cl₄-MB, respectively.     

Matrix-isolation spectra of chlorine nitrate

High-resolution FTIR-isolation spectra of chlorine nitrate in nitrogen and argon matrices have been studied and a full analysis based on planar ClONO₂ and known impurities carried out. No evidence for isomers of ClONO₂ has been found; if present, their concentrations must be less than 1% of parent ClONO₂.     

Matrix-isolation FT-IR and theoretical investigation of the competitive intramolecular hydrogen bonding in 5-methyl-3-nitro-2-hydroxyacetophenone

The paper presents the conformational, vibrational and hydrogen bond characteristics of 5-methyl-3-nitro-2-hydroxyacetophenone studied with the combined matrix-isolation FT-IR spectroscopic and theoretical (DFT/B3LYP/6-31++G^**) technique. Theoretical calculations predict three stable conformations of the studied compound. Only two of these conformations could be identified experimentally using the matrix-isolation FT-IR technique. The conformation with the intramolecular hydrogen bond OH^…ON has been found to be more stable than the conformation with the OH^…OC type of hydrogen bond by 7.28 kJ/mol. The complete assignment of the experimental spectra could be performed based on the theoretical calculations including the normal coordinate analysis and isotopic substitution.     

Matrix-isolation study and ab initio calculations of the structure and spectra of hydroxyacetone

The structure of hydroxyacetone (HA) isolated in an argon matrix (at 12 K) and in a neat solid phase (at 12-175 K) was characterized by using infrared (IR) spectroscopy. The interpretation of the experimental results was supported by high-level quantum chemical calculations, undertaken by using both ab initio (MP2) and density functional theory methods. A potential-energy surface scan, carried out at the MP2/6-311++G(d,p) level of theory, predicted four nonequivalent minima, Cc, Tt, Tg, and Ct, all of them doubly degenerate by symmetry. The energy barriers for conversion between most of the symmetrically related structures and also between some of the nonequivalent minima (e.g., Tg --> Tt and Ct --> Tt) are very small and stay below the zero-point vibrational level associated with the isomerization coordinate in the higher-energy form in each pair. Therefore, only Cc and Tt conformers have physical significance, with populations of 99 and 1%, respectively, in gas phase at room temperature. For the matrix-isolated compound, only the most stable Cc conformer was observed. On the other hand, the polarizable continuum model calculations indicated that in water solution, the population of Tt and Ct conformers might be high enough (ca. 6 and 11%, respectively) to enable their experimental detection, thus supporting the conclusions of a previous IR spectroscopy study [ Spectrochim. Acta A 2005, 61, 477] in which the presence of more than one HA conformer in aqueous solution was postulated. The signatures of these minor conformers, however, do not appear in the spectra of the neat HA crystal, and the crystal structure was rationalized in terms of centrosymmetric hydrogen-bonded dimers consisting of two Cc-like units. Finally, we calculated (1)H, (13)C, and (17)O NMR chemical shifts at different levels of theory and found them to agree with available experimental data.     

FT-IR and FT-Raman vibrational spectra and molecular structure investigation of nicotinamide: A combined experimental and theoretical study

In this work, the experimental and theoretical spectra of nicotinamide (C₆H₆N₂O) are studied. FT-IR and FT-Raman spectra of title molecule in the liquid phase have been recorded in the region 4000–100 cm^?1. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree–Fock and density functional method (B3LYP) with the 6-31+G*(d, p) and 6-31++G* (d, p)basis set. The vibrational frequencies have been calculated and scaled values have been compared with the experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found in good agreement. The DFT-B3LYP/6-31++G (d, p) calculations have been found are more reliable than the ab initio HF/6-31+G (d, p) calculations for the vibrational study of nicotinamide. The optimized geometric parameters (bond lengths and bond angles) are compared with experimental values of the molecule. The alteration of vibrational bands due to the substitutions in the base molecule is also investigated from their characteristic region of linked spectrum.     

Matrix-isolation FT-IR spectroscopic study and theoretical DFT(B3LYP)/6-31++G** calculations of the vibrational and conformational properties of tyrosine

The complicated conformational isomerism of tyrosine is studied by experimental matrix-isolation FT-IR spectroscopy combined with theoretical DFT(B3LYP)/6-31++G** calculations. Not less than 18 possible conformations of tyrosine have been considered theoretically. The results revealed that the most and the less stable forms of neutral tyrosine have the same conformation of the main part of amino acid (conformation II) but they differ in orientation of the phenyl ring. The calculated values of the relative energies suggest that all conformations would be detectable in the experimental spectrum. However, it appeared that it is not possible to distinguish in the experimental spectrum between the bands due to the forms with the same conformation of the main part of amino acid but a different orientation of the phenol ring.     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been recorded in the region 4000–400 cm⁻¹ and 3500–50 cm⁻¹, respectively. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

Matrix isolation FTIR spectroscopic and theoretical study of dimethyl sulfite

The preferred conformations of dimethyl sulfite and their vibrational spectra were studied by matrix-isolation Fourier transform infrared spectroscopy and theoretical methods (density functional theory (DFT) and Moller-Plesset (MP2), with basis sets of different sizes, including the quadruple-zeta, aug-cc-pVQZ basis). Five minima were found at these levels of theory. At the MP2/6-31++G(d,p) and DFT/B3LYP/aug-cc-pVQPZ levels, the GG conformer (where the O-S-O-C dihedral angles are 73.2 and 70.8 degrees ) resulted in the conformational ground state. At the highest level of theory used, the GT conformer (O-S-O-C = +68.5 and -173.2 degrees ) is 0.83 kJ mol(-1) higher in energy than the GG form, while conformer GG' (O-S-O-C = +85.7 and -85.7 degrees ) has a relative energy of 1.18 kJ mol(-1). The remaining two conformers (G'T and TT) are high-energy forms and not experimentally relevant. In consonance with the theoretical predictions, conformer GG was found to be the most stable conformer in the gaseous phase as well as in the low-temperature matrices. Annealing of the argon matrices first promotes the GG'-->GT isomerization, which is followed by conversion of GT into the most stable conformer. There is no evidence of occurrence of GG'-->GG direct conversion in the low-temperature matrices. On the other hand, during deposition of the xenon matrices conformer GG' totally converts to conformer GT. Two observations demonstrated this fact: no evidence of bands corresponding to GG' were observed in xenon matrices and the GG/GT intensity ratio became similar to the GG/(GT + GG') intensity ratio observed in argon matrices. All these results could be explained by taking into account the relative values of the theoretically predicted energy barriers for the different isomerization processes: GG'-->GT, 1.90 kJ mol(-1); GT-->GG, 9.64 kJ mol(-1); and GG'-->GG, 19.46 kJ mol(-1).     

Density functional theory study of the FT-IR spectra of phthalimide and N-bromophthalimide

Fourier transform infrared (FT-IR) spectra of phthalimide and N-bromophthalimide have been recorded in the range of 4000-400 cm-1. With the hope of providing more and effective information on the fundamental vibrations, a normal coordinate analysis has been performed on phthalimide and N-bromophthalimide, by assuming C2v symmetry. Density functional theory (DFT)-Beck3-Lee-Yang-Parr (B3LYP) levels with 6-31G* and 6-311+G** basis sets have been employed in quantum chemical analysis. The computational frequencies are in good agreement with the observed results. The theoretical spectra obtained along with intensity data agree well with the observed spectra.     

Preparation and FT-IR spectra of calcium bilirubinate

In this investigation two calcium bilirubinates compounds, Ca(HBR)₂·H₂O and Ca(BR)·2H₂O, were prepared. Their Fourier transform infrared spectra were measured in KBr discs and in fluorolube and nujol mulls, respectively. The results suggest that it is better to identify the Ca(HBR)₂·H₂O and Ca(BR)·2H₂O with fluorolube and/or nujol mulls when examining mixtures (e.g. gallstone).     

Solid-state vibrational spectra and theoretical study of alaninamide acetate

Solid-state IR and Raman spectroscopic elucidation of alaninamide acetate is preformed by means of the possibilities of linear-polarized IR and Raman methods. The experimental assignment is compared with theoretical vibrational analysis with the intention to explain the influence of intermolecular interactions in solid phase on the spectroscopic properties of the compound studied. The 1H and ¹³C NMR spectra in solution are compared with the corresponding ones of alanine, studying the amidation effect on the chemical shift signals in the alanine moieties.     

FT-IR and NMR investigation of 1-phenylpiperazine: a combined experimental and theoretical study

FT-IR and (1)H, (13)C, DEPT, COSY, NOESY, HETCOR, INADEQUATE NMR spectra of 1-phenylpiperazine (pp) have been reported for the first time except for its (1)H NMR spectrum. The vibrational frequencies and (1)H, (13)C NMR chemical shifts of pp (C(10)H(14)N(2)) have been calculated by means of the Hartree-Fock (HF) and Becke-Lee-Yang-Parr (BLYP) or Becke-3-Lee-Yang-Parr (B3LYP) density functional methods with 6-31G(d) and 6-31G(d,p) basis sets, respectively. Comparison between the experimental and the theoretical results indicates that density functional B3LYP method is superior to the scaled HF and BLYP approach for predicting vibrational frequencies and NMR properties.     

Matrix-isolation infrared spectroscopic and theoretical studies on reactions of laser-ablated germanium atoms with water molecules

Laser-ablated germanium atoms have been codeposited at 4 K with water molecules in excess argon. Adduct and insertion products, such as Ge(H2O), HGeOH, HGeO, H2GeO, GeOH, Ge(OH)2, HGeOGeH, and HGeGeO, have been formed in the present experiments and characterized by using infrared spectroscopy on the basis of the results of the isotopic shifts, mixed isotopic splitting patterns, stepwise annealing, change of reagent concentration and laser energy, and comparison with theoretical predictions. Density functional theory calculations have been performed on these molecules and the corresponding transition states. The agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts supports the identification of these molecules from the matrix infrared spectra. Plausible reaction mechanisms have been proposed to account for the formation of these molecules.     

FT-IR, FT-raman and SERS spectra of L-proline

IR, Raman and surface-enhanced Raman scattering (SERS) spectra of L-proline were recorded and analyzed. The molecular plane assumes a tilted orientation with respect to the metal surface. The vibrational wavenumbers and corresponding vibrational assignments are examined theoretically using the Gaussian 03 set of quantum chemistry codes.     

FT-IR spectra of proteins at low temperatures

Infrared spectra of several globular proteins have been recorded in fluid solutions (hydro-alcoholic mixtures) in the temperature range –110° C to 30° C. In the case of hemoglobin, which has a highly ordered secondary structure, smaller spectral changes are observed which are compatible with distortions of its helices. In contrast to this,-casein, a protein with mostly unordered structure, undergoes a much larger change whereby low temperature induces folding of the protein chains.Issued as NRCC No. 28929     

The vibrational spectra and structures of dimethyl oxaloacetate and dimethyl oxaloacetate-d2

The complete vibrational spectra of dimethyl oxaloacetate and dimethyl oxaloacetate-d₂ have been recorded and analyzed. The i.r. spectra were recorded at liquid N₂ as well as ambient temperature. Tentative vibrational assignments are proposed based on an enol structure in the crystalline phase. In solution, dimethyl oxaloacetate exists as a tautomeric mixture of keto and enol forms. Evidence for the existence of different enol conformers in CCl₄ and CS₂ solutions is also presented.     

A theoretical study of the UV spectra of dithienyls and thiophene

A calculation by the self-consistent MO method of the UV spectra of thiophene, 2,2′-, 3,3′-, and 2,3′-dithienyl is described. For the dithienyls the local energy method developed by Longuet-Higgins and Murrell is applied. Only the π-electrons are considered explicitly and the zero differential overlap approximation is used. Values are given for the transition energies and oscillator strengths of thiophene, the dithienyls and some cyclopentadithiophenes, and for the angles of twist of the dithienyls in non-polar solution. For thiophene a reasonable charge distribution is obtained and the bond-orders lead to bond lengths in good agreement with experiment.     

A theoretical study of the electronic spectra of pyridine and phosphabenzene

The electronic excitation spectra of pyridine and phosphabenzene have been studied using theoretical methods. The electronic states are described by wave functions derived from second-order perturbation theory based on multiconfigurational reference functions. The study includes singlet and triplet valences excited states as well as a number of Rydberg states. For both molecules the transition energies to the two lowest * excited singlet states are known from experiment and reproduced with an accuracy of 0.15 eV or better, while then * transition energies are predicted with a somewhat uncertain error of about 0.2 eV. The calculations suggest the lowestn * transition detected experimentally in pyridine corresponds to an adiabatic transition. 43 electronic states have been determined in each of the molecules.