Theoretical prediction of gas-phase infrared spectra of imidazo[1,2-a]pyrazinediones and imidazo[1,2-a]imidazo[1,2-d]pyrazinediones derived from glycine

Imidazo[1,2-a]pyrazine-3,6-diones and imidazo[1,2-a]imidazo[1,2-d]pyrazine-3,8-diones can be produced by pyrolysis of simple amino acids. While such bicyclic and tricyclic amidines were detected and characterized by IR spectroscopy for some alpha-substituted amino acids, the parent systems composed of glycine fragments are unknown up to now. IR spectra for five amidines derived from glycine were calculated by using different semi-empirical (PM3, AM1, MNDO and MINDO/3), HF, and hybrid DFT (B3LYP, B3P86 and B3PW91) methods in conjunction with 6-31G(d) basis set (for HF and DFT). Vibration frequencies in the experimental IR spectra were predicted based upon the B3LYP data, by correcting the calculated wavenumbers by a scaling factor of 0.959. The behavior of most characteristic bands (nu(CX), nu(NH), etc.) and their shifts with respect to such bands in the spectra of alanine and alpha-aminoisobutyric acid derivatives studied before, are discussed. Performance of the semi-empirical methods was tested, bearing in mind possible future needs for IR spectra predictions for larger molecular systems of similar chemical nature; the use of MINDO/3 and MNDO is recommended. A basis set effect on the B3LYP fundamental vibration frequencies for hexahydroimidazo[1,2-a]pyrazine-3,6-dione was studied by varying Pople basis sets from minimal STO-3G to 6-311++G(d, p). No significant improvements were found beyond the 6-31G(d) basis set, which thus can be recommended to predict IR spectra for the amidines and similar molecules.     

Potential energy distributions and potential scans for the internal rotation of two rotors in 3,3-dichloro and 3,3,3-trichloropropanals.

The conformational behavior and structural stability of 3,3-dichloropropanal and 3,3,3-trichloropropanal were investigated by ab initio calculations. The 6-311 + + G** basis set was employed to include polarization and diffuse functions in the calculations at B3LYP level. From the calculation, the trans conformer of 3,3,3-trichloropropanal was predicted to be the predominant conformer with about 2 kcal mol(-1) of energy lower than the cis form. Additionally, 3,3 dichloro-propanal was predicted to exist as a mixture of three stable conformers. The potential function scans were calculated for the two molecules from which the rotational barriers could be estimated. The vibrational frequencies were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations for the conformers of the two molecules. Vibrational Raman and infrared spectra of the mixture of the stable conformers were computed at 300 K.     

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.     

X-ray,vibrational spectra and density functional studies on cynacure

The solid-state X-ray diffraction, FT-IR and FT-Raman measurements of cynacure have been performed. Optimized molecular structures and normal vibrations of cynacure and 2-(methylthio)aniline have been calculated in the gas phase at the B3LYP/6-311++G** level. Scaling factors that bring computational gas-phase frequencies in closer agreement with the solid-state experimental data have been calculated for each vibration type. The observed IR and Raman bands of cynacure and 2-(methylthio)aniline have been assigned in the frameworks of the calculated mode frequencies as well as the calculated IR and Raman intensities. The assignments of the normal modes of cynacure have been compared with those of the benzene and 2-(methylthio)aniline modes. The effects of the substitution on the benzene vibrational frequencies have been investigated. 2-(Methylthio)aniline and cynacure both have four stable conformers. The calculated ground-state energetics and vibrational spectra of 2-(methylthio)aniline and cynacure suggest the coexistence of their stable conformers at the room temperature.     

An infrared study of solid glycine in environments of astrophysical relevance

The conversion from neutral to zwitterionic glycine is studied using infrared spectroscopy from the point of view of the interactions of this molecule with polar (water) and non-polar (CO(2), CH(4)) surroundings. Such environments could be found on astronomical or astrophysical matter. The samples are prepared by vapour-deposition on a cold substrate (25 K), and then heated up to sublimation temperatures of the co-deposited species. At 25 K, the neutral species is favoured over the zwitterionic form in non-polar environments, whereas for pure glycine, or in glycine/water mixtures, the dominant species is the latter. The conversion is easily followed by the weakening of two infrared bands in the mid-IR region, associated to the neutral structure. Theoretical calculations are performed on crystalline glycine and on molecular glycine, both isolated and surrounded by water. Spectra predicted from these calculations are in reasonable agreement with the experimental spectra, and provide a basis to the assignments. Different spectral features are suggested as probes for the presence of glycine in astrophysical media, depending on its form (neutral or zwitterionic), their temperature and composition.     

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.     

Vibrational spectra and rotational isomerism of bis(N-2-chloroethyl)nitramine

The IR and Raman spectra of bis(N-2-chloroethyl)nitramine (BCENA) in the liquid and crystalline states and in CCl₄ and CH₃CN solutions are studied. The spectra are compared, and it is concluded that BCENA exists as a mixture of conformers of different polarities in the liquid state and as one less polar conformer in the crystalline state. To determine the conformations corresponding to the total electron energy minima and interpret the vibrational spectrum of BCENA, we performed an ab initio quantum chemical calculation of the BCENA molecule in the Hartree-Fock approximation using the 3–21G* and 6–31G* basis sets. Out of twelve possible conformations five are stable; the most stable conformer is C₂(GG). The frequencies and forms of normal vibrations of stable conformers are calculated using scaled quantum chemical force fields. The calculated and experimental frequencies are compared, and the relations between the frequencies of skeletal stretching and bending vibrations are analyzed. It is concluded that the BCENA crystal is formed by the C₂ (GG) conformer. The vibrational spectrum is interpreted, and the frequencies are assigned to vibrations of conformers differing in form. Translated fromZhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 303–317, March–April, 1997.     

Accurate theoretical IR and Raman spectrum of Al2O2 and Al2O3 molecules

The accurate harmonic vibration frequencies together with the infrared (IR) and Raman intensities of the most stable conformers of Al₂O₂ and Al₂O₃ molecules have been calculated by the density functional theory (DFT) method with B3LYP exchange–correlation potential and using a set of the augmented correlated consistent basis sets up to quintuple order. The anharmonic vibration frequencies of the non-linear Al₂O₂ molecule have also been calculated. The obtained equilibrium geometrical parameters, harmonic and anharmonic vibration frequencies along with the IR and Raman intensities good converge to their limits with increasing the size of the used basis set. A comparison of the calculated harmonic and anharmonic vibrational frequencies with the available experimental ones points out that the small differences between the calculated harmonic and experimental frequencies can be further substantially reduced when calculations of the anharmonic vibrational frequencies will be available for all types of molecular geometries.     

Infrared photodissociation spectroscopy of electrosprayed ions in a Fourier transform mass spectrometer

Previous gas-phase methods for infrared photodissociation spectroscopy (IRPD) require sample volatility. Our method instead uses electrospray ionization to introduce even large nonvolatile molecules into a Fourier transform mass spectrometer, where extended (>15 s) ion storage makes possible high sensitivity spectral measurements with an OPO laser over a range of 3050-3800 cm(-1). The spectra of 22 gaseous proton-bound amino acid complexes are generally correlated with the H-stretching frequencies established for O-H and N-H functional groups in solution. For theoretical structure predictions of the Gly2H+ and N-acylated Asp2H+ dimers, IRPD spectra clearly differentiate between the predicted lowest energy conformers. In contrast to solution, in the gas phase the glycine zwitterion is approximately 20 kcal/mol less stable than the neutral; however, glycine is clearly zwitterionic in the gaseous GlyLysH+ dimer. The level of theory is inadequate for the larger Lys2H+ dimer, as all low energy predicted structures have free carboxyl O-H groups, in contrast to the IR spectrum. IRPD appears to be a promising new technique for providing unique information on a broad range of biomolecular and other gaseous ions, especially on noncovalent bonding involving O-H and N-H groups.     

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm(-1) and 50-3500 cm(-1), respectively. In addition, the IR spectra in CCl(4) at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.     

Simulation of the Raman spectra of zwitterionic glycine + nH2O (n = 1, 2, …, 5) by means of DFT calculations and comparison to the experimentally observed Raman spectra of glycine in aqueous medium

Raman spectra of an aqueous solution of glycine (Gly) have been recorded in the range of 400-2000 cm⁻¹. In aqueous solution, glycine molecules exist in their zwitterionic form, having two opposite charged poles, COO⁻ and NH₃⁺. The zwitterionic structure of glycine (ZGly) is stabilized by the hydrogen bond interaction of water (W) molecules. In the present report, we have optimized the ground state geometries of different hydrogen bonded complexes of [ZGly + (W)_n=1-5] in aqueous medium using DFT calculations at the B3LYP/6-311++G(d) level of theory. A comparative discussion on the structural details and binding energies (BEs) of each conformer has been also done. The theoretical Raman spectra were calculated corresponding to the most stable [ZGly + (W)_n=1-5] conformers. The theoretically simulated Raman spectra of each stable conformer were compared with experimentally observed Raman spectra to explore the number of water molecules needed for stabilizing the structure of ZGly. The theoretically simulated Raman spectra corresponding to the most stable conformer of [ZGly + (W)₅] having a BE of −22.8 kcal/mol, are matching nicely with the experimentally observed Raman spectra. Thus, on the basis of the above observations, we conclude that the conformer, [ZGly + (W)₅] is the most probable conformer in the aqueous medium. We also believe that in the conformer, [ZGly + (W)₅] the five water molecules are arranged around the ZGly in such a way that the effect of steric hindrance is less compared to the other conformers. The dipole-dipole interaction potential (DDP) is also calculated corresponding to the strongest hydrogen bond for each [ZGly + (W)_n=1-5] conformer.     

Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene

In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.     

Conformational search for zwitterionic leucine and hydrated conformers of both the canonical and zwitterionic leucine using the DFT-CPCM model

The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.     

Conformational dependence of Raman frequencies and intensities in alkanes and polyethylene

Raman vibrational frequencies and intensities of octane, dodecane and hexadecane conformers have been calculated using quantum mechanical ab initio methods. The results agree with various trends observed in the experimental spectra of alkanes, as well as several observations from the experimental Raman spectra of polyethylenes. The present data suggest that ab initio calculated Raman data on alkanes provide valuable information regarding the interpretation of polymer Raman spectra, in particular concerning issues where interpretation based on experimental verification is not possible.     

Conformational stability and vibrations of aminopropylsilanol molecule

Density functional theory (DFT), using the B3-LYP/6-31G(d,p) method have been used to investigate the conformation and vibrational spectra of aminopropylsilanetriol (APST) NH2CH2CH2CH2Si(OH)3. The potential function for CCCSi torsion gives rise to two distinct conformers trans and gauche. The predicted energy of the more stable trans conformer is 337 cm-1 less than the energy of gauche conformer. The calculated barriers to the conformation interchange are: 1095, 2845 and 438 cm-1 for the trans to gauche, gauche to gauche and gauche to trans conformers, respectively. For the trans conformer the potential energy curve for the Si(OH)3 groups torsion in APST has been calculated changing the HOSiC dihedral angle. The barrier for the internal rotation of 3065 cm-1 has been obtained. The optimized molecular structure of APST dimer calculated for trans conformer has a SiOSi angle of 143.2 degrees, and a SiOSi bond length of 0.164 nm. A complete vibrational assignment for both conformers as well as for trans-dimer is supported by the normal coordinate analysis, calculated IR intensities as well as Raman activities. On the basis of the results, the vibrational spectra of APST aqueous solution and APST polymer have been analyzed. The average error between the observed and calculated frequencies is 14 cm-1.     

FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine

The Fourier transform Raman and Fourier transform infrared spectra of 5-bromo-2-nitropyridine were recorded in the solid phase. The equilibrium geometry, natural atomic charges, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. A detailed interpretations of the infrared and Raman spectra of 5-bromo-2-nitropyridine is reported on the basis of the calculated potential energy distribution (PED). The theoretical spectrograms for the Raman and IR spectra of the title molecule have been constructed.     

FT-IR, FT-Raman spectra and ab initio DFT vibrational analysis of p-bromophenoxyacetic acid

The Fourier transform Raman and Fourier transform infrared spectra of p-bromophenoxyacetic acid were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) method with the 6-31G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of p-bromophenoxyacetic acid is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

IR Low‐Temperature Matrix and ab Initio Study on β‐Alanine Conformers

For the first time the argon‐matrix low‐temperature FTIR spectra of β‐alanine are recorded. They reveal a quite complicated spectral pattern which suggests the presence of several β‐alanine conformers in the matrix. To interpret the spectra, the eighteen β‐alanine conformers, stable in the gas phase, are estimated at the B3LYP and MP2 levels combined with the aug‐cc‐pVDZ. Ten low‐energy structures are reoptimized at the QCISD/aug‐cc‐pVDZ and B3LYP and MP2 levels by using the aug‐cc‐pVTZ basis sets. Assignment of the experimental spectra is undertaken on the basis of the calculated B3LYP/aug‐cc‐pVDZ anharmonic IR frequencies as well as careful estimation of the conformer population. The presence of at least three β‐alanine conformers is demonstrated. The detailed analysis of IR spectra points to the possible presence of five additional β‐alanine conformers.     

Vibrational spectra of pyrazole in various aggregate states and their interpretation

The selection of the fundamental frequencies of pyrazole and the assignment of them to various types of vibrations were made on the basis of a comparison of the IR and Raman spectra of pyrazole and some of its isotopically substituted derivatives in various aggregate states and in the form of complexes with CdCl₂. The assignment was confirmed by prior calculation of the frequencies and forms of the vibrations of pyrazole.     

Experimental and theoretical studies on vibrational spectra of 4-(2-furanylmethyleneamino)antipyrine, 4-benzylideneaminoantipyrine and 4-cinnamilideneaminoantipyrine

This work deals with the IR and Raman spectroscopy of 4-(2-furanylmethyleneamino) antipyrine (FAP), 4-benzylideneaminoantipyrine (BAP) and 4-cinnamilideneaminoantipyrine (CAP) by means of experimental and quantum chemical calculations. The equilibrium geometries, harmonic frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-31G(d) basis set. The comparisons between the calculated and experimental results covering molecular structures, assignments of fundamental vibrational modes and thermodynamic properties were investigated. The optimized molecular geometries have been compared with the experimental data obtained from XRD data, which indicates that the theoretical results agree well with the corresponding experimental values. For the three compounds, comparisons and assignments of the vibrational frequencies indicate that the calculated frequencies are close to the experimental data, and the IR spectra are comparable with some slight differences, whereas the Raman spectra are different clearly and the strongest Raman scattering actives are relative tightly to the molecular conjugative moieties linked through their Schiff base imines. The thermodynamic properties (heat capacities, entropies and enthalpy changes) and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized strucutres.