Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.     

Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C₃H₇N₆⁺·C₈H₅O₄⁻) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000–100 cm⁻¹ region where the theoretical evaluation and assignment of all observed bands were made.     

Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

Molecular structure and vibrational assignment of 2-,4-,6-methylquinoline by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments of 2-,4-,6-methylquinoline (2-,4-,6-mq) in the ground state were performed by HF and DFT/B3LYP levels of theory using the 6-31++G(d,p) basis set. Harmonic and anharmonic vibrational frequencies were calculated. 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 by using parallel quantum mechanic solutions program. The general agreements between the observed and calculated frequencies are shown.     

Molecular structure, IR and NMR spectra of 2,6 distyrylpyridine by density functional theory and ab initio Hartree-Fock calculations

Vibrational frequencies and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of 2,6 distyrylpyridine (C21H17N) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. These methods are proposed as a tool to be applied in the structural characterization of 2,6 distyrylpyridine (C21H17N). The title compound has C2v point group, thus providing useful support in the interpretation of experimental IR data. In addition, obtained results were related to the linear correlation plot of experimental 13C NMR, 1H NMR chemical shifts values and IR data.     

Molecular structure, vibrational and chemical shift assignments of 8-hydroxy-1-methylquinolinium iodide hydrate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, (1)H and (13)C NMR chemical shift values of 8-hydroxy-1-methylquinolinium iodide monohydrate [(C(10)H(10)NO)(+)I(-)H(2)O] in the ground state were performed by HF and B3LYP levels of theory using the LanL2DZ basis set. The optimized bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by HF and DFT methods, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The title compound [(C(10)H(10)NO)(+)I(-)H(2)O] have been studied theoretically in the 4, 000-200 cm(-1) region and the assignment of all the observed bands were made. The analysis of the infrared spectra indicates that there are some structure-spectra correlations. These methods are proposed as a tool to be applied in the structural characterization of 8-hydroxy-1-methylquinolinium iodide monohydrate [(C(10)H(10)NO)(+)I(-)H(2)O], and thus providing useful support in the interpretation of experimental NMR data.     

Molecular structure and vibrational analysis of 3-Ethylpyridine using ab initio HF and density functional theory (B3LYP) calculations

The FT-Raman and FT-IR spectra for 3-Ethylpyridine (3-EP) have been recorded in the region 4000-100 cm(-1) and compared with the harmonic vibrational frequencies calculated using HF/DFT (B3LYP) method by employing 6-31G(d,p) and 6-311++G(d,p) basis set with appropriate scale factors. IR intensities and Raman activities are also calculated by HF and DFT (B3LYP) methods. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values of some substituted benzene. The experimental geometrical parameters show satisfactory agreement with the theoretical prediction from HF and DFT. The scaled vibrational frequencies at B3LYP/6-311++G(d,p) seem to coincide with the experimentally observed values with acceptable deviations. The theoretical spectrograms (IR and Raman) have been constructed and compared with the experimental FT-IR and FT-Raman spectra. Some of the vibrational frequencies of the pyridine are effected upon profusely with the C2H5 substitutions in comparison to pyridine and these differences are interpreted.     

Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods

Ab initio and density functional theory (DFT) calculations were performed for obtaining fundamental vibrational frequencies of methylamine, CH3NH2, and its deuterated variants CH3ND2, CD3NH2, and CD3ND2. The calculations were carried out using the CCSD(T) coupled cluster approximation with cc-pVTZ and cc-pVQZ basis sets, and by the DFT method with the semiempirical hybrid functional B97-1 with polarization consistent pc-2 and pc-3 basis sets. Reasonable performance of the DFT harmonic and ab initio harmonic calculations was found, which improved considerably upon combination of the harmonic fundamental frequencies with anharmonic corrections from the smaller, pc-2, basis. The computed anharmonic fundamental frequencies of methylamine isotopologues agree very well with the experimental values and represent a useful tool for assignment and analysis of the dominant resonances.     

Molecular structure and vibrational spectra of indole and 5-aminoindole by density functional theory and ab initio Hartree–Fock calculations

The molecular geometry and vibrational frequencies of indole and 5-aminoindole in the ground state have been calculated by using the Hartree–Fock and density functional method with 6-311++G(d,p) basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of indole and 5-aminoindole with the calculated results by density functional and Hartree–Fock methods indicates that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems. The theoretical spectrograms for FT-IR spectrum of 5-aminoindole have been constructed.     

FT-IR, NIR-FT-Raman and gas phase infrared spectra of 3-aminoacetophenone by density functional theory and ab initio Hartree-Fock calculations

The gas phase infrared spectrum of 3-aminoacetophenone (3AAP) was measured in the range 5000-500cm(-1) and with a resolution of 0.5cm(-1). The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 3AAP were recorded in the solid phase. Geometry optimizations were done without any constraint and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and density functional theory (DFT) levels invoking 6-311G(2df 2p) basis set and the results are compared with the experimental values. Harmonic-vibrational wavenumber was also calculated for the minimum energy conformer at ab initio and DFT levels using 6-31G(d,p) basis set and the results are compared with related molecules. With the help of specific scaling procedures, the observed vibrational wavenumbers in gas phase, FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrogram for the FT-IR spectra of the title molecule is also constructed.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-mercaptopropanoic acid

2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.     

Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions

Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.     

Analysis of the vibrational spectra of 1-methyluracil and its isotopic derivatives by ab initio calculations

The vibrational spectrum of 1-methyluracil trapped in an argon matrix has been analysed based on ab initio Hartree—Fock SCF calculations with a split-valence 4–21 basis set. The directly computed theoretical harmonic force field was scaled with empirical scale factors which were transferred from uracil (except for the methyl vibrational modes) to provide an a priori prediction of fundamental frequencies and intensities. The average deviations between experiment and prediction were 9.8 cm⁻¹ for the in-plane vibrations and 18.3 cm⁻¹ for the ring out-of-plane modes. After a few corrections of assignment of the observed spectrum, a new set of scale factors was optimized to give the best force field available from combined consideration of the experimental and theoretical information. These scale factors reduced the average deviations to 6.7 cm⁻¹ for the in-plane modes and to 11.7 cm⁻¹ for the out-of-plane ones. The vibrational spectra of seven isotopic derivatives (-2¹⁸0, -4¹⁸0, -3d, -5d, -6d, -5, 6d₂ and -CD₃) of 1-methyluracil were predicted with the force field resulting from the optimized set of scale factors, and compared with the crystal-phase experimental data. A few misassignments in the experimental isotopic spectra have been corrected. Vibrational absorption intensities have been computed and compared with experiment and with an earlier calculation.     

Structure and vibrational frequencies of 1-naphthaldehyde based on density functional theory calculations

The mid and far FTIR and Raman spectra were measured in the liquid state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) and standard B3LYP/6-311+G** basis set combination. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical (SQM) force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Unambiguous vibrational assignment of all the fundamentals was made using the total energy distribution (TED).     

Modeling structures and vibrational frequencies for dinitrosyl iron complexes (DNICs) with density functional theory

The biochemical and physiological importance of nitric oxide (NO) in signaling and vasodilation has been studied for several decades. The discovery of both protein-bound and free low molecular weight dinitrosyl iron complexes (DNICs) suggests that such compounds might play roles in biological NO storage and transport. These complexes have important distinguishing spectroscopic features, including EPR and M?ssbauer spectra, and NO vibrational frequencies (ν((NO))). The latter are particularly sensitive to modifications of the ligand environment and metal oxidation states. Examinations of functionals and basis sets delineate their effect on the NO vibrational frequencies and allow development of a methodology to calculate these frequencies in other DNICs. Three complexes of the form (L)(CO)Fe(NO)(2) (L = CO, N,N'-dimethyl-imidazol-2-ylidene (IMe) or 1-methylimidazole (MeImid)), where {Fe(NO)(2)}(10) is in its reduced form, have been used to calibrate the vibrational frequencies. The functional BP86 paired with a basis set of SDD/ECP on the metal and 6-311++G(d,p) on the ligand atoms exhibits the most accurate results, with deviations from experimental vibrational frequencies of no more than ±40 cm(-1). Subsequent investigations were performed on a series of diiron trinitrosyl complexes of the form {Fe(NO)}(7)-{Fe(NO)(2)}(9) bridged by sulfurs, namely, [(ON)Fe(μ-S,S-C(6)H(4))(2)Fe(NO)(2)](-), [Fe(NO)(2){Fe(NS(3))(NO)}-μ-S,S'], and [(ON)Fe(bme-dach)Fe(NO)(2)-μ-S,S'](+), with the ideal functional/basis set pair determined via the aforementioned test set. The ground state energetics (singlet/triplet/singlet, respectively), geometric parameters, and nitrosyl vibrational frequencies were calculated. The results for the former two complexes correlated well with the experimental work, and in contrast with what was reported in an earlier computational study, a stable triplet ground state structure was optimized for [Fe(NO)(2){Fe(NS(3))(NO)}-μ-S,S']. For [(ON)Fe(bme-dach)Fe(NO)(2)-μ-S,S'](+), whose synthesis and structure were recently reported, the geometric parameters, vibrational frequencies, and total energies compare well to experimental ones and favor a singlet ground state.     

Vibrational spectra and molecular structure of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one by density functional theory and ab initio Hartree-Fock calculations

The vibrational frequencies and molecular geometry of (R)- and (rac)-4-phenly-1,3-oxazolidin-2-one (4-POO) in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths are described better by HF while bond angles are reproduced more accurately by DFT (B3LYP). Comparison of the observed fundamental vibrational frequencies of (R)-POO and (rac)-4-POO and calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems.     

Efficient evaluation of analytic vibrational frequencies in Hartree-Fock and density functional theory for periodic nonconducting systems

We report a method for the efficient evaluation of analytic energy second derivatives with respect to in-phase nuclear coordinate displacements within Hartree-Fock and Kohn-Sham density functional theories using Gaussian orbitals and periodic boundary conditions. The use of an atomic orbital formulation for all computationally challenging steps allows us to adapt the direct space fast multipole method for the Coulomb-type infinite summations. Our implementation also exploits the local character of the exact Hartree-Fock exchange in nonconducting systems. Exchange-correlation contributions are computed using extensive screening and fast numerical quadratures. We benchmark our scheme for in-phase vibrational frequencies of a trans-polyacetylene chain, a two-dimensional boron nitride sheet, and bulk diamond with the 6-31G** basis set and various density functionals. A study of computational scaling with the size of the unit cell for trans-polyacetylene reveals subquadratic scaling for our scheme.