Vibrational properties and DFT calculations of formamidine-templated Co and Fe formates

Experimental Raman and IR spectra of [NH₂-CH-NH₂][M(HCOO)₃] (M = Co, Fe), containing formamidinium cations [NH₂-CH-NH₂]⁺ (FMD⁺) were recorded at room temperature. In order to assign the vibrational modes corresponding to the FMD⁺ cation, the three-parameter hybrid B3LYP density functional method has been used with the 6-311G(2d,2p) basis to derive the vibrational wavenumbers (harmonic and anharmonic), infrared intensities and Raman scattering activities of formamidine molecule and FMD⁺ cation. The performed calculations revealed that protonation should affect most significantly the ν(CH), ρ(NH₂), ω(NH₂) and τ(NH₂) modes, which are expected to shift towards higher wavenumbers after protonation.     

Vibrational assignment of the Raman active modes of 1,10-phenanthroline-5,6-dione using DFT calculations

A complete assignment of the Raman active modes of 1,10-phenanthroline-5,6-dione in the 100-4000 cm(-1) spectral region is reported. Intense well resolved spectra of solid phendione with high S/N are reported. Assignment of the normal modes with appropriate symmetry representation symbols was achieved by employing density functional theory calculations. Our calculations were modeled on results previously reported for phenanthroline. Results of the B3LYP calculations were consistent and established that phendione possess sixty fundamentals.     

Vibrational anharmonic calculations in solution: performance of various DFT approaches

We report anharmonic spectra calculated for formaldehyde in acetonitrile solution using the quartic force field obtained for various DFT/solvent coupled models. A statistical study has been carried out for each mode by using several classes of DFT functionals and comparing them to the reference ab-initio CCSD(T)/cc-pVQZ calculations. Results lead to the recommended use of hybrid functionals associated with the 6-31+G** basis set and the Polarized Continuum model (PCM) to predict the expected shifts relative to the gas phase.     

pH-dependent Raman study of pyrrole and its vibrational analysis using DFT calculations

Raman spectra of pyrrole in aqueous medium at different pH values, 2.5, 5.5, 7.5 and 10.5 were recorded in the two spectral regions, 1,040-1,160 cm(-1) and 3,300-3,360 cm(-1) and pH dependence of the linewidth, peak position and intensity of the Raman bands corresponding to the ring breathing and symmetric nu(N-H) stretching modes were examined. A linear pH dependence of the peak positions for the ring breathing mode and a maximum at nearly neutral pH (7.5) for the symmetric nu(N-H) normal mode is observed, whereas the linewidth (FWHM) shows almost no variation with the change of pH. A slight decrease in the wavenumber position of the nu(N-H) mode at pH value >7.5 indicates that the influence of deprotonation is small, which results from a weak interaction between the reference molecule and the surrounding environment. The density functional theory (DFT) calculations were made primarily to obtain the optimized geometry and vibrational spectra of pyrrole in the ground electronic state using B3LYP functional and the highest level basis set 6-311++G(d,p). The assignments of the normal modes of pyrrole were made on the basis of potential energy distribution (PED). The calculations were also performed on protonated and deprotonated structures of pyrrole.     

Vibrational spectra and fundamental structural assignments from HF and DFT calculations of methyl benzoate

The Fourier transform Raman and Fourier transform infrared spectra of methyl benzoate (MB) were recorded in the liquid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, depolarization ratios, reduced masses were calculated by Hartree-Fock (HF) and 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. The thermodynamic functions of the title compound were also performed at HF/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of methyl benzoate is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Vibrational assignment of the spectral data and thermodynamic properties of 2-chloro-4-fluorobenzophenone using DFT quantum chemical calculations

The FT-Raman (3500-100 cm⁻¹) and FT-IR (4000-450 cm⁻¹) spectra of 2-chloro-4-fluorobenzophenone were recorded in the solid phase. Density functional theory calculations with B3LYP/6-31G (d, p) basis set was used to determine the ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities and Raman activities of this compound. Potential energy distributions (PEDs) and normal modes, for the spectral data computed at B3LYP/6-31G (d, p) level, have also been obtained from force-field calculations. The wavenumbers found after scaling of the force field showed very good agreement with the experimentally determined values. A comparison of the theoretical spectra and experimental FT-IR and FT-Raman spectra of the title molecule has been made and full vibrational assignments of the observed spectra have been proposed. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated.     

Vibrational spectroscopic studies and DFT calculations on tribromoacetate and tribromoacetic acid in aqueous solution

Aqueous solutions of sodium tribromoacetate (NaCBr3CO2) and its corresponding acid (CBr3COOH) have been studied using Raman and infrared spectroscopy. The spectra of the species in solution were assigned according to symmetry Cs. Characteristic bands of CBr3CO2-(aq) and the tribromoacetic acid, CBr3COOH(aq), are discussed. For the hydrated anion, the CO2 group, the symmetric CO2 stretching mode at 1332 cm(-1) and the asymmetric stretching mode at 1651 cm(-1) are characteristic while the CO mode at 1730 cm(-1) is characteristic for the spectra of the acid. The stretching mode, νC-C at 912cm(-1) for CBr3CO2-(aq) is 10 cm(-1) lower in the anion compared with that of the acid. These characteristic modes are compared to those in acetate, CH3CO2-(aq). Coupling of the modes are fairly extensive and therefore DFT calculations have been carried out in order to compare the measured spectra with the calculated ones. The geometrical parameters such as bond length and bond angles of the tribromoacetate, and tribromoacetic acid have been obtained and may be compared with the ones published for other acetates and their conjugated acids. CBr3COOH(aq) is a moderately strong acid and the pKa value derived from quantitative Raman measurements is equal to -0.23 at 23°C. The deuterated acid CBr3COOD in heavy water has been measured as well and the assignments were given.     

Vibrational transition moment directions of a terminally p-nitrobenzyl substituted long-chain alkanethiol by polarized infrared spectra and DFT calculations

Transition moment directions of the vibrational states of nitro and carbonyl groups of p-nitrobenzyl-16-mercaptohexadecanoate are evaluated by infrared linear dichroism (IR LD) to be further exploited as film orientation markers in self-assembled monolayers (SAMs) that the respective compound forms on metal surfaces. DFT calculations followed by a complete normal coordinate analysis were employed to assist in the vibrational bands assignments. The analysis of the experimental IR LD spectra in conjunction with the step-wise reduction procedure of Thulstrup–Eggers indicated that the transition moment directions of the antisymmetric NO₂ stretching and the carbonyl stretching modes are collinear, and confirmed previous results that those of the symmetric and the antisymmetric NO₂ stretching vibrations are not exactly mutually perpendicular.     

Conformational study of monomeric 2,3-butanediols by matrix-isolation infrared spectroscopy and DFT calculations

The FT-IR spectra of two diastereomers of 2,3-butanediol, (R,S) and (S,S), isolated in low-temperature argon and xenon matrixes were studied, allowing the identification of two different conformers for each compound. These conformers were characterized by a +/-gauche arrangement around the O-C-C-O dihedral angle, thus enabling the establishment of a very weak intramolecular hydrogen bond of the O...H-O type. No other forms of these compounds were identified in matrixes, despite the fact that these four conformers had calculated relative energies from 0 to 5.1 kJ mol(-1) and were expected to be thermally populated from 50 to 6% in the gaseous phase of each compound. The nonobservation of additional conformers was explained in terms of low barriers to intramolecular rotation, resulting in the conformational relaxation of the compounds during deposition of the matrixes. The barriers to internal rotation of the OH groups were computed to be less than 4 kJ mol(-1) and are easily overcome in matrixes within the family of conformers with the same heavy atom backbone. The barriers for intramolecular rearrangement of the O-C-C-O dihedral angle in both diastereomers were calculated to range from 20 to 30 kJ mol(-1). Interconversions between the latter conformers were not observed in matrixes, even after annealing up to 65 K. Energy calculations, barriers, and calculated infrared spectra were carried out at the DFT(B3LYP)/6-311++G theory. Additional MP2/6-311++G calculations of energies and vibrational frequencies were performed on the most relevant conformers. Finally, independent estimations of the hydrogen-bond enthalpy in the studied molecules were also obtained based on theoretical structural data and from vibrational frequencies (using well-established empirical correlations). The obtained values for -DeltaH for both diastereomers of 2,3-butanediol amount to ca. 6-8 kJ mol(-1).     

Vibrational spectra of triiodomesitylene: combination of DFT calculations and experimental studies. Effects of the environment

A study of the internal vibrations of triiodomesitylene (TIM) is presented. It is known from X-rays diffraction at 293 K that the molecule has nearly D(3h) symmetry because of the large delocalization of the methyl protons. By using Raman and infrared spectra recorded at room temperature, a first assignment is done by comparing TIM vibrations with those of 1,3,5-triiodo- and 1,3,5-trimethyl-benzene. This assignment is supported by DFT calculations by using the MPW1PW91 functional with the LanL2DZ(d,p) basis set and assuming C(3h) symmetry. The agreement between the calculated and experimental frequencies is very good: always better than 97% for the observed skeletal vibrations. The calculations overestimate the methyl frequencies by 7%, and experiment shows only broad features for these excitations. Because a neutron diffraction study had established that the TIM conformation at 14 K is not exactly trigonal, new theoretical calculations were done with C(s) symmetry. This shows that all previous E' and E' modes of vibration are split by 2-12 cm(-1). This is confirmed by infrared, Raman, and inelastic neutron scattering spectra recorded below 10 K. Apart from two frequencies, all the TIM skeleton vibrations have been detected and assigned by using C(s) symmetry. For the methyl vibrations, experiment has confirmed the splitting of the previously degenerate modes; only some small discrepancies remain in the assignment. This is partly due to the difference of the model conformation used in the calculations and the crystallographic one. All these results confirm that each of the three methyl groups has not only its own tunnel splitting but also a different specific spectroscopic behavior for all the molecular modes.     

Analysis of XPS and XES of diamond and graphite by DFT calculations using model molecules

X‐ray photoelectron and emission spectra (XPS and XES) of diamond and graphite have been analyzed by deMon density‐functional theory (DFT) calculations using the model adamantane derivative (C₁₀H₁₂(CH₃)₄) and pyrene (C₁₆H₁₀) molecules, respectively. The theoretical valence photoelectron and C Kα X‐ray emission spectra for the allotrope are in good accordance with the experimental ones. The combined analysis of the valence XPS and C Kα XES enables us to divide the valence electronic distribution into the individual contributions for pσ‐, and pπ‐bonding MOs of the diamond and graphite, respectively. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 102–108, 2001     

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity,coupling and methyl group tunneling

The Raman, IR and INS spectra of 1,3-dibromo-2,4,6-trimethylbenzene (DBMH) were recorded in the 80–3200 cm⁻¹ range. The molecular conformation and vibrational spectra of DBMH were computed at the MPW1PW91/LANL2DZ level. Except for the methyl 2 environment, the agreement between the DFT calculations and the neutron diffraction structure is almost perfect (deviations < 0.01 Å for bond lengths, <0.2° for angles). The frequencies of the internal modes of vibration were calculated with the harmonic and anharmonic approximations; the later method yields results that are in remarkable agreement with the spectroscopic data, resulting in a confident assignment of the vibrational bands. Thus, no scaling is necessary. The coupling, in phase or anti-phase, of the motions of symmetrical CBr and CMe bonds is highlighted. Our DFT calculations suggest that the torsion of methyl groups 4 and 6 is hindered in deep wells, whereas methyl group 2 is a quasi-free rotor. The failure of the calculations to determine the frequencies of the methyl torsional modes is explained as follows: DFT does not consider the methyl spins and assumes localization of the protons, whereas the methyl groups must be treated as quantum rotors.     

Vibrational characterization of L-leucine phosphonate analogues: FT-IR, FT-Raman, and SERS spectroscopy studies and DFT calculations

This study reports the Raman (FT-Raman) and absorption infrared (FT-IR) spectra, based on calculated wavenumbers and normal modes of vibrations, of the following compounds: L-Leu-D-NH-CH(Me)-PO(3)H(2) (LI), L-Leu-NH-C(Me)(2)-PO(3)H(2) (LII), L-Leu-D-NH-CH(Et)-PO(3)H(2) (LIII), L-Leu-L-NH-CH(Et)-PO(3)H(2) (LIV), L-Leu-L-NH-CH(EtOH)-PO(3)H(2) (LV), L-Leu-NH-C(Me)(Et)-PO(3)H(2) (LVI), L-Leu-L-NH-CH(PrA)-PO(3)H(2) (LVII), L-Leu-L-NH-CH(c-Pr)-PO(3)H(2) (LVIII), L-Leu-L-NH-CH(t-Bu)-PO(3)H(2) (LIX), L-Leu-L-NH-CH(BuA)-PO(3)H(2) (LX), L-Leu-L-NH-CH(c-Bu)-PO(3)H(2) (LXI), and L-Leu-L-NH-C(Adm)-PO(3)H(2) (LXII). The equilibrium geometries and vibrational wavenumbers were calculated using density functional theory (DFT) at the B3LYP, 6-311++G** level using Gaussian 03, Raint, GaussSum 0.8, and Gar2ped software. We briefly compare and analyze the experimental and calculated vibrational wavenumbers in the range 4000-400 cm(-1). In addition, the Raman wavenumbers are compared to those from the surface-enhanced Raman scattering (SERS) spectra for the phosphono analogues of l-leucine (l-Leu) adsorbed on a colloidal silver surface in an aqueous solution. The geometries of these molecules etched on the silver surface were deduced from observed changes in both the intensity and broadness of Raman bands in the spectra of the bound versus free species. For example, LVI appears to adsorb onto the colloidal silver particles mainly through the amine group and amide bond, which assists in the adsorption process, whereas LII shows strongly enhanced SERS bands due to the rocking, twisting, and stretching vibrations of the N(amid)C(sg)(Me)(2)P fragment, suggesting that this peptide's interaction with the silver surface occurs mainly via this fragment. On the other hand, the most dominant SERS bands of LIII and LIV due to the P═O bond stretches reflect P═O···Ag complex formation.     

A conformational study of hydroxylated isoflavones by vibrational spectroscopy coupled with DFT calculations

The conformational preferences of a series of hydroxylated isoflavones were studied by optical vibrational spectroscopy (FTIR and Raman) coupled with density functional theory (DFT) calculations. Special attention was paid to the effect of the hydroxyl substitution, due to the importance of this group in the biological activity of these systems. The isoflavones investigated – daidzein, genistein and formononetin – were shown to exist in distinct conformations in the solid state, namely regarding the orientation of the hydroxylic groups at C⁷ and within the catechol moiety, that are determinant factors for their conformational behaviour and antioxidant ability. In the light of the most stable conformers obtained for each molecule, a complete assignment of their experimental vibrational spectra was performed.     

Configuration and conformation of alfentanil hydrochloride. Conformational study by NMR and theoretical calculations

The configurational and conformational structure of alfentanil hydrochloride (1) was studied by nuclear magnetic resonance and theoretical calculations. Compound 1 is best described by equilibrium between two stereoisomeric piperidinium rings with the N‐substituent always being in equatorial position. Nuclear magnetic resonance spectra demonstrate that, depending on the solvent, 1 adopts the conformation with an axial methoxymethylene group. Computations were crucial in determining the importance of the transannular attractive interaction between the positive charge at the piperidinium N‐atom and the methoxymethyl group in position 4. Copyright © 2014 John Wiley & Sons, Ltd.     

Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT

Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.     

Structure-property correlation of CdSe clusters using experimental results and first-principles DFT calculations

Structures and properties of CdSe quantum dots (clusters) up to a diameter of approximately 2 nm were investigated by combining experimental absorption, photoluminescence (PL), and X-ray diffraction (XRD) spectroscopies as well as ab initio DFT calculations. These CdSe clusters were nucleated and grown from solutions containing respective cadmium and selenium precursors following the hot-injection technique that allows one to obtain size-controlled CdSe clusters having PL efficiency up to 0.5. The DFT calculations were performed at the B3LYP/Lanl2dz level and followed by time-dependent TDDFT calculations to estimate n energy singlet transitions. On the basis of the results of these experimental and theoretical studies, an approach to determine whether the proposed cluster with a mean diameter of approximately 2 nm is more physically reasonable is discussed. It was shown that the minimum nucleus of a CdSe cluster consists of (CdSe)(3) with a six-membered ring and planar structure. No PL is observed for this structure. The formation of the next stable cluster depends on whether hexadecylamine (HDA) was used for the growth of the CdSe clusters. In the absence of HDA, the second cluster was found to be (CdSe)(6) characterized by a broad PL spectrum, while in the presence of HDA, it was found to be (CdSe)(n) (where n > or = 14) with a sharp PL spectrum.     

Structural and spectroscopic study of the Br2...3-Br-pyridine complex by DFT calculations

The structure and the Raman vibrational spectrum of the complex Br(2)...3-Br-pyridine are determined by DFT calculations using different parametrizations. The calculations are performed taking into account the effects of the dichloromethane as solvent by the CPCM method. A value of 39 kJ mol(-1) for the formation enthalpy and of 1 kJ mol(-1) for the formation free energy at room temperature in presence of the solvent is found. The predicted Raman spectrum is compared with the experimental one and the essential features of the spectrum are well reproduced by the B3LYP parametrization. The intensity changes of the bands when going from the free moieties to the complex are also generally correctly predicted by the theoretical treatment.     

Vibrational spectra and structure of 1-phenyltetrazole and 5-chloro-1-phenyltetrazole: A combined study by low temperature matrix isolation and solid state FTIR spectroscopy and DFT calculations

Infrared spectra of 1-phenyltetrazole (C₇N₄H₆) and 5-chloro-1-phenyltetrazole (C₇N₄H₅Cl) isolated in argon matrixes (T=8 K) and in the solid state (at room temperature) were studied. DFT(B3LYP)/6-31G* calculations predict the minimum energy conformation of 1-phenyltetrazole as being non-planar, with the two rings (phenyl and tetrazole) twisted by 29°. For 5-chloro-1-phenyltetrazole, the optimized dihedral angle between the two rings is larger (48°). The theoretically calculated IR spectra of both compounds fit well the spectra observed experimentally. This allowed a reliable assignment of observed IR absorption bands.     

Elucidating the mass spectrum of the retronecine alkaloid using DFT calculations

Pyrrolizidine alkaloids are natural molecules playing important roles in different biochemical processes in nature and in humans. In this work, the electron ionization mass spectrum of retronecine, an alkaloid molecule found in plants, was investigated computationally. Its mass spectrum can be characterized by three main fragment ions having the following m/z ratios: 111, 94, and 80. In order to rationalize the mass spectrum, minima and transition state geometries were computed using density functional theory. It was showed that the dissociation process includes an aromatization of the originally five‐membered ring of retronecine converted into a six‐membered ring compound. A fragmentation pathway mechanism involving dissociation activation barriers that are easily overcome by the initial ionization energy was found. From the computed quantum chemical geometric, atomic charges, and energetic parameters, the abundance of each ion in the mass spectrum of retronecine was discussed.