Infrared spectrum, DFT: pBP86/DN** and NCA vibrational calculations of 2-methylthiosemicarbazide copper(II) nitrate [Cu(2MeTSC)2(NO3)2

To elucidate tentative assignments of metal-ligand modes of thiosemicarbazide complexes, a structural study and a assignment of the normal vibrations of 2-methylthiosemicarbazide copper(II) nitrate, [Cu(2MeTSC)(2)(NO(3))(2)] have been done through the ab initio DFT: pBP86/DN** procedure, and through the normal coordinate analysis (NCA). In the vibrational calculations, the elongated CuONO(2) bonds of the nitrate groups were considered in the CS and CN tautomers of the complex. DFT calculations had revealed that the infrared spectra can be well interpreted through the CN tautomer, failing in the prediction of the -NO(2) group wavenumbers. A little difference stabilization energy for the tautomers were found: for the CN tautomer was E=-3487,36376a.u., and for the CS tautomer, E=-3473,93598a.u. The observed combination bands at 1763.0 and at 1754.0 cm(-1) are an indicative that the -NO(3)(-) groups acts as monodentate ligands. Calculations had confirmed the experimental assignment of the infrared spectrum.     

Fourier transform infrared spectrum, vibrational analysis and structural determinations of the trans-bis(glycine)nickel(II) complex by means of the RHF/6-311G and DFT:B3LYP/6-31G and 6-311G methods

The trans-bis(glycine)nickel(II) complex was synthesized, and the Fourier transform infrared spectra in the regions 4000-370 cm(-1) and 700-30 cm(-1) were measured. Band deconvolution analysis and the second derivative of the infrared spectrum were also performed. The determination of the geometrical structure in the trans position of the glycine ligands around Ni(II) for the trans-bis(glycine)nickel(II) complex as well as the vibrational assignment were assisted by RHF/6-311G and by Density Functional Theory calculations, DFT:B3LYP/6-31G and 6-311G basis sets. A full discussion of the framework vibrational modes was done using as criteria the geometry study of distorted structures generated for the vibrational modes. Incidentally, Normal Coordinate Analysis was carried out for the Ni(N)(2)(O)(2) structural fragment. The calculated DFT spectra in the high- and low-energy regions agree with the observed ones.     

FT-IR vibrational spectrum and DFT:B3LYP/6-311G structure and vibrational analysis of bis-serinenickel(II) complex: [Ni(Ser)2

The bis-serinenickel(II) complex was synthesized, and the Fourier-transforms infrared spectra in the regions 4000-370 and 700-30 cm(-1) was measured. The second derivative spectra and band deconvolution analysis was also obtained. Density functional theory calculations, DFT:B3LYP/6-311G, were performed for the determination of geometrical structure and vibrational assignment for the bis-serinenickel(II) complex. A full discussion of the framework vibrational modes was done using as criteria the geometry study of distorted structures generated for the vibrational modes. Incidentally, the normal coordinate analysis was carried out for the Ni(N)2(O)2 structural fragment. The calculated DFT spectra in the high and low energy regions agree well with the observed ones.     

Multiple structures and dynamics of [CpRu(CO)2]2 and [CpFe(CO)2]2 in solution revealed with two-dimensional infrared spectroscopy

Two-dimensional infrared (2DIR) spectroscopy is applied to both (Cp)(2)Fe(2)(CO)(4) and its ruthenium analog (Cp)(2)Ru(2)(CO)(4) in order to study the vibrational dynamics of these two systems. Combining the results of 2DIR spectroscopy and DFT calculations, the different structural forms of both the iron and the ruthenium complexes were characterized, furthering the previous assignment of the linear IR spectrum by determining the transition frequencies associated with the different isomeric forms. Monitoring the time-dependent amplitudes of the cross peaks enabled the observation of equilibrium energy transfer dynamics between different vibrational modes of the cis-B (Cp)(2)Fe(2)(CO)(4) and the gauche-NB (Cp)(2)Ru(2)(CO)(4) complexes. Treating the energy transfer as an equilibrium process, we extracted the rate constants associated with both the uphill and the downhill transfer of vibrational energy, finding that the difference in the rate constants of the two metal complexes maps to the difference in the energy gap between the two modes involved.     

Nuclear resonance vibrational spectra of five-coordinate imidazole-ligated iron(II) porphyrinates

Nuclear resonance vibrational spectra have been obtained for six five-coordinate imidazole-ligated iron(II) porphyrinates, [Fe(Por)(L)] (Por = tetraphenylporphyrinate, octaethylporphyrinate, tetratolylporphyrinate, or protoporphyrinate IX and L = 2-methylimidazole or 1,2-dimethylimidazole). Measurements have been made on both powder and oriented crystal samples. The spectra are dominated by strong signals around 200-300 cm(-1). Although the in-plane and out-of-plane vibrations are seriously overlapped, oriented crystal spectra allow their deconvolution. Thus, oriented crystal experimental data, along with density functional theory (DFT) calculations, enable the assignment of key vibrations in the spectra. Molecular dynamics are also discussed. The nature of the Fe-N(Im) vibrations has been elaborated further than was possible from resonance Raman studies. Our study suggests that the Fe motions are coupled with the porphyrin core and peripheral groups motions. Both peripheral groups and their conformations have significant influence on the vibrational spectra (position and shape).     

Estimate of the vibrational contribution to the entropy change associated with the spin transition in the d4 systems [MnIII(pyrol)3tren] and [CrII(depe)2I2

The vibrational contribution to DeltaS of the low-spin ((3)T(1)) to high-spin ((5)E) spin transition in two 3d(4) octahedral systems [Mn(III)(pyrol)(3)tren] and [Cr(depe)(2)I(2)] have been estimated by means of DFT calculations (B3LYP/CEP-31G) of the vibrational normal-modes frequencies. The obtained value at the transition temperature for the Mn(iii) complex is DeltaS(vib)(44 K) = 6.3 J K(-1) mol(-1), which is comparable with the proposed Jahn-Teller contribution of R ln3 = 9.1 J K(-1) mol(-1) and which is approximately half of the experimentally determined 13.8 J K(-1) mol(-1). The corresponding value for the Cr(ii) complex is DeltaS(vib)(171.45 K) = 46.5 J K(-1) mol(-1), as compared to the experimental value of 39.45 J K(-1) mol(-1). The analysis of the vibrational normal modes reveals that for the d(4) systems under study, contrary to Fe(ii) d(6) systems, not all metal-ligand stretching vibrations make a contribution. For the Mn(iii) complex, the only vibration that contributes to DeltaS(vib) involve the nitrogens occupying the Jahn-Teller axis, while in the case of Cr(ii) the contributing vibrations involve the Cr-I bonds. Low-frequency modes due to ring vibrations, metal-ligand bending and movement of the molecule as a whole also contribute to the vibrational entropy associated with the spin transition.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

FT-IR and FT-Raman spectra and vibrational investigation of 4-chloro-2-fluoro toluene using ab initio HF and DFT (B3LYP/B3PW91) calculations

FT-IR (4000-100 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectra of solid sample of 4-chloro-2-fluoro toluene (4Cl2FT) have been recorded using Bruker IFS 66 V spectrometer. Ab initio-HF (HF/6-311++G (d, p)) and DFT (B3LYP/6-311++G and B3PW91/6-311++G (d, p)) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities. The vibrational frequencies are calculated and scaled values are compared with FT-IR and FT-Raman experimental values. The isotropic HF and DFT analyses showed good agreement with experimental observations. The differences between the observed and scaled wave number values of most of the fundamentals are very small in B3LYP than HF. Comparison of the simulated spectra provides important information about the ability of the computational method (B3LYP) to describe the vibrational modes. The influences of substitutions on the geometry of molecule and its normal modes of vibrations have also been discussed. The changes made by substitutions on the benzene are much responsible for the non-linearity of the molecule. This is an attractive entity for the future studies of non-linear optics.     

Naked five-coordinate Fe(III)(NO) porphyrin complexes: vibrational and reactivity features

Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the dianion of 5,10,15,20-tetrakis-phenyl-porphyrin and TPFPP is the dianion of 5,10,15,20-tetrakis-pentafluorophenyl-porphyrin, have been obtained as isolated species by the gas phase reaction of NO with [Fe(III)(TPP)](+) and [Fe(III) (TPFPP)](+) ions delivered in the gas phase by electrospray ionization, respectively. The so-formed nitrosyl complexes have been characterized by vibrational spectroscopy also exploiting (15)N-isotope substitution in the NO ligand. The characteristic NO stretching frequency is observed at 1825 and 1859 cm(-1) for [Fe(III)(TPP)(NO)](+) and [Fe(III)(TPFPP)(NO)](+) ions, respectively, providing reference values for genuine five-coordinate Fe(III)(NO) porphyrin complexes differing only for the presence of either phenyl or pentafluorophenyl substituents on the meso positions of the porphyrin ligand. The vibrational assignment is aided by hybrid density functional theory (DFT) calculations of geometry and electronic structure and frequency analysis which clearly support a singlet spin electronic state for both [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+) complexes. Both TD-DFT and CASSCF calculations suggest that the singlet ground state is best described as Fe(II)(NO(+)) and that the open-shell AFC bonding scheme contribute for a high-energy excited state. The kinetics of the NO addition reaction in the gas phase are faster for [Fe(III)(TPFPP)](+) ions by a relatively small factor, though highly reliable because of a direct comparative evaluation. The study was aimed at gaining vibrational and reactivity data on five-coordinate Fe(III)(NO) porphyrin complexes, typically transient species in solution, ultimately to provide insights into the nature of the Fe(NO) interaction in heme proteins.     

Structure and vibrational frequencies of 2-butanimine

The conformational behavior and structural stability of 2-butanimine were investigated by utilizing ab initio calculations with 6-311++G** basis set at HF, MP2, B3LYP and BLYP levels. The vibrational frequencies of 2-butanimine were computed. Complete vibrational assignments were made on the basis of normal coordinate calculations for stable conformer of the molecule. HF results without scaled quantum mechanical (SQM) force field procedure considered are in bad agreement with experimental values. Of the two DFT methods, BLYP reproduces the observed fundamental frequencies most satisfactorily with the mean absolute deviation of the non-CH stretching modes less than 21.3 cm(-1). The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

Quantitative vibrational dynamics of iron in nitrosyl porphyrins

We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.     

Synthesis, IR spectra, crystal structure and DFT studies on 1-acetyl-3-(4-chlorophenyl)-5-(4-methylphenyl)-2-pyrazoline

1-Acetyl-3-(4-chlorophenyl)-5-(4-methylphenyl)-2-pyrazoline has been synthesized and characterized by elemental analysis, IR and X-ray single crystal diffraction. Density functional (DFT) calculations have been carried out for the title compound by using the B3LYP method at the 6-311G** basis set level. The calculated results show that the predicted geometry can reproduce well the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they are supported each other. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C(0)(p, m), S(0)(m), H(0)(m) and temperatures.     

Experimental Raman spectra of dilute and laser-light-sensitive [Rh(4)(CO)(9)(mu-CO)(3)] and [(mu(4)-eta(2)-3-hexyne)Rh(4)(CO)(8)(mu-CO)(2)]. Comparison with theoretically predicted spectra

The reaction of [Rh(4)(CO)(9)(mu-CO)(3)] with 3-hexyne to form the butterfly cluster [(mu(4)-eta(2)-3-hexyne)Rh(4)(CO)(8)(mu-CO)(2)] was monitored viain-situ Raman spectroscopy using an NIR laser source, at room temperature and under atmospheric argon using n-hexane as solvent. The collected raw spectra were deconvoluted using band-target entropy minimization (BTEM). The pure component mid-Raman spectra of the [Rh(4)(CO)(9)(mu-CO)(3)] and the butterfly cluster [(mu(4)-eta(2)-3-hexyne)Rh(4)(CO)(8)(mu-CO)(2)], were reconstructed with a high signal-to-noise ratio. Full geometric optimization and Raman vibrational prediction were carried out using DFT. The experimental and predicted Raman spectra were in good agreement. In particular, the far-Raman vibrational modes in the region 100-280 cm(-1) provided characterization of the metal-metal bonds and direct confirmation of the structural integrity of the polynuclear frameworks in solution.     

How nitrogenase shakes--initial information about P-cluster and FeMo-cofactor normal modes from nuclear resonance vibrational spectroscopy (NRVS)

Nitrogenase catalyzes a reaction critical for life, the reduction of N(2) to 2NH(3), yet we still know relatively little about its catalytic mechanism. We have used the synchrotron technique of (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the dynamics of the Fe-S clusters in this enzyme. The catalytic site FeMo-cofactor exhibits a strong signal near 190 cm(-)(1), where conventional Fe-S clusters have weak NRVS. This intensity is ascribed to cluster breathing modes whose frequency is raised by an interstitial atom. A variety of Fe-S stretching modes are also observed between 250 and 400 cm(-)(1). This work is the first spectroscopic information about the vibrational modes of the intact nitrogenase FeMo-cofactor and P-cluster.     

Density functional theory calculations and vibrational spectral analysis of 3,5-(dinitrobenzoic acid)

The FT-IR and Raman spectra of 3,5-dinitrobenzoic acid (DNBA) have been recorded and analyzed. The equilibrium geometry, various bonding and harmonic vibrational wavenumbers have been calculated with the help of density functional theory (DFT) method. Most of the vibrational modes are observed in the expected range. Mulliken population analysis shows the interactions C-N-O?H-C and C-O?H-C. The most possible interaction is explained using natural bond orbital (NBO) analysis. The strengthening and polarization of the CO bond increases due to the degree of conjugation. HOMO-LUMO energy and the thermodynamic properties are also evaluated.     

Theoretical studies on vibrational spectra of some mixed carbonyl-halide complexes of Osmium(II)

The vibrational spectra of Os(CO)(6)(2+) and some of its mixed carbonyl-halide complexes, cis-Os(CO)(2)X(4)(2-), fac-Os(CO)(3)X(3)(-) and Os(CO)(5)X(+) (X=F, Cl, Br and I), have been systematically investigated by ab initio RHF and density functional B3LYP methods with LanL2DZ and SDD basis sets. The calculated vibrational frequencies of complexes Os(CO)(6)(2+), cis-Os(CO)(2)X(4)(2-) and fac-Os(CO)(3)X(3)(-) are evaluated via comparison with the experimental values. In infrared frequency region, the C-O stretching vibrational frequencies calculated at B3LYP level with two basis sets are in good agreement with the observed values with deviations less than 5%. In the far-infrared region, the B3LYP/SDD method achieved the best results with deviations less than 9% for Os-X stretching and less than 8% for Os-C stretching vibrational frequencies. The vibrational frequencies for Os(CO)(5)X(+) that have not been experimentally reported were predicted.     

Thermal, vibrational and EPR studies of Cu(II) bromide bis(p-methylaniline) and bis(m-methylaniline) complexes

[CuBr(2)(pMA)(2)] and [CuBr(2)(mMA)(2)] complexes (pMA: p-methylaniline, mMA: m-methylaniline) have been prepared and characterized by elemental analyses, thermogravimetric analyses, magnetic moment measurements, and IR, Raman and EPR spectroscopic studies. Coordination effects on the vibrational spectra of the ligands have been investigated. The room temperature EPR spectra of the complexes and their simulated spectra are also discussed in detail. The vibrational and EPR spectral studies suggest that the coordination sphere around Cu(II) consist of a distorted tetragonal structure.     

Theoretical study of the vibrational spectra of the hydrogen-bonded systems between pyridine-3-carboxamide (nicotinamide) and DMSO

The vibrational characteristics (vibrational frequencies and infrared intensities) for the hydrogen-bonded systems of nicotinamide (NA(Z) and NA(E)) with dimethyl sulfoxide (DMSO) have been predicted using ab initio SCF/6-31G(d,p) and DFT (BLYP/6-311++G(d,p)) calculations. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between nicotinamide (NA(Z) and NA(E)) and DMSO leads to large red shifts of the stretching vibrations for the hydrogen-bonded N-H bonds of nicotinamide and very strong increase in their IR intensity. The results from the BLYP/6-311++G(d,p) calculations show that the predicted red shifts of the nu(s)(NH) and nu(as)(NH) vibrations for the complex NA(E)-DMSO (1:2) (Deltanu(as)(NH)=-186 cm(-1) and Deltanu(s)(NH)=-198 cm(-1)) are in better agreement with the experimentally measured. The magnitudes of the wavenumber shifts are indicative of strong NH...O hydrogen-bonded interactions in both complexes. The calculations predict an increase of the IR intensity of nu(s)(NH) and nu(as)(NH) vibrations in the complexes up to 14 times. Having in mind that in more cases the predicted changes in the vibrational characteristics for the complexes studied are very near, it could be concluded that both conformers of nicotinamide, Z-conformer and E-conformer, are present in the solution forming the hydrogen-bonded complexes with DMSO.     

Analysis of vibrational spectra of chlorotoluene based on density function theory calculations

The conformational behavior and structural stability of chlorotoluene were investigated by utilizing ab initio calculations with 6-31G* basis set at restricted Hartree-Fock (RHF) and density function theory (DFT) levels. The vibrational frequencies of chlorotoluene were computed at the RHF and DFT levels. Complete vibrational assignments were made on the basis of normal coordinate calculations for stable conformer of the molecule. RHF results without scaled quantum mechanical (SQM) force field procedure considered are in bad agreement with experimental values. Of the five DFT methods, BLYP reproduces the observed fundamental frequencies most satisfactorily with the mean absolute deviation of the non-CH stretching modes less than 10 cm(-1). Two hybrid DFT methods are found to yield frequencies, which are generally higher than the observed fundamental frequencies. When the calculated results are compared with 'experimental' frequencies, B3LYP method is found to be slightly more accurate for C-H stretching modes. The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

FT-IR and FT-Raman, vibrational assignments, molecular geometry, ab initio (HF) and DFT (B3LYP) calculations for 1,3-dichlorobenzene

The FT-IR and FT-Raman vibrational spectra of 1,3-dichlorobenzene (1,3-DCB) have been recorded using Bruker IFS 66 V Spectrometer in the range 4000-100 cm(-1). A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry, vibrational frequencies, atomic charges, dipole moment, rotational constants and several thermodynamic parameters in the ground state were calculated using ab initio Hartree-Fock (HF) and DFT (B3LYP) methods with 6-31++G (d, p) and 6-311++G (d, p) basis sets. With the help of different scaling factors, the observed vibrational wave numbers in FT-IR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wave numbers in the expected range. The inductive effect of Chlorine atoms in the benzene molecule has also been investigated.