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.     

Zn2+ has a primary hydration sphere of five: IR action spectroscopy and theoretical studies of hydrated Zn2+ complexes in the gas phase

Complexes of Zn(2+)(H(2)O)(n), where n = 6-12, are examined using infrared photodissociation (IRPD) spectroscopy, blackbody infrared radiative dissociation (BIRD), and theory. Geometry optimizations and frequency calculations are performed at the B3LYP/6-311+G(d,p) level along with single point energy calculations for relative energetics at the B3LYP, B3P86, and MP2(full) levels with a 6-311+G(2d,2p) basis set. The IRPD spectrum of Zn(2+)(H(2)O)(8) is most consistent with the calculated spectrum of the five-coordinate MP2(full) ground-state (GS) species. Results from larger complexes also point toward a coordination number of five, although contributions from six-coordinate species cannot be ruled out. For n = 6 and 7, comparisons of the individual IRPD spectra with calculated spectra are less conclusive. However, in combination with the BIRD and laser photodissociation kinetics as well as a comparison to hydrated Cu(2+) and Ca(2+), the presence of five-coordinate species with some contribution from six-coordinate species seems likely. Additionally, the BIRD rate constants show that Zn(2+)(H(2)O)(6) and Zn(2+)(H(2)O)(7) complexes are less stable than Zn(2+)(H(2)O)(8). This trend is consistent with previous work that demonstrates the enthalpic favorability of the charge separation process forming singly charged hydrated metal hydroxide and protonated water complexes versus loss of a water molecule for complexes of n ≤ 7. Overall, these results are most consistent with the lowest-energy structures calculated at the MP2(full) level of theory and disagree with those calculated at B3LYP and B3P86 levels.     

Spectroscopic analysis of 2-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-ylimino)-2-(4-nitro-phenyl) acetonitrile

The optimized geometry and vibrational frequencies of 2-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-ylimino)-2-(4-nitro-phenyl) acetonitrile (DOPNA) were obtained by ab initio DFT/B3LYP level with complete relaxation in the potential energy surface using 6-31G and 6-311G basis sets. The Fourier-transform infrared (FT-IR) spectrum of DOPNA has been recorded in the region 4000-400 cm(-1). The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR spectrum. The calculated frequencies are in comparable agreement with the experimental frequencies. The calculated energy span between the HOMO and the LUMO of DOPNA is 2.94 and 2.87eV by B3LYP/6-31G and B3LYP/6-311G, respectively.     

Molecular geometry as a source of chemical information. 3. How H-bonding affects aromaticity of the ring in the case of phenol and p-nitrophenol complexes: a B3LYP/6-311+G study

Molecular geometries of phenol and p-nitrophenol (ArOH) interacting with fluoride were optimized at the B3LYP/6-311+G level of theory taking as constraints the planarity of the systems and the linearity of the O...H...F moiety. For p-nitrophenol complexes, the substituent effect stabilization energy (SESE) was computed, and for all systems aromaticity indices, HOMA, and out-of-plane components of NICS(1) and NICS(1)(zz)() were calculated. SESE values depend strongly on the O...F distance, the same as both aromaticity indices. Variation in HOMA values for the studied ArOH...F(-) complexes is within the range of 0.55 to approximately 1.0 and for NICS(1)(zz)() between -12 and -26 ppm. It was also found that a decrease in aromaticity is well correlated with the variations of C-O bond length.     

Experimental and DFT 1H NMR study of conformational equilibria in trans-4',7-dihydroxyisoflavan-4-ol and trans-isoflavan-4-ol

The solution-state conformational equilibria of trans-4',7-dihydroxyisoflavan-4-ol (1) and trans-isoflavan-4-ol (2) were assessed based on the temperature dependence of their vicinal coupling constants J(H)(-)(2)(alpha)(,H)(-)(3) and J(H-3,H)(-)(4) in comparison to values calculated with density functional theory (DFT) methods at the B3LYP/cc-pVTZ//B3LYP/6-31G(d,p) level of theory. For each half-chair conformer, several rotamers with respect to the C-4 hydroxyl and C-3 phenyl were calculated and the overall diequatorial-to-diaxial ratio at 298 K was assessed as 66:34 for 1 and 73:27 for 2. The syntheses of 1 and 2 are described.     

Structure, stability and vibrational spectrum of the hydrogen-bonded complex between HNO3 and H2O. Ab initio and DFT studies

The structure, stability and vibrational spectrum of the binary complex between HONO2 and H2O have been investigated using ab initio calculations at SCF and MP2 levels with different basis sets and B3LYP/6-31G(d,p) calculations. Full geometry optimization was made for the complex studied. It was established that the hydrogen-bonded H2O...HONO2 complex has a planar structure. The corrected values of the dissociation energy at the SCF and MP2 levels and B3LYP calculations are indicative of relatively strong OH...O hydrogen-bonded interaction. The changes in the vibrational characteristics (vibrational frequencies and infrared intensities) arising from the hydrogen bonding between HONO2 and H2O have been estimated by using the ab initio calculations at SCF and MP2 levels and B3LYP/6-31G(d,p) calculations. It was established that the most sensitive to the complexation is the stretching O-H vibration from HONO2. In agreement with the experiment, its vibrational frequency in the complex is shifted to lower wavenumbers. The predicted frequency shift with the B3LYP/6-31G(d,p) calculations (-439 cm(-1)) is in the best agreement with the experimentally measured (-498 cm(-1)). The intensity of this vibration increases dramatically upon hydrogen bonding. The ab initio calculations at the SCF level predict an increase up to five times; at the MP2 level up to 10 times and the B3LYP/6-31G(d,p) predicted increase is up to 17 times. The good agreement between the predicted values of the frequency shifts and those experimentally observed show that the structure of the hydrogen-bonded complex H2O...HONO2 is reliable.     

Complete basis set B3LYP NMR calculations of CDCl3 solvent's water fine spectral details

The assignment of singlet at 1.55 ppm and the 1:1:1 triplet at 1.519 ppm to H(2)O and HOD in the 400 MHz (1)H NMR spectrum of CDCl(3) solvent were supported by complete basis set (CBS) GIAO-B3LYP calculated chemical shift and the CBS B3LYP estimated (2)J(D,H) spin-spin coupling constant (SSCC). The CBS fitting of B3LYP/cc-pCVxZ and B3LYP/pcJ-n predicted SSCC values, the accurate value of (2)J(D,H) = -1.082 +/- 0.030 Hz of HOD in chloroform-d(1) and the H/D isotopic shift of 0.0307(1) ppm were reported for the first time. The agreement between CBS B3LYP predicted chemical shift, spin-spin values and experiment was good.     

FT-IR vibrational spectrum and DFT:B3LYP/6-31G structure and vibrational analysis of guanidinoaceticserinenickel(II) complex: [Ni(GAA)(Ser)

Vibrational assignment and structural determination for the guanidinoaceticserinenickel(II) complex have been made through DFT:B3LYP/6-31G calculations. 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 co-ordinate treatments have been made in order to clarify the assignments 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.     

Fourier-transform infrared and Raman spectra of cysteine dichloride cadmium(II) anion DFT: B3LYP/3-21G(d) structural and vibrational calculations

The cysteine dichloride cadmium(II) potassium was synthesized and the structural analysis was carried out through the following methods: determination of the C, H, N, S and O contents, thermogravimetry, infrared and Raman spectra. Assuming Cd-S, Cd-O (O-carboxilate) and Cd-N bonds, several hypothetical structures were calculated by means DFT: B3LYP/3-21G(d) quantum mechanical method. The calculations shows that the Cd-S and Cd-N central bonds are favoured in the anion complex formation [Cd(Cys)Cl2]-, being the stabilization energy 55.52 kcal mol(-1) lower than isotopomers with Cd-S and Cd-O central bonds. Features of the infrared and Raman spectra confirm the theoretical structural prediction. Full assignment of the vibrational spectra is proposed based on the DFT procedure, and in order to confirm the C-H, N-H, C-C, C-N, Cd-N, Cd-S and Cd-Cl stretching and the HNH and HCH bending, a normal coordinate analysis based on local symmetry force field for -SC(H2)C-, -CdN(H2)C- and -SCd(Cl2)N- fragments was carried out.     

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

2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR 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. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.     

Experimental infrared spectra of Cl-(ROH) (R = H, CH3, CH3CH2) complexes in the gas-phase

Infrared multiple photon dissociation spectra for the chloride ion solvated by either water, methanol or ethanol have been recorded using an FTICR spectrometer coupled to a free-electron laser, and are presented here along with assignments to the observed bands. The assignments made to the Cl(-)/H(2)O, Cl(-)(CH(3)OH), and Cl(-)(CH(3)CH(2)OH) spectra are based on comparison with the neutral H(2)O, CH(3)OH, and CH(3)CH(2)OH spectra, respectively. This work confirms that a band observed around 1400 cm(-1) in the Cl(-)(H(2)O) spectrum is not due to the Ar tag in Ar predissociation spectra. The carrier of this band is, most likely, the first overtone of the OHCl bend. Based on the position of the overtone in the IRMPD spectrum, 1375 cm(-1), the fundamental must occur very close to 700 cm(-1) and observation of this band should aid theoretical treatments of the spectrum of this complex. B3LYP/6-311++G(2df,2pd) calculations are shown to reproduce the IRMPD spectra of all three solvated chloride species. They also predict that attaching one or two Ar atoms to the Cl(-)(H(2)O) complex results in a shift of no more than a few wavenumbers in the fundamental bands for the bare complex, in agreement with previous experiment. For both alcohol-Cl(-) complexes, the S(N)2 "backside attack" isomers are not observed and Cl(-) is predicted theoretically, and confirmed experimentally, to be bound to the hydroxyl hydrogen. For Cl(-)(CH(3)CH(2)OH), the trans and gauche conformers are similar in energy, with the gauche conformer predicted to be thermodynamically favoured. The experimental infrared spectrum agrees well with that predicted for the gauche conformer but a mixture of gauche and anti conformers cannot be ruled out based on the experimental spectra nor on the computed thermochemistry.     

Experimental and computational studies on the molecular energetics of chlorobenzophenones

The standard (p degrees = 0.1 MPa) molar enthalpies of formation, Delta(f)H(m)degrees, of crystalline 2-, 3- and 4-chlorobenzophenone and 4,4'-dichlorobenzophenone were derived from the standard molar energies of combustion, Delta(c)U(m)degrees, in oxygen, to yield CO(2)(g), N(2)(g), and HCl x 600H(2)O(l), at T = 298.15 K, measured by rotating bomb combustion calorimetry. The Calvet high-temperature vacuum sublimation technique was used to measure the enthalpy of sublimation, Delta(cr)(g)H(m)degrees, of the compound 2-chlorobenzophenone. For the other three compounds, the standard molar enthalpies of sublimation, at T = 298.15 K were derived by the Clausius-Clapeyron equation, from the temperature dependence of the vapor pressures of these compounds, measured by the Knudsen-effusion technique. From the values of Delta(f)H(m)degrees and Delta(cr)(g)H(m)degrees, the standard molar enthalpies of formation of all the compounds, in the gaseous phase, Delta(f)H(m)degrees (g), at T = 298.15 K, were derived. These values were also calculated by using the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d) computational approach.     

Theoretical proton affinity and fluoride affinity of nerve agent VX

Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -ΔE ～ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(═O)(Me)-S-(CH(2))(2)-N(+)(iPr)═CHMe] product and the destruction product forming Et-O-P(═O)(Me)-SMe + CH(2)═N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(═O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -ΔE ～ 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems.     

Energetics of the O-H bond and of intramolecular hydrogen bonding in HOC6H4C(O)Y (Y = H, CH3, CH2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds

The energetics of the phenolic O-H bond in a series of 2- and 4-HOC 6H 4C(O)Y (Y = H, CH3, CH 2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH 3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds and of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y, was investigated by using a combination of experimental and theoretical methods. The standard molar enthalpies of formation of 2-hydroxybenzaldehyde (2HBA), 4-hydroxybenzaldehyde (4HBA), 2'-hydroxyacetophenone (2HAP), 2-hydroxybenzamide (2HBM), and 4-hydroxybenzamide (4HBM), at 298.15 K, were determined by micro- or macrocombustion calorimetry. The corresponding enthalpies of vaporization or sublimation were also measured by Calvet drop-calorimetry and Knudsen effusion measurements. The combination of the obtained experimental data led to Delta f H m (o)(2HBA, g) = -238.3 +/- 2.5 kJ.mol (-1), DeltafHm(o)(4HBA, g) = -220.3 +/- 2.0 kJ.mol(-1), Delta f H m (o)(2HAP, g) = -291.8 +/- 2.1 kJ.mol(-1), DeltafHm(o)(2HBM, g) = -304.8 +/- 1.5 kJ.mol (-1), and DeltafHm(o) (4HBM, g) = -278.4 +/- 2.4 kJ.mol (-1). These values, were used to assess the predictions of the B3LYP/6-31G(d,p), B3LYP/6-311+G(d,p), B3LYP/aug-cc-pVDZ, B3P86/6-31G(d,p), B3P86/6-311+G(d,p), B3P86/aug-cc-pVDZ, and CBS-QB3 methods, for the enthalpies of a series of isodesmic gas phase reactions. In general, the CBS-QB3 method was able to reproduce the experimental enthalpies of reaction within their uncertainties. The B3LYP/6-311+G(d,p) method, with a slightly poorer accuracy than the CBS-QB3 approach, achieved the best performance of the tested DFT models. It was further used to analyze the trends of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y evaluated by the ortho-para method and to compare the energetics of the phenolic O-H bond in 2- and 4-HOC 6H 4C(O)Y compounds. It was concluded that the O-H bond "strength" is systematically larger for 2-hydroxybenzoyl than for the corresponding 4-hydroxybenzoyl isomers mainly due to the presence of the intramolecular O...H hydrogen bond in the 2-isomers. The observed differences are, however, significantly dependent on the nature of the substituent Y, in particular, when an intramolecular H-bond can be present in the radical obtained upon cleavage of the O-H bond.     

Structural study on 2,2'-(methylimino)bis(N,N-dioctylacetamide) complex with Re(VII)O4- and Tc(VII)O4- by 1H NMR, EXAFS, and IR spectroscopy

The structures of the complex of 2,2'-(methylimino)bis(N,N-dioctylacetamide) (MIDOA) with M(VII)O(4)(-) (M = Re and Tc), which were prepared by liquid-liquid solvent extraction, were investigated by using (1)H nuclear magnetic resonance (NMR), extended X-ray absorption fine structure (EXAFS), and infrared (IR) spectroscopy. The (1)H NMR spectra of the complex of MIDOA with Re(VII)O(4)(-) prepared in the organic solution suggest the transfer of a proton from aqueous to organic solution and the formation of the H(+)MIDOA ion. The EXAFS spectra of the complexes of H(+)MIDOA with Re(VII)O(4)(-) and Tc(VII)O(4)(-) show only the M-O coordination of the aquo complexes, suggesting that the chemical state of M(VII)O(4)(-) was unchanged during the extraction process. The results from (1)H NMR and EXAFS, therefore, provide evidence of M(VII)O(4)(-)···H(+)MIDOA complex formation in the organic solution. The IR spectra of Re(VII)O(4)(-)···H(+)MIDOA and Tc(VII)O(4)(-)···H(+)MIDOA were analyzed based on the structures and the IR spectra that were calculated at the B3LYP/cc-pVDZ level. Comparison of the observed and calculated IR spectra demonstrates that an intramolecular hydrogen bond is formed in H(+)MIDOA, and the M(VII)O(4)(-) ion interacts with H(+)MIDOA through multiple C-H(n)···O hydrogen bonds.     

Vibrational assignments, normal coordinate analysis, B3LYP calculations and conformational analysis of methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate

The Raman and infrared spectra of solid methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate (MAMPC, C7H8N4S3) were measured in the spectral range of 3700-100 cm(-1) and 4000-200 cm(-1) with a resolution of 4 and 0.5 cm(-1), respectively. Room temperature 13C NMR and (1)H NMR spectra from room temperature down to -60 °C were also recorded. As a result of internal rotation around C-N and/or C-S bonds, eighteen rotational isomers are suggested for the MAMPC molecule (Cs symmetry). DFT/B3LYP and MP2 calculations were carried out up to 6-311++G(d,p) basis sets to include polarization and diffusion functions. The results favor conformer 1 in the solid (experimentally) and gaseous (theoretically) phases. For conformer 1, the two -CH3 groups are directed towards the nitrogen atoms (pyrazole ring) and CS, while the -NH2 group retains sp2 hybridization and C-CN bond is quasi linear. To support NMR spectral assignments, chemical shifts (δ) were predicted at the B3LYP/6-311+G(2d,p) level using the method of Gauge-Invariant Atomic Orbital (GIAO) method. Moreover, the solvent effect was included via the Polarizable Continuum Model (PCM). Additionally, both infrared and Raman spectra were predicted using B3LYP/6-31G(d) calculations. The recorded vibrational, 1H and 13C NMR spectral data favors conformer 1 in both the solid phase and in solution. Aided by normal coordinate analysis and potential energy distributions, confident vibrational assignments for observed bands have been proposed. Moreover, the CH3 barriers to internal rotations were investigated. The results are discussed herein are compared with similar molecules whenever appropriate.     

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.     

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.