Determination of molecular structure in solution using vibrational circular dichroism spectroscopy: the supramolecular tetramer of S-2,2'-dimethyl-biphenyl-6,6'-dicarboxylic acid

The infrared (IR) and vibrational circular dichroism (VCD) spectra of S-2,2'-dimethyl-biphenyl-6,6'-dicarboxylic acid, S-1, in CDCl(3) solution are concentration-dependent, showing that oligomerization occurs with increasing concentration. DFT calculations support the conclusion that the oligomer formed is the cyclic tetramer (S-1)(4), in which S-1 monomers are linked by hydrogen(H)-bonded (COOH)(2) moieties. Due to the existence of two inequivalent tautomeric conformations of each (COOH)(2) moiety, six inequivalent conformations of (S-1)(4) are possible. B3LYP/6-31G* DFT calculations predict that the conformation "aaab", possessing three equivalent (COOH)(2) conformations, a, and one tautomeric conformation, b, has the lowest free energy. B3LYP/6-31G* IR and VCD spectra vary substantially with conformation. The B3LYP/6-31G* IR and VCD spectra of the C=O stretch modes of "aaab" are in excellent agreement with the experimental spectra, while those of all other conformations exhibit poor agreement, confirming the prediction that the "aaab" conformation is the predominant conformation. Comparison of the calculated IR and VCD spectra of the six conformations to the experimental spectra in the range 1100-1600 cm(-1) further supports this conclusion. The study is the first to use VCD spectroscopy to determine the structure of a supramolecular species.     

Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin

The normal-mode spectrum for the four-coordinated heme compound Fe(II) octaethylporphyrin, Fe(OEP), has been determined by refining force constants to the experimental Fe vibrational density of states measured with nuclear resonance vibrational spectroscopy (NRVS). Convergence of the calculated spectrum to the data was achieved by first imposing D4 symmetry on the model structure as well as the force constants, progressively including different internal coordinates of motion, then allowing the true Ci (or S2) point group symmetry of the C(i)1 Fe(OEP) crystal structure. The NRVS-refined normal modes are in good agreement with Raman and IR spectra at high frequencies. Prior density functional theory predictions for a model porphyrin are similar to the core modes computed with the best-fit force field, but significant differences between D4 and Ci modes underline the sensitivity of porphyrin Fe normal modes to structural details. Some differences between the Ci best fit and the NRVS data can be attributed to intermolecular contacts not included in the normal-mode analysis.     

Analysis of the normal modes of molecules with D3h symmetry: Infrared spectra of monomeric s-triazine and cyanuric acid

Normal modes of s-triazine and cyanuric acid were calculated at the DFT(B3LYP)/6-311++G(d,p) level. These modes were analyzed in terms of potential energy distribution (PED), computed using a specially designed set of symmetry coordinates. The normal-mode analysis was described in detail and the PED matrix definition used in the calculations was provided. Particular attention has been devoted to the degenerate vibrations. The experimental infrared spectra of s-triazine and cyanuric acid isolated in low-temperature Ar matrices have been recorded and interpreted by comparison with the theoretically predicted normal modes. In the spectrum of matrix-isolated s-triazine, the IR bands originating from ¹³C and ¹⁵N isotopologues with one of the ring atoms substituted by a rare isotope were detected. These bands were identified thanks to the excellent agreement between the experimentally observed and theoretically predicted isotope shifts.     

Vibrational spectra of the trifluoromethylsulfinate anion and scaled quantum mechanical force fields for CF3SO2- and CF3SeO2-

The infrared and Raman spectra of KCF(3)SO(2) were obtained and the observed spectral features assigned to the expected normal modes of vibration. Besides, the vibrational properties of the CF(3)SO(2)(-) and CF(3)SeO(2)(-) related anions were studied by means of density functional theory (DFT) techniques. After obtaining the optimized geometrical parameters and conformations, the vibrational wavenumbers and the associated force constants were calculated. The original force fields in cartesian coordinates were transformed to local symmetry coordinates and subsequently scaled to reproduce the experimental wavenumbers. Some trends observed in the force constants of the studied species and of the related CF(3)SO(3)(-) anion could be explained by the differences in geometrical parameters.     

An experimental value for the B(1u) C-H stretch mode in benzene

We here present experimental infrared spectra on two (C(6)H(6))(C(6)D(6)) benzene dimer isomers in the gas phase. The spectra show that the two benzene molecules in the dimer are symmetrically inequivalent and have distinct IR signatures. One of the two molecules is in a site of low symmetry, which leads to the IR activation of fundamental modes that are IR forbidden by symmetry in the monomer. In the spectra, all four fundamental C-H stretch modes of benzene are observed. Modes in the dimer are shifted up to 3 cm(-1) to the red, compared to the modes that are known for the monomer. For the nu(13) B(1u) C-H stretch fundamental mode of benzene, a first experimental value of 3015(+2) (-5) cm(-1) is determined, in excellent agreement with anharmonic frequency calculations presented here.     

Excited-state distortions of cyclometalated Ir(III) complexes determined from the vibronic structure in luminescence spectra

The luminescence spectra of [(tpy)(2)Ir(CN-t-Bu)2](CF(3)SO(3)) in methylcyclohexane glass and frozen n-nonane at 15 K reveal well-resolved vibronic fine structure. The vibronic peaks are assigned by comparison with the vibrational frequencies obtained from Raman and IR spectra and those obtained using DFT electronic structure calculations. The magnitudes of the distortions along the normal coordinates are calculated by fitting the emission spectra using the time-dependent theory of spectroscopy. Broadening effects and the MIME frequency observed at room temperature are interpreted. The most highly distorted normal modes involve atomic motions on the tpy ligand, consistent with the metal to ligand/ligand centered assignment of the electronic transition.     

Vibrational frequencies and structural determinations of tetrachlorobutatriene

The normal mode frequencies and corresponding vibrational assignments of tetrachlorobutatriene in D2h symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of the six types of motion (C=C stretch, CCl2 scissors, CCl2 twist, CCl2 wag, CCl2 rock, and C=C=C bend) predicted by a group theoretical analysis. By comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors is derived.     

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH2CH2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6-311++G* basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C2h and C2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G* basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.     

Vibrational frequencies and structural determinations of 1,5-dicarba-closo-pentaborane(5)

The normal mode frequencies and corresponding vibrational assignments of 1,5-dicarba-closo-pentaborane(5) are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of six types of motion predicted by a group theoretical analysis (C-H stretch, B-H stretch, B-B stretch, B-C stretch, C-H wag, and B-H wag) utilizing the D(3h) symmetry of the molecule. By comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors is derived. Theoretical IR and Raman intensities are reported.     

Fourier transform infrared and Raman spectra of N-di-isopropylphosphorylguanidine (DPG)

The Fourier transform infrared and the Fourier transform Raman spectra of N-di-isopropylphosphorylguanidine (DPG) in the solid state and in aqueous solution were recorded and analyzed. Assuming Cs symmetry for different structural fragment of the molecule, the experimental and calculated band assignments of the nu(NH), delta(HNH), delta(CNH), nu(C=N), nu(PN), nu(CN), nu(PO) and nu(OC) normal modes suggested that the DPG exists as a tautomeric contribution of the phosphorylamine (I) and N-phosphorylimine (II) structural forms. [structures: see text]     

Vibrational frequencies and structural determination of trichloroboroxine

The normal mode frequencies and corresponding vibrational assignments of trichloroboroxine (B3O3Cl3) in D3h symmetry are examined theoretically using the Gaussian 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of five types of motion (B-Cl stretch, B-O stretch, B-Cl bend, O-B-O bend, and B(OOCl) umbrella motion) predicted by a group theoretical analysis. By comparing the vibrational frequencies with IR and Raman spectra available in the literature, a set of scaling factors is derived. Molecular orbitals and bonding are examined.     

Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory

Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2)(2)(H(2)O)(2)] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn(2)(CCA2)(4)(H(2)O)(2)] structure. Experimental and calculated (1)H, (13)C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.     

Spectroscopic and theoretical studies on nickel(II) complex of maleonitriledithiolate and 2,2'-bipyridine

The complete IR spectra of the title complex Ni(mnt)(bpy) (mnt=maleonitriledithiolate, bpy=2,2'-bipyridine) and a new method to analyze vibrational spectra for such a complicated metal complex are reported in this paper. The molecular geometry, binding, electronic structure and spectroscopic property of it have been studied in detail by theoretical calculations. The geometry optimization from PM3 calculations give that this molecule is of a planar structure with the symmetry point group C(2v) and its ground state is the spin triplet state. The vibrational and electronic spectra were calculated by PM3 and ZINDO/S methods, respectively. The scientific method of analyzing vibrational spectra is established herein by giving main fixed points and pivotal vibrational units. Besides the regular symbols, the new defined symbols eta and M play an important role in describing the vibration modes accurately and vividly.     

Spectroscopic and density functional studies of the dinitrosyl metalloporphyrin complexes Fe(P)(NO)2 and Ru(P)(NO)2

Experimental evidence including infrared spectra for the formation of the dinitrosyl metalloporphyrin complexes M(P)(NO)(2) (M = Ru or Fe, P = tetraphenylporphyrin (TPP), octaethylporphyrin (OEP), or tetra-m-tolylporphryin (TmTP)) is described. Although observation of a single NO stretching band in the IR spectrum of each M(P)(NO)(2) complex first suggested a centrosymmetric (D(4)(h)() or C(2)(h)()) structure, DFT geometry optimizations and frequency calculations of model complexes indicate that the trans-syn (C(2)(v)()) conformation should be more stable. The frequency calculations resolve the apparent ambiguity in the IR spectra in terms of the relative oscillator strengths of the predicted IR bands.     

Infrared spectroscopic studies of siderophore-related hydroxamic acid ligands adsorbed on titanium dioxide

The adhesion of bacteria to metal oxide and other mineral surfaces may involve bacterial siderophores, many of which contain hydroxamic acid (Ha) ligands. The adsorption behavior of the siderophore-related ligands acetohydroxamic acid, N-methylformohydroxamic acid, N-methylacetohydroxamic acid, and 1-hydroxy-2-piperidone on titanium dioxide thin films has been investigated using in situ ATR-IR spectroscopy with variation of concentration and pH. All the ligands were found to adsorb strongly on the TiO2 surface as hydroxamate ions and form bidentate surface complexes. Vibrational modes involving C=O stretching and N-O stretching of these ligands were assigned by comparing observed IR spectra with those calculated by the density functional method at the B3LYP/6-31+G(d) level. Calculated spectra of the complex [Ti(Ha)(OH)4]-, used to model the TiO2 surface, were compared with observed spectra of adsorbed hydroxamic acids. These results suggest that hydroxamic acid ligands in siderophores would be expected to bind to metal (oxide) and mineral surfaces during bacterial adhesion processes.     

Ab initio-based all-mode two-dimensional infrared spectroscopy of a sugar molecule

To construct two-dimensional infrared (2D IR) spectra having all vibrational modes of a molecule included is still quite challenging, both experimentally and theoretically. Here we report an ab initio-based all-mode 2D IR spectra simulation approach. Using deuterated glycolaldehyde (CH2OHCDO), the smallest sugar as a model molecule, we have calculated correlation 2D IR spectrum of its entire 3N-6 (N=8) normal modes in the mid-to-far-IR region (4000-0 cm(-1)), using quantum chemical anharmonic frequency and anharmonicity computations in conjunction with time-domain third-order nonlinear response functions. The calculated 2D IR spectra were found to contain a network of structural and dynamical parameters of the molecule. It is found that certain spectral regions, once enlarged, show features that are in reasonable agreement with limited but already available single- and dual-frequency 2D IR experimental results. The extension of narrow-band 2D IR spectroscopy into the full mid-to-far-IR regime would allow us to characterize the structural distributions and dynamics of molecular complexes in condensed phases with sufficient number of parameters.     

Hydrolysis of uranyl(VI) in acidic and basic aqueous solutions using a noncomplexing organic base: a multivariate spectroscopic and statistical study

In the field of actinide aqueous chemistry, this work aims to resolve some controversy about uranyl(VI) hydroxide species present in basic aqueous solutions. We revisit the Raman, IR, and UV-visible spectra with two new approaches. First, Raman, IR and UV data were recorded systematically from aqueous solutions with the noncomplexing electrolyte (C(2)H(5))(4)NNO(3) at 25 °C and 0.1 MPa ([U(total)] = 0.005-0.105 M) in H(2)O and D(2)O over a wide range of -log mH(D)(+) between 2.92 and 14.50. Second, vibrational spectra (IR and Raman) of basic solutions in H(2)O and D(2)O were analyzed using the Bayesian Positive Source Separation method to estimate pure spectra of individual species. In D(2)O solutions, the new spectroscopic data showed the occurrence of the same species as those in H(2)O. As observed for the wavenumber of the symmetric stretching mode, the wavenumber characteristic of the O═U═O antisymmetric stretching mode decreases as the number of OH(D)(-) ligands increases. These kinds of data, completed by (1) analysis of the signal widths, (2) persistence of the apparent exclusion rule between IR and Raman spectra of the uranyl species stretching modes, and (3) interpretation of the absorption UV-visible spectra, allow discussion of the chemistry, structures, and polynuclearity of uranyl(VI) species. In moderate basic solutions, the presence of two trimers is suggested. In highly basic solutions ([OH(-)] ≈ 3 M), the two monomers UO(2)(OH)(4)(2-) and UO(2)(OH)(5)(3-) are confirmed to be in good agreement with earlier EXAFS and NMR results. The occurrence of the UO(2)(OH)(6)(4-) monomer is also suggested from the more basic solutions investigated.     

Quantum chemistry-based analysis of the vibrational spectra of five-coordinate metalloporphyrins [M(TPP)Cl

Vibrational properties of the five-coordinate porphyrin complexes [M(TPP)(Cl)] (M = Fe, Mn, Co) are analyzed in detail. For [Fe(TPP)(Cl)] (1), a complete vibrational data set is obtained, including nonresonance (NR) Raman, and resonance Raman (RR) spectra at multiple excitation wavelengths as well as IR spectra. These data are completely assigned using density functional (DFT) calculations and polarization measurements. Compared to earlier works, a number of bands are reassigned in this one. These include the important, structure-sensitive band at 390 cm(-1), which is reassigned here to the totally symmetric nu(breathing)(Fe-N) vibration for complex 1. This is in agreement with the assignments for [Ni(TPP)]. In general, the assignments are on the basis of an idealized [M(TPP)]+ core with D(4h) symmetry. In this Work, small deviations from D(4h) are observed in the vibrational spectra and analyzed in detail. On the basis of the assignments of the vibrational spectra of 1, [Mn(TPP)(Cl)] (2), and diamagnetic [Co(TPP)(Cl)] (3), eight metal-sensitive bands are identified. Two of them correspond to the nu(M-N) stretching modes with B(1g) and Eu symmetries and are assigned here for the first time. The shifts of the metal sensitive modes are interpreted on the basis of differences in the porphyrin C-C, C-N, and M-N distances. Besides the porphyrin core vibrations, the M-Cl stretching modes also show strong metal sensitivity. The strength of the M-Cl bond in 1-3 is further investigated. From normal coordinate analysis (NCA), force constants of 1.796 (Fe), 0.932 (Mn), and 1.717 (Co) mdyn/A are obtained for 1-3, respectively. The weakness of the Mn-Cl bond is attributed to the fact that it only corresponds to half a sigma bond. Finally, RR spectroscopy is used to gain detailed insight into the nature of the electronically excited states. This relates to the mechanism of resonance enhancement and the actual nature of the enhanced vibrations. It is of importance that anomalous polarized bands (A(2g) vibrations), which are diagnostic for vibronic mixing, are especially useful for this purpose.     

Infrared photodissociation spectroscopy of mononuclear iron carbonyl anions

The infrared photodissociation spectroscopy of mass-selected mononuclear iron carbonyl anions Fe(CO)(n)(-) (n = 2-8) were studied in the carbonyl stretching frequency region. The FeCO(-) anion does not fragment when excited with infrared light. Only a single IR active band was observed for the Fe(CO)(2)(-) and Fe(CO)(3)(-) anions, consistent with theoretical predictions that these complexes have linear D(∞h) and planar D(3h) symmetry, respectively. The Fe(CO)(4)(-) anion is the most intense peak in the mass spectra and was characterized to have a completed coordination sphere with high stability. Anion clusters larger than n = 4 were determined to involve a Fe(CO)(4)(-) core anion that is progressively solvated by external CO molecules. Three CO stretching vibrational fundamentals were observed for the Fe(CO)(4)(-) core anion, indicating that the Fe(CO)(4)(-) anion has a C(3v) structure. All the carbonyl stretching frequencies of the Fe(CO)(n)(-) anion complexes are red-shifted with respect to those of the corresponding neutrals.     

Infrared, Raman, and inelastic neutron scattering spectra of dodecahedrane: an I(h) molecule in T(h) site symmetry

The Raman spectrum of crystalline dodecahedrane, C20H20, a species of nominal I(h) symmetry, exhibits splitting of the H(g) Raman active modes. The Raman inactive gerade vibrations of G(g), T(1g), and T(2g) symmetry are found to have weak Raman activity. The IR forbidden vibrations of T(2u), G(u), and H(u) type have moderate IR activity. All of this is consistent with the T(h) site symmetry. A treatment of the structure and vibrations of dodecahedrane using a periodic lattice DFT method results in a slightly distorted T(h) structure with six C-C bonds that are 0.001 A longer than the other 24. The vibrational spectrum computed for this structure exhibits splittings of the H(g) modes that are consistent with the observed spectra, but the computed splittings are larger than observed in room-temperature data. A complex pattern observed in the C-H stretching region is assigned. The inelastic neutron scattering spectrum calculated from the computed normal modes for the T(h) molecule in the lattice agrees quantitatively with experiment when overtone and combination transitions are included and allowance is made for anharmonicity of the C-H stretch motion. Finally, it is argued that the existing crystallographic determination of the average C-C bond length of 1.544 A is shortened by disorder and should be revised upward to agree with the computed value of 1.558 A.