RESUMO
IR and Raman spectra of eugenol, isoeugenol and methyl eugenol have been obtained in the liquid phase. Vibrational spectroscopic results are discussed in relation to computed structures and spectra of the low energy conformations of these molecules obtained from DFT calculations at the B3LYP/cc-pVTZ level. Although computed differences in vibrational spectra for the different conformers were generally small, close examination, in conjunction with the experimental spectra, enabled conformational analysis of all three molecules. Anharmonic contributions to computed vibrational spectra were obtained from calculations of cubic and quartic force constants at the B3LYP/DZ level. This permitted the determination of the anharmonic fundamentals for comparison with the experimental IR and Raman band positions, leading to an excellent fit between calculated and experimental spectra. Band assignments were obtained in terms of potential energy distributions (ped's).
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RATIONALE: Ion mobility spectrometry-mass spectrometry (IMS-MS) offers an opportunity to combine measurements and/or calculations of the collision cross-sections and subsequent mass spectra with computational modelling in order to derive the three-dimensional structure of ions. IMS-MS has previously been reported to separate two components for the compound norfloxacin, explained by protonation on two different sites, enabling the separation of protonated isomers (protomers) using ion mobility with distinguishable tandem mass spectrometric (MS/MS) data. This study reveals further insights into the specific example of norfloxacin and wider implications for ion mobility mass spectrometry. METHODS: Using a quadrupole ion mobility time-of-flight mass spectrometer, the IMS and MS/MS spectra of norfloxacin were recorded and compared with theoretical calculations using molecular modelling (density functional theory), and subsequent collision cross-section calculations using projection approximation. RESULTS: A third significant component in the ion mobilogram of norfloxacin was observed under similar experimental conditions to those previously reported. The presence of the new component is convoluted by co-elution with another previously observed component. CONCLUSIONS: This case demonstrates the potential of combined IMS-MS/MS with molecular modelling information for increased understanding of 'small-molecule' fragmentation pathways.
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The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.
Assuntos
Alanina/química , Simulação por Computador , Glicina/química , Modelos Químicos , Teoria Quântica , Análise Espectral Raman/métodos , Ligação de Hidrogênio , Soluções/química , Espectrofotometria Infravermelho/métodos , Termodinâmica , Vibração , Água/químicaRESUMO
The IR, resonance Raman (RR) and electronic spectra of two phenylazonaphthol pigments, LRC Scarlet and 4BL Red, have been measured and assignments of the vibrational and electronic spectra were facilitated by ab initio calculation s at the B3-LYP/DZ level. Vibrational spectra indicate that the major species in the solid state are the hydrazo tautomers. Electronic spectra are in accordance with the nature of the electronic transitions predicted by time-dependent B3-LYP/DZ calculations.
Assuntos
Naftóis/química , Espectrofotometria Infravermelho/métodos , Análise Espectral Raman/métodos , Corantes/química , Elétrons , Modelos Químicos , Modelos Moleculares , Pigmentação , SoftwareRESUMO
Surface-enhanced resonance Raman scattering (SERRS) from the alpha-diimine complexes [Ru(bpm)(3)](2+) and [Ru(bpz)(3)](2+) is reported for the first time at a roughened silver electrode. In both cases, a possible adsorbate orientation has been proposed involving binding through nitrogen lone pair electrons to the silver surface, based on changes in band positions upon adsorption. The SERRS spectra of [Ru(bpm)(3)](2+) were found to change slightly with a change in applied potential. The relative intensity of the nu(C6C6') band was found to be dependent on both excitation wavelength and applied potential. This was ascribed to an active charge transfer (CT) mechanism operating synergistically with the electromagnetic mechanism. No such CT activity was observed in [Ru(bpz)(3)](2+). It is tentatively suggested that this behavior may arise from the different modes of adsorption of the two complexes.
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Rational design and synthesis of an IGD peptidomimetic substrate with significant motogenic activity.
Assuntos
Mimetismo Molecular , Peptídeos/síntese química , Motivos de Aminoácidos , Sequência de Aminoácidos , Anticorpos Anti-Idiotípicos/química , Relação Dose-Resposta a Droga , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Homologia de Sequência de AminoácidosRESUMO
IR spectra of N-methylpyrrole (NMP) have been measured following adsorption on, and subsequent desorption from, SiO(2), TiO(2), ZrO(2), SiO(2)-Al(2)O(3), H-mordenite, and sepiolite. Three modes of adsorption have been observed: (i) hydrogen bonding to surface hydroxyl groups, (ii) electron transfer at Lewis acidic surface sites, and (iii) proton transfer at Brønsted acidic surface sites. Protonation of NMP was detected only for adsorption on SiO(2)-Al(2)O(3) and H-mordenite, indicating the presence of Brønsted acidic sites with pK(a) values =-2.90. The results establish that the adsorption of NMP can provide useful information regarding the nature of surface acidity on oxides which is complementary to that obtained from other probe molecules such as NH(3) and pyridine.
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The adsorption of 2-chloropyridine on SiO(2), TiO(2), ZrO(2), SiO(2)-Al(2)O(3) and H-mordenite has been studied by IR spectroscopy. The different modes of interaction with oxide surfaces, i.e. hydrogen-bonding and adsorption at Brønsted or Lewis acid sites, was modelled by ab initio calculations at the B3LYP/DZ+(d) level. Adsorption on SiO(2) results in hydrogen bonding to surface hydroxyl groups, whereas the spectra obtained following adsorption on TiO(2) and ZrO(2) display evidence for electron transfer at Lewis acidic surface sites. Protonation of 2-chloropyridine at Brønsted acidic sites was detected only for adsorption on SiO(2)-Al(2)O(3) and H-mordenite, indicating the presence of Brønsted acidic sites on these oxide surfaces with pK(a) values =0.70. IR studies of 2-chloropyridine adsorption can provide useful information regarding the nature of surface acidity on oxides which is complementary to that obtained from other probe molecules such as NHs and pyridine.
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Óxidos/química , Piridinas/química , Adsorção , Óxido de Alumínio/química , Dióxido de Silício/química , Espectrofotometria Infravermelho/métodos , Espectroscopia de Infravermelho com Transformada de Fourier , Titânio/química , Zircônio/químicaRESUMO
Solid-state Raman and IR spectra of two polymorphic forms of each of three fenamates (flufenamic acid, mefenamic acid and tolfenamic acid) display subtle but highly reproducible differences. Many of these spectral differences can be ascribed to different conformations of these molecules, involving two of four possible orientations of one substituted benzene ring with respect to the other. Interpretation of the vibrational spectra in terms of conformational differences has been facilitated by DFT calculations at the B3LYP/cc-pVDZ level for each conformer. The calculated spectra are compared with the experimental spectra in order to identify the conformers present in two polymorphic forms in each case, and detailed band assignments are obtained from the DFT calculations.
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Fenamatos/química , Conformação Molecular , Análise Espectral Raman , Ácido Flufenâmico/química , Ácido Mefenâmico/química , Modelos Moleculares , Teoria Quântica , Espectrofotometria Infravermelho , Termodinâmica , Vibração , ortoaminobenzoatos/químicaRESUMO
Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the anions of urazole and 4-methylurazole, and their N-deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of both anions can be interpreted using a model that incorporates hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. In the case of the urazole anion it is shown that deprotonation occurs primarily at N1 rather than N4, but there is also evidence for the second tautomer both in the solid state and in aqueous solution. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.
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Ânions/química , Espectrofotometria Infravermelho/métodos , Análise Espectral Raman/métodos , Triazóis/química , Simulação por Computador , Ligação de Hidrogênio , Estrutura Molecular , Teoria Quântica , VibraçãoRESUMO
Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.
Assuntos
Aminoácidos/química , Ácido Aspártico/química , Ácido Glutâmico/química , Espectrofotometria Infravermelho/métodos , Análise Espectral Raman/métodos , Amidas/química , Físico-Química/métodos , Ligação de Hidrogênio , Espectroscopia de Ressonância Magnética , Espectrometria de Massas/métodos , Conformação Molecular , Peptídeos/química , Solventes/química , Espectroscopia de Infravermelho com Transformada de Fourier , VibraçãoRESUMO
The surface-enhanced Raman scattering (SERS) spectra of rhodanine adsorbed on silver nanoparticles have been examined using 514.5 and 632.8 nm excitation. There is evidence that, under the experimental conditions used, rhodanine undergoes a nanoparticle surface-induced reaction resulting in the formation of a dimeric species via the active methylene group in a process which is analogous to the Knoevenagel reaction. The experimental observations are supported by DFT calculations at the B3-LYP/cc-pVDZ level. Calculated energies for the interaction of the E and Z isomers of the dimers of rhodanine with silver nanoparticles support a model in which the (intra-molecular hydrogen bonded) E isomer dimer is of lower energy than the Z isomer. A strong band, at 1566 cm(-1), in the SERS spectrum of rhodanine is assigned to the nu(C double bond C) mode of the dimer species.
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Teoria Quântica , Rodanina/análogos & derivados , Rodanina/química , Prata/química , Ressonância de Plasmônio de Superfície/métodos , Dimerização , Estrutura Molecular , Fotoquímica , Análise Espectral Raman , Propriedades de SuperfícieRESUMO
For the first time, a full scaled quantum chemical normal coordinate analysis has been performed on [Ru(LL')(3)](2+) complexes, where LL' = 2,2'-bipyrazine (bpz) or 2,2'-bipyrimidine (bpm). Geometric structures were fully optimized using density functional theory and an effective core potential basis set. The infrared and Raman spectra were calculated using the optimized geometries. The results of the calculations provide a highly satisfactory fit to the experimental infrared and Raman spectra, and the potential energy distributions allow a detailed understanding of the vibrational bands therein.
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The IR and resonance Raman spectra of the nickel(II) complexes of dibenzo[b,i][1,4,8,11]tetraaza[14]annulene (TAA) and 5,7,12,14-tetramethyldibenzo[b,i][1,4,8,11]tetraaza[14]annulene (TMTAA) have been measured and compared with ab initio calculations of the vibrational wavenumbers at the B3-LYP level using the LanL2DZ basis set. An excellent fit is found between the experimental and calculated data, enabling precise vibrational assignments to be made. Surface-enhanced resonance Raman spectra were obtained following adsorption on Ag electrodes, with potentials in the range -0.1 to -1.1 V vs Ag/AgCl. There is evidence for contributions from both the electromagnetic and charge transfer (CT) surface enhancement mechanisms. The data indicate that variations in band intensities with electrode potential can be interpreted in terms of the CT mechanism.