Showing papers on "Infrared spectroscopy published in 2007"

Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures

Abstract: Infrared spectroscopy is one of the oldest and well established experimental techniques for the analysis of secondary structure of polypeptides and proteins. It is convenient, non-destructive, requires less sample preparation, and can be used under a wide variety of conditions. This review introduces the recent developments in Fourier transform infrared (FTIR) spectroscopy technique and its applications to protein structural studies. The experimental skills, data analysis, and correlations between the FTIR spectroscopic bands and protein secondary structure components are discussed. The applications of FTIR to the secondary structure analysis, conformational changes, structural dynamics and stability studies of proteins are also discussed.

Fourier Transform Infrared Spectrometry

Abstract: The theory and instrumentation for Fourier transform infrared spectrometry are discussed. These instruments measure infrared spectra of the same quality as spectra measured on grating spectrometers in about one thousandth of the time. Their sensitivity advantage for spectra measured in equal times is between a factor of 10 and 100. Commercial spectrometers are now available from nine vendors in North America. Important areas of chemistry include atmospheric monitoring, surface chemistry, and on-line identification of chromatographically separated materials. Many new biochemical and biomedical applications are also becoming apparent, including investigations of phase transitions in lipids and studies of the biocompatibility of implant polymers.

Mott Transition in VO2 Revealed by Infrared Spectroscopy and Nano-Imaging

Abstract: Electrons in correlated insulators are prevented from conducting by Coulomb repulsion between them. When an insulator-to-metal transition is induced in a correlated insulator by doping or heating, the resulting conducting state can be radically different from that characterized by free electrons in conventional metals. We report on the electronic properties of a prototypical correlated insulator vanadium dioxide in which the metallic state can be induced by increasing temperature. Scanning near-field infrared microscopy allows us to directly image nanoscale metallic puddles that appear at the onset of the insulator-to-metal transition. In combination with far-field infrared spectroscopy, the data reveal the Mott transition with divergent quasi-particle mass in the metallic puddles. The experimental approach used sets the stage for investigations of charge dynamics on the nanoscale in other inhomogeneous correlated electron systems.

Determining Beta Sheet Crystallinity in Fibrous Proteins by Thermal Analysis and Infrared Spectroscopy

Abstract: We report a study of self-assembled beta-pleated sheets in B. mori silk fibroin films using thermal analysis and infrared spectroscopy. B. mori silk fibroin may stand as an exemplar of fibrous proteins containing crystalline beta-sheets. Materials were prepared from concentrated solutions (2−5 wt % fibroin in water) and then dried to achieve a less ordered state without beta-sheets. Crystallization of beta-pleated sheets was effected either by heating the films above the glass transition temperature (Tg) and holding isothermally or by exposure to methanol. The fractions of secondary structural components including random coils, alpha-helices, beta-pleated sheets, turns, and side chains were evaluated using Fourier self-deconvolution (FSD) of the infrared absorbance spectra. The silk fibroin films were studied thermally using temperature-modulated differential scanning calorimetry (TMDSC) to obtain the reversing heat capacity. The increment of the reversing heat capacity ΔCp0(Tg) at the glass transition fo...

DRIFT study of manganese/ titania-based catalysts for low-temperature selective catalytic reduction of NO with NH3.

Abstract: Manganese oxides and iron-manganese oxides supported on TiO2 were prepared by the sol−gel method and used for low-temperature selective catalytic reduction (SCR) of NO with NH3. Base on the previous study, Mn(0.4)/TiO2 and Fe(0.1)−Mn(0.4)/TiO2 were then selected to carry out the in situ diffuse reflectance infrared transform spectroscopy (DRIFT) investigation for revealing the reaction mechanism. The DRIFT spectroscopy for the adsorption of NH3 indicated the presence of coordinated NH3 and NH4+ on both of the two catalysts. When NO was introduced, the coordinated NH3 on the catalyst surface was consumed rapidly, indicating these species could react with NO effectively. When NH3 was introduced into the sample preadsorbed with NO + O2, SCR reaction would not proceed on Mn(0.4)/TiO2. However, for Fe(0.1)−Mn(0.4)/TiO2 the bands due to coordinated NH3 on Fe2O3 were formed. Simultaneously, the bidentate nitrates were transformed to monodentate nitrates and NH4+ was detected. And NO2 from the oxidation of NO on ...

Size-dependent structural transformations of hematite nanoparticles. 1. Phase transition.

Abstract: Using Fourier Transform InfraRed (FTIR) spectroscopy, Raman spectroscopy, X-ray diffraction (XRD), and Transmission Electron Microscopy (TEM), we characterize the structure and/or morphology of hematite (α-Fe2O3) particles with sizes of 7, 18, 39 and 120 nm. It is found that these nanoparticles possess maghemite (γ-Fe2O3)-like defects in the near surface regions, to which a vibrational mode at 690 cm−1, active both in FTIR and Raman spectra, is assigned. The fraction of the maghemite-like defects and the net lattice disorder are inversely related to the particle size. However, the effect is opposite for nanoparticles grown by sintering of smaller hematite precursors under conditions when the formation of a uniform hematite-like structure throughout the aggregate is restricted by kinetic issues. This means that not only particle size but also the growth kinetics determines the structure of the nanoparticles. The observed structural changes are interpreted as size-induced α-Fe2O3 ↔ γ-Fe2O3 phase transitions. We develop a general model that considers spinel defects and absorbed/adsorbed species (in our case, hydroxyls) as dominant controls on structural changes with particle size in hematite nanoparticles, including solid-state phase transitions. These changes are represented by trajectories in a phase diagram built in three phase coordinates—concentrations of spinel defects, absorbed impurities, and adsorbed species. The critical size for the onset of the α → γ phase transition depends on the particle environment, and for the dry particles used in this study is about 40 nm. The model supports the existence of intermediate phases (protohematite and hydrohematite) during dehydration of goethite. We also demonstrate that the hematite structure is significantly less defective when the nanoparticles are immersed in water or KBr matrix, which is explained by the effects of the electrochemical double layer and increased rigidity of the particle environment. Finally, we revise the problem of applicability of IR spectroscopy to the lattice vibrations of hematite nanoparticles, demonstrating that structural comparison of different samples is much more reliable if it is based on the Eu band at about 460 cm−1 and the spinel band at 690 cm−1, instead of the A2u/Eu band at about 550 cm−1 used in previous work. The new methodology is applied to analysis of the reported IR spectra of Martian hematite.

Adsorption properties of HKUST-1 toward hydrogen and other small molecules monitored by IR

Abstract: Among microporous systems metal organic frameworks are considered promising materials for molecular adsorption. In this contribution infrared spectroscopy is successfully applied to highlight the positive role played by coordinatively unsaturated Cu2+ ions in HKUST-1, acting as specific interaction sites. A properly activated material, obtained after solvent removal, is characterized by a high fraction of coordinatively unsaturated Cu2+ ions acting as preferential adsorption sites that show specific activities towards some of the most common gaseous species (NO, CO2, CO, N2 and H2). From a temperature dependent IR study, it has been estimated that the H2 adsorption energy is as high as 10 kJ mol−1. A very complex spectral evolution has been observed upon lowering the temperature. A further peculiarity of this material is the fact that it promotes ortho–para conversion of the adsorbed H2 species.

Attenuated Total Reflectance Fourier Transform Infrared Analysis of Fly Ash Geopolymer Gel Aging

Abstract: Structural changes in fly ash geopolymers activated with different sodium hydroxide and silicate concentrations are investigated using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy over a period of 200 days. A strong correlation is found between the concentration of silicate monomer in the activating solution and the position of the main Si−O−T stretching band in the FTIR spectrum, which gives an indication of the relative changes in the gel Si/Al ratio. The FTIR spectra of geopolymer samples with activating solution concentrations of up to 1.2 M SiO2 indicate that an Al-rich gel forms before the final gel composition is reached. The time required for the system to reach a steady gel composition depends on the silicate activating solution concentration and speciation. Geopolymers activated with solutions containing predominantly high-order silicate species rapidly reach a steady gel composition without first forming an Al-rich gel. A minimum silicate monomer concentration...

Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D2O

Abstract: We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D2O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.

Synthesis and properties of magnesium tetrahydroborate, Mg(BH4)2

Abstract: Mg(BH4)2 is one of the few complex hydrides which have the potential to meet the requirements for hydrogen storage materials, because it contains 14.9 mass% H and has suitable thermodynamic properties. It has not been investigated for hydrogen storage applications yet. In this study, several ways to synthesize solvated and desolvated magnesium tetrahydroborate by wet chemical and mechanochemical methods were tested and compared. A direct synthesis by a reaction of MgH2 with aminoboranes yields magnesium tetrahydroborate quantitatively and in pure form. The method is also applicable to the synthesis of other tetrahydroborates. The products were characterized by elemental analysis, in situ X-ray diffraction (XRD), infrared spectroscopy (FTIR), and thermal analysis methods, such as thermogravimetric analysis (TGA-DSC) and high-pressure calorimetry under a hydrogen atmosphere (HP-DSC).

Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide.

Abstract: The capability of 2D IR spectroscopy to elucidate time-evolving structures is enhanced by a programmable mid-IR pulse shaper that greatly improves the ease, speed, and accuracy of data collection. Traditional ways of collecting 2D IR spectra are difficult to implement, cause distorted peak shapes, and result in poor time resolution and/or phase problems. We report on several methods for collecting 2D IR spectra by using a computer-controlled germanium acoustooptic modulator that overcomes the above problems. The accuracy and resolution of each method is evaluated by using model metal carbonyl compounds that have well defined lineshapes. Furthermore, phase cycling can now be employed to largely alleviate background scatter from heterogeneous samples. With these methods in hand, we apply 2D IR spectroscopy to study the structural diversity in amyloid fibers of aggregated human islet amyloid polypeptide (hIAPP), which is involved with type 2 diabetes. The 2D IR spectra reveal that the β-sheet fibers have a large structural distribution, as evidenced by an inhomogeneously broadened β-sheet peak and strong coupling to random coil conformations. Structural diversity is an important characteristic of hIAPP because it may be that partly folded peptides cause the disease. This experiment on hIAPP is an example of how computer generation of 2D IR pulse sequences is a key step toward automating 2D IR spectroscopy, so that new pulse sequences can be implemented quickly and a diverse range of systems can be studied more easily.

Infrared spectroscopy of organometallic ions in the gas phase: from model to real world complexes.

Abstract: Gas phase mid-infrared spectroscopy of molecular ions can nowadays be performed with high performance mass spectrometers coupled to free electron lasers (FEL). The wide and continuous tunability of highly intense FELs in the mid-infrared region can be exploited for performing infrared multiple photon dissociation (IRMPD) spectroscopy of molecular ions. This review will focus on gas phase IRMPD spectroscopic investigations aiming at probing the structure and the reactivity of transition metal complexes. The performance of infrared spectroscopy for characterizing the coordination mode of polydentate ligands and the spin state of the metal will be illustrated. Infrared spectroscopy has also been exploited to probe the reactivity of metal complexes, and a special attention will be given to the infrared spectroscopy of reactive intermediates.

Experimental vibrational study of imidazolium-based ionic liquids: Raman and infrared spectra of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and 1-ethyl-3-methylimidazolium ethylsulfate.

Abstract: The vibrational structure of two room-temperature ionic liquids with the cation 1-ethyl-3-methylimidazolium [EMIM] and the respective anions bis(trifluoromethylsulfonyl)imide [TFSI] and ethylsulfate [EtOSO3] is investigated. In particular, attenuated total reflection (ATR) infrared (IR) as well as Raman spectra in the spectral range from 500 to 3500 cm−1 have been recorded and analyzed. Moreover, the depolarization ratios of the Raman lines are determined. The individual peaks are assigned to the corresponding vibrational modes of the molecules. While the CH stretching region around 3000 cm−1 is dominating in Raman spectra, it is remarkably weak in IR spectra. Finally, the results for 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are compared to previous studies of single ions available in the literature. This comparison shows good agreement.

Modification of the surfaces of Wyoming montmorillonite by the cationic surfactants alkyl trimethyl, dialkyl dimethyl, and trialkyl methyl ammonium bromides.

Abstract: Surfaces of a Wyoming SWy-2 sodium montmorillonite were modified using microwave radiation through intercalation with the cationic surfactants octadecyltrimethylammonium bromide, dimethyldioctadecylammonium bromide, and methyltrioctadecylammonium bromide by an ion exchange mechanism. Changes in the surfaces and structure were characterized using X-ray diffraction (XRD), thermal analysis (TG) and infrared (IR) spectroscopy. Different configurations of surfactants within montmorillonite interlayer are proposed based on d(001) basal spacings. A range of surfactant molecular environments within the surface-modified montmorillonite are proposed based upon their thermal decomposition. IR spectroscopy using a smart endurance single bounce diamond attenuated total reflection (ATR) cell has been used to study the changes in the spectra of CH asymmetric and symmetric stretching modes of the surfactants to provide more information of the surfactant molecular configurations.

Spectroscopy of synthetic Mg-Fe pyroxenes I: Spin-allowed and spin-forbidden crystal field bands in the visible and near-infrared

Abstract: Understanding the fundamental crystal chemical controls on visible and near-infrared reflectance spectra of pyroxenes is critical to quantitatively assessing the mineral chemistry of pyroxenes viewed by remote sensing. This study focuses on the analysis ofspectroscopic measurements of a comprehensive set of synthetic Mg-Fe pyroxenes from the visible through the near-infrared (0.3-2.6 μm) to address the constraints of crystal structure and Fe^2+ content on spin-forbidden and spin-allowed crystal field absorptions in Ca-freeorthopyroxenes. The chemistry and oxidation state of the synthetic pyroxenes are characterized. Coordinated Mssbauer spectroscopy is used to determine site occupancy of Fe^2+ in the M1 and M2 crystallographic sites. Properties of visible and near-infrared absorption bands of the synthetic pyroxenes are quantified using the modified Gaussian model. The 1 and 2 μm spin-allowed crystal field absorption bands move regularly with increasing iron content, defining a much tighter trend than observed previously. A spin-allowed crystal field absorption band at 1.2 μm is explicitly verified, even at low total iron contents, indicating that some portion of Fe^2+ resides in the M1 site. The 1.2 μm band intensifies and shifts to longer wavelengths with increasing iron content. At visible wavelengths, spin-forbidden crystal field absorptions are observed in all iron-bearing samples. The most prominent absorption near 506 nm, attributed to iron in the M2 site, shifts to slightly longer wavelengths with iron content. The purity and extent of this pyroxene series allows visible wavelength absorption bands to be directly assigned to specific transitions of Fe^2+ in the M1 and M2 sites.

Tryptophan-based peptides to synthesize gold and silver nanoparticles: a mechanistic and kinetic study.

Abstract: Synthetic oligopeptides with a tryptophan residue at the C-terminus have been used for the synthesis of gold and silver nanoparticles at pH 11. The tryptophan residue in the peptides is responsible for the reduction of metal ions to the respective metals, possibly through electron transfer. A mechanistic pathway has been proposed to explain the reductive properties of the tryptophan moiety of the peptide based on some spectroscopic techniques, such as UV-visible and fluorescence spectroscopy. This study reveals that some of the peptide molecules are converted to its corresponding ditryptophan, kynurenine form and some cross-linked products, all of which are highly fluorescent species. The resultant peptide-functionalized metal nanoparticles have also been characterized by UV-visible spectroscopy, transmission electron microscopy, and Fourier transform IR spectroscopy and thermogravimatric analysis.

Spectroscopic Methods in Organic Chemistry

Abstract: Download Area for Lecturers: www.thieme.de/specials/hmz_en.html This book provides the necessary equipment for the application of spectroscopic methods in organic chemistry, as required as part of chemistry courses in all universities. The following methods are explained and examples given: * UV/Vis Spectroscopy, derivative Spectroscopy, chirooptical methods CD and ORD. * Aggregated molecules, charge transfer complexes, conjugated oligomers. * Infrared (IR) and Raman Spectroscopy, Fourier transform IR spectroscopy, and GC/IRcombination methods. * Nuclear Magnetic Resonance Spectroscopy (NMR), 1H-, 13C-, 19F-, 15N- und 31P-NMR, spin decoupling, triple resonance, INDOR difference spectroscopy, 2D- and 3D-NMR, COSY, TOCSY, ROESY and NOESY spectra, NOE, INEPT, and DEPT technique, DEPTQ, HETCOR, HRMAS, INADEQUATE and lanthanide shift reagents, simulation and calculation of spectra, and the combination of separation and NMR methods. The new 2D NMR techniques TOCSY, HMQC and HMBC, more examples and a guide to completely assign all 1H and 13C NMR signals of a given substrate. * Mass spectrometry (MS), electron impact and chemical ionization (EI and CI), fast atom bombardment (FAB), electrospray und thermospray ionization (ESI and TSI), MS/MS technique (MSn), field ionization and field desorption (FI and FD), atmospheric pressure chemical ionization (APCI), MALDI TOF technique, GC/MS, LC/MS, and HPLC-UV(DAD)-APCI combination MS/MS technique. Fourier transform ion cyclotron resonance MS (FT-ICR-MS). The layout and many tables help to introduce the reader to spectroscopy. The extensive and thorough approach makes the text the first choice both as a companion for the professional chemists and as a refresher course in practical spectroscopy. The second English edition is a translation of the 7th German edition, in which several major alterations and didactic improvements have been made. For further information on our chemistry products, please visit: Thieme Chemistry.

Replication and Coating of Silica Templates by Hydrothermal Carbonization

Abstract: Hierarchical carbon materials with functional groups residing at the surface are prepared for the first time by using nanostructured silica materials as templates in combination with hydrothermal carbonization at mild temperatures (180 °C). Different carbon morphologies (e.g., macroporous casts, hollow spheres, carbon nanoparticles, and mesoporous microspheres) can be obtained by simply altering the polarity of the silica surface. The surface functionality and hydrophilicity of the resulting materials are assessed by Fourier transform IR spectroscopy, X-ray photoelectron analysis, and water porosimetry. Raman spectroscopy and X-ray diffraction measurements show that the materials are of the carbon-black type, similar to charcoal.

Measuring Molecular Order in Poly(3-alkylthiophene) Thin Films with Polarizing Spectroscopies

Abstract: We measured the molecular order of poly(3-alkylthiophene) chains in thin films before and after melting through the combination of several polarized photon spectroscopies: infrared (IR) absorption, variable angle spectroscopic ellipsometry (SE), and near-edge X-ray absorption fine structure (NEXAFS). The data from the various techniques can be uniformly treated in the context of the dielectric constant tensor e for the film. The combined spectroscopies allow determination of the orientation distribution of the main-chain axis (SE and IR), the conjugated π system normal (NEXAFS), and the side-chain axis (IR). We find significant improvement in the backbone order of the films after recrystallization of the material at temperatures just below the melting temperature. Less aggressive thermal treatments are less effective. IR studies show that the changes in backbone structure occur without significant alteration of the structure of the alkyl side chains. The data indicate that the side chains exhibit signifi...

Ultrafast 2D-IR vibrational echo spectroscopy: A probe of molecular dynamics

Abstract: Ultrafast two dimensional infrared (2D-IR) vibra- tional echo spectroscopy has emerged as a powerful method for the study of molecular dynamics under thermal equilibrium con- ditions occurring on ultrafast time scales. Here, we describe ex- perimental details of 2D-IR vibrational echo spectroscopy in- cluding the experimental setup, pulse sequence, heterodyne de- tection, and extraction of the mainly absorptive part of the 2D- IR spectrum. As an experimental example, the measurements of the hydrogen bond dynamics of neat water and water in a high concentration of NaBr solution are presented and compared. The experiments are performed on OD stretching vibration of dilute HOD in H2O to eliminate contributions from vibrational exci- tation transport. A new experimental observable for extracting dynamical information that yields the frequency-frequency cor- relation function is presented. The observable is the inverse of the center line slope (CLS) of the 2D spectrum, which varies from a maximum of 1 to 0 as spectral diffusion proceeds. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first radiation field-matter interaction. Comparisons of the dynamics obtained from the data on water and the concentrated NaBr solutions show that the hydrogen bond dynamics of water around ions are much slower than in bulk water.