CH Vibrational Modes Research Articles

Hydrogen-related defects in diamond: A comparison between observed and calculated FTIR spectra

A comprehensive and up-to-date compilation of observed and calculated hydrogen (H)-related peaks that occur in the near- and middle-infrared spectra of diamond is presented. The experimental database contains >300 observed peaks attributed to H-related impurities in natural diamond. The database of calculated peaks includes data from first-principles simulations of the FTIR spectra of different VxNyHz defects in diamond and contains >300 peaks that correspond to different C-H, N-H, and B-H vibrational modes for each VxNyHz defect. Less than ~10 % of observed H-related peaks have been assigned to specific defects. Consequently, the computational database was constructed to better understand the properties of different VxNyHz defects that may correspond to different observed peaks. In general, hydrogen-rich diamonds with a dominant Type Ib character and thus poorly aggregated N, show a larger number of low-intensity, H-related peaks compared to diamonds with a dominant Type Ia character. For example, ~51 % of observed H-related peaks are only observed in Type Ib diamonds, ~9 % of peaks are only observed in diamonds with a dominant Type Ia character and ~40 % of peaks are observed in both Type Ia and Type Ib diamonds. There is a major increase in the number of distinct H-related peaks in Type IaA + Ib diamonds compared to Type Ib diamonds suggesting N-aggregation processes responsible for the formation of A-centers may also produce many distinct VxNyHz defects capable of trapping H. There is a major decrease in the number of H-related peaks in Type IaA > Ib diamonds compared to Type IaA + Ib diamonds suggesting that many of the VxNyHz defects associated with the initial production of A-centers become unstable with increasing mantle residence time and the progressive loss of C-centers. These defects likely combine (or disaggregate and then re-combine) to form fewer, relatively more intense, H-related peaks observed in Type IaA > Ib diamonds. Many of these peaks persist through continued annealing in the mantle and are observed in Type IaA, IaAB, and IaB diamonds. Our data suggests that N and H incorporation are not correlated during diamond growth and that in the early stages of diamond residence, H is incorporated into many distinct VxNyHz defects that involve C- and A-centers. With continued residence and annealing, and the progressive formation A-centers and loss of C-centers, these defects aggregate to form relatively fewer, presumably more stable, VxNyHz defects such as VN3H.

Nonlinear optical properties and spectroscopic analysis of NB-pyrrole isosteres: Theoretical investigation

The nonlinear optical properties and spectroscopic analysis of mono and double NB- substituted pyrrole, namely: PN3B2 - PN3B4 - PN2B3 - PN2B4 - PN3,4N2,5, and PN2,5B3,4 have been investigated using two levels of theory: MP2/6-311+G (2df,2p) and DFT B3LYP/6-311++G(d,p). The vibrational spectra spam the range of 400 – 4000 cm−1, where each structure possesses 9 stretching, 8 bending, and 7 torsions modes, with only CH vibrational modes appeared in the mono-substituted group. The energy gap of the mono-substituted group is generally lower than that the double-substituted one. The most stable PN3B2 and PN3,4B2,5 isosteres show the maximum excitation energy and blueshift wavelengths. In solution, the bands are redshifted. The largest chemical shifts for the PN3B4 isostere's NH1 and BH1 protons are found at 8.5 and 4.8 ppm, respectively. The polarizability improves linearly as a function of the dipole moment. The PN2B4 introduces the highest dipole moment and consequently the polarizability, while PN3B2 shows opposite trend.

Intermolecular interaction study of l-Threonine in polar aprotic Solvent: Experimental and theoretical study

The present paper accounts for the interacting nature of CO, CH and OH vibrational modes of l-Threonine in polar aprotic solvent Dimethyl Formamide(DMF) using Raman spectroscopic and infrared(IR) techniques. The intermolecular interaction between l-Threonine and DMF are analyzed using Density Functional Theory (DFT), IEFPCM and M062X methods, each with a basis set 6–311++G (d, p)to predict the favourable interacting sites of the two molecules and to validate the experimental data with the theoretical calculations. The variation in peak frequencies has been explained for neat l-Threonine and their interactions at different concentrations (0.1 M, 0.3 M, 0.5 M, 0.7 M and 0.9 M). The wavenumbers of all the stretching modes (CO, CH and OH) shows a redshift. The intensity and the topology parameters of the intermolecular hydrogen bond at the bond critical points have been analyzed using the AIM theory of DFT and M062X methods. The intermolecular hydrogen bonding for the mentioned complexes and the study of the surface charge that encompasses the molecular cavity has also been carried out using the IEF-PCM solvation model under the same basis set. Electronic properties such as MEP surface study, frontier orbital analysis, and their corresponding energy gap have also been analyzed using DFT calculation. The frequencies derived from the computational and experimental data are found in good correlation to each other.

Raman spectroscopic analysis of oral cells in the high wavenumber region

Raman spectroscopy can provide a molecular-level signature of the biochemical composition and structure of cells with submicrometer spatial resolution and could be useful to monitor changes in composition for early stage and non-invasive cancer diagnosis, both ex-vivo and in vivo. In particular, the fingerprint spectral region (400–1800cm−1) has been shown to be very promising for optical biopsy purposes. However, limitations for discrimination of dysplastic and inflammatory processes based on the fingerprint region have been demonstrated. In addition, the Raman spectral signal of dysplastic cells is one important source of misdiagnosis of normal versus pathological tissues. The high wavenumber region (2800–3600cm−1) provides more specific information based on NH, OH and CH vibrations and can be used to identify the subtle changes which could be important for discrimination of samples. In this study, we demonstrate the potential of the high-wavenumber spectral region in this context by collecting Raman spectra of nucleolus, nucleus and cytoplasm from oral epithelial cancer (SCC-4) and dysplastic (DOK) cell lines and from normal oral epithelial primary cells, in vitro, in water immersion, which were then analyzed by principal components analysis as a method to discriminate the spectra. Analysis was performed before and after digital subtraction of the bulk water signal. In the normal cell line, the three subcellular regions are well differentiated before water subtraction, although the discrimination of the two nuclear regions is less well defined after water subtraction. Comparing the respective subcellular regions of the three cell lines, before water subtraction, the cell lines can be discriminated using sequential PCA and Feature Discriminant Analysis with up to ~100% sensitivity and 97% specificity for the cytoplasm, which is improved to 100% sensitivity and 99% specificity for the nucleus. The results are discussed in terms of discrimination comparing the CH vibrational modes of nucleic acids, proteins and lipids. The potential role of the OH vibrations, considering free water and confined water, in the discrimination of cell cultures and pathological processes are also discussed.

Temperature dependent Raman and X-ray diffraction studies of anhydrous milk fat

Raman spectroscopy was used to characterize the polymorphs and liquid state of anhydrous milk fat, with emphasis placed on the thermal evolution of the ester carbonyl stretching modes (1800–1700cm−1) and the comparative study of the Raman-active CC (1660cm−1) and CH (3000–2700cm−1) vibrational modes. Specific Raman signatures in the crystalline phase were found and attributed to the coexistence of two groups of triglycerides. This was confirmed using differential scanning calorimetry and X-ray diffraction methods. In the ester carbonyl band, the effect of changing temperature on both the number of modes and new defined intensity ratios was studied and enabled polymorph discrimination. CH stretching signals increased with polymorph stability, indicating the dominance of antisymmetric CH methylene vibrations as the anhydrous milk fats crystal lattice became more ordered. The change in intensity of the CH stretching bands as a function of temperature was used to probe the order-disorder transition.

The influence of wavelength, temporal sequencing, and pulse duration on resonant infrared matrix-assisted laser processing of polymer films

We have carried out a systematic investigation of laser ablation plume interactions in resonant infrared matrix-assisted pulsed laser evaporation. The laser source utilized in this study was a mid-infrared OPO capable of dual sequential ns pulses with adjustable delay ranging from 1 to 100 μs. This unique capability enabled us both to probe the ablation plume with a second laser pulse, and to effectively double the laser fluence. The primary ablation target used for this study consisted of poly(methyl methacrylate) dissolved in a binary mixture of methanol and toluene. Both the critical thermodynamic and optical properties of the binary mixture were determined and used to interpret our results. We found that deposition rates associated with single pulse irradiation tracks with the optical absorption coefficient in the spectral range from 2,700 to 3,800 nm. In the case of dual sequential pulses, discrepancies in this trend have been linked to the rate of change in the optical absorption coefficient with temperature. The influence of fluence on deposition rate was found to follow a sigmoidal dependence. Surface roughness was observed to have a diametrically opposed trend with pulse delay depending on whether the OH or CH vibrational mode was excited. In the case of CH excitation, we suggest that the rougher films are due to the absorbance of the second pulse by droplets within the plume containing residual solvent which leads to the formation of molecular balloons and hence irregularly shaped features on the substrate.

Crown ethers at the aqueous solution–air interface: 1. Assignments and surface spectroscopy

The surface of aqueous solutions of 4-Nitro Benzo-15-Crown-5 (NB15C5) and Benzo-15-Crown-5 (B15C5) has been studied using the surface sensitive technique vibrational sum frequency spectroscopy (VSFS). The NO, CN, COC and CH vibrational modes of these compounds at the air-water interface as well as OH vibrational modes of the surface water hydrating this compound have been targeted in order to obtain molecular information about arrangement and conformation of the adsorbed crown ether molecules at the air-water interface. The CH(2) vibrational modes of crown ethers have been identified and found to be split due to interaction with ether oxygen. The spectra provide evidence for the existence of a protonated crown complex moiety at the surface leading to the appearance of strongly ordered water species. The interfacial water species are influenced by the resulting charged interface and by the strong Zundel polarizability due to tunneling of the proton species between equivalent sites within the crown ring.

Cation–anion–water interactions in aqueous mixtures of imidazolium based ionic liquids

We have examined the cation–anion–water interactions in aqueous mixtures of imidazolium ionic liquids (ILs) over the whole composition range using FTIR spectroscopy. Changes in the peak positions or band areas of OH vibrational modes of water and CH vibrational modes of imidazolium cation as a function of IL concentration indicated a diminishing trend in hydrogen-bonding network of water and qualitative changes in solution structures. 1H NMR chemical shifts of C(2)H, HC(4)C(5)H and alkyl chain protons of imidazolium cation provided useful information about the comparative strength of cation–anion–water interactions.

Role of the Succinate Skeleton in the Disorder–Order Transition of AOT and Its Analogous Molecules: Detection by Infrared Absorption Spectra of the Configurations Arising from the Difference in Torsion Angles of the Succinate Skeleton

Abstract The IR spectra in the 1300–1450 cm−1 region, which reflect the CH and CH2 deformation vibrational modes of the succinate skeleton, have been investigated in detail for sodium dialkylsulfonates (alkyl groups: ethyl, n-propyl, n-butyl, n-hexyl, n-heptyl, n-octyl, n-decyl, and n-dodecyl) and sodium 1,2-bis(2-ethylhexyl)sulfosuccinate (sodium 1,2-bis(2-ethylhexyloxycarbonyl)ethanesulfonate) (AOT). The results have provided clear evidence that two configurations, arising from the difference in the torsion angles of the succinate skeleton, are preferentially stabilized in aqueous solution as well as in the solid state, depending upon the concentration. Thus, the IR spectra of this region can be used as a powerful tool for elucidation of the mechanism of the disorder–order transition in aggregate systems of AOT or its homologs at the molecular level.

Photochemistry and Photo-Induced Ultrafast Dynamics at Metal Surfaces

Abstract This account describes excitation mechanisms and ultrafast nuclear dynamics at metal surfaces induced upon photon irradiation. After reviewing possible excitation mechanisms for photochemistry of adsorbates on metal surfaces, we discuss the ultra-violet photochemistry of saturated hydrocarbons, i.e., methane and cyclohexane, on metal surfaces. Although these alkanes in the gas phase do not absorb photons at ≈6 eV, CH bond dissociation takes place upon 6.4-eV photon irradiation on metal surfaces. Hybridization between CH antibonding orbitals of the alkanes and metal bands, forming a new band across the Fermi level, is proposed to be responsible for both the photochemistry and CH vibrational mode softening. Since electronic relaxation at metal surfaces takes place very rapidly, most of excited adsorbates do not proceed to dissociation and/or desorption, but rather they are vibrationally excited. To probe photo-induced nuclear motions in real time, we developed femtosecond (fs) time-resolved second harmonic generation spectroscopy on metal surfaces. This method was used to explore the dynamics of photo-excited coherent vibration at Pt(111) surfaces covered with alkali-metal atoms. Irradiation of fs pump-laser pulses induced coherent vibrational motions of the stretching vibration of alkali atoms with respect to the metal surface and the Rayleigh modes of the Pt surface, which manifest themselves in modulations of second harmonic intensity of probe pulses. We also demonstrated that selective excitation of a phonon mode can be achieved by using tailored light pulse trains.

Photochemistry of cyclohexane on Cu(111)

The photochemistry of cyclohexane on Cu(111) and its excitation mechanism have been studied by temperature-programmed desorption, ultraviolet and X-ray photoelectron spectroscopy. Cyclohexane weakly adsorbed on Cu(111) has been known to show a broadened and redshifted CH stretching band, i.e., CH vibrational mode softening. Although no dehydrogenation takes place thermally on this surface and by the irradiation of photons at 5.0 eV, adsorbed cyclohexane is dissociated to cyclohexyl and hydrogen by the irradiation of photons at 6.4 eV. This is a marked contrast to cyclohexane in the gas phase where the onset of absorption is located at 7 eV. When the surface irradiated by 6.4-eV photons is further annealed, cyclohexyl is dehydrogenated to form cylcohexene that desorbs at 230 K. The systematic measurements of photochemical cross sections at 6.4 eV with linearly polarized light as a function of incident angle indicate that the electronic transition from the highest occupied band of cyclohexane to a partially occupied hybridized band near the Fermi level is responsible for the photochemistry. The hybridized band is formed by the interactions between the electronic states of cyclohexane and the metal substrate. The role of the hybridized band in the photochemistry and the CH vibrational mode softening is discussed.

Iodine insertion in pentacene thin films investigated by infrared and Raman spectroscopy

Vibrational and electronic properties of iodine doped pentacene thin films were studied by Raman and infrared measurements. The observation of the polaronic transition in charged pentacene gives access to the reorganization energy of the pentacene molecules. Iodine insertion induces a modification of the CH vibrational modes located at the end and along the pentacene molecules. At low doping level, iodide ions are intercalated between the two-dimensional pentacene layers. At high doping level, iodine is inserted inside the layers of pentacene in an irreversible way, which is expected to decrease charge transport performance.

Charge Reversal Behavior at the CaF2/H2O/SDS Interface as Studied by Vibrational Sum Frequency Spectroscopy

We report in situ spectroscopic measurements of charge reversal behavior and surfactant bilayer formation at the salt/aqueous solution interface as the aqueous surfactant concentration is varied. The studies, which employ vibrational sum frequency spectroscopy to measure the vibrational response of sodium dodecyl sulfate and water at the CaF2/H2O interface, demonstrate the complex nature of the adsorption process which includes monomer adsorption, surfactant bilayer formation, surfactant restructuring, surface charge reversal, and water reorientation. These effects have been monitored directly for the first time by taking advantage of the spectroscopy and the nonlinear phase relationships between the CH and OH vibrational modes. The results provide important insight into the adsorption mechanism that is central to processes such as mineral ore flotation and separation, waste processing, and petroleum recovery.

Vibrational modes of CH bonds in n-paraffin molecular chains: an algebraic description

We apply the one-dimensional vibron model to compute energies and infrared intensities of CH vibrational modes (stretching and bending states) of n-paraffin molecules. We consider the possible onset of interactions between different kinds of bending motions as well as that of anharmonic resonances between CH stretching modes and CH bending overtone/combination vibrations.

Non-invasive measurement of corneal hydration.

To investigate the feasibility of a confocal Raman spectroscopic technique for the noncontact assessment of corneal hydration in vivo in two legally blind subjects. A laser beam (632.8 nm; 15 mJ) was maintained on the cornea using a microscope objective lens (25x magnification, NA=0.5, f=10 mm) both for focusing the incident light as well as collecting the Raman backscattered light, in a 180 degrees backscatter configuration. An optical fiber, acting as the confocal pinhole for elimination of light from out-of-focus places, was coupled to a spectrometer that dispersed the collected light onto a sensitive array-detector for rapid spectral data acquisition over a range from 2,890 to 3,590 cm(-1). Raman spectra were recorded from the anterior 100 to 150 microm of the cornea over a period of time before and after topical application of a mild dehydrating solution. The ratio between the amplitudes of the signals at 3,400 cm(-1) (OH-vibrational mode of water) and 2,940 cm(-1) (CH-vibrational mode of proteins) was used as a measure of corneal hydration. High signal-to-noise ratio (SNR 25) Raman spectra were obtained from the human corneas using 15 mJ of laser light energy. Qualitative changes in the hydration of the anterior-most part of the corneas could be observed as a result of the dehydrating agent. Confocal Raman spectroscopy could potentially be applied clinically as a noncontact tool for the assessment of corneal hydration in vivo.

The formation of the copper/polyphenylquinoxaline interface: An HREELS study

AbstractThe interaction of copper with the surface of polyphenylquinoxaline is investigated with high resolution electron energy loss spectroscopy. The metal deposition is found to affect several features, in particular the elastic peak and the CH vibrational modes associated with the aromatic groups. Diffusion of copper to the bulk is observed upon thermal treatment.

X-Ray and Fourier-transform infrared studies of 1,8-bis(dimethylaminomethyl)naphthalene. Comparison with 1,8-bis(dimethylamino)naphthalene

The X-ray structure of a proton sponge, 1,8-bis(dimethylaminomethyl)naphthalene (DMAMN) has been determined and its FTIR spectrum investigated. The results are compared with previously reported data on 1,8-bis(dimethylamino)naphthalene (DMAN). The X-ray results show that in DMAMN, the naphthalene ring is almost planar in contrast with DMAN. The IR spectra of these two molecules are markedly different and the decrease in the intensity of some ring and CH vibrational modes in DMAMN is discussed as a function of the higher symmetry of the naphthalene skeleton of the molecule.

Surface phonons and CH vibrational modes of diamond (100) and (111) surfaces.

The surface phonons and CH vibrational structure of diamond (100) and (111) surfaces have been examined using high-resolution electron-energy-loss spectroscopy. Experimental phonon features of (2\ifmmode\times\else\texttimes\fi{}1)-reconstructed diamond surfaces [H-free (100) and partially H-terminated (111)] agree well with scaled phonon frequencies of theoretically predicted modes for similarly reconstructed silicon surfaces. Several modes not detected on silicon surfaces are observed on diamond surfaces, in agreement with scaled theoretical calculations. Vibrational spectra from hydrogen-terminated diamond (1\ifmmode\times\else\texttimes\fi{}1) surfaces reveal several types of ${\mathrm{CH}}_{\mathit{x}}$ species, including ${\mathit{sp}}^{3}$ hybridized methyl and methylene groups, and olefinic (${\mathit{sp}}^{2}$ hybridized) methylene groups. On heating to \ensuremath{\sim}1473 K, hydrogen desorbs readily from the (100) surface. Complete removal of hydrogen from the (111) surface by repeated annealing to \ensuremath{\sim}1473 K was impossible, although (2\ifmmode\times\else\texttimes\fi{}1) reconstruction had already occurred.

Infrared total internal reflection spectroscopy of dimethylcadmium on chemically passivated silicon surfaces

The chemistry of dimethylcadmium (DMCd) on chemically passivated silicon surfaces is monitored through changes in the infrared spectra of the CH vibrational modes in both chemically and physically adsorbed molecules. Total internal reflection of the IR probe beam was employed to isolate the surface-molecule signal from that due to ambient gas-phase molecules. Excimer laser irradiation of the adsorbed DMCd at 248 nm under conditions appropriate for Cd film deposition resulted in changes in the observed spectra which indicate a high hydrocarbon content in the deposited metal layer.

Infrared total internal reflection spectroscopy of dimethylcadmium on silicon

The surface chemistry of dimethylcadmium (DMCd) on silicon surfaces is monitored through changes in the infrared spectra of both chemically and physically adsorbed molecules. A technique involving total internal reflection of the IR probe beam was employed to isolate the surface‐molecule signal from that due to ambient gas‐phase molecules. Fourier‐transformed infrared spectra of DMCd on silicon were recorded in the region from 2.0 to 5.0 μm, where the CH vibrational modes of the molecule occur. Excimer laser irradiation of the molecules at 248 nm under conditions appropriate for Cd film deposition resulted in changes in the observed spectra due to dissociation of both surface and gas‐phase molecules.