Stretching Mode Region Research Articles

Linear and Non-Linear Middle Infrared Spectra of Penicillin G in the CO Stretching Mode Region

In this work we report the linear and non-linear IR spectral response characterization of the CO bonds of PenicillinG sodium salt in D2O and in DMSO−d6 solutions. In order to better characterize the spectral IR features in the CO stretching region, broadband middle infrared pump-probe spectra are recorded. The role of hydrogen bonds in determining the inhomogeneous broadening and in tuning anharmonicity of the different types of oscillators is exploited. Narrow band pump experiments, at the three central frequencies of β−lactam, amide and carboxylate CO stretching modes, identify the couplings between the different types of CO oscillators opening the possibility to gather structural dynamic information. Our results show that the strongest coupling is between the β−lactam and the carboxylate CO vibrational modes.

Structural evolution of water and hydroxyl groups during thermal, mechanical and chemical treatment of high purity natural quartz.

Fused silica crucibles are commonly used in the fabrication process of solar grade silicon ingots. These crucibles are manufactured from high purity natural quartz sand and as a consequence, their properties are influenced by the presence of water and hydroxyls in the raw quartz. In this work, diffuse reflectance IR, 1H magic angle spinning NMR, and Raman spectroscopy were used to investigate the influence of thermal treatment on water and hydroxyl groups in high purity natural quartz sand. Most of the water in dry sand is present in the form of closed inclusions within the quartz grains which were detected in Raman imaging studies, even after thermally treating the samples at 600 °C. Only after heating to 900 °C did this water completely vanish, most likely as a result of rupturing of the inclusions. However, newly formed OH groups, identified as isolated and hydrogen bound OH were observed as products of the reaction between water and quartz. Similarly, liquid water was observed in NMR spectra even after treatment at 600 °C while at temperatures >900 °C, only non-interacting silanol groups were present. The comparison of the temperature dependence of the IR and NMR spectra also yields insight into the assignment of the OH stretching mode region of the IR spectrum in this system. The intensity of water related bands decreases while the intensity of OH bands first increases and then decreases with increasing temperature. The band intensity of Al-rich defects as well as the characteristic feature at 3200 cm−1 does not follow the temperature dependence of typical water peaks. It is also shown that leaching the quartz sand in HF solution helps to remove water from inclusions, likely by forming pathways for fluid flow inside the quartz grains. Milling of the samples caused formation of an additional type of hydroxyl group, possibly due to partial amorphisation of the surfaces of the quartz grains surface during the process. The results improve the basis for a knowledge-based processes development for the processing of high purity natural quartz.

Analysis of the Interfacial Molecular Behavior of a Lubrication Film of n-Dodecane Containing Stearic Acid under Lubricating Conditions by Sum Frequency Generation Spectroscopy.

The molecular behavior of n-dodecane with added stearic acid at a friction interface was studied using sum frequency generation (SFG) spectroscopy and a tribometer. In the case of n-dodecane with stearic acid, under dynamic conditions, a strong peak from the symmetric stretching vibrational mode of methylene, which was not observed under static conditions, appears. However, this strong methylene peak was not observed in the case of only n-dodecane. The SFG spectrum in the C-H stretching mode region of n-dodecane-d26 with stearic acid in the dynamic condition was analogous to that in the static condition. These results indicate that the interfacial structure of stearic acid does not change under sliding condition. The n-dodecane on a stearic acid adsorption film is highly aligned. Moreover, from the sliding direction dependence of the SFG measurements, the molecular orientation of n-dodecane was deduced: n-dodecane on stearic acid adsorption films orient parallel to the sliding direction. These results have shown that the stearic acid adsorption film behaves as solid-like, which has also been mentioned in previous studies. Further, our results revealed a new function of stearic acid: the stearic acid adsorption film induces the formation of a well-defined n-dodecane interfacial structure and forces the n-dodecane molecules to orient along the sliding direction at the friction interface.

Two‐dimensional Raman spectroscopy study of ionogel phase formation in long‐chain ionic liquid/water systems

The phase behavior of the imidazolium‐based room temperature ionic liquids (RTILs) 1‐decyl‐3‐methyl‐imidazolium bromide and chloride ([C10mim][Br], [C10mim][Cl]) were studied by 2D Raman correlation spectroscopy and principal component analysis. The hydrogen‐bonded network changes and the liquid crystalline ionogel phase formation were observed when water content was continuously increased in the system, and the Raman shift of C–H stretching modes in spectra was monitored. The extent of liquid crystalline ionogel phase was determined from the discontinuities in the concentration dependencies. The focus to the Raman bands originated from the imidazolium ring C–H stretching mode region (3000–3200 cm−1) when water content in the IL was increased allowing to determine the lower border of ionogel phase formation in RTIL/water systems. The upper border of the ionogel phase was determined when main attention was carried out to the Raman bands originated from the O–H stretching vibration region (3200–3800 cm−1). The hypothesis of weaker hydrogen bonds involving the C(4)‐H and C(5)‐H groups and stronger hydrogen bonds of the C(2)‐H groups was supported by Raman results. Copyright © 2016 John Wiley & Sons, Ltd.

Effect of Headgroup on the Physicochemical Properties of Phospholipid Bilayers in Electric Fields: Size Matters

The effect of molecular structure on ensemble structure of phospholipid films has been investigated. Bilayers of dimyristoyl phosphatidylethanolamine (DMPE) were prepared on Au(111) electrodes using Langmuir-Blodgett and Langmuir-Schaeffer deposition. Capacitance and charge density measurements were used to investigate the adsorption behavior and barrier properties of the lipid bilayers. In situ polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) was employed to investigate the organization of the molecules within the bilayer. DMPE bilayers exhibit lower capacitance than bilayers formed from the related lipid, dimyristoyl phosphatidylcholine (DMPC). The infrared data show that these results can be explained by structural differences between the bilayers formed from each molecule. DMPE organizes into bilayers with hydrocarbon chains tilted at a smaller angle to the surface normal, which results in a thicker film. The hydrocarbon chains contain few conformational defects. Spectra in the carbonyl and phosphate stretching mode regions indicate low solvent content of DMPE films. Both of these effects combine to produce films with lower capacitance and enhanced barrier properties. The results are explained in terms of the differences in structure between the constituent molecules.

Raman Spectroscopic Study of Aggregation Process of Antibiotic Amphotericin B Induced by H+, Na+, and K+ Ions

The normal and the preresonance Raman effects (NR and PRR) of spectroscopy have been used to monitor and explain the aggregation processes of amphotericin B (AmB) in aqueous solution at different pH values and containing the K(+) and Na(+) ions. The resonance-enhanced and normal vibrational Raman spectra were recorded with a semiconductor laser (ex 785 nm) and an argon laser (ex 514.5 nm) for investigation of interactions between AmB chromophores. The essential difference between the samples stimulated by resonance-enhanced and by near-infrared was in the C=C stretching mode region of polyene chain. The processes connected with the aggregation of AmB led to changes in the chromophore, which were only visible as a remarkable broadening of the band centered at 1558 cm(-1). The understanding of possible physical mechanisms responsible for the molecular aggregation of the drug is important from the pharmaceutical applicability standpoint.

Understanding Morphology-Dependent Polymer Aggregation Properties and Photocurrent Generation in Polythiophene/Fullerene Solar Cells of Variable Compositions

We fabricate poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) thin film solar cells of variable weight/weight (w/w) compositions (i.e., 1:1 to 1:4) to systematically perturb polymer packing (aggregation) properties and assess their impact on local electronic structure and photocurrent generation efficiency. A combination of absorption spectroscopy and resonance Raman spectroscopic and photocurrent imaging techniques are used to quantify and spatially map morphology-dependent cofacial, π−π aggregated P3HT chains and correlate these structures to local photocurrent production characteristics. On average, increasing the PCBM weight fraction results in blue shifts and broadening for absorption and Raman spectra in the dominant P3HT C═C stretching mode region (∼1450−1470 cm−1), whereas symmetric stretching C—C modes show decreased intensities and red shifts. P3HT/PCBM absorption spectra are fitted near the resolved P3HT onset region using a weakly coupled H-aggregate model that reveals decreases in the relative amounts of aggregated/unaggregated P3HT chains as well as interchain exciton coupling in the aggregated component. Raman bands of P3HT C═C modes can likewise be decomposed into contributions from both aggregated (IC═Cagg.) and unaggregated (IC═Cun.) chains, and like absorption spectra, IC═Cagg./IC═Cun. values decrease with increased PCBM content. Combined Raman and photocurrent imaging studies of 1:1 P3HT/PCBM devices reveal that most aggregated (ordered) P3HT chains reside primarily outside PCBM-rich regions, but this, surprisingly, reverses for >1:1 PCBM w/w loadings where all aggregated P3HT chains reside within PCBM-rich regions. This effect is attributed to a change in the type of P3HT aggregation from inter- to primarily intrachain (or self-aggregated) that is supported by decreases in the interchain exciton coupling parameter from absorption fits as well as Raman C—C and C═C (agg.) frequency maps. The results reveal not only the importance of the polymer aggregation state but also its spatial location in the film that together have a large impact on charge transport properties and material performance.

Rovibrational spectrum of the Ne–N 2O van der Waals complex in the 1285 cm −1 region

The rovibrational spectrum of the Ne–N 2O van der Waals complex has been recorded in the symmetric stretching mode region of the N 2O monomer (∼1285 cm −1) using a tunable diode laser spectrometer in conjunction with an astigmatic multi-pass cell and a pulsed supersonic slit jet. The spectra of both 20Ne–N 2O and 22Ne–N 2O isotopomers are assigned and analyzed using a Watson S-reduced asymmetric-rotor Hamiltonian. The rotational and centrifugal constants for the excited vibrational state are accurately determined. The band-origin of the spectrum is determined to be ν 0 = 1285.12251(18) cm −1 for 20Ne–N 2O and 1285.12363(27) cm −1 for 22Ne–N 2O, which shows a blue-shift of 0.21921 cm −1 for 20Ne–N 2O and 0.22033 cm −1 for 22Ne–N 2O from that of the N 2O monomer, respectively.

Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation study.

The sum-frequency generation (SFG) spectrum from the water/[1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine] (DMPC) interface in the OH stretching mode region of water is simulated and shows three spectral peaks which are assigned to different environments. The weak 3590 cm(-1) peak is attributed to a few water molecules coupled to the glycerol backbone of DMCP. The 3470 cm(-1) feature comes from the top water layer adjacent to the hydrophilic headgroup of DMPC. The 3290 cm(-1) peak arises from the near-bulk water nonadjacent to DMPC. The stretching mode corresponding to the 3290 cm(-1) peak is strongly coupled to the neighboring water molecules. In contrast, the 3470 cm(-1) mode is decoupled from the surrounding water molecules, and the orientation of water is governed by DMPC. This decoupling explains the slow relaxation dynamics of water measured in the time-resolved SFG experiment. Despite the similarity of the SFG spectra, the peak origins of water/lipid and water/vapor interfaces are different.

Vibrational structure of the polyunsaturated fatty acids eicosapentaenoic acid and arachidonic acid studied by infrared spectroscopy

The spectroscopic discrimination of the two structurally similar polyunsaturated C20 fatty acids (PUFAs) 5,8,11,14,17-eicosapentaenoic acid and 5,8,11,14-eicosatetraenoic acid (arachidonic acid) is shown. For this purpose their vibrational structures are studied by means of attenuated total reflection (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The fingerprint regions of the recorded spectra are found to be almost identical, while the C–H stretching mode regions around 3000cm−1 show such significant differences as results of electronic and molecular structure alterations based on the different degree of saturation that both fatty acids can be clearly distinguished from each other.

Femtosecond Measurements of Vibrational Circular Dichroism and Optical Rotatory Dispersion Spectra

Heterodyne-detected spectral interferometry with fs IR pulses measures vibrational optical activity free-induction-decay fields. By utilizing Brewster's angle germanium polarizers with ultimate extinction ratio over almost the entire IR frequency range, the complex vibrational optical activity susceptibility of small organic chiral molecules in the CC stretching mode region is characterized (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Observation of surface enhanced IR absorption coefficient in alkanethiol based self-assembled monolayers on GaAs(001)

Alkanethiol self-assembled monolayers (SAMs) of various methylene group chain lengths [HS–(CH2)n–CH3] (n=9,11,13,15,17) were fabricated on the GaAs(001) surface followed by characterization using Fourier transform infrared spectroscopy. Modal analysis of the CH2 stretching mode region (2800–3000 cm−1) showed that linear scaling of the n-dependent factors accurately reproduced the spectral data, supporting a chain-length consistent physical model upon which a measurement of the absorption coefficient was based. Evaluated from the linearity of the absorbance data, a peak coefficient of 3.5×104 cm−1 was obtained and a domain for ordered self-assembly was assigned for values n>9. Compared with measurements of the absorption coefficient made in the liquid phase, the SAM phase coefficient was determined to be about six times greater. This enhancement effect is discussed in terms of contributions relating to the locally ordered environment and is largely attributed to the chemical properties of the interface. We believe this to be the first demonstration of IR spectral enhancement of a molecular species chemisorbed on the semiconductor surface.

Infrared and Raman studies of manganese dihydrogen phosphate dihydrate, Mn(H 2PO 4) 2·2H 2O. Part II: Region of the internal OH group vibrations

Infrared and Raman spectra of Mn(H 2PO 4) 2·2H 2O and of series of deuterated analogues recorded at room temperature (RT) and at the boiling temperature of liquid nitrogen (LNT) have been presented and analyzed with respect to the OH vibrations. In the OH stretching mode region ABC bands behaviour is observed in accordance with the structural data for presence of a short hydrogen bond (2.609 Å). It is presumed that the A band of the ABC trio most probably originates from the stretching OH vibrations of strongly hydrogen bonded POH(1) group, but the contribution of the second POH(2) group and the water molecule should be also considered. The strength of the four hydrogen bonds as deduced from the infrared wavenumbers of the isotopically isolated OD groups has been discussed in terms of the respective O···O distances, the hydrogen bond acceptor capability of the oxygen atoms, the hydrogen bond donor strength of the H 2PO 4 ions and water molecules and the hydrogen bond acceptor angles. The influence of the cooperative effect has been also analyzed.

Pharmacodynamic Assessment of Histone Deacetylase Inhibitors: Infrared Vibrational Spectroscopic Imaging of Protein Acetylation

Infrared spectroscopy identifies molecules by detection of vibrational patterns characteristic of molecular bonds. We apply this approach to measure protein acetylation after treatment with histone deacetylase inhibitors. The anticancer activity of histone deacetylase inhibitors (HDACi) is ascribed to the hyperacetylation of both core nucleosomal histones and nonhistone proteins critical to the maintenance of the malignant phenotype (Marks, P. A.; Richon, V. M.; Breslow, R.; Rifkind, R. A. Curr. Opin. Oncol. 2001, 13, 477-483; Mai, A.; Massa, S.; Rotili, D.; Cerbara, I.; Valente, S.; Pezzi, R.; Simeoni, S.; Ragno, R. Med. Res. Rev. 2005, 25, 261-309). After incubation of the peripheral blood mononuclear cells (PBMCs) in vitro with the HDACi SNDX-275, a benzamide drug derivative, vibrational spectral changes in the methyl and methylene stretching mode regions, which reflect concentration-dependent increases in protein acetylation, were detected and quantified. We applied these metrics, based upon spectral differences, to peripheral blood mononuclear cells from patients treated in vivo with this agent. The data demonstrate a new approach to a sensitive assessment of global molecular modifications that is independent of antibodies, requires minimal cell processing, and is easily adapted to high-throughput screening.

Laser Raman spectroscopy of THF clathrate hydrate in the temperature range 90–300 K

In situ Raman and Fourier transform infrared (FTIR-NIR) spectroscopic studies on tetrahydrofuran (THF-C 4H 8O) clathrate hydrate (CH) were reported. The Raman results in lattice (64 cm −1), ring breathing and C–H stretching mode regions are in conformity with earlier reports, while the FTIR (NIR) studies in second order mode region were reported for the first time. Comparison of the results indicate that the band assigned to ring breathing mode around 922 cm −1 (in Raman) and corresponding second order mode in NIR around 4295 cm −1 broadens and shifts in enclathrated THF. The ring breathing mode at lower temperatures ( T < 120 K) is highly asymmetric and splits into two and are due to different host–guest interactions at lower temperatures.

Infrared and Raman spectra of magnesium ammonium phosphate hexahydrate ( struvite) and its isomorphous analogues. IV. FTIR spectra of protiated and partially deuterated nickel ammonium phosphate hexahydrate and nickel potassium phosphate hexahydrate

The Fourier transform infrared spectra recorded from room temperature down to the boiling temperature of liquid nitrogen of two struvite analogues, nickel ammonium phosphate hexahydrate (NiNH 4PO 4·6H 2O) and nickel potassium phosphate hexahydrate (NiKPO 4·6H 2O) and their partially deuterated analogues were analyzed and compared to the previously studied spectra of struvite and its potassium analogue. In the stretching mode region of the water molecules and ammonium ions, a broad asymmetric and deuteration sensitive band appears, which is an indication for strong hydrogen bonds in the structure of NiNP. In the LNT difference spectra of samples with low deuterium content (≈2–3% D), several bands appear between 2520 and 2080 cm −1 due to vibrations of isotopically isolated HDO molecules and NH 3D + ions. The most significant difference between the two studied spectra is between 2350 and 2250 cm −1 where additional bands from ND stretching modes of isotopically isolated NH 3D + ions are expected in the spectrum of NiNP. In the region of ν 3(PO 4) modes one strong, slightly asymmetric, temperature-sensitive band appears above 1000 cm −1 in both spectra. The analysis of the RT and LNT spectra of the protiated and partially deuterated compounds, the band at around 575 cm −1 is assigned to the ν 4(PO 4) modes and the remaining ones as due to librational and translational modes of the water molecules.

Control and FTIR Analysis of CO Diffusion on Pt(997) Surface

Using collision with energy-controlled rare gas atoms, the control and analysis of the diffusion of molecules on the surface was performed in an ultra high vacuum chamber with Fourier-transform infrared (FTIR) spectrometer and a supersonic molecular beam apparatus. A stepped Pt(997) surface was exposed to CO molecules and subsequently to energy-controlled Ne or Ar atoms. There was no change in the CO stretching mode region of the FTIR spectrum of the Pt(997) surface after Ne atoms having an average translational energy of 0.23 eV were collided with it. However, when Ne atoms having an average translational energy of 0.56 eV were collided with the surface, the intensity of the peak assigned to the CO stretching mode at terrace sites decreased, while that at step sites increased with increasing the exposure to the Ne atoms. This indicates that CO molecules adsorbed at the terrace sites migrate laterally to the step sites upon collision with high-energy Ne atoms. In addition, it was shown that the direction of diffusion can be controlled, the diffusion of the molecule in particular chemisorbed state can be activated, and the activation energy of diffusion can be estimated. A new method to examine the diffusion of adsorbates by the use of the collision with energy-controlled atoms is proposed.

Collision-induced migration of CO on Pt(9 9 7) surface

Lateral displacement of adsorbates induced by collisions with energy-controlled rare gas atoms was examined in an ultra high vacuum chamber using Fourier-transform infrared (FTIR) spectroscopy and a supersonic molecular beam apparatus. A stepped Pt(9 9 7) surface was exposed to CO molecules and subsequently to energy-controlled Ne or Ar atoms. There was no change in the CO stretching mode region of the FTIR spectrum of the Pt(9 9 7) surface after Ne atoms having an average translational energy of 0.23 eV were collided with it. However, when Ne atoms having an average translational energy of 0.56 eV were collided with the surface, the intensity of the peak assigned to the CO stretching mode at terrace sites decreased, while that at step sites increased with increasing the exposure to the Ne atoms. This is the demonstration of collision-induced migration, showing that CO molecules adsorbed at the terrace sites migrate laterally to the step sites upon collision with high-energy Ne atoms. In addition, the experimental results demonstrate the existence of an additional energy barrier for jumps across the steps. This investigation demonstrates an advantage of using a molecular beam for studying adsorbate migration.

Conformational differences in protein disulfide linkages between normal hair and hair from subjects with trichothiodystrophy: A quantitative analysis by Raman microspectroscopy

Raman spectra of normal hair shafts and hair shafts from patients exhibiting trichothiodystrophy (TTD) were obtained using line focus laser illumination. Because hair from TTD patients has a significant decrease in the content of the sulfur-containing amino acids in comparison to normal hair, the 550-500 cm(-1) disulfide stretching mode region of the Raman spectrum was examined in detail. A quantitative spectral analysis demonstrates significant increases in the two energetically less favored gauche-gauche-trans (g-g-t) and trans-gauche-trans (t-g-t) forms. These observations suggest that the increased amounts of these less stable disulfide conformers are contributing factors to or associated with the hair brittleness observed for this congenital disorder. Structure-spectra correlations for the three dominant disulfide conformers are confirmed by quantum chemical calculations using modern density functional theory (DFT).

High-Resolution IR Spectroscopy of the N 2O–H 2O and N 2O–D 2O van der Waals Complexes

We report high-resolution infrared vibrational–rotational spectra of the weakly bound complexes N 2O–H 2O and N 2O–D 2O in the higher frequency N 2O stretching mode region (ν 3=2223.756693(124) cm −1). The measurements were carried out using a free jet expansion in combination with a lead salt diode laser spectrometer. Rotational constants, quartic centrifugal distortion constants, and band origins have been derived for both isotopomers. The geometrical structure is determined using isotopic substitution. The deduced structure shows evidence for a second hydrogen bond interaction within the complex. The nonrigidity of the complexes gives rise to an internal rotation of the water molecule around its own C 2 v symmetry axis. For N 2O–H 2O, a tunneling splitting arising from this internal motion has been observed in the spectra. According to symmetry considerations, the observed splitting in the spectrum of N 2O–H 2O corresponds to the difference between the tunneling frequencies in the ground and vibrationally excited states.