Infrared Absorption Frequencies Research Articles

Direct Observation of MAX1 Self‐Assembly via Site‐Specific Carbon‐Deuterium Infrared Probes

The physical characterization of molecules that self-assemble presents a challenge, particularly when associated with phase separation or precipitation. Infrared (IR) spectroscopy has been shown to be a non-perturbative method for monitoring folding dynamics, accentuated by the sensitivity of the bond stretch frequencies of site-specific IR probes to changes in local molecular environment.1 Site-specific incorporation of probes that absorb in the “transparent window” region of the biomolecular IR spectrum has been widely used to gain insight into protein electrostatics, structure, folding, and conformational dynamics. To expand the use of IR probes for the investigation of time-resolved kinetic processes, such as self-assembly, carbon-deuterium (C-D) bonds were incorporated into five different positions of a twenty-residue MAX1 β-hairpin peptide and the site-specific kinetics of gelation were examined after stopped-flow mixing using FTIR detection. MAX1 peptide hydrogels are biocompatible and clinically relevant for application in tissue regeneration and drug delivery.2 Steady state IR absorption frequencies and linewidths of C-D bonds at all labeled positions indicate, as expected, that the labeled side chains occupy a hydrophobic region of the hydrogel; furthermore, the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. The changes in the absorption spectra of C-D bonds induced by gelation were reliably followed as function of time and the site-specific time constants for the gel transition show that MAX1 gelation occurs as a cooperative process with no lag phase. We believe that stopped-flow FTIR spectroscopy is equally applicable for other transparent window IR probes and can be extended to other time-resolved applications, such as protein folding and enzyme kinetics. 1. Adhikary, R., J. Zimmermann, and F.E. Romesberg, Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev, 2017. 117(3): p. 1927-1969. 2. Schneider, J.P., et al., Responsive Hydrogels from the intramolecular Folding and Self-Assembly of a Designed Peptide. J. of Am. Chem. Soc., 2002. 124: p. 15030-15037.

A rapid, spatially dispersive frequency comb spectrograph aimed at gas phase chemical reaction kinetics

This New Views article will highlight some recent advances in high sensitivity gas detection using direct infrared absorption frequency comb laser spectroscopy, with a focus on frequency comb use in chemical reaction kinetics and our own contribution to this field. Our recently implemented detection technique uses a combination of a 12.9 GHz free spectral range virtually imaged phased array and diffraction grating to spatially disperse the mid-infrared frequency comb onto a camera. Individual frequencies or ‘comb teeth’ of a 250 MHz repetition-rate frequency comb are able to be resolved. High molecular sensitivity is achieved by increasing the interaction path length using a Herriott multipass cell. High spectral resolution, broadband spectral coverage, and high molecular sensitivity are all achieved on an adjustable 1–50 µs timescale, making this frequency comb apparatus ideal for measuring chemical reaction kinetics where multiple absorbing species can be monitored simultaneously. This New Views article will also discuss some of the challenges and decisions that chemists might face in implementing this advanced physics technology in their own laboratory. Spatially dispersed 250 MHz mid-infrared frequency comb laser, with absorption of some frequencies by a dilute sample of methane.

Effect of a Magnetic Field on Photocatalytic Degradation of Rhodamine B Over g-C3N4

Magnetic fields have potential applications in photocatalysis. However, there is limited research on the effect of magnetic fields on heterogeneous photocatalysis, and the action mechanism remains unclear. In this study, the photocatalytic degradation of rhodamine B over g-C3N4 in an aqueous solution was investigated, and the adsorption and photocatalytic activity were analyzed in the absence and presence of a magnetic field. Furthermore, the infrared absorption frequency of the bending vibration of water was measured in real-time. The results show that the adsorption and photocatalytic efficiencies were positively correlated with the magnetic field intensity in the range of 0∼2 T, while high-intensity magnetic fields (4∼8 T) played an inhibitory role. In addition, the infrared absorption frequencies of water exhibited a red-shift under 1 T and 2 T magnetic fields at 37 °C, while the absorption frequencies under 4 T and 8 T magnetic fields were the same as that in the absence of magnetic fields. The effects of the magnetic field on the g-C3N4 photocatalytic efficiency and water infrared absorption frequency were similar, suggesting that the effect of the magnetic field on the water structure may be one factor affecting the g-C3N4 photocatalytic efficiency.

Vibrational relaxation of small anions in a polymer film

Steady-state and ultrafast vibrational spectroscopy can help to elucidate the interactions between small anions and their environment because the anions’ infrared absorption frequencies and vibrational energy relaxation (VER) times depend strongly on those interactions. Their strong infrared absorptions also make many of these anions promising candidates for strong coupling to optical fields. Here, we report the vibrational energy relaxation of dicyanamide (DCA) in H2O and D2O and find that the so-called solvent isotope effect on VER is not as pronounced as for other anions. In addition, we report the infrared spectroscopy and VER lifetimes of DCA, N3−, and NCS− embedded in a polyelectrolyte polymer. We find that the polymer matrix accelerates VER in a similar fashion to H2O, but the detailed mechanism of this acceleration remains unclear.

Phase transition, structural, mechanical and thermal properties of erbium pnictides under pressure

In this article, we have investigated the high-pressure structural phase transition of erbium pnictides (ErX; X = N, P and As). An extended interaction potential model has been developed (including the zero-point energy effect in three-body interaction potential model). Phase transition pressures are associated with a sudden collapse in volume. The phase transition pressures and associated volume collapses have been predicted successfully. The elastic constants, their combinations and pressure derivatives are also reported. The pressure behaviour of elastic constants, bulk modulus and shear modulus have been presented and discussed. Moreover, the thermophysical properties such as molecular force constant (f), infrared absorption frequency (υ 0), Debye temperature (θ D) and Grunneisen parameter (γ) have also been predicted.

Residual compressive stress induced infrared-absorption frequency shift of hexagonal boron nitride in cubic boron nitride films prepared by plasma-enhanced chemical vapor deposition

The effects of compressive stress on the TO phonon frequencies of hexagonal boron nitride (hBN) in cubic BN (cBN) films were investigated using infrared absorption spectroscopy, showing that the B–N stretching vibration of hBN at 1380 cm−1 shifted to high wavenumbers under biaxial compressive stress with the rate 2.65 cm−1 per GPa, while the B–N–B bending vibration near 780 cm−1 shifted to low wavenumbers with the rate −3.45 cm−1/GPa. The density functional perturbation theoretical calculation was carried out to check the above phonon frequencies under stress for two typical orientations of hBN crystallite. The results are shown to be in fair agreement with the experimental data. Our results suggest that the residual compressive stress accumulated in cBN films can be evaluated from the IR peak position near 780 cm−1.

A Jigsaw Classroom Activity for Learning IR Analysis in Organic Chemistry

A modified jigsaw classroom activity is presented for the integrated study of functional groups and their characteristic infrared absorption frequencies. Students individually performed semiempirical studies on the vibrational frequencies of an assigned molecule and compared the results to an experimental spectrum from a database. The results of these studies were discussed in a small group exercise to discover the spectral features that are most useful in identifying particular functional groups and their relationship to structures.

Controlled, Stepwise Reduction and Band Gap Manipulation of Graphene Oxide.

Graphene oxide (GO) has drawn tremendous interest as a tunable precursor in numerous areas, due to its readily manipulable surface. However, its inhomogeneous and nonstoichiometric structure makes achieving chemical control a major challenge. Here, we present a room-temperature based, controlled method for the stepwise reduction of GO, with evidence of sequential removal of each organic moiety. By analyzing signature infrared absorption frequencies, we identify the carbonyl group as the first to be reduced, while the tertiary alcohol takes the longest to be completely removed from the GO surface. Controlled reduction allows for progressive tuning of the optical gap from 3.5 eV down to 1 eV, while XPS spectra show a concurrent increase in the C/O ratio. This study is the first step toward selectively enhancing the chemical homogeneity of GO, thus providing greater control over its structure, and elucidating the order of removal of functional groups and hydrazine-vapor reduction.

Combined ATR-FTIR and DFT Study of Cyclohexanone Adsorption on Hydrated TiO2 Anatase Surfaces

The adsorption of cyclohexanone on different planes ((100), (101), and (001)) of anatase TiO2, with variable level of hydration, was evaluated by density functional theory (DFT) calculations. Surface hydration was found to affect the cyclohexanone adsorption enthalpy and the calculated infrared absorption frequencies of the preferred adsorbed configurations considerably. A good correlation was found between two experimentally observed absorption frequencies at 1694 and at 1681 cm–1 of cyclohexanone adsorbed on TiO2, determined by attenuated total reflection Fourier transform infrared (ATR-FTIR), and frequencies calculated for conformations of cyclohexanone interacting with the (101) surface with low and intermediate levels of hydration, respectively. The corresponding adsorption enthalpies of these adsorbed conformations amount to −23.5 and −37.0 kJ/mol, respectively. In addition, DFT calculations show that cyclohexanone physisorption on hydrated (100) yields an adsorption enthalpy of −89.4 kJ/mol. This might be a conformation contributing to irreversible adsorption of cyclohexanone known to occur experimentally after photocatalytic activation of TiO2. Other phenomena of relevance to irreversible adsorption are also briefly discussed.

Quantitative structure–property relationship study for the prediction of characteristic infrared absorption of carbonyl group of commonly used carbonyl compounds

Quantitative structure–property relationship (QSPR) study was applied to the prediction of the characteristic infrared absorption frequency of carbonyl group ( ν C O ) of 65 commonly used carbonyl compounds using linear heuristic method (HM) and non-linear radial basis function neural network (RBFNN) based on their structures alone. HM was used both for pre-selecting molecular descriptors and for developing the linear model. The statistical parameters provided by the HM model were R 2 = 0.873, R CV 2 = 0.838 , F = 67.348, and RMS = 16.267. The five molecular descriptors selected by HM method were used as inputs for RBFNN to establish the non-linear model. The RBFNN model's results were: R 2 = 0.943, R CV 2 = 0 .911 , F = 880.885, and RMS = 10.310. The proposed models were evaluated for predictive ability with an external validation set, and the statistical parameters obtained were R EXT 2 = 0.876 , F = 56.732, RMS = 19.754 for HM and R EXT 2 = 0 .908 , F = 79.010, RMS = 13.748 for RBFNN. The results indicate that the simple linear model can be used to predict ν C O of carbonyl compounds, while the non-linear model can give more accurate results.

Theoretical analysis of static properties of mixed ionic crystal: NH4Cl1−x Br x

In the present paper, we have investigated the static properties of the mixed ionic crystal NH4Cl1ixBrx using three-body potential model (TBPM) by the application of Vegard's law. The results for the mixed crystal counterparts are also in fair agreement with the pseudo-experimental data generated from the application of Vegard's law. The results for the end point members (x = 0 and 1) are in good agreement with the experi- mental data. The results on compressibility, molecular force constant, infrared absorption frequencies and Debye temperature are presented probably for the flrst time for these mixed crystal counterparts.

GC-IRD studies on regioisomeric ring substituted methoxy methyl phenylacetones related to 3,4-methylenedioxyphenylacetone

The methoxy methyl phenylacetones share an isobaric relationship (equivalent mass but different elemental composition) to the controlled precursor substance 3,4-methylenedioxyphenylacetone (3,4-methylenedioxyphenyl-2-propanone; 3,4-MDP-2-P). The ten ring substituted methoxy methyl phenylacetones are resolved by capillary gas chromatography on a modified cyclodextrin stationary phase. All ten regioisomeric ketones eluted before the controlled precursor substance 3,4-methylenedioxyphenylacetone. The vapor phase infrared spectra generated from the capillary column effluent clearly differentiated 3,4-MDP-2-P from the various methoxy methyl phenylacetones. Additionally the methoxy methyl phenylacetones provide unique individual infrared spectra. Infrared absorption frequencies and patterns confirmed the relative position of the methoxy-group and the acetone side-chain for the regioisomeric ketones.

Competing quantum effects in the dynamics of a flexible water model

Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which the intramolecular interactions were described using simple harmonic functions. To demonstrate this, we introduce a new simple point charge model for liquid water, q-TIP4P/F, in which the O-H stretches are described by Morse-type functions. We have parametrized this model to give the correct liquid structure, diffusion coefficient, and infrared absorption frequencies in quantum (path integral-based) simulations. The model also reproduces the experimental temperature variation of the liquid density and affords reasonable agreement with the experimental melting temperature of hexagonal ice at atmospheric pressure. By comparing classical and quantum simulations of the liquid, we find that quantum mechanical fluctuations increase the rates of translational diffusion and orientational relaxation in our model by a factor of around 1.15. This effect is much smaller than that observed in all previous simulations of empirical water models, which have found a quantum effect of at least 1.4 regardless of the quantum simulation method or the water model employed. The small quantum effect in our model is a result of two competing phenomena. Intermolecular zero point energy and tunneling effects destabilize the hydrogen-bonding network, leading to a less viscous liquid with a larger diffusion coefficient. However, this is offset by intramolecular zero point motion, which changes the average water monomer geometry resulting in a larger dipole moment, stronger intermolecular interactions, and a slower diffusion. We end by suggesting, on the basis of simulations of other potential energy models, that the small quantum effect we find in the diffusion coefficient is associated with the ability of our model to produce a single broad O-H stretching band in the infrared absorption spectrum.

A Study on the Coordinative Versatility of the Zwitterionic S,N,S Ligand EtNHC(S)­Ph2P=NPPh2C(S)NEt in Its Anionic, Neutral and Cationic Forms – Determination of Absolute pKa Values in CH2Cl2 of RhI Complexes

AbstractThe coordination properties of EtNHC(S)Ph2P=NPPh2C(S)NEt (HEtSNS) towards RhI species derived from [Rh(CO)2Cl]2 and [Rh(cod)Cl]2 (cod = 1,5‐cyclooctadiene) were studied. This ligand is an amphoteric zwitterion, which forms the H2EtSNS+ cation upon protonation and the EtSNS– dianion–cation upon deprotonation. All three forms coordinate to metal centers. Their geometrical versatility allows many coordination fashions: S‐monodentate; S,S‐bidentate (with a bite angle spanning from 90 to 180°); S,N,S‐tridentate; N,N,N‐tridentate; and S,S‐bridging, as determined by X‐ray diffraction methods. The [Rh(CO)EtSNS] complex is a biprotic base; its conjugated acids are [Rh(CO)HEtSNS]+ and [Rh(CO)H2EtSNS]2+, and their pKa values were determined in dichloromethane solutions. In this triad of compounds, which are geometrically similar, the RhI metal center features variable charge density as confirmed by the νCO infrared absorption frequency.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Properties and pervaporation separation of hydroxyl‐terminated polybutadiene‐based polyurethane/poly(methyl metharcylate) interpenetrating networks membranes

AbstractHydroxyl‐terminated polybutadiene (HTPB), 4,4′‐dicyclohexyl methane diiscyanate (H12MDI), and 1,4‐butane diol are used to synthesize polyurethane (PU) solutions by two‐stage process. Interpenetrating networks (IPNs) of HTPB‐based PU and poly(methyl methacrylate) (PMMA) with HTPB/MMA (wt/wt % ratio) = 2.0, 1.5, 1.0, 1.5, 0.8, and 0.6, which are designated as IPN1 to IPN5, respectively, are synthesized by sequential polymerization technique. Thermal properties, tensile strength, and contact angle of membranes increase with the increase of MMA content, while the elongation of membranes show the reverse trend. Characterization of membranes are investigated by CC/CO absorption ratio and infrared absorption frequency shiftment. These PU and IPN membranes are used for the separation of ethanol/water and isopropanol/water solution by pervaporation test. IPN3 membrane possesses the largest pervaporation permeability and the separation factor. The pervaporation results of ethanol/water feed has the same trend as that of isopropyl alcohol (IPA)/water solution. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007

Synthetic, Infrared, 1H and 13C NMR Spectral Studies on N-(2/3/4-Substituted Phenyl)-2,4-Disubstituted Benzenesulphonamides, 2,4-(CH3)2/2-CH3-4-Cl/2,4-Cl2C6H3SO2NH(i-XC6H4) (i-X = H, 2-CH3, 3-CH3, 4-CH3, 2-Cl, 3-Cl, 4-Cl, 4-F, 4-Br)

Twenty six N-(2/3/4-substituted phenyl)-2,4-disubstituted benzenesulphonamides of the general formulae 2,4-(CH3)2C6H3SO2NH(i-XC6H4), 2-CH3-4-ClC6H3SO2NH(i-XC6H4) and 2,4- Cl2C6H3SO2NH(i-XC6H4), where i-X = H, 2-CH3, 3-CH3, 4-CH3, 2-Cl, 3-Cl, 4-Cl, 4-F or 4-Br, have been prepared, characterized and their infrared spectra in the solid state and 1H and 13C NMR spectra in solution studied. The infrared N-H stretching vibrational frequencies vary in the range 3298 - 3233 cm−1. Asymmetric and symmetric SO stretching vibrations appear in the ranges 1373 - 1311 cm−1 and 1177 - 1140 cm−1, respectively, while C-S, S-N and C-N stretching absorptions vary in the ranges 840 - 812 cm−1, 972 - 908 cm−1 and 1295 - 1209 cm−1, respectively. The various 1H and 13C NMR chemical shifts are assigned to the protons and carbon atoms of the two benzene rings in line with those for similar compounds. The incremental shifts due to the groups in the parent compounds have been computed by comparing the chemical shifts of the protons or carbon atoms in these compounds with those of benzene or aniline, respectively. The computed incremental shifts and other data were used to calculate the 1H and 13C NMR chemical shifts of the substituted compounds in three different ways. The calculated chemical shifts by the three methods compared well with each other and with the observed chemical shifts. It is observed that there are no particular trends in the variation of either the infrared absorption frequencies or the chemical shifts with the nature or site of substitution.

Water vapour sorption by the pedal mucus trail of a land snail

The hydrophilicity of pedal mucus trails deposited by snails influences the settlement of marine organisms and can potentially influence the trailing and homing mechanisms of terrestrial snails. The composition of pedal mucus deposited as a trail on a solid substrate by the giant African land snail ( Achatina marginata) has been probed non-invasively using infrared ellipsometry. The primary chemical groups in the mucus (in its native state) have been identified through their characteristic infrared absorption frequencies. Water vapour sorption in the mucus trails in equilibrium with the atmosphere was measured as a function of the relative humidity (RH). When RH=84%, the mucus contains 53 volume percent water. The water sorption isotherm of the mucus trail can be described through a Flory–Huggins polymer/solvent interaction parameter of χ=0.54±0.1, which is comparable to the value for some synthetic hydrophilic polymers, such as poly(vinyl pyrrolidone).

Synthesis of polyesteramides by palladium-catalyzed carbonylation–polycondensation of aromatic diiodides and amino alcohols

Abstract Polyesteramides were prepared by palladium-catalyzed carbonylation–polycondensation reaction of aromatic diiodides and amino alcohols. Several polyesteramides with moderate intrinsic viscosity were synthesized in excellent yields using different substrates and characterized. All polymers exhibited characteristic infrared absorption frequencies corresponding to amide and ester carbonyl groups. The effects of reaction parameters such as carbon monoxide pressure, solvent, base, temperature, etc. on the yield and intrinsic viscosity of the polyesteramide obtained were investigated using the carbonylation of 4,4′-diiodobiphenyl and 3-aminopropan-1-ol as a model polymerization reaction. The rate of carbonylation as well as intrinsic viscosity of the resulting polyesteramide increased with increase in the carbon monoxide pressure. Under optimized reaction conditions, the catalyst could be recycled efficiently several times without any loss in activity leading to very high cumulative turnover numbers (>10 3 ) that are almost two orders of magnitude higher than those reported for similar reactions.

Overcoming problems of density and thickness measurements in FTIR volatile determinations: a spectroscopic approach

The Beer–Lambert law is traditionally used to determine water and carbon concentrations in glasses from their infrared (IR) spectra. In practice, this method requires estimation of the thickness and density of the glass as well as the calibration of the molecular absorptivities of the species concerned. All of these parameters can be sources of practical difficulties and analytical uncertainty. These weaknesses in the application of the Beer–Lambert law have been overcome by an empirical analysis of the infrared spectra. Using a set of 292 spectra obtained on 113 natural and experimental tholeiitic glasses (SiO2 48.5–51 wt%; water contents 0–4000 ppm H2O), it can be shown that the thickness–density (ρ d) product of a glass sample can be directly and reliably inferred from its IR spectrum. This allows the Beer–Lambert law to be rewritten. The new form no longer requires thickness or density estimations to determine volatile contents. Moreover, if needed, the thickness of the glass slab can also be accurately determined from the IR spectra. This new method is developed for quantitative determination of water concentrations in MORB glasses but can also be applied to any minor species (carbon, sulfur, etc.) provided it is active in the IR domain and that a suitable independent frequency of IR absorption can be identified. Precision is about 60 ppm H2O on O–H− contents. This method, tested on natural and experimental MORB-type glasses, can be applied to any chemical composition provided a set of reference spectra is available.

Stress dependence of infrared absorption frequencies and oscillator strengths of acceptors confined in GaAs/AlGaAs quantum wells

Infrared absorption of acceptors confined in a GaAs/AlGaAs quantum well (QW) has been calculated in the presence of an external stress. The absorption frequency and oscillator strength of the dominating infrared transitions of acceptors confined in the QW are examined. The effects of the confined QW potential and the applied stress on the acceptor binding energies are investigated. A simple relation between the acceptor ground state splitting and the first heavy hole-light hole subband splitting is obtained for a GaAs/AlGaAs QW.