Enhancing the information content of vibrational spectra through sample perturbation

Infrared and Raman band frequencies, intensities and line shapes are often sensitive to the local molecular environment determined by molecular conformation, surrounding matrix, temperature, pressure, etc. The variety of local environments experienced by a condensed-phase molecule can lead to vibrational spectra with broad bands containing many overlapped spectral features. The spectral resolution of these overlapped features can be enhanced by making perturbations to the sample environment. Examples of perturbations which can be applied to the sample to enhance the information content of infrared spectra are changes in temperature, concentration and mechanical strain. In each instance, the spectra obtained as a function of the perturbation can be cross-correlated to produce a two-dimensional correlation map defined by two independent wavenumber axes. in this representation, infrared bands which respond to the perturbation in a similar or different manner can be clearly identified. This information can be used to help resolve overlapped bands and make unambiguous band assignments.     

Vibrational circular dichroism studies of molecular conformation and association of dipeptides

Vibrational circular dichroism (VCD) and infrared (IR) absorption spectra in the NH stretching region have been measured for the dipeptides, R′COAANHR′'(R′ = Me and tertBu; AA = Ala, Leu, Val and Phe; R′' = Me, isoBu and neoPe). Analyses of the VCD and absorption spectra indicated that the VCD bands for the NH stretching are quite sensitive to the state of hydrogen bonding as well as the local conformation of oligopeptides. VCD spectra exhibit a negative VCD band at 3420-3405 cm⁻¹ due to the C₅ conformer with an intramolecularly hydrogen-bonded five-membered ring. The intermolecularly hydrogen-bonded NH stretching vibration exhibits a characteristic negative—positive couplet from the high wavenumber side due to the antiparallel C₅C₅ dimer formation. Hydrogen-bonded oligomers beyond the dimer formed in highly concentrated solutions give rise to an additional negative VCD band on the lower wavenumber side of the hydrogen-bonded absorption band.     

Intercomparison of simultaneously obtained infrared (4.8 microm) and visible (515-715 nm) ozone spectra using ACE-FTS and MAESTRO

Laboratory ozone absorption spectra were measured simultaneously in the visible (515-715 nm) and infrared (2070-2140 cm(-1)) spectral regions using SCISAT-1's MAESTRO (Measurement of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) and ACE-FTS (Atmospheric Chemistry Experiment-Fourier Transform Spectrometer) spectrometers. An intercomparison of these measurements was used to assess the relative accuracy of HITRAN absolute line strengths, for which there was a 4% change between the 2000 and 2004 versions. Results reported here show that Chappuis band cross section strengths are more consistent with the HITRAN 2004 4.8 microm band line strengths than with the 2000 compilation.     

Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.     

Influence of temperature and pressure on shape and shift of impurity optical bands in polymer glasses

The shape, broadening, and shift of optical absorption spectra of molecular impurity centers in polymer glasses are considered in terms of inhomogeneous energy distributions and coupling of electronic transitions to vibrations. Persistent spectral hole burning was applied for frequency-selective probing of zero-phonon lines. The shift and broadening of spectral holes were studied between 5 and 50 K and by applying a hydrostatic He gas pressure up to 200 bar. Broadband absorption spectra were recorded between 5 and 300 K in poly(methyl methacrylate) and polyethylene. In addition to "normal" thermal broadening, due to the first- and second-order electron phonon coupling, several narrowing components were predicted on the basis of frequency dependent hole behavior. Thermal expansion of the matrix and the relaxation of local strains, previously accumulated on cooling below the glass temperature can lead to shrinking of the inhomogeneous width. A Voigt treatment of absorption band shapes reveals that the Gaussian component can indeed suffer remarkable narrowing. Inhomogeneous band shapes and the frequency-dependent thermal and baric line shifts were rationalized with the aid of a pair of two-body Lennard-Jones potentials. The shift of potential well minima is a crucial factor influencing solvent shifts, inhomogeneous band shapes, pressure shift coefficients, and quadratic electron phonon coupling constants.     

Determination of molecular line parameters for acrolein (C(3)H(4)O) using infrared tunable diode laser absorption spectroscopy

Acrolein (C(3)H(4)O) molecular line parameters, including infrared (IR) absorption positions, strengths, and nitrogen broadened half-widths, must be determined since they are not included in the high resolution transmission (HITRAN) molecular absorption database of spectral lines. These parameters are required for developing a quantitative analytical method for measuring acrolein in a single puff of cigarette smoke using tunable diode laser absorption spectroscopy (TDLAS). The task is complex since acrolein has many highly overlapping infrared absorption lines in the room temperature spectrum and the cigarette smoke matrix contains thousands of compounds. This work describes the procedure for estimating the molecular line parameters for these overlapping absorption lines in the wavenumber range (958.7-958.9 cm(-1)) using quantitative reference spectra taken with the infrared lead-salt TDLAS instrument at different pressures and concentrations. The nitrogen broadened half-width for acrolein is 0.0937 cm(-1)atm(-1) and to our knowledge, is the first time it has been reported in the literature.     

Taking apart the two-dimensional infrared vibrational echo spectra: more information and elimination of distortions

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe the fast structural evolution of molecular systems under thermal equilibrium conditions. Structural dynamics are tracked by observing the time evolution of the 2D-IR spectrum, which is caused by frequency fluctuations of vibrational mode(s) excited during the experiment. However, there are a variety of effects that can produce line shape distortions and prevent the correct determination of the frequency-frequency correlation function (FFCF), which describes the frequency fluctuations and connects the experimental observables to a molecular level depiction of dynamics. In addition, it can be useful to analyze different parts of the 2D spectrum to determine if dynamics are different for subensembles of molecules that have different initial absorption frequencies in the inhomogeneously broadened absorption line. Here, an important extension to a theoretical method for extraction of the FFCF from 2D-IR spectra is described. The experimental observable is the center line slope (CLSomega(m)) of the 2D-IR spectrum. The CLSomega(m) is obtained by taking slices through the 2D spectrum parallel to the detection frequency axis (omega(m)). Each slice is a spectrum. The slope of the line connecting the frequencies of the maxima of the sliced spectra is the CLSomega(m). The change in slope of the CLSomega(m) as a function of time is directly related to the FFCF and can be used to obtain the complete FFCF. CLSomega(m) is immune to line shape distortions caused by destructive interference between bands arising from vibrational echo emission, from the 0-1 vibrational transition (positive), and from the 1-2 vibrational transition (negative) in the 2D-IR spectrum. The immunity to the destructive interference enables the CLSomega(m) method to compare different parts of the bands as well as comparing the 0-1 and 1-2 bands. Also, line shape distortions caused by solvent background absorption and finite pulse durations do not affect the determination of the FFCF with the CLSomega(m) method. The CLSomega(m) can also provide information on the cross correlation between frequency fluctuations of the 0-1 and 1-2 vibrational transitions.     

Noise in FT-IR spectral data processing

A series of exploratory works on resolution enhancement, precision in wavenumber, integrated band intensity measures, and noise level control were performed on FT-IR spectra using standard mathematical techniques of data processing. In this communication, the infrared (IR) absorption band corresponding to the ν₈ mode of dichloromethane, CH₂Cl₂, was studied in benzene solution.Fourier self-deconvolution of the CH₂Cl₂ ν₈ band was carried out using standard software supplied for the purpose. Second and fourth derivative spectra were obtained with the “Nicolet” software parameter “DR1”. Self-deconvolution in Fourier space and derivative techniques were used to decrease the band full-width at half-height (FWHH) and achieve an apparent band resolution enhancement.The total area under the self-deconvoluted band is not exactly the same as under the original band. Under optimum self-deconvolution conditions, the integrated area increases by 6.9 % as compared with the out-of-phane CH bending W(CH₂) original band. However, a linear relationship between the integrated area of the self-deconvoluted band and FWHH of the original Lorentzian component was observed.The applicability and potential advantages of the self-deconvolution and derivation methods in spectral data processing are strongly limited by the noise level or signal-to-noise ratio (SNR) of the original IR spectra.     

The effect of optical substrates on micro-FTIR analysis of single mammalian cells

The study of individual cells with infrared (IR) microspectroscopy often requires living cells to be cultured directly onto a suitable substrate. The surface effect of the specific substrates on the cell growth—viability and associated biochemistry—as well as on the IR analysis—spectral interference and optical artifacts—is all too often ignored. Using the IR beamline, MIRIAM (Diamond Light Source, UK), we show the importance of the substrate used for IR absorption spectroscopy by analyzing two different cell lines cultured on a range of seven optical substrates in both transmission and reflection modes. First, cell viability measurements are made to determine the preferable substrates for normal cell growth. Successively, synchrotron radiation IR microspectroscopy is performed on the two cell lines to determine any genuine biochemically induced changes or optical effect in the spectra due to the different substrates. Multivariate analysis of spectral data is applied on each cell line to visualize the spectral changes. The results confirm the advantage of transmission measurements over reflection due to the absence of a strong optical standing wave artifact which amplifies the absorbance spectrum in the high wavenumber regions with respect to low wavenumbers in the mid-IR range. The transmission spectra reveal interference from a more subtle but significant optical artifact related to the reflection losses of the different substrate materials. This means that, for comparative studies of cell biochemistry by IR microspectroscopy, it is crucial that all samples are measured on the same substrate type.

Study of anomalous infrared properties of nanomaterials through effective medium theory

Effective medium theory is introduced into a three-layer model to study the anomalous IR properties of nanostructured Pt films. A composite system is set up for the nanostructured film together with adsorbates and water around it. The anomalous IR spectral features, which exhibit a transition from enhanced (or normal) IR absorption to Fano-type bipolar line shape and, finally, to enhanced anomalous IR absorption (the abnormal infrared effects) along with the change in structure and size of nanomaterials, as observed through experiments for CO molecule adsorption, are elucidated by an increase in the volume fraction of metal in the composite system and the effective thickness of the composite system. The theoretical simulation results illustrate that the spectral line shape of IR absorption depends strongly on the volume fraction of metal, while the intensity of the IR band is directly proportional to the effective thickness. This study has revealed, through a physical optical aspect of interaction of CO molecules with nanostructured metal films, one of the possible origins of anomalous IR properties and has shed light on interpreting the peculiar properties of nanomaterials.     

20种α-氨基酸的太赫兹光谱及其分子结构的相关性

应用太赫兹时域光谱(THz-TDS)技术, 在室温下对构成蛋白质的20种基本氨基酸的多晶粉末压片样品进行了光谱测试分析. 结果表明, 所有氨基酸对THz波反应非常灵敏, 在0.2-3.0 THz的有效频谱范围内, 表现出各自特征吸收峰, 故而利用THz光谱可以有效地区别不同种类的氨基酸. 我们以新数据验证和补充了前人的研究结果, 建立了以氨基酸分子结构及其THz光谱特征为基础的分类方案, 讨论并揭示了氨基酸分子的结构差异与其THz吸收光谱之间的相关性. 认知这些相关性将有助于鉴定氨基酸分子, 促进THz光谱学的理论研究以及在生物医学领域的推广应用.     

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.     

Voltage-induced infrared spectra from polymer field-effect transistors

Charge-induced infrared absorption spectra from the metal-insulator-semiconductor diodes fabricated with aluminum oxide, poly(p-xylylene), and SiO₂ as gate dielectric and regioregular poly(3-octylthiophene) as organic semiconductor have been measured in situ with reflection or transmission configurations by the FT-IR difference-spectrum method. The observed bands have been attributed to the carriers injected into the polymer layers under the application of minus gate bias. The wavenumber of the band around 1300 cm⁻¹ depends on the gate voltage, indicating that the structure of the carriers depends on the carrier concentration. There exist upper limits in the concentrations of the injected carriers. In situ infrared absorption measurements provide the information about the injected carriers, which affect the properties and the functions of polymer field-effect devices.     

Determination of molecular line parameters for acrolein (C3H4O) using infrared tunable diode laser absorption spectroscopy

Acrolein (C₃H₄O) molecular line parameters, including infrared (IR) absorption positions, strengths, and nitrogen broadened half-widths, must be determined since they are not included in the high resolution transmission (HITRAN) molecular absorption database of spectral lines. These parameters are required for developing a quantitative analytical method for measuring acrolein in a single puff of cigarette smoke using tunable diode laser absorption spectroscopy (TDLAS). The task is complex since acrolein has many highly overlapping infrared absorption lines in the room temperature spectrum and the cigarette smoke matrix contains thousands of compounds. This work describes the procedure for estimating the molecular line parameters for these overlapping absorption lines in the wavenumber range (958.7–958.9 cm⁻¹) using quantitative reference spectra taken with the infrared lead-salt TDLAS instrument at different pressures and concentrations. The nitrogen broadened half-width for acrolein is 0.0937 cm⁻¹ atm⁻¹ and to our knowledge, is the first time it has been reported in the literature.     

Hydrogen-bonding between pyrimidine and water: a vibrational spectroscopic analysis

We present an experimental and a theoretical study on hydrogen-bonding between pyrimidine and water as the H-donor. The degree of hydrogen-bonding in this binary system varies with mixture composition. This was monitored experimentally by polarization-resolved linear Raman spectroscopy with the pyrimidine ring breathing mode nu1 as a marker band. A subsequent quantitative line shape analysis of the isotropic Raman intensity for 24 pyrimidine/water mixtures clearly revealed a splitting into three spectral components upon dilution with water. The two additional peaks have been assigned to distinct groups of hydrogen-bonded species that differ in the number of pyrimidine nitrogen atoms (N) involved in hydrogen-bonding to water hydrogen atoms (H). From the integrated Raman intensities for "free" and "hydrogen-bonded" pyrimidine, a concentration profile for these species was established. Our assignments and interpretations are supported by quantum mechanical calculations of structures and by vibrational spectra for pyrimidine and 10 pyrimidine/water complexes with increasing water content. Also, accurate structure-spectra correlations for different cluster subgroups have been determined; within each particular cluster subgroup the water content varies, and a perfect negative correlation between NH hydrogen-bond distances and nu1 wavenumbers was observed.     

High resolution infrared spectra of H2-Kr and D2-Kr van der Waals complexes

Infrared spectra of weakly bound hydrogen-krypton complexes have been studied at high spectral resolution (0.04 cm(-1)) using a long-path (154 m) low temperature (100 K) absorption cell and a Fourier transform spectrometer. In addition to spectra from the regions of the H(2) and D(2) fundamental vibrational bands in the midinfrared, the results also include the region of the pure rotational S(0)(0) transition of H(2) in the far infrared. A total of 219 measured line positions from these spectra have been fully assigned to specific quantum transitions and form the basis for determining a greatly improved semiempirical three-dimensional intermolecular potential energy surface for hydrogen-krypton in an accompanying paper.     

High resolution FTIR spectrum of the nu1 band of DCOOD

Accurate spectral information on formic acid has wide application to radioastronomy since it was the first organic acid found in interstellar space. In this work, the infrared absorption spectrum of the nu1 band of deuterated formic acid (DCOOD) has been measured on a Bomem DA3.002 Fourier transform spectrometer in the wavenumber region 2560-2690 cm(-1) with a resolution of 0.004 cm(-1). A total of 292 infrared transitions have been assigned in this hybrid type A and B band centred at 2631.8736 +/- 0.0004 cm(-1). The assigned transitions have been fitted to give a set of eight rovibrational constants for the nu1 = 1 state with a standard deviation of 0.00078 cm(-1).     

POLARIZED UV-ABSORPTION SPECTRA OF RETINAL ISOMERS-I. MEASUREMENTS IN EXTREMELY THIN MONOCRYSTAL PLATELETS

Abstract Crystals of all- trans retinal and both different forms of 11- cis , 12-s- cis retinal were grown on quartz slides with faces (101), (001) and (101), respectively, forming thin platelets of less than 0.2 μm thickness. Polarized UV absorption spectra at room temperature were measured in the range from 20 to 43 × 10³ cm⁻¹ with a microscope-spectrophotometer. In this spectral range three diffuse absorption bands were observed for all crystal types at similar wave numbers. A main absorption band was found at 25–28 × 10³ cm⁻¹, and two further bands at 32–34 and 38–40 × 10³ cm⁻¹. In case of all- trans retinal the latter band is by far the weakest in this spectral range. Additionally, the crystal spectrum of all- trans retinal shows a shoulder at the low wavenumber side of the main band which cannot be resolved in the corresponding solution spectrum. In the crystal spectra of 11- cis , 12-s- cis retinal, however, only a strong dissymmetry is observed at this side of the main band.     

Carbon dioxide versus xenon as a mobile phase for flow cell packed column SFC/FT-IR

Xenon is compared to carbon dioxide as a mobile phase for super critical fluid chromatography/Fourier transform infrared spectrometry. The study showed xenon to be comparable to carbon dioxide in terms of resulting chromatography for non-polar analytes. Xenon was confirmed to be a very poor mobile phase, however, for polar analytes. It was determined that small wavenumber shifts in the infrared spectra of probe analytes occurred as either the density or temperature of the mobile phase was increased. The degree of these shifts was often similar for xenon and carbon dioxide. Analyte spectra for five different compounds were produced in both super critical xenon and carbon dioxide and compared to condensed phase and vapor phase library spectra. In all cases, carbon dioxide spectra were readily matched to their corresponding vapor phase spectra, despite having blanked portions of the spectrum due to carbon dioxide infrared absorption. Xenon produced technically superior spectra without such blanked regions, but at a much higher economical cost than carbon dioxide and with no real improvement in terms of library matching.     

Investigation of the spectral,optical and surface morphology properties of the N,N′‐Dipentyl‐3,4,9,10‐perylenedicarboximide small molecule for optoelectronic applications

The spectral and optical properties of the solutions of the N,N′‐Dipentyl‐3,4,9,10‐perylenedicarboximide (PTCDI‐C5) small molecule for different molarities were investigated in detail. The significant spectral parameters such as molar/mass extinction coefficients, absorption coefficient, electric dipole line strength, and oscillator strength of the PTCDI‐C5 molecule were calculated. The absorption bands of PTCDI‐C5 show vibronic structures with seven peaks at 2.08, 2.35, 2.53, 2.70, 2.86, 3.32, and 3.86 eV, respectively. The electronic spectra of the PTCDI‐C5 can be characterized by two basic regions as visible and Soret band. Effects of the molarities on the significant many optical parameters were investigated in detail. The direct and indirect allowed optical band gaps of the PTCDI‐C5 decrease with increasing molarity. Then, surface morphology properties were investigated and calculated roughness parameters of the PTCDI‐C5 film. Finally, we discussed for optoelectronic applications of these parameters, and this study was compared with the similar and related studies in the literature. Copyright © 2015 John Wiley & Sons, Ltd.