Set-up for time-resolved step-scan FTIR spectroscopy of noncyclic reactions

We have established a novel technique, which allows the application of time-resolved step-scan FTIR difference spectroscopy on noncyclic reactions. Cyclic reactions are ideally suited for the step-scan technique. However, it is difficult to apply the step-scan technique to noncyclic reactions, because the investigated process has to be repeated at about 1000 sampling positions of the interferogram. Consequently, to investigate noncyclic systems the sample has to be renewed at every sampling position. In the presented novel approach the IR-beam and the excitation laser-beam are focused to a very small diameter of 200 μm. Thereby, only a small segment of the sample, which has an overall diameter of 15 mm, is excited and probed. By moving the sample, which is mounted on an x-y-stage, to different nonexcited segments the reaction can be repeated until a complete interferogram data set is recorded. In so far as the typically used flow cells are concerned their optical pathlength is too large to perform difference spectroscopy. We use 4 μm thin films to depress the water background absorption of biological samples. As test, the well known photo-cyclic reactions of bacteriorhodopsin are measured. No systematic errors appear in the difference spectra. Because of intensity loss by the IR-microscope the signal-to-noise ratio is about 5 times less as compared to conventional step-scan measurements. For the first time, the technique is then applied to a noncyclic reaction, the photolysis of caged ATP. The successful performance with 10 μs time-resolution now opens the door for many new applications of step-scan FTIR measurements to noncyclic reactions.     

Fourier-transform infrared study of the switching process in a ferroelectric liquid crystalline polymer

The implementation of the step-scan technique on our FT-IR spectrometer enabled us to follow the electric-field induced reorientation dynamics of different molecular segments of a ferroelectric liquid crystalline polymer on a sub-millisecond time scale. It was detected that not only the mesogen but also the spacer and at least part of the backbone take part in the reorientation process.     

Dynamic ft-ir spectroscopy of polymer films and liquid crystals

The use of continuous-scan and step-scan Fourier transform infrared (FT-IR) spectroscopic techniques to study the dynamics of the response of polymer films and liquid crystals to external perturbations is described here. The first application of dynamic stepscan FT-IR deals with the response of various polymer films to sinusoidally modulated tensile strain. In these experiments, a small amplitude sinusoidal stress is applied to a polymeric film and the transition dipole responses are monitored as a phase lag with respect to the external perturbation. The degree of deformation is small enough to cause only linear reversible responses to the sample. The main advantage of the technique is that it can provide valuable information at the molecular level that can be used to interpret the macroscopic properties of the polymeric material under investigation. Results for heterogeneous polymers include semicrystalline high density/low density polyethylene blends and the micro-phase separated copolymer Kraton^r̀ are presented. In addition, continuous-scan stroboscopic FT-IR was used to explore the submolecular (functional group) contributions to the reorientation dynamics of the liquid crystal director in response to pulsed (DC) electric fields. For the nematic liquid crystal molecules, 4-pentyl-4'-cyanobiphenyl (5CB) and 4-pentyl-4'-cyanophenylcyclohexane (5PCH), the individual response of the rigid and floppy parts was examined.     

Matrix merging arrangements for the study protein dynamics by time-resolved step-scan Fourier transform infrared spectroscopy and multivariate curve resolution

In this paper, we propose the construction of merging arrangements for combining the information from various runs as a powerful approach to improve the resolution. The bacteriorhodopsin (bR) photocycle has been chosen in this study as an example dealing with the protein dynamics monitored by means of time-resolved step-scan FT-IR spectroscopy. The possibilities of matrix merging are evaluated and results are compared with those from the analysis of individual and augmented matrices. As a conclusion, this strategy provides excellent results for the analysis of this type of time-resolved FT-IR data.     

Ordering and mobility of ferroelectric liquid crystal dimer as studied by FT-IR spectroscopy with 2D-IR correlation analysis

Both a conservative rapid-scan FT-IR technique and a novel step-scan FT-IR technique with 2D correlation analysis were used to study the orientation and the mobility of a ferroelectric liquid crystal dimer during switching under an electric field. The detailed mutual arrangements of different molecular segments (mesogen, poly(methylene) chain, polysiloxane chain) in a smectic C* phase were derived from the static spectra. It was shown that the long mesogen axis, the average poly(methylene) and the average polysiloxane chain axes do not coincide with each other. The hindered rotation of the carbonyl group is confirmed. Time-resolved FT-IR technique was used to follow the segmental motion with a time resolution of 5 μs. The temperature and electric field strength dependencies of the mobility of these segments are discussed. 2D correlation analysis of time-resolved data reveals small differences in the behavior of the carbonyl and the benzoic rings in the mesogen moieties, that can be explained as differences in the orientation distribution functions of these moieties.     

Applications of FT-IR/microscopy in forensic analysis

The technique of FT-IR/microscopy is applied to a variety of problems faced by the forensics chemist. These are as varied as the identification of drugs and fibers to the assignment of the origin of a paint sample. Our efforts in the effective utilization of FT-IR/microscopy in this area and usage of new data bases to aid in identifications are discussed.     

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

A prerequisite for the understanding of functional molecules like proteins is the elucidation of their structure under reaction conditions. Chiral vibrational spectroscopy is one option for this purpose, but provides only indirect access to this structural information. By first‐principles calculations, we investigate how Raman optical activity (ROA) signals in proteins are generated and how signatures of specific secondary‐structure elements arise. As a first target we focus on helical motifs and consider polypeptides consisting of twenty alanine residues to represent α‐helical and 3₁₀‐helical secondary‐structure elements. Although ROA calculations on such large molecules have not been carried out before, our main goal is the stepwise reconstruction of the ROA signals. By analyzing the calculated ROA spectra in terms of rigorously defined localized vibrations, we investigate in detail how total band intensities and band shapes emerge. We find that the total band intensities can be understood in terms of the reconstructed localized vibrations on individual amino acid residues. Two different basic mechanisms determining the total band intensities can be established, and it is explained how structural changes affect the total band intensities. The band shapes can be rationalized in terms of the coupling between the localized vibrations on different residues, and we show how different band shapes arise as a consequence of different coupling patterns. As a result, it is demonstrated for the chiral variant of Raman spectroscopy how collective vibrations in proteins can be understood in terms of well‐defined localized vibrations. Based on our calculations, we extract characteristic ROA signatures of α helices and of 3₁₀‐helices, which our analysis directly relates to differences in secondary structure.     

Time-resolved Fourier transform infrared spectrometry using a microfabricated continuous flow mixer: application to protein conformation study using the example of ubiquitin

We report on the use of time-resolved Fourier transform infrared spectroscopy (FT-IR) to study chemically induced conformational changes of proteins using the example of ubiquitin. For this purpose a micromachined mixer is coupled to a conventional IR transmission cell with a pathlength of 25 microm and operated in both the continuous and the stopped-flow mode. This experimental set-up allows the elucidation of reaction pathways in the time frame of about 500 milliseconds to seconds with little reagent consumption and low pressure. For continuous flow measurements employed in the time frame from 0.5 to 1.4 s the reaction time is determined by the flow rate used as the connection between the point of confluence in the micromixer and the flow cell was kept constant in all experiments. For stopped-flow experiments (>1.4 s) the time is determined by data acquisition of the rapid scanning infrared spectrometer. Ubiquitin, a small well-known protein with 76 amino acid residues, changes its conformation from native to A-state with the addition of methanol under low pH conditions. We investigated the conformational change in the time frame from 0.5 to 10 s by mixing ubiquitin (20% methanol-d(4)) with an 80% methanol-d(4) solution at pD 2 by evaluating the time dependent changes in the amide I band of the protein.     

Observations of different triplet conformations in time-resolved infrared spectra of alkyl phenylglyoxylates

Two different conformations of the triplet state of alkyl phenylglyoxylates were observed by means of time-resolved step-scan FT-IR spectroscopy. The amplitude of the peak corresponding to the sterically hindered conformation decreases as the size of the alkyl group increases. Both conformations exhibit similar reactivity in intermolecular hydrogen abstraction, but only one of them undergoes Norrish Type II photoelimination.     

Assessment of a Large Enzyme–Drug Complex by Proton‐Detected Solid‐State NMR Spectroscopy without Deuteration

Solid‐state NMR spectroscopy has recently enabled structural biology with small amounts of non‐deuterated proteins, largely alleviating the classical sample production demands. Still, despite the benefits for sample preparation, successful and comprehensive characterization of complex spin systems in the few cases of higher‐molecular‐weight proteins has thus far relied on traditional ¹³C‐detected methodology or sample deuteration. Herein we show for a 29 kDa carbonic anhydrase:acetazolamide complex that different aspects of solid‐state NMR assessment of a complex spin system can be successfully accessed using a non‐deuterated, 500 μg sample in combination with adequate spectroscopic tools. The shown access to protein structure, protein dynamics, as well as biochemical parameters in amino acid sidechains, such as histidine protonation states, will be transferable to proteins that are not expressible in E. coli.     

Docking of photosystem I subunit C using a constrained geometric simulation

The elucidation of assembly pathways of multi-subunit protein complexes is a problem of great interest in structural biology and biomolecular modeling. In this study, we use a new computer algorithm for the simulation of large-scale motion in proteins to dock the subunit PsaC onto Photosystem I. We find that a complicated docking pathway involving multiple conformational changes can be quickly simulated by actively targeting only a few residues at a time to their target positions. Simulations for two possible docking scenarios are explored, and experimental approaches to distinguish between them are discussed.     

FT-IR detection in gas chromatography

Fourier-transform infrared (FT-IR) spectroscopy plays a small, though occasionally crucial, role as a detection technique in gas chromatography (GC). FT-IR can be used as a universal, a selective and a specific detection method, but a major drawback is its lack of sensitivity. The power of GC/FT-IR is the unique structural information that can be extracted from the spectral data and that cannot be obtained from any other method. As a consequence, GC/FT-IR is mainly applied as an additional tool to GC/MS, for isomer discrimination and structure elucidation of compounds with closely-related structures.     

TReNDS—Software for reaction monitoring with time-resolved non-uniform sampling

NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods—correlation experiments—are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time-consuming, and thus, the reaction-monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single-scan or fast-sampling experiments). Recently, the technique of time-resolved non-uniform sampling (TR-NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on-the-fly processing during the reaction. In this paper, we introduce TReNDS: free, user-friendly software kit for acquisition and processing of TR-NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR-NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.     

Absolute Minimal Sampling in High‐Dimensional NMR Spectroscopy

Standard three‐dimensional Fourier transform (FT) NMR experiments of molecular systems often involve prolonged measurement times due to extensive sampling required along the indirect time domains to obtain adequate spectral resolution. In recent years, a wealth of alternative sampling methods has been proposed to ease this bottleneck. However, due to their algorithmic complexity, for a given sample and experiment it is often hard to determine the minimal sampling requirement, and hence the maximal achievable experimental speed up. Herein we introduce an absolute minimal sampling (AMS) method that can be applied to common 3D NMR experiments. We show for the proteins ubiquitin and arginine kinase that for widely used experiments, such as 3D HNCO, accurate carbon frequencies can be obtained with a single time increment, while for others, such as 3D HN(CA)CO, all relevant information is obtained with as few as 6 increments amounting to a speed up of a factor 7–50.     

Electric field standing wave effects in FT-IR transflection spectra of biological tissue sections: Simulated models of experimental variability

The so-called electric field standing wave effect (EFSW) has recently been demonstrated to significantly distort FT-IR spectra acquired in a transflection mode, both experimentally and in simulated models, bringing into question the appropriateness of the technique for sample characterization, particularly in the field of spectroscopy of biological materials. The predicted effects are most notable in the regime where the sample thickness is comparable to the source wavelength. In this work, the model is extended to sample thicknesses more representative of biological tissue sections and to include typical experimental factors which are demonstrated to reduce the predicted effects. These include integration over the range of incidence angles, varying degrees of coherence of the source and inhomogeneities in sample thickness. The latter was found to have the strongest effect on the spectral distortions and, with inhomogeneities as low as 10% of the sample thickness, the predicted distortions due to the standing wave effect are almost completely averaged out. As the majority of samples for biospectroscopy are prepared by cutting a cross section of tissue resulting in a high degree of thickness variation, this finding suggests that the standing wave effect should be a minor distortion in FT-IR spectroscopy of tissues. The study has important implications not only in optimization of protocols for future studies, but notably for the validity of the extensive studies which have been performed to date on tissue samples in the transflection geometry.     

Inductively coupled plasma-atomic emission spectrometry: Analytical assessment of the technique at the beginning of the 90's

The main application of the inductively coupled plasma (ICP) today is in atomic emission spectroscopy (AES), as an excitation spectrochemical source, although uses of an ICP for fluorescence as just an atomiser, and specially for mass spectrometry, as an ionization source, are rocketing in the last few years.Since its inception, only a quarter of a century ago, ICP-AES has rapidly evolved to one of the preferred routine analytical techniques for convenient determination of many elements with high speed, at low levels and in the most varied samples. Perhaps its comparatively high kinetic temperature (capable of atomising virtually every compound of any sample), its high excitation and ionisation temperatures, and its favourable spatial structure at the core of the ICP success.By now, the ICP-AES can be considered as having achieved maturity in that a huge amount of analytical problems can be tackled with this technique, while no major or fundamental changes have been adopted for several years. Despite this fact, important driving forces are still in operation to further improve the ICP-AES sensitivity, selectivity, precision, sample throughput, etc. Moreover, proposals to extend the scope of the technique to traditionally elusive fields (e.g. non-metals and organic compound analysis) are also appearing in the recent literature.In this paper the state of the art, the last developments and the expectations in trying to circumvent the limitations of the ICP-AES (on the light of literature data and personal experience) are reviewed.     

Investigation of fungal deterioration of synthetic paint binders using vibrational spectroscopic techniques

The deterioration of synthetic polymers caused by biological process is usually evaluated by visual inspection and measuring physical effects. In contrast to this approach, we have applied vibrational spectroscopies to study the biodegradation of the synthetic resins. 29 synthetic resins used as paint binding media, including acrylic, alkyd and poly(vinyl acetate) polymers, were examined for potential susceptibility to fungal degradation using the standard method ASTM G21-96(2002). In addition, the degraded resins were analysed by Raman spectroscopy, FT-IR and FT-IR photoacoustic spectroscopy. Almost all the acrylic resins studied proved to be resistant to microbial attack, while all alkyd resins and some poly(vinyl acetates) turned out to be biodegradable. Within a few days of inoculation Aspergillus niger was the most copious fungus on the biodegraded resins. A comparison of the IR and Raman spectra of control and biodegraded resins did not show any differences, but photoacoustic spectroscopy revealed additional bands for the fungal-degraded resins, consistent with the presence of fungal-derived substances. The additional bands in the photoacoustic spectra were due to the presence of Aspergillus niger and melanin, a fungal pigment. Since IR photoacoustic spectroscopy can be also a suitable technique for the chemical characterisation of binding media, the same spectroscopic analysis can be employed to both characterise the material and obtain evidence for fungal colonization. Microbial growth on Sobral 1241ML (alkyd resin) after 28 d (growth rating 4) compared with the non-inoculated resin.     

Quantitative Structural Constraints for Organic Powders at Natural Isotopic Abundance Using Dynamic Nuclear Polarization Solid‐State NMR Spectroscopy

A straightforward method is reported to quantitatively relate structural constraints based on ¹³C–¹³C double‐quantum build‐up curves obtained by dynamic nuclear polarization (DNP) solid‐state NMR to the crystal structure of organic powders at natural isotopic abundance. This method relies on the significant gain in NMR sensitivity provided by DNP (approximately 50‐fold, lowering the experimental time from a few years to a few days), and is sensitive to the molecular conformation and crystal packing of the studied powder sample (in this case theophylline). This method allows trial crystal structures to be rapidly and effectively discriminated, and paves the way to three‐dimensional structure elucidation of powders through combination with powder X‐ray diffraction, crystal‐structure prediction, and density functional theory computation of NMR chemical shifts.     

A novel vertical attenuated total reflectance photochemical flow-through reaction cell for Fourier transform infrared spectroscopy

A unique photochemical cell design and two experiments are presented, which illustrate the usefulness of flow-through attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy as a technique for investigating photochemical reactions at the mineral-water interface. The kinetics of the photolysis reaction of potassium oxalate (K(2)C(2)O(4)) in a ferric iron solution and oxalate adsorbed onto goethite (alpha-FeOOH) were investigated to show the capabilities of the cell. Due to complicated kinetics, the adsorption experiment demonstrates not only the types of complex problems, that may exist at the mineral-water interface, but also the ability for this novel cell design to address them.