Methods for extracting biochemical information from bacterial Raman spectra: an explorative study on Cupriavidus metallidurans

In this study, we explore Raman spectra of bacteria for their biochemical information. Therefore, a database of biomolecules was used and several approaches were applied such as the study of difference spectra, the calculation dot products, the usage of coefficients obtained from an EMSC procedure and the application of 2D correlation spectroscopy. These methods were applied on a dataset containing Raman spectra of Cupriavidus metallidurans LMG 1195 in five stages of its growth, aiming to extract information about the evolution of cell components during growth. EMSC coefficients seemed to be most promising for tracking metabolic products and the results were often confirmed by difference spectra or by 2D correlation spectroscopy.     

Raman spectroscopic study of bacterial endospores

Endospores and endospore-forming bacteria were studied by Raman spectroscopy. Raman spectra were recorded from Bacillus licheniformis LMG 7634 at different steps during growth and spore formation, and from spore suspensions obtained from diverse Bacillus and Paenibacillus strains cultured in different conditions (growth media, temperature, peroxide treatment). Raman bands of calcium dipicolinate and amino acids such as phenylalanine and tyrosine are more intense in the spectra of sporulating bacteria compared with those of bacteria from earlier phases of growth. Raman spectroscopy can thus be used to detect sporulation of cells by a characteristic band at 1,018 cm^–1 from calcium dipicolinate. The increase in amino acids could possibly be explained by the formation of small acid-soluble proteins that saturate the endospore DNA. Large variations in Raman spectra of endospore suspensions of different strains or different culturing conditions were observed. Next to calcium dipicolinate, tyrosine and phenylalanine, band differences at 527 and 638 cm^–1 were observed in the spectra of some of the B. sporothermodurans spore suspensions. These bands were assigned to the incorporation of cysteine residues in spore coat proteins. In conclusion, Raman spectroscopy is a fast technique to provide useful information about several spore components. Figure A difference spectrum between Raman spectra of B. licheniformis LMG 7634 cultured for 6 days and 1 day, together with the reference Raman spectrum of calcium dipicolinate     

Comparison of multivariate calibration models for glucose,urea, and lactate from near-infrared and Raman spectra

Partial least-squares (PLS) calibration models have been generated from a series of near-infrared (near-IR) and Raman spectra acquired separately from sixty different mixed solutions of glucose, lactate, and urea in aqueous phosphate buffer. Independent PLS models were prepared and compared for glucose, lactate, and urea. Near-IR and Raman spectral features differed substantially for these solutes, with Raman spectra enabling greater distinction with less spectral overlap than features in the near-IR spectra. Despite this, PLS models derived from near-IR spectra outperformed those from Raman spectra. Standard errors of prediction were 0.24, 0.11, and 0.14 mmol L⁻¹ for glucose, lactate, and urea, respectively, from near-IR spectra and 0.40, 0.42, and 0.36 mmol L⁻¹ for glucose, lactate, and urea, respectively, from Raman spectra. Differences between instrumental signal-to-noise ratios were responsible for the better performance of the near-IR models. The chemical basis of model selectivity was examined for each model by using a pure component selectivity analysis combined with analysis of the net analyte signal for each solute. This selectivity analysis showed that models based on either near-IR or Raman spectra had excellent selectivity for the targeted analyte. The net analyte signal analysis also revealed that analytical sensitivity was higher for the models generated from near-IR spectra. This is consistent with the lower standard errors of prediction.     

Raman and photoacoustic infrared spectra of fluorene derivatives: Experiment and calculations

Raman and photoacoustic (PA) infrared spectra of fluorene and four derivatives (2,3-benzofluorene, 2-methylfluorene, 2-ethylfluorene and 1,8-dimethylfluorene) were recorded and analyzed in this investigation. Mid- and far-infrared PA spectra were examined from about 2000 to 100 cm⁻¹. The Raman spectra spanned the same wavenumber range. Observed bands in both PA and Raman spectra were compared with DFT (harmonic) and variational (anharmonic) calculations, and with published spectra. The DFT calculations provided single-molecule frequencies, whereas the variational method yielded results for both monomeric and dimeric species. Many previously unknown bands, including numerous features due to combination and overtone transitions, were identified and assigned in this work.     

Detection of structurally similar adulterants in botanical dietary supplements by thin-layer chromatography and surface enhanced Raman spectroscopy combined with two-dimensional correlation spectroscopy

Thin-layer chromatography (TLC) coupled with surface enhanced Raman spectroscopy (SERS) has been widely used for the study of various complex systems, especially for the detection of adulterants in botanical dietary supplements (BDS). However, this method is not sufficient to distinguish structurally similar adulterants in BDS since the analogs have highly similar chromatographic and/or spectroscopic behaviors. Taking into account the fact that higher cost and more time will be required for comprehensive chromatographic separation, more efforts with respect to spectroscopy are now focused on analyzing the overlapped SERS peaks. In this paper, the combination of a TLC–SERS method with two-dimensional correlation spectroscopy (2DCOS), with duration of exposure to laser as the perturbation, is applied to solve this problem.     

Structural insights of catalytic intermediates in dialumene based CO_2 capture: Evidences from theoretical resonance Raman spectra

CO_2 capture is considered as one of the most ideal strategies for solving the environmental issues and against global warming.Recently,experimental evidence has suggested that aluminum double bond(dialumene) species can capture CO_2 and further convert it into value-added products.However,the catalytic application of these species is still in its infancy.Both the dynamics mechanism of CO_2 fixation and the detailed structures of catalytic intermediates are not well understood.In this work,we investigate the structure dependent resonance Raman(RR) signals for different reaction intermediates.Ab-initio simulations of spontaneous resonance Raman(spRR) and time-domain stimulated resonance Raman(stRR) give spectral signatures correlated to the existence of different intermediates during the CO_2-dialumene binding process.The unique Raman vibronic feature s contain rich structural information with high temporal resolution,enabling to monitor the transient catalytic intermediates under reaction conditions.Our work shows that RR can be used to monitor intermediates during the dialumene based CO_2 capture reaction.The spectral features not only provide insight into the structural information of intermediate species,but also allow a deeper understanding of the dynamical details of this kind of catalytic process.     

Regularity modes in Raman spectra of polyolefins: Part I. Propylene/olefin copolymers

Behavior of the regularity modes of isotactic polypropylene is analyzed in Raman spectra of a number of random propylene/olefin copolymers. The regularity modes at 809, 841, 973, 998, and 1220 cm⁻¹ decrease in intensity with growth of the content of the incorporated monomer. For the lines at 809, 973, and 1220 cm⁻¹ the rate of intensity damping varies depending on the structure of the incorporated monomer. The type of the incorporated monomer has inconsiderable effect on the evolution of intensity of the regularity bands at 841 and 998 cm⁻¹. Anomalous behavior of the mode at 1220 cm⁻¹ was observed for the propylene/1-butene copolymers.     

A comparison of surface-enhanced infrared and surface-enhanced Raman spectra of pyrazine adsorbed on polycrystalline gold electrodes

The adsorption of pyrazine at a polycrystalline Au film electrode has been investigated using in situ surface-enhanced infrared absorption spectroscopy (SEIRAS), chronocoulometry, and ac impedance. Combining the SEIRA data and the thermodynamic data (the surface charge density of the electrode and the relative Gibbs surface excess of pyrazine), pyrazine was found to adsorb on the surface with a vertical end-on configuration via one N atom. The SEIRA spectra were compared with published surface-enhanced Raman (SER) spectra of pyrazine in order to clarify the reason for the breakdown of the Raman selection rule in the SER spectra. The activation of originally Raman-forbidden modes in the SER spectra is well explained by a photo-driven charge-transfer mechanism. The charge-transfer is deduced to be from filled metal states near the Fermi level to the first and second excited states of pyrazine. It is emphasized that the comparative SEIRA and SER studies are important for a better understanding of the electrochemical interface.     

The Diversity of Linear Conjugated Polyenes and Colours in Nature: Raman Spectroscopy as a Diagnostic Tool

This review is centered on the linear conjugated polyenes, which encompasses chromatic biomolecules, such as carotenoids, polyunsaturated aldehydes and polyolefinic fatty acids. The linear extension of the conjugated double bonds in these molecules is the main feature that determines the spectroscopic properties as light-absorbing. These classes of compounds are responsible for the yellow, orange, red and purple colors which are observed in their parent flora and fauna in nature. Raman spectroscopy has been used as analytical tool for the characterization of these molecules, mainly due to the strong light scattering produced by the delocalized pi electrons in the carbon chain. In addition, conjugated polyenes are one of the main target molecular species for astrobiology, and we also present a brief discussion of the use of Raman spectroscopy as one of the main analytical tools for the detection of polyenes extra-terrestrially.     

Advances in surface-enhanced Raman spectroscopy for analysis of pharmaceuticals: A review

Recently, Raman spectroscopy become a popular and potential analytical technique for the analysis of pharmaceuticals as a result of its advancement. The innovation of laser technology, Fourier Transform-Raman spectrometers with charge coupled device (CCD) detectors, ease of sample preparation and handling, mitigation of sub-sampling problems using different geometric laser irradiance patterns and invention of different optical components of Raman spectrometers are contributors of the advancement of Raman spectroscopy. Transmission Raman Spectroscopy is a useful tool in pharmaceutical analysis to address the problems related with sub-sampling in conventional Raman back scattering. More importantly, the development of surface-enhanced Raman scattering (SERS) has been a prominent advancement for Raman spectroscopy to be applied for pharmaceuticals analysis as it avoids the inherent insensitivity and fluorescence problems. As the active pharmaceutical ingredients (APIs) contain aromatic or conjugated domains with strong Raman scattering activity, Raman spectroscopy is an attractive alternative conventional analytical method for pharmaceuticals. Coupling of Raman spectroscopy with separation techniques is also another advancement applied to reduce or avoid possible spectral interferences. Therefore, in this review, transmission Raman spectroscopy, SERS, and SERS coupled with various separation techniques for pharmaceutical analysis are presented.     

Can Raman Optical Activity Separate Axial from Local Chirality? A Theoretical Study of Helical Deca‐Alanine

Motivated by experimental work on the distinction of protein secondary structure motifs by Raman optical activity (ROA) spectroscopy, we demonstrate using density functional theory that axial chirality in structures with different local chirality can be filtered out by ROA spectroscopy. To this purpose, two diastereomers of right-handed helical deca-alanine, the (all-S) and the (R,S,R,S,R,S,R,S,R,S) form, are compared. Furthermore, we suggest to interpret calculated ROA spectra of large molecules in terms of vibrational bands rather than individual peaks. This is due to the non-homogeneous effect of the harmonic approximation as well as of the chosen electronic structure method onto the vibrational frequencies, which in a dense region of many vibrations will strongly determine the shape of the spectrum. In addition, the calculated ROA spectrum of (all-S)-deca-alanine is compared to the experimental spectrum of poly-(L)-alanine in solution.     

Regularity modes in Raman spectra of polyolefins: Part II. Polyethylene and ethylene copolymers

In this work, the thermal behavior of the regularity modes in Raman spectra of polyethylene with different densities and random ethylene/1-hexene copolymers with varying content of comonomer are studied. We demonstrate especially that the vibrational modes at 1062 and 2850 cm^↙1 are related to a critical sequence length of trans-conformers of 6⬜8 CH₂ groups, while the modes at 1130, 1170, 1295, and 2883 cm^↙1 indicate a critical sequence length of trans-conformers of 18 CH₂ groups. Upon increasing the 1-hexene content in the ethylene/1-hexene copolymers, the evolution of the intensities of the Raman modes at 1062, 1130, 1170, 1295, and 1417 cm^↙1, normalized to the intensity of the band at 2850 cm^↙1, is similar to the evolution of the intensities of the same modes in the Raman spectra of low density polyethylene at increasing temperature. This observation however contrasts with that in the Raman spectra of polyethylenes with middle and high densities. We suppose that these results can be explained by similarities in the structure of non-crystalline areas of low density polyethylene and the ethylene/1-hexene copolymers, which contain significant amounts of short sequences of trans-conformers.     

Ti2: accurate determination of the dissociation energy from matrix resonance Raman spectra and chemical interaction with noble gases

UV-visible and resonance Raman spectra of Ti(2) isolated in Ar, Kr, and Xe matrices at temperatures of 10 K were measured by using the 514 nm line of an Ar ion laser. The data show that the Ti(2) molecule interacts strongly with Xe, leading to a significant weakening of the Ti[bond]Ti bond strength. The f(Ti[bond]Ti) force constant decreases in the series Ar>Kr>Xe, from 232.8 Nm(-1) in Ar and 225.5 Nm(-1) in Kr to 199.7 Nm(-1) in Xe. Additional experiments in an Ar matrix containing 2 % of Xe indicate the formation of a molecule of the formula Ti(2)Xe. Our spectra for Ti(2) in an Ar matrix give evidence for several previously not observed members of the Stokes progression. The sum of experimental data allows for an improved estimation of the dissociation energy on the basis of a LeRoy-Bernstein-Lam analysis. A dissociation energy of 1.18 eV was derived from this analysis. The UV-visible data give evidence of the vibrational levels of an excited state of Ti(2).     

Experimental and theoretical IR,Raman, NMR spectra of 2‐, 3‐, and 4‐nitrobenzoic acids

The influence of the position of nitro group toward the carboxylic group on the vibration structure of the molecule was estimated. Optimized geometrical structures were calculated (HF, B3PW91, B3LYP). Experimental and theoretical FT‐IR, FT‐Raman, and nuclear magnetic resonance (NMR) spectra of the title compounds were recorded and analyzed. The most important vibrational bands of nitro and carboxyl groups and the benzene ring were assigned. Wavenumbers and intensities for the three acids studied were compared and discussed. Data of chemical shifts in ¹H and ¹³C NMR spectra of 2‐, 3‐, and 4‐nitrobenzoic acids were analyzed in comparison with benzoic acid molecule. The calculated parameters are compared with experimental characteristics of these molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Super-resolution and Raman chemical imaging: from multiple low resolution images to a high resolution image

Imaging in Raman spectroscopy is a valuable tool for analytical chemistry. Although molecular characterization at micron level is achieved for many applications, it usually fails producing chemical images of micron size samples as expected in chemical, environmental and biological analysis. The aim of the work is to introduce the potential of super-resolution in vibrational spectroscopic imaging. This original chemometrics approach uses several low resolution images of the same sample in order to retrieve a higher resolution chemical image. It is thus possible to overcome in a certain way some physical and instrumentals limitations. To illustrate the methodology, sub-micronic details of a Si/Au sample are retrieved from low resolution images with different super-resolution algorithms. The better results are obtained with Iterative L2/Bilateral Total Variation regularization method. The use of a regularization procedure gives also better results since its first property is to preserve edges during the reconstruction of the super-resolved image. This concept of chemical image data processing should open new analytical opportunities.     

Trans-esterification of fatty acids from microorganisms and human blood serum by trimethylsulfonium hydroxide (TMSH) for GC analysis

Summary Trimethylsulfonium hydroxide (TMSH) can convert fatty acids into the corresponding fatty acid methyl esters (FAMEs) in a single step. These fatty acids may also be bound in biomolecules such as phospholipids and/or glycerides. Complex mixtures of saturated and unsaturated FAMEs which may contain hydroxy and cylopropyl groups are obtained by trans-esterification; they can easily be separated in most cases by capillary GC. When FAMEs are generated from different microorganisms e.g. bacteria the patterns of the chromatograms are characteristic. Examples of characteristic patterns of bacteria with different cell wall structures are shown. The described method of transesterification can also be applied directly to blood serum without sophisticated sample pretreatment. The profiles of the chromatograms match well those described in the literature obtained by other methods of trans-esterification or sample preparation.     

Raman and Neutron Scattering Study of Partially Deuterated L‐Alanine: Evidence of a Solid‐Solid Phase Transition

Raman and neutron experiments using specific isotope labeling were combined in order to study the dynamics and structure of L ‐alanine. Inelastic neutron and Raman scattering data of C₂H₄(ND₂)CO₂D are discussed in relation to the doubling of the lattice parameter a observed by means of neutron powder diffraction in C₂D₄ (NH₂)CO₂H. The major changes accompanying the phase transition are found in the vibrational frequencies involving the torsional vibration τ(CO₂^?), which is clearly affected by the hydrogen bonds between the protons of the ammonium group and the oxygen atoms of the carboxylate group. At lower temperatures the rearrangement of identifiable hydrogen bonds induces changes in the bending vibration δ(ND₃), confirming some orientational disorder.     

Selective preparation of terminal alkenes from aliphatic carboxylic acids by a palladium-catalysed decarbonylation-elimination reaction

Trialkylamines were used as additives in the decarbonylation-elimination reaction catalysed by the combination of palladium(II) chloride and DPE-Phos. Aliphatic carboxylic acids were transformed at relatively low temperature into terminal alkenes in high yield and high selectivity, without the need for distillation, thereby avoiding isomerisation.