Vibrational spectroscopy of fossils

Over the last two decades, there has an been increasing interest in applying vibrational spectroscopy in palaeontological research. For example, this chemical analytical technique has been used to elucidate the chemical composition of a wide variety of fossils, including Archaean putative microfossils, stromatolites, chitinozoans, acritarchs, fossil algae, fossil plant cuticles, putative fossil arthropods, conodonts, scolecodonts and dinosaur bones. The insights provided by these data have been equally far ranging: to taxonomically identify a fossil, to determine biogenicity of a putative fossil, to identify preserved biologically synthesized compounds and to elucidate the preservational mechanisms of fossil material. Vibrational spectroscopy has clearly been a useful tool for investigating various palaeontological problems. However, it is also a tool that has been misapplied and misinterpreted, and thus, this review is dedicated to providing a palaeontologist who is new to vibrational spectroscopy with a basic understanding of these techniques, and the types of chemical information that can be obtained. Two example applications of these techniques are discussed in detail, one looking into fossil palynomorph taxonomy and other into the enigmatic Burgess Shale‐type preservation.     

My remembrances of H.G. Khorana: exploring the mechanism of bacteriorhodopsin with site-directed mutagenesis and FTIR difference spectroscopy

H.G. Khorana’s seminal contributions to molecular biology are well-known. He also had a lesser known but still major influence on current application of advanced vibrational spectroscopic techniques such as FTIR difference spectroscopy to explore the mechanism of bacteriorhodopsin and other integral membrane proteins. In this review, I provide a personal perspective of my collaborative research and interactions with Gobind, from 1982 to 1995 when our groups published over 25 papers together which resulted in an early picture of key features of the bacteriorhodopsin proton pump mechanism. Much of this early work served as a blueprint for subsequent advances based on combining protein bioengineering and vibrational spectroscopic techniques to study integral membrane proteins.     

Vibrational optical activity: From discovery and development to future challenges

Vibrational optical activity (VOA) consisting of infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA) was predicted, discovered, and confirmed between 1971 and 1975. My path to VOA was mentored by three pioneers of chirality and vibrational spectroscopy: Professors Albert Moscowitz, Warner L. Peticolas, and Philip J. Stephens, and while they are no longer alive today, the Chirality Medal, my award address, and this paper are dedicated to each of them. Since the discovery of VOA, a number of key advances have made possible the current era of widespread applications. The principal instrumental advances were Fourier-transform VCD (FT-VCD) and multichannel charge coupled detector (CCD) ROA. Computational advances include the first complete quantum chemistry formulation of VCD leading to the magnetic field perturbation (MFP) and the nuclear velocity perturbation (NVP) theories. The strength of VOA is the comparison between measured and calculated spectra that enables the determination of absolute configuration and solution-state conformations. More recently, VCD has uncovered supramolecular chirality in amyloid fibrils and ROA to high-order protein structure. Future challenges for VOA include describing the effects of weak intermolecular interactions, transfer of chirality, solvent effects, supramolecular chirality, and the generation of nuclear velocity electron current density.     

Comparison between high definition FT‐IR,Raman and AFM‐IR for subcellular chemical imaging of cholesteryl esters in prostate cancer cells

The family of vibrational spectroscopic imaging techniques grows every few years and there is a need to compare and contrast new modalities with the better understood ones, especially in the case of demanding biological samples. Three vibrational spectroscopy techniques (high definition Fourier‐transform infrared [FT‐IR], Raman and atomic force microscopy infrared [AFM‐IR]) were applied for subcellular chemical imaging of cholesteryl esters in PC‐3 prostate cancer cells. The techniques were compared and contrasted in terms of image quality, spectral pattern and chemical information. All tested techniques were found to be useful in chemical imaging of cholesterol derivatives in cancer cells. The results obtained from FT‐IR and Raman imaging showed to be comparable, whereas those achieved from AFM‐IR study exhibited higher spectral heterogeneity. It confirms AFM‐IR method as a powerful tool in local chemical imaging of cells at the nanoscale level. Furthermore, due to polarization effect, p‐polarized AFM‐IR spectra showed strong enhancement of lipid bands when compared to FT‐IR.     

Vibrational spectroscopic studies to acquire a quality control method of Eucalyptus essential oils

This article presents a novel and original approach to analyze in situ the main components of Eucalyptus oil by means of Raman spectroscopy. The obtained two-dimensional Raman maps demonstrate a unique possibility to study the essential oil distribution in the intact plant tissue. Additionally, Fourier Transform (FT)-Raman and attenuated total reflection (ATR)-IR spectra of essential oils isolated from several Eucalyptus species by hydrodistillation are presented. Density Functional Theory (DFT) calculations were performed in order to interpret the spectra of the essential oils of the Eucalyptus species. It is shown that the main components of the essential oils can be recognized by both vibrational spectroscopic techniques using the spectral information of the pure terpenoids. Spectroscopic analysis is based on the key bands of the individual volatile substances and therefore allows one to discriminate different essential oil profiles of several Eucalyptus species. It has been found that the presented spectroscopic data correlate very well with those obtained by gas chromatography (GC) analysis. All these investigations are helpful tools to generate a fast and easy method to control the quality of the essential oils with vibrational spectroscopic techniques in combination with DFT calculations.     

Rational design of thiolated polyenes as trifunctional Raman reporter molecules in surface‐enhanced Raman scattering nanotags for cytokine detection in a lateral flow assay

The characteristic vibrational spectroscopic fingerprint of Raman reporter molecules adsorbed on noble metal nanoparticles is employed for the identification of target proteins by the corresponding surface‐enhanced Raman scattering (SERS) nanotag‐labeled antibodies. Here, we present the modular synthesis of thiolated polyenes with two to five C═C double bonds introduced via stepwise Wittig reactions. The experimental characterization of their electronic and vibrational properties is complemented by density functional theory calculations. Highly SERS‐active nanotags are generated by using the thiolated polyenes as Raman reporter molecules in Au/Au core/satellite supraparticles with multiple hot spots. The cytokines IL‐1β and IFN‐γ are detected in a duplex SERS‐based lateral flow assay on a nitrocellulose test strip by Raman microscopy. The thiolated polyenes are suitable for use in immuno‐SERS applications such as point‐of‐care testing as well as cellular and tissue imaging.     

Differential Imaging of Biological Structures with Doubly-resonant Coherent Anti-stokes Raman Scattering (CARS)

Coherent Raman imaging techniques have seen a dramatic increase in activity over the past decade due to their promise to enable label-free optical imaging with high molecular specificity ¹. The sensitivity of these techniques, however, is many orders of magnitude weaker than fluorescence, requiring milli-molar molecular concentrations ^1,2. Here, we describe a technique that can enable the detection of weak or low concentrations of Raman-active molecules by amplifying their signal with that obtained from strong or abundant Raman scatterers. The interaction of short pulsed lasers in a biological sample generates a variety of coherent Raman scattering signals, each of which carry unique chemical information about the sample. Typically, only one of these signals, e.g. Coherent Anti-stokes Raman scattering (CARS), is used to generate an image while the others are discarded. However, when these other signals, including 3-color CARS and four-wave mixing (FWM), are collected and compared to the CARS signal, otherwise difficult to detect information can be extracted ³. For example, doubly-resonant CARS (DR-CARS) is the result of the constructive interference between two resonant signals ⁴. We demonstrate how tuning of the three lasers required to produce DR-CARS signals to the 2845 cm^-1 CH stretch vibration in lipids and the 2120 cm^-1 CD stretching vibration of a deuterated molecule (e.g. deuterated sugars, fatty acids, etc.) can be utilized to probe both Raman resonances simultaneously. Under these conditions, in addition to CARS signals from each resonance, a combined DR-CARS signal probing both is also generated. We demonstrate how detecting the difference between the DR-CARS signal and the amplifying signal from an abundant molecule''s vibration can be used to enhance the sensitivity for the weaker signal. We further demonstrate that this approach even extends to applications where both signals are generated from different molecules, such that e.g. using the strong Raman signal of a solvent can enhance the weak Raman signal of a dilute solute.     

Vibrational spectroscopy of seaweed galactans

Information from classical infrared spectroscopy studies has been of significance for characterizing seaweed galactans. The development of Fourier transform infrared spectroscopy and of Fourier transform laser Raman spectroscopy has produced great advances in the application of vibrational spectroscopy to the structural study of polysaccharides. Computational facilities in the spectrometers allow the arithmetic manipulations of the spectra. The second-derivative mode in the FT IR spectrocopy provided more information by increasing the number and resolution of the bands in the spectra as compared to the parent ones. A review of literature data on vibrational spectroscopy of sulfated polysaccharides and new results are presented. Agar-type polymers showed two diagnostic bands in the second-derivative mode in the region 800–700 cm^–1. Carrageenans exhibited a number of bands in the region 1600–1000 cm^–1. Fourier transform laser Raman spectroscopy in the solid state gave well-defined characteristic spectra of agar and carrageenans. Both techniques can be applied to small samples in the solid state and allow differentiation in a few minutes between agar and carrageenan-type seaweed galactans. The second-derivative mode of the FT IR spectra can be applied to distinguish agar-producing from carrageenan-producing seaweeds. The spectra on KBr pellets of dried, ground agarophyte and carrageenophyte seaweed samples showed the same bands as the corresponding polysaccharides.     

Theoretical and pH dependent surface enhanced Raman spectroscopy study on caffeine

The surface enhanced Raman spectroscopy (SERS) spectrum of caffeine is recorded on a silver colloid at different pH values. It is discussed on the basis of the SERS "surface selection rules" in order to characterize its vibrational behavior on such a biological artificial model. To improve the previous assignments in the Raman spectrum and for a reliable, detailed analysis of SERS spectra, density functional theory calculations (structural parameters, harmonic vibrational wavenumbers, total electron density, and natural population analysis of the molecule) are performed for the anhydrous form of caffeine and the results are discussed. The predicted geometry and vibrational Raman spectra are in good agreement with the experimental data. The flat orientation of the mainly chemisorbed caffeine attached through the pi electrons and the lone pair of nonmethylated N atoms of the imidazole ring are proposed to occur at neutral and basic pH values. At acid pH values caffeine is probably adsorbed on the Ag surface through one or both oxygen atoms, more probably through the O atom of the conjugated carbonyl group with an end-on orientation. However, the changes in the overall SERS spectral pattern seem to indicate the electromagnetic mechanism as being the dominant one.     

Vibrational two-photon microscopy for tissue imaging: Short-wave infrared surface-enhanced resonance hyper-Raman scattering

Multiphoton microscopy using short-wave infrared (SWIR) radiation offers nondestructive and high-resolution imaging through tissue. Two-photon fluorescence (TPF), for example, is commonly employed to increase the penetration depth and spatial resolution of SWIR imaging, but the broad spectral peaks limit its multiplexing capabilities. Hyper-Raman scattering, the vibrational analog of TPF, yields spectral features on the order of 20 cm^?1 and reporter-functionalized noble metal nanoparticles (NPs) provide a platform for both hyper-Raman signal enhancement and selective targeting in biological media. Herein we report the first tissue imaging study employing surface-enhanced resonance hyper-Raman scattering (SERHRS), the two-photon analog of surface-enhanced resonance Raman scattering. Specifically, we employ multicore gold-silica NPs (Au@SiO₂ NPs) functionalized with a near infrared-resonant cyanine dye, 3,3′-diethylthiatricarbocyanine iodide as a SERHRS reporter. SWIR SERHRS spectra are efficiently acquired from mouse spleen tissue. SWIR SERHRS combines two-photon imaging advantages with narrow vibrational peak widths, presenting future applications of multitargeted bioimaging.     

Raman,FT-IR spectroscopic analysis and first-order hyperpolarisability of 3-benzoyl-5-chlorouracil by first principles

3-Benzoyl-5-chlorouracil (3B5CU), a biologically active synthetic molecule, has been analysed at DFT/6-311+ + G(d,p) level and reported for the first time as a potential candidate for nonlinear optical (NLO) applications. The optimised skeleton of 3B5CU molecule is non-planar. The frontier orbital energy gap, dipole moment, polarisability and first static hyperpolarisability have been calculated. The first static hyperpolarisability is found to be almost 15 times higher than that of urea. The high value of first static hyperpolarisability (2.930 × 10^? 30 e.s.u.) due to the intra-molecular charge transfer in 3B5CU has been discussed using first principles. A complete vibrational analysis of the molecule has been performed by combining the experimental Raman, FT-IR spectral data and the quantum chemical calculations. In general, a good agreement of calculated modes with the experimental ones has been obtained. The strong vibrational modes contributing towards NLO activity, involving the whole charge transfer path, have been identified and analysed.     

Polysaccharide-polynucleotide complexes VIII. Cation-induced complex formation between polyuridylic acid and schizophyllan

Raman spectroscopy has recently been applied ex vivo and in vivo to address various biomedical issues such as the early detection of cancers, monitoring of the effect of various agents on the skin, determination of atherosclerotic plaque composition, and rapid identification of pathogenic microorganisms. This leap in the number of applications and the number of groups active in this field has been facilitated by several technological advancements in lasers, CCD detectors, and fiber-optic probes. However, most of the studies are still at the proof of concept stage. We present a discussion on the status of the field today, as well as the problems and issues that still need to be resolved to bring this technology to hospital settings (i.e., the medical laboratory, surgical suites, or clinics). Taken from the viewpoint of clinicians and medical analysts, the potential of Raman spectroscopic techniques as new tools for biomedical applications is discussed and a path is proposed for the clinical implementation of these techniques.     

Raman ChemLighter: Fiber optic Raman probe imaging in combination with augmented chemical reality

Raman spectroscopy using fiber optic probe combines non‐contacted and label‐free molecular fingerprinting with high mechanical flexibility for biomedical, clinical and industrial applications. Inherently, fiber optic Raman probes provide information from a single point only, and the acquisition of images is not straightforward. For many applications, it is highly crucial to determine the molecular distribution and provide imaging information of the sample. Here, we propose an approach for Raman imaging using a handheld fiber optic probe, which is built around computer vision–based assessment of positional information and simultaneous acquisition of spectroscopic information. By combining this implementation with real‐time data processing and analysis, it is possible to create not only fiber‐based Raman imaging but also an augmented chemical reality image of the molecular distribution of the sample surface in real‐time. We experimentally demonstrated that using our approach, it is possible to determine and to distinguish borders of different bimolecular compounds in a short time. Because the method can be transferred to other optical probes and other spectroscopic techniques, it is expected that the implementation will have a large impact for clinical, biomedical and industrial applications.      

Cell (A549)-particle (Jasada Bhasma) interactions using Raman spectroscopy

Current methods for the evaluation of cell interactions with particles are nonspecific, slow, and invasive to the cells. Raman spectroscopy is a noninvasive technique, and is used in the present study to investigate particle-cell interactions. The main focus of the present study is to employ Raman spectroscopy for investigating the interaction of human lung adenocarcinoma cell line (A549) with the particulate system Jasada Bhasma, a traditional Indian medicine. Jasada Bhasma is a unique preparation of zinc and is traditionally used for the treatment of various diseases like diabetes, age-related eye diseases, and as a health promotional tonic. The Raman spectral analysis is executed by identifying the difference in intracellular DNA/RNA, and proteins and lipids concentration between particles--treated and untreated cells. Comparison between Bhasma-treated and -untreated cells indicates that vibrational peaks corresponding to the DNA/RNA molecule show a significant increase in cells treated with the Jasada Bhasma. Apart from the DNA molecule, several other vibrational peaks related to the protein molecules also show a significant increase in A549 cells after treatment with Bhasma. These results indicate that Bhasma treatment of A549 possibly delays DNA degradation and enables retention of higher amount of protein molecules in the cells.     

Imaging the invisible—Bioorthogonal Raman probes for imaging of cells and tissues

A revolutionary avenue for vibrational imaging with super‐multiplexing capability can be seen in the recent development of Raman‐active bioortogonal tags or labels. These tags and isotopic labels represent groups of chemically inert and small modifications, which can be introduced to any biomolecule of interest and then supplied to single cells or entire organisms. Recent developments in the field of spontaneous Raman spectroscopy and stimulated Raman spectroscopy in combination with targeted imaging of biomolecules within living systems are the main focus of this review. After having introduced common strategies for bioorthogonal labeling, we present applications thereof for profiling of resistance patterns in bacterial cells, investigations of pharmaceutical drug‐cell interactions in eukaryotic cells and cancer diagnosis in whole tissue samples. Ultimately, this approach proves to be a flexible and robust tool for in vivo imaging on several length scales and provides comparable information as fluorescence‐based imaging without the need of bulky fluorescent tags.     

CDSpecTech: A single software suite for multiple chiroptical spectroscopic analyses

The program CDSpecTech was developed to facilitate the analysis of chiroptical spectra, which include the following: vibrational circular dichroism (VCD) and corresponding vibrational absorption (VA) spectra; vibrational Raman optical activity (VROA) and corresponding vibrational Raman spectra; electronic circular dichroism (ECD) and corresponding electronic absorption (EA) spectra. In addition, the program allows for generating optical rotatory dispersion (ORD) as the Kramers–Kronig transform of ECD spectra. The simulation of theoretical spectra from transition strengths can be achieved using different bandshape profiles. The experimental and simulated theoretical spectra can be visually compared by displaying them together. A unique feature of CDSpecTech is performing spectral analysis using the ratio spectra; i.e., the dimensionless dissymmetry factor (DF) spectrum, which is the ratio of CD to absorption spectra, and the dimensionless circular intensity difference (CID) spectrum, which is the ratio of VROA to vibrational Raman spectra. The quantitative agreement between experimental and simulated theoretical spectra can also be assessed from the numerical similarity overlap between them. Two different similarity overlap methods are available. The program uses a graphical user interface which allows for ease of use and facilitates the analysis. All these features make CDSpecTech a valuable tool for the analysis of chiroptical spectra. The program is freely available on the World Wide Web.     

Selected latest applications of molecular spectroscopy in natural product analysis

The field of molecular vibrational spectroscopy applied to natural products is advancing extremely fast. Traditionally applied separation techniques (LC-, μ-LC–MS, GC, CE-MS) offer the advantages of high selectivity/sensitivity, but their application for routine quality control is limited due to long analyses times. Therefore, molecular spectroscopy in combination with multivariate analysis (MVA) enjoys excellent reputation, because of the fast and non-invasive measurement enabling the analysis of several physical and chemical parameters simultaneously. Near infrared (NIR; 4.000–10.000 cm⁻¹), attenuated total reflection (ATR; 400–4.000 cm⁻¹), Raman and far ultraviolet (FUV;120–200 nm) spectroscopy have permanently increased their efficiencies for quality control of predominantly food stuff, but also of other natural products including mainly medicinal plants. All four techniques enable not only a quantitative analysis of potent ingredients, but also qualitative fingerprint analysis for the discrimination of, e.g., species and/or geographic origin, respectively. Thereby, each individual spectroscopic technique possesses its specific strength. Powerful miniaturized portable spectrometers based on linear variable tuneable filter (LVTF) or micro-electro-mechanical systems (MEMS) are helpful in order to prevent consumers from deception on one hand, on the other hand they represent powerful analytical instruments for measurements in the field. 2-Dimensional correlation spectroscopy (2DCOS) represents a powerful technique for monitoring the dynamics of a system including temperature stability, extraction procedures etc. Imaging and mapping spectroscopy using infrared radiation and/or Raman scattering are not only suitable for classification of food stuff including e.g. maize kernels and/or coffee beans, but also for localizing the distribution of ingredients down to a resolution of 4 μm.In the present contribution, the latest progresses of the different techniques are introduced and their applicability in the fields of natural product analysis will be discussed in detail by distinct selected applications.     

Fingerprint‐to‐CH stretch continuously tunable high spectral resolution stimulated Raman scattering microscope

Stimulated Raman scattering (SRS) microscopy is a label‐free method generating images based on chemical contrast within samples, and has already shown its great potential for high‐sensitivity and fast imaging of biological specimens. The capability of SRS to collect molecular vibrational signatures in bio‐samples, coupled with the availability of powerful statistical analysis methods, allows quantitative chemical imaging of live cells with sub‐cellular resolution. This application has substantially driven the development of new SRS microscopy platforms. Indeed, in recent years, there has been a constant effort on devising configurations able to rapidly collect Raman spectra from samples over a wide vibrational spectral range, as needed for quantitative analysis by using chemometric methods. In this paper, an SRS microscope which exploits spectral shaping by a narrowband and rapidly tunable acousto‐optical tunable filter (AOTF) is presented. This microscope enables spectral scanning from the Raman fingerprint region to the Carbon‐Hydrogen (CH)‐stretch region without any modification of the optical setup. Moreover, it features also a high enough spectral resolution to allow resolving Raman peaks in the crowded fingerprint region. Finally, application of the developed SRS microscope to broadband hyperspectral imaging of biological samples over a large spectral range from 800 to 3600 cm^?1, is demonstrated.     

Nonlinear vibrational microscopy applied to lipid biology

Optical microscopy is an indispensable tool that is driving progress in cell biology. It still is the only practical means of obtaining spatial and temporal resolution within living cells and tissues. Most prominently, fluorescence microscopy based on dye-labeling or protein fusions with fluorescent tags is a highly sensitive and specific method of visualizing biomolecules within sub-cellular structures. It is however severely limited by labeling artifacts, photo-bleaching and cytotoxicity of the labels. Coherent Raman Scattering (CRS) has emerged in the last decade as a new multiphoton microscopy technique suited for imaging unlabeled living cells in real time with high three-dimensional spatial resolution and chemical specificity. This technique has proven to be particularly successful in imaging unstained lipids from artificial membrane model systems, to living cells and tissues to whole organisms. In this article, we will review the experimental implementations of CRS microscopy and their application to imaging lipids. We will cover the theoretical background of linear and non-linear vibrational micro-spectroscopy necessary for the understanding of CRS microscopy. The different experimental implementations of CRS will be compared in terms of sensitivity limits and excitation and detection methods. Finally, we will provide an overview of the applications of CRS microscopy to lipid biology.