Fourier transform infrared (FTIR) spectroscopy is a powerful and widely used technique for studying an extensive range of substances, including investigations of their nature and behaviour under a gamut of conditions. IR spectra are characteristic of the bonds in molecular species (or extended bonded structures such as in solid lattices); they are therefore often used to 'fingerprint' substances and determine their identity, quality, impurities, and changes. However, samples containing a significant proportion of water present a particular challenge to FTIR spectroscopy due to its extensive absorption. Here, we concentrate on the special considerations that have to be taken if aqueous solutions are to be examined.

Fluorescence spectroscopy is widely used to characterise materials and investigate their behaviour. Here is presented a brief overview of the types of fluorescence spectrometers and their main components.

Fluorescence polarization techniques have proved to be a very useful method of investigating the environment and motion of fluorescent molecules and fluorophores within larger macromolecules. In this article the basic phenomena underlying fluorescence polarization and anisotropy, together with their relationships, are discussed.

The absolute stereochemistry of chiral molecules is ideally established to atomic resolution by X-ray crystallographic analysis. However, chiroptical spectroscopies, namely electronic circular dichroism (ECD), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD) and Raman optical activity (ROA), play important complementary roles in establishing relative and absolute sterochemistries as well as allowing determinations of optical purity. A brief summary of chiroptical spectroscopies is presented, along with guidance to their advantages and disadvantages. The application of ECD to verifying that single crystals selected for crystallographic analysis are indeed representative of bulk material is described.

Recent developments in spatially resolved infrared spectroscopy and imaging are summarized. These cover studies of catalysis, polymer structure, biomedical applications, and investigations of art works.

Ultra-violet-visible absorption spectroscopy and Circular Dichroism (CD) spectroscopy are widely used techniques for identifying and studying inorganic materials. Here is presented a brief overview of some of the features of this area.

Ultra violet, visible and near infra red absorption spectroscopy is widely used to characterise materials and investigate their behaviour. Here is presented a brief overview of the types of absorption spectrometers and their main components.

Circular dichroism (CD) is the differential absorption of left and right circularly polarized light by a chiral substance. The phenomenon can occur for all wavelengths of light and results in vibrational CD (VCD) in the infrared region and electronic CD (ECD) in the ultraviolet and visible regions, corresponding to the different excitations induced in a molecule by the light; Raman optical activity (ROA) is the analogous phenomenon for Raman scattering. The VCD and ROA techniques are described elsewhere in this encyclopedia; the section here concentrates on the instrumentation for ECD. The basis of CD, the main features of ECD spectrometers, and optimal methodology for obtaining spectra are described.

Polymorphism is an important solid state feature which affects many scientific fields ranging from mineralogy, metallurgy, and materials science through to the food and pharmaceutical industries. This article presents how vibrational spectroscopies, namely Infrared and Raman, are used to detect and characterize different polymorphic forms. Some examples covering different fields are shown.

Second Edition of the Encyclopedia of Spectroscopy and Spectrometry pulls key information into a single source for quick access to answers and/or in-depth examination of topics. SPEC-2 covers theory, methods, and applications for researchers, students, and professionals - combining proven techniques and new insights for comprehensive coverage of the field. The content is available in print and online via ScienceDirect, the latter of which offers optimal flexibility, accessibility, and usability through anytime, anywhere access for multiple users and superior search functionality. No other work gives analytical and physical (bio)chemists such unprecedented access to the literature. With 30% new content, SPEC-2 maintains the 'authoritative, balanced coverage' of the original work while also breaking new ground in spectroscopic research. The key features of the book include: incorporates more than 150 color figures, 5,000 references, and 300 articles (30% of which are new), for a thorough examination of the field; highlights new research and promotes innovation in applied areas ranging from food science and forensics to biomedicine and health; and features a new co-editor: David Koppenaal of Pacific Northwest National Laboratory, Washington, USA, whose work in atomic mass spectrometry has been recognized internationally.

ABSTRACT TNF is a primitive protein that has emerged from more than 550 million years of evolution. Our bioinformatics study of TNF from nine different taxa in vertebrates revealed several conserved regions in the TNF sequence. By screening overlapping peptides derived from human TNF to determine their role in three different TNF-induced processes – apoptosis, necrosis and NF-κB stimulation – we found that TNF conserved regions are mostly related to cell death rather than NF-κB stimulation. Among the most conserved regions, peptides (P)12, P13 and P1213 (comprising P12 and P13) induced apoptosis, whereas P14, P15, P16 and P1516 (comprising P15 and P16) induced necrosis. Cell death induced by these peptides was not through binding to the TNF receptor. P16-induced necrosis was mainly through disruption of the cell membrane, whereas P1213-induced apoptosis involved activation of TRADD followed by formation of complex II. Finally, using a monoclonal antibody and a mutant TNF protein, we show that TNF-induced apoptosis is determined by a conserved linear sequence that corresponds to that within P1213. Our results reveal the determinant sequence that is key to the TNF primitive function of inducing apoptosis.

Proteins are used as drugs against different pathologies because of their potential specificity of action with fewer side effects. However, their production and successful storage imposes a greater challenge compared to small molecule drugs. Though the determination of protein thermal stability is commonly used to find the optimum storage conditions for biopharmaceuticals, a multi-technique approach should be applied more often when investigating complex systems to understand the structure of the species that contribute to the different transitions, thereby gaining insight about the processes of both unfolding and aggregation. This knowledge is crucial for identifying those conformational changes which are likely to lead to aggregation/degradation allowing a more rational approach to biopharmaceutical production and formulation. This is particularly important in the case of multi-domain proteins, such as IgGs, which can undergo multiple transitions due to independent unfolding of the domains. In this work, we have followed the thermal denaturation of a monoclonal antibody by using different biophysical techniques with complementary strengths, providing an example of how the information gathered suggests a way to intervene to stabilise the wanted conformation (monomeric protein). Indeed, in this particular case, an optimisation of storage conditions based on only thermal stability studies would have led to the stabilisation of an undesired product, a population of low molecular weight oligomers.

Circular dichroism (CD) is the differential absorption of left and right circularly polarized light by a chiral substance. The phenomenon can occur for all wavelengths of light and results in ‘vibrational’ CD (VCD) in the infra-red region and ‘electronic’ CD (ECD) in the ultra violet and visible regions, corresponding to the different excitations induced in a molecule by the light; ‘Raman optical activity' (ROA) is the analogous phenomenon for Raman scattering. This chapter concentrates on ECD and describes the theory, instrumentation and some examples.

All the chiroptical techniques used to characterize and investigate chiral molecules rely on either linearly or circularly polarized light (CPL) in some manner. For example, circular dichroism (CD) is the differential absorption of left and right CPL by a chiral substance. The phenomenon can occur for all wavelengths of light and results in 'vibrational' CD (VCD) in the infra-red region and 'electronic' CD in the ultra violet and visible regions, corresponding to the different excitations induced in a molecule by the light. Raman optical activity is the analogous phenomenon for Raman scattering. Optical rotatory dispersion and polarimetry rely on the effects of chiral substances on plane-polarized light. This section provides the background to such polarized light and their relationships with each other.

The rotation of the plane of linearly polarized light by a chiral substance is probably the most generally known physical phenomenon of chirality, leading to the common usage of the term 'optically active' when referring to chiral compounds. The monitoring of this phenomenon either at a single wavelength, as in polarimetry, or over a spectrum of wavelengths, as in optical rotatory dispersion, finds extensive use in characterizing the stereochemistry of chiral molecules and provides the basis of the d/l and (+)/(−) notations of enantiomers. This chapter presents the basis of optical rotation, its molecular aspects, and instrumentation and illustrates these with some examples.

This article describes the efficient synthesis of the first generation of branched sugar amino acid (SAA) oligomers in solution phase via two main routes: by the use of a standard coupling reagent and via the use of active ester intermediates. Benzyl-protected dimeric carbopeptoid and methyl-protected dimeric and tetrameric, hexameric and octameric carbopeptoids were obtained from a branched δ-3,5-trans-tetrahydrofuran (THF) SAA and methyl-protected dimeric and tetrameric carbopeptoids were synthesised from a branched δ-3,5-cis-THF SAA. These systems are of interest because of their potential to display foldameric properties reminiscent of those observed in α-peptides and proteins. Amongst their many uses, foldamers provide simpler models in the study of the factors which induce the folding and unfolding of proteins and, ultimately, potential insights into their functioning.

The structure of a short fragment of the human HIV-1 membrane glycoprotein gp41 has been examined using a combination of parallel tempering molecular dynamics (PTMD) and far UV circular dichroism spectroscopy. The aim is to resolve conflicting reports on the solution state conformational bias in this membrane proximal domain spanning the epitope for the 2F5 monoclonal antibody. We conclude that gp41(659-671) exhibits conformational plasticity in which competing folding propensities are present and can be influenced by local microenvironment. Contrary to previous reports, the 3(10) helix does not emerge as a dominant motif from either simulation or experiment, and this peptide is therefore not a model system for this fold type. Other fold groups such as turn motifs are identifiable at elevated temperatures in the PTMD trajectories and are potentially relevant in antibody binding. Helical populations in pure water are significantly overestimated according to the CHARMM parametrization. However, circular dichroism (CD) data show that helices are promoted in membrane mimetic solvents. As this is a membrane proximal peptide, the helical motif may well have physiological significance.