Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C-18O labelling, polarised infrared spectroscopy and molecular combing

A novel combination of site-specific isotope labelling, polarised infrared spectroscopy and molecular combing reveal local orientational ordering in the fibril-forming peptide YTIAALLSPYSGGRADS. Use of 13C-18O labelled alanine residues demonstrates that the Nterminal end of the peptide is incorporated into the cross-beta structure, while the C-terminal end shows orientational disorder

Separating heart and brain: on the reduction of physiological noise from multichannel functional near-infrared spectroscopy (fNIRS) signals

Objective. Functional near-infrared spectroscopy (fNIRS) is an emerging technique for the in vivo assessment of functional activity of the cerebral cortex as well as in the field of brain–computer interface (BCI) research. A common challenge for the utilization of fNIRS in these areas is a stable and reliable investigation of the spatio-temporal hemodynamic patterns. However, the recorded patterns may be influenced and superimposed by signals generated from physiological processes, resulting in an inaccurate estimation of the cortical activity. Up to now only a few studies have investigated these influences, and still less has been attempted to remove/reduce these influences. The present study aims to gain insights into the reduction of physiological rhythms in hemodynamic signals (oxygenated hemoglobin (oxy-Hb), deoxygenated hemoglobin (deoxy-Hb)). Approach. We introduce the use of three different signal processing approaches (spatial filtering, a common average reference (CAR) method; independent component analysis (ICA); and transfer function (TF) models) to reduce the influence of respiratory and blood pressure (BP) rhythms on the hemodynamic responses. Main results. All approaches produce large reductions in BP and respiration influences on the oxy-Hb signals and, therefore, improve the contrast-to-noise ratio (CNR). In contrast, for deoxy-Hb signals CAR and ICA did not improve the CNR. However, for the TF approach, a CNR-improvement in deoxy-Hb can also be found. Significance. The present study investigates the application of different signal processing approaches to reduce the influences of physiological rhythms on the hemodynamic responses. In addition to the identification of the best signal processing method, we also show the importance of noise reduction in fNIRS data.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this “light-switch” effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280–1450 cm-1, which characterise both the emissive “bright” and the non-emissive “dark” excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the “dark” excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the “bright” state are observed for both L- and D enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the L enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Long-lived excited-state dynamics of i-motif structures probed by time-resolved infrared spectroscopy

UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ~300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.

Infrared and Raman selection rules for cyclopentane

Infra-red and Raman selection rules are obtained for the cyclopentane molecule, on the assumption that it has a free pseudo-rotation with a large potential hump at the D5h configuration. The selection rules obtained, which concern the vibrational, pseudo-rotational, and rotational quantum numbers, are summarized in tables 1, 2 and 3.

Gas-solid reactions of single crystals: a study of the reaction of bromine with single crystals of trans-cinnamic acid and a range of its derivatives by infrared and Raman microspectroscopy

Single crystals of trans-cinnamic acid and of a range of derivatives of this compound containing halogen substituents on the aromatic ring have been reacted with 165 Torr pressure of bromine vapour in a sealed desiccator at 20 degrees C for 1 week. Infrared and Raman microspectroscopic examination of the crystals shows that bromination of the aliphatic double bond, but not of the aromatic ring, has occurred. It is demonstrated also that the reaction is truly gas-solid in nature. A time-dependent study of these reactions shows that they do not follow a smooth diffusion-controlled pathway. Rather the reactions appear to be inhomogeneous and to occur at defects within the crystal. The reaction products are seen to flake from the surface of the crystal. It is shown, therefore, that these are not single crystal to single crystal transitions, as have been observed previously for the photodimerisation of trans-cinnamic acid and several of its derivatives. It is shown that there are no by-products of the reaction and that finely ground samples react to form the same products as single crystals.

Characterization and identification of mixed-metal phosphates in soils: the application, of Raman spectroscopy

The development of protocols for the identification of metal phosphates in phosphate-treated, metal-contaminated soils is a necessary yet problematical step in the validation of remediation schemes involving immobilization of metals as phosphate phases. The potential for Raman spectroscopy to be applied to the identification of these phosphates in soils has yet to be fully explored. With this in mind, a range of synthetic mixed-metal hydroxylapatites has been characterized and added to soils at known concentrations for analysis using both bulk X-ray powder diffraction (XRD) and Raman spectroscopy. Mixed-metal hydroxylapatites in the binary series Ca-Cd, Ca-Pb, Ca-Sr and Cd-Pb synthesized in the presence of acetate and carbonate ions, were characterized using a range of analytical techniques including XRD, analytical scanning electron microscopy (SEM), infrared spectroscopy (IR), inductively coupled plasma-atomic emission spectrometry (ICP-AES) and Raman spectroscopy. Only the Ca-Cd series displays complete solid solution, although under the synthesis conditions of this study the Cd-5(PO4)(3)OH end member could not be synthesized as a pure phase. Within the Ca-Cd series the cell parameters, IR active modes and Raman active bands vary linearly as a function of Cd content. X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) suggest that the Cd is distributed across both the Ca(1) and Ca(2) sites, even at low Cd concentrations. In order to explore the likely detection limits for mixed-metal phosphates in soils for XRD and Raman spectroscopy, soils doped with mixed-metal hydroxylapatites at concentrations of 5, 1 and 0.5 wt.% were then studied. X-ray diffraction could not confirm unambiguously the presence or identity of mixed-metal phosphates in soils at concentrations below 5 wt.%. Raman spectroscopy proved a far more sensitive method for the identification of mixed-metal hydroxylapatites in soils, which could positively identify the presence of such phases in soils at all the dopant concentrations used in this study. Moreover, Raman spectroscopy could also provide an accurate assessment of the degree of chemical substitution in the hydroxylapatites even when present in soils at concentrations as low as 0.1%.

Analysis of red and yellow ochre samples from Clearwell Caves and Catalhoyuk by vibrational spectroscopy and other techniques

Ochre samples excavated from the neolithic site at Qatalhoyuk, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Qatalhoyuk contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals. (C) 2003 Elsevier B.V. All rights reserved.

Analysis of red and yellow ochre samples from Clearwell Caves and Catalhoyuk by vibrational spectroscopy and other techniques

Ochre samples excavated from the neolithic site at Qatalhoyuk, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Qatalhoyuk contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals. (C) 2003 Elsevier B.V. All rights reserved.

Infrared linear dichroism spectroscopy on amyloid fibrils aligned by molecular combing

We report the use of molecular combing as an alignment method to obtain macroscopically oriented amyloid fibrils on planar surfaces. The aligned fibrils are studied by polarized infrared spectroscopy. This gives structural information that cannot be definitively obtained from standard infrared experiments on isotropic samples, for example, confirmation of the characteristic cross-beta amyloid core structure, the side-chain orientation from specific amino acids, and the arrangement of the strands within the fibrils, as we demonstrate here. We employed amyloid fibrils from hen egg white lysozyme (HEWL) and from a model octapeptide. Our results demonstrate molecular combing as a straightforward method to align amyloid fibrils, producing highly anisotropic infrared linear dichroism (IRLD) spectra.

Assessment of the consistency of H2O line intensities over the near-infrared using sun-pointing ground-based Fourier transform spectroscopy

We report on the consistency of water vapour line intensities in selected spectral regions between 800–12,000 cm−1 under atmospheric conditions using sun-pointing Fourier transform infrared spectroscopy. Measurements were made across a number of days at both a low and high altitude field site, sampling a relatively moist and relatively dry atmosphere. Our data suggests that across most of the 800–12,000 cm−1 spectral region water vapour line intensities in recent spectral line databases are generally consistent with what was observed. However, we find that HITRAN-2008 water vapour line intensities are systematically lower by up to 20% in the 8000–9200 cm−1 spectral interval relative to other spectral regions. This discrepancy is essentially removed when two new linelists (UCL08, a compilation of linelists and ab-initio calculations, and one based on recent laboratory measurements by Oudot et al. (2010) [10] in the 8000–9200 cm−1 spectral region) are used. This strongly suggests that the H2O line strengths in the HITRAN-2008 database are indeed underestimated in this spectral region and in need of revision. The calculated global-mean clear-sky absorption of solar radiation is increased by about 0.3 W m−2 when using either the UCL08 or Oudot line parameters in the 8000–9200 cm−1 region, instead of HITRAN-2008. We also found that the effect of isotopic fractionation of HDO is evident in the 2500–2900 cm−1 region in the observations.

Identification of forged Bank of England £20 banknotes using IR spectroscopy

Bank of England notes of £20 denomination have been studied using infrared spectroscopy in order to generate a method to identify forged notes. An aim of this work was to develop a non-destructive method so that a small, compact Fourier transform infrared spectrometer (FT-IR) instrument could be used by bank workers, police departments or others such as shop assistants to identify forged notes in a non-lab setting. The ease of use of the instrument is the key to this method, as well as the relatively low cost. The presence of a peak at 1400 cm−1 arising from νasym () from the blank paper section of a forged note proved to be a successful indicator of the note’s illegality for the notes that we studied. Moreover, differences between the spectra of forged and genuine £20 notes were observed in the ν(OH) (ca. 3500 cm−1), ν(CH) (ca. 2900 cm−1) and ν(CO) (ca. 1750 cm−1) regions of the IR spectrum recorded for the polymer film covering the holographic strip. In cases where these simple tests fail, we have shown how an infrared microscope can be used to further differentiate genuine and forged banknotes by producing infrared maps of selected areas of the note contrasting inks with background paper.

The two-dimensional anharmonic oscillator III: the CCC bending mode of C3O2

Newly observed data on the rotational constants of carbon suboxide in excited vibrational states of the low-wavenumber bending vibration ν7 have been successfully interpreted in terms of the two-dimensional anharmonic oscillator wavefunctions associated with this vibration. By combining these results with published infrared and Raman spectra the vibrational assignment has been extended and a refined bending potential for ν7 has been derived: this has a minimum at a bending angle of about 24° at the central C atom, with an energy maximum at the linear configuration some 23 cm−1 above the minimum. From similar data on the combination and hot bands of ν7 with ν4 (1587 cm−1) and ν2 (786 cm−1) the effective ν7 bending potential has also been determined in the one-quantum excited states of ν4 and ν2. The effective ν7 potential shows significant changes from the ground vibrational state; the central hump in the ν7 potential surface is increased to about 50 cm−1 in the v4 = 1 state, and decreased to about 1 cm−1 in the v2 = 1 state. In the light of these results vibrational assignments are suggested for most of the observed bands in the infrared and Raman spectra of C3O2.