Comparing protein–ligand interactions in solution and single crystals by Raman spectroscopy

By using a Raman microscope, we show that it is possible to probe the conformational states in protein crystals and crystal fragments under growth conditions (in hanging drops). The flavin cofactor in the enzyme para-hydroxybenzoate hydroxylase can assume two conformations: buried in the protein matrix (“in”) or essentially solvent-exposed (“out”). By using Raman difference spectroscopy, we previously have identified characteristic flavin marker bands for the in and out conformers in the solution phase. Now we show that the flavin Raman bands can be used to probe these conformational states in crystals, permitting a comparison between solution and crystal environments. The in or out marker bands are similar for the respective conformers in the crystal and in solution; however, significant differences do exist, showing that the environments for the flavin's isoalloxazine ring are not identical in the two phases. Moreover, the Raman-band widths of the flavin modes are narrower for both in and out conformers in the crystals, indicating that the flavin exists in a more limited range of closely related conformational states in the crystal than in solution. In general, the ability to compare detailed Raman data for complexes in crystals and solution provides a means of bridging crystallographic and solution studies.

A few selected applications of surface nonlinear optical spectroscopy.

As a second-order nonlinear optical process, sum-frequency generation is highly surface-specific and accordingly has been developed into a very powerful and versatile surface spectroscopic tool. It has found many unique applications in different disciplines and thus provided many exciting new research opportunities in surface and surface-related science. Selected examples are discussed here to illustrate the power of the technique.

Low concentrations of diacylglycerol promote the binding of apolipophorin III to a phospholipid bilayer: a surface plasmon resonance spectroscopy study.

The binding of the exchangeable apolipoprotein apolipophorin III (apoLp-III) to an egg phosphatidylcholine bilayer as a function of the concentration of diacylglycerol (DG) in the bilayer was studied by surface plasmon resonance spectroscopy. At a DG concentration of 2 mol % in the bilayer, the binding of apoLp-III reached saturation. Under saturating conditions, apoLp-III forms a closely packed monolayer approximately 55 A thick, in which each molecule of protein occupies approximately 500 A2 at the membrane surface. These dimensions are consistent with the molecular size of the apoLp-III molecule determined by x-ray crystallography, if apoLp-III binds to the bilayer with the long axis of the apoLp-III normal to the membrane surface. In the absence of protein, the overall structure of the lipid bilayer was not significantly changed up to 2.5 mol% DG. However, at 4 and 6 mol % DG, the presence of nonbilayer structures was observed. The addition of apoLp-III to a membrane containing 6 mol % DG promoted the formation of large lipid-protein complexes. These data support a two-step sequential binding mechanism for binding of apoLp-III to a lipid surface. The first step is a recognition process, consisting of the adsorption of apoLp-III to a nascent hydrophobic defect in the phospholipid bilayer caused by the presence of DG. This recognition process might depend on the presence of a hydrophobic sensor located at one of the ends of the long axis of the apoLp-III molecule but would be consolidated through H-bond and electrostatic interactions. Once primary binding is achieved, subsequent enlargement of the hydrophobic defect in the lipid surface would trigger the unfolding of the apolipoprotein and binding via the amphipathic alpha-helices. This two-step sequential binding mechanism could be a general mechanism for all exchangeable apolipoproteins. A possible physiological role of the ability of apoLp-III to bind to lipid structures in two orientations is also proposed.

The Relationship Between Cadwaladerite Al(OH)2Cl∙4H2O and Lesukite Al2(OH)5Cl∙2H2O as Investigated by SEM, PXRD, FTIR and Raman Spectroscopy

Cadwaladerite (Al(OH)2Cl∙4H2O) collected from Cerro Pintados, Chile described by Gordon in 1941 is designated as “doubtful” by the IMA. Material collected from the same locality in 2015 resembling the description of cadwaladerite gave a powder XRD pattern similar to lesukite (Al2(OH)5Cl∙2H2O). However, Gordon provided no X-ray data for his material from Cerro Pintados. In order to determine whether cadwaladerite and lesukite are the same mineral species, measurements were made on a suite of samples from various localities. A portion of the material collected by Gordon in 1941 was also obtained from the Mineralogical Museum of Harvard University. Type material of lesukite from a fumarolic environment at the Tolbachik Fissure in Kamchatka, Russia was obtained as well as lesukite from the Maria Mine, Chile (Arica Province) and a previously undescribed locality for lesukite (Barranaca del Sulfato, Mejillones Peninsula, Antofagasta Province). All samples are yellow to yellow-orange in colour and all exhibit small cubic crystals (up to 50µm), even Gordon’s cadwaladerite which was thought to be amorphous. The Chilean samples are all associated with halite and sometimes with anhydrite. These five samples were studied by SEM, FTIR, powder XRD, and Raman spectroscopy. A ratio of Al:Cl less than or equal to 1.3:1 was observed for all the samples, including measurements made on lesukite from the Russian locality Vergasova et al. studied in 1997, and determined to have a 2:1 ratio. SEM-EDS analyses also show all samples to have minor iron substitution, as well as copper substitution in two samples. FTIR spectra are very similar for all samples. Raman spectroscopy done on both samples collected in Cerro Pintados and the Russian lesukite gave similar spectra. Powder XRD analyses on all samples showed spectra identified to be lesukite, including Gordon’s cadwaladerite. Crystal cell parameters calculated from powder XRD ranged from 19.778Å to 19.878Å. Results using modern instrumental techniques confirm Gordon’s cadwaladerite, collected in 1939 and described in 1941, and lesukite are the same mineral species.

Characterization and Degradation of Fatty Acid Methyl Esters and Biodiesel in Artificial Seawater Under UV Exposure Using Raman Spectroscopy

Thesis (Master's)--University of Washington, 2016-06

Enhanced Raman amplifier flatness with nonlinear broadening over non-standard transmission fibre

Nonlinear CW pump broadening over non-standard transmission fibre is used for the first time to achieve improved gain flatness in a single-pump broadband Raman amplifier. As an illustration of the benefits that can be obtained from this approach, a threefold increase in the bandwidth for 0.1 dB gain variation is reported when the broadened pump is used to produce 9.2 dB on-off gain over 25 km LEAF fibre. © 2005 Elsevier B.V. All rights reserved.

Enhanced Raman amplifier gain performance with HNLF broadening

Nonlinear CW pump broadening over non-standard transmission fiber is used for the first time to achieve superior gain variation performance in a single-pump broadband Raman amplifier. A threefold increase in the bandwidth for 0.1 dB gain variation is reported.

Characterisation of Organic Matter in the Torridonian Using Raman Spectroscopy

Postprint

The Relationship Between Cadwaladerite Al(OH)2Cl∙4H2O and Lesukite Al2(OH)5Cl∙2H2O as Investigated by SEM, PXRD, FTIR and Raman Spectroscopy

Cadwaladerite (Al(OH)2Cl∙4H2O) collected from Cerro Pintados, Chile described by Gordon in 1941 is designated as “doubtful” by the IMA. Material collected from the same locality in 2015 resembling the description of cadwaladerite gave a powder XRD pattern similar to lesukite (Al2(OH)5Cl∙2H2O). However, Gordon provided no X-ray data for his material from Cerro Pintados. In order to determine whether cadwaladerite and lesukite are the same mineral species, measurements were made on a suite of samples from various localities. A portion of the material collected by Gordon in 1941 was also obtained from the Mineralogical Museum of Harvard University. Type material of lesukite from a fumarolic environment at the Tolbachik Fissure in Kamchatka, Russia was obtained as well as lesukite from the Maria Mine, Chile (Arica Province) and a previously undescribed locality for lesukite (Barranaca del Sulfato, Mejillones Peninsula, Antofagasta Province). All samples are yellow to yellow-orange in colour and all exhibit small cubic crystals (up to 50µm), even Gordon’s cadwaladerite which was thought to be amorphous. The Chilean samples are all associated with halite and sometimes with anhydrite. These five samples were studied by SEM, FTIR, powder XRD, and Raman spectroscopy. A ratio of Al:Cl less than or equal to 1.3:1 was observed for all the samples, including measurements made on lesukite from the Russian locality Vergasova et al. studied in 1997, and determined to have a 2:1 ratio. SEM-EDS analyses also show all samples to have minor iron substitution, as well as copper substitution in two samples. FTIR spectra are very similar for all samples. Raman spectroscopy done on both samples collected in Cerro Pintados and the Russian lesukite gave similar spectra. Powder XRD analyses on all samples showed spectra identified to be lesukite, including Gordon’s cadwaladerite. Crystal cell parameters calculated from powder XRD ranged from 19.778Å to 19.878Å. Results using modern instrumental techniques confirm Gordon’s cadwaladerite, collected in 1939 and described in 1941, and lesukite are the same mineral species.

High-Throughput Prediction of Acacia and Eucalypt Lignin Syringyl/Guaiacyl Content Using FT-Raman Spectroscopy and Partial Least Squares Modeling

High-throughput techniques are necessary to efficiently screen potential lignocellulosic feedstocks for the production of renewable fuels, chemicals, and bio-based materials, thereby reducing experimental time and expense while supplanting tedious, destructive methods. The ratio of lignin syringyl (S) to guaiacyl (G) monomers has been routinely quantified as a way to probe biomass recalcitrance. Mid-infrared and Raman spectroscopy have been demonstrated to produce robust partial least squares models for the prediction of lignin S/G ratios in a diverse group of Acacia and eucalypt trees. The most accurate Raman model has now been used to predict the S/G ratio from 269 unknown Acacia and eucalypt feedstocks. This study demonstrates the application of a partial least squares model composed of Raman spectral data and lignin S/G ratios measured using pyrolysis/molecular beam mass spectrometry (pyMBMS) for the prediction of S/G ratios in an unknown data set. The predicted S/G ratios calculated by the model were averaged according to plant species, and the means were not found to differ from the pyMBMS ratios when evaluating the mean values of each method within the 95 % confidence interval. Pairwise comparisons within each data set were employed to assess statistical differences between each biomass species. While some pairwise appraisals failed to differentiate between species, Acacias, in both data sets, clearly display significant differences in their S/G composition which distinguish them from eucalypts. This research shows the power of using Raman spectroscopy to supplant tedious, destructive methods for the evaluation of the lignin S/G ratio of diverse plant biomass materials. © 2015, The Author(s).

Raman Spectroscopy and DFT calculations for the Electronic Structure Characterization of Conjugated Polymers

In the last three decades, there has been a broad academic and industrial interest in conjugated polymers as semiconducting materials for organic electronics. Their applications in polymer light-emitting diodes (PLEDs), polymer solar cells (PSCs), and organic field-effect transistors (OFETs) offer opportunities for the resolution of energy issues as well as the development of display and information technologies1. Conjugated polymers provide several advantages including low cost, light weight, good flexibility, as well as solubility which make them readily processed and easily printed, removing the conventional photolithography for patterning2. A large library of polymer semiconductors have been synthesized and investigated with different building blocks, such as acenes or thiophene and derivatives, which have been employed to design new materials according to individual demands for specific applications. To design ideal conjugated polymers for specific applications, some general principles should be taken into account, including (i) side chains (ii) molecular weights, (iii) band gap and HOMO and LUMO energy levels, and (iv) suited morphology.3-6 The aim of this study is to elucidate the impact that substitution exerts on the molecular and electronic structure of π-conjugated polymers with outstanding performances in organic electronic devices. Different configurations of the π-conjugated backbones are analyzed: (i) donor-acceptor configuration, (ii) 1D lineal or 2D branched conjugated backbones, and (iii) encapsulated polymers (see Figure 1). Our combined vibrational spectroscopy and DFT study shows that small changes in the substitution pattern and in the molecular configuration have a strong impact on the electronic characteristics of these polymers. We hope this study can advance useful structure-property relationships of conjugated polymers and guide the design of new materials for organic electronic applications.

Raman spectroscopy study of the transformation of the carbonaceous skeleton of a polymer-based nanoporous carbon along the thermal annealing pathway

We report a multi-wavelength Raman spectroscopy study of the structural changes along the thermal annealing pathway of a poly(furfuryl alcohol) (PFA) derived nanoporous carbon (NPC). The Raman spectra were deconvoluted utilizing G, D, D′, A and TPA bands. The appropriateness of these deconvolutions was confirmed via recovery of the correct dispersive behaviours of these bands. It is proposed that the ID/IG ratio is composed of two parts: one associated with the extent of graphitic crystallites (the Tuinstra–Koenig relationship), and a second related to the inter-defect distance. This model was used to successfully determine the variation of the in-plane size and intra-plane defect density along the annealing pathway. It is proposed that the NPC skeleton evolves along the annealing pathway in two stages: below 1600 °C it was dominated by a reduction of in-plane defects with a minor crystallite growth, and above this temperature growth of the crystallites accelerates as the in-plane defect density approaches zero. A significant amount of transpolyacetylene (TPA)-like structures was found to be remaining even at 2400 °C. These may be responsible for resistance to further graphitization of the PFA-based carbon at higher temperatures.

New insight on the underdrawing of 16th Flemish-Portuguese easel paintings by combined surface analysis and microanalytical techniques

This paper focusses on the study of the underdrawings of 16th century easel paintings attributed to the workshop of the Portuguese-Flemish Master Frei Carlos. This investigation encompasses multidisciplinary research that relates the results of surface exams (infrared reflectography, standard light photography and infrared photography) with analytical investigations. The surface analysis of Frei Carlos’ underdrawings by infrared reflectography has shown heterogeneous work, revealing two different situations: (1) an abundant and expressive underdrawing, revealing a Flemish influence and (2) a simple and outlined underdrawing. This preliminary research raised an important question related to this Portuguese-Flemish workshop and to the analytical approach: Is the underdrawing's heterogeneity, as observed in the reflectograms, related to different artists or is this rather an effect that is produced due to the use of different materials in the underdrawing's execution? Consequently, if different materials were used, how can we have access to the hidden underdrawings? In order to understand the reasons for this dissemblance, chemical analysis of micro-samples collected in underdrawing areas and representing both situations were carried out by optical microscopy, micro Fourier transform infrared spectroscopy (μ-FTIR), scanning electron microscopy coupled with energy dispersive X-ray spectrometry (SEM-EDX) and micro-Raman spectroscopy (μ-Raman). Taking into account the different possibilities and practical and theoretical limitations of surface and punctual examinations in the study of easel painting underdrawings, the methodology of research was adjusted, sometimes resulting in a re-analysis of experimental results. This research shows the importance of combining multispectral surface exams and chemical analysis in the understanding of the artistic creative processes of 16th century easel paintings.