UV Resonance Raman Spectroscopy Research Articles

π‐π stacking interactions mediate molecular recognition between arginine and tryptophan containing peptides derived from human islet polypeptide

AbstractCation‐π interactions, often found in protein assemblies, are characterized by favorable electrostatic interactions between an aromatic π‐electron surface and a positively charged species. There are evidences that reveal the importance of cation‐π interactions between arginine and aromatic residues in protein structure and function. In this paper, the effect of cation‐π interactions on the aggregation propensity of peptides derived from human islet polypeptide (hIAPP) was explored using UV resonance Raman and fluorescence spectroscopy. By employing an analog of hIAPP22–29 in which Phe‐23 is replaced with tryptophan (NWGAILSS), we were able to demonstrate an increase in the amyloidogenic propensity of this mutant in the presence of Zn2+ that is attributable to cation‐π interactions. In contrast, no cation‐π interactions were observed when the cationic F23R analog of hIAPP22–29 (NRGAILSS) was allowed to interact with NWGAILSS. From these observations, it was surmised that in these peptides, the dominant interaction between arginine and tryptophan involves the π‐cloud of the guanidino group and the indole ring, not cation‐π interactions. The spectroscopic data, supported by density functional theory‐based simulation results, suggest that arginine‐tryptophan interaction involves π‐π stacking where the guanidino group is oriented parallel to the indole ring. These hydrophobic interactions, coupled with the hydrotropic effect of the guanidine functionality of arginine, led to a delay in the aggregation kinetics of NWGAILSS. These unique interactions were further exploited to design a peptide inhibitor of full‐length amylin self‐assembly.

Hydration water and ionic aggregation in aqueous solutions of imidazolium-based protic ionic liquids

Water molecules, present as additive or as contaminant of Protic Ionic Liquids (PILs), can compete for the hydrogen bond sites leading to important modifications of the local order of these liquids and to the modulation of their physical–chemical properties. In this work, aqueous solutions of a set of N-methylimidazolium-based PILs [MIM][X] (X = NO3−, TfO−, HSO4−, and Cl−) were investigated by deep UV Resonance Raman (UVRR) spectroscopy in the water-rich domain where ionic aggregates and bulk-like water coexist. A differential method was used to analyze the OH stretching profile to extract the so-called solute-correlated (SC) spectrum, which is particular informative of the hydration features of the PILs. Moreover, specific bands of the cation, sensitive to the hydrogen bonding, were comparatively investigated. The progressive evolution from solvent-separated ion pairs (SIP) and/or solvent-shared ion pairs (SSIP) to contact ion pairs (CIP) and/or larger ionic aggregates can be monitored as a function of the hydration level, in the water-rich domain. Our approach showed that, in the high-diluted regime, the hydration environment around the [MIM] cation does not depend on the type of anion. Moreover, [MIM][NO3] and [MIM][TfO] showed cation-water (ionic) H-bonds at the NH site stronger than the cation–anion (double-ionic) ones. The analysis of SC Raman spectra points out the formation of cation–anion H-bonds (through the CH ring groups), stronger than cation-water ones, upon PILs concentration increase, especially evident in the case of [MIM][Cl]. The H-bond strength between the anion and hydration water is found to decrease following the order: [Cl] ∼ [HSO4] > [NO3] > [TfO]. Chloride ions tend to perturb a larger number of water molecules than the other anions. The number of perturbed water molecules decreases at increasing PIL concentration, showing a larger dependence for [MIM][Cl], consistently with its larger propensity to form ionic aggregates. The unique response of [MIM][Cl] to hydration found by analyzing SC-UVRR data is related to the synergy of different factors such as the anion reduced size (higher charge density), spherical symmetry, and high H-bond basicity.

Synchrotron-based UV resonance Raman spectroscopy probes size confinement, termination effects, and anharmonicity of carbon atomic wires

Vibrational and electronic properties and anharmonicity of sp-carbon atomic wires (i.e., polyynes) have been studied using resonance Raman spectroscopy, focusing on the confinement effects connected to their structure (length and termination). We exploited the fine tunability of the synchrotron radiation to resonantly excite short H-, CH3-, and CN-capped carbon atomic wires at their vibronic transitions in the deep UV. We report for the first time the resonance Raman spectra of size-selected CH3-capped polyynic wires (HCnCH3, n = 8–12) and CN-capped wires (HC6CN and HC12CN). We observed that the degree of π-electron conjugation increases with the wire length and is related to the specific termination. The analysis of multiple quanta Raman overtone bands shows that the anharmonic correction of the vibrational potential energy becomes increasingly relevant as the wire length increases. Finally, studying the vibronic lines of the UV absorption spectra allows the determination of an effective displacement parameter between the minima of the ground and the low-lying excited state, proving that the strong electron-phonon coupling of these systems is sensitive to chain length and termination.

Deep UV resonance Raman spectroscopy for sensitive detection and quantification of the fluoroquinolone antibiotic drug moxifloxacin and the β-lactam meropenem in human plasma

Quantification of antibiotics in body fluids is of major clinical interest. A sensitive detection of the fluoroquinolone moxifloxacin and the β-lactam meropenem in the complex matrix human blood plasma was achieved with help of deep UV resonance Raman spectroscopy. Multivariate curve resolution was applied for quantification and low limits of detection in order of magnitude of the clinical concentration were detected in human plasma. Moxifloxacin and meropenem were detected down to minimum concentrations of 4 µM (2 mg/L) and 2 µM (1 mg/L). The acquired results and the benefits of enhanced Raman spectroscopy, i.e., short analysis time, small sample volume, and high sensitivity with the potential for multicomponent detection based on multivariate quantification, will pave the path as future point-of-care approach for sensitive detection of antibiotics in complex body fluids.

Comparative investigation of chemical and structural properties of charred fir wood samples by Raman and FTIR spectroscopy as well as X-ray-micro-CT technology

Abstract Wood surface charring is a treatment method commonly employed to enhance weather protection and aesthetic appearance of building exteriors. This study aims to investigate the differences between two wood surface charring processes: the traditional Japanese method known as Yakisugi and an alternative charring technique industrially manufactured with a gas burner. The objective of the study was to assess whether a thicker layer after Yakisugi treatment has any advantages over a thinner layer after the alternative process. Vibrational spectroscopy techniques including UV resonance Raman (UVRR) and Fourier transform infrared (FTIR) spectroscopy, were utilized in conjunction with X-ray-micro-CT analysis. The findings revealed that ATR-FTIR spectroscopy detected the degradation of carbohydrates and changes in lignin within the charred surface, although both processes exhibited similar vibrational contributions. In contrast, UVRR spectroscopy provided insights into the carbonized layers, revealing spectral differences indicating variations in temperature during the charring processes. X-ray micro-CT analysis visually highlighted significant differences in the coal layers, suggesting distinct combustion profiles. Remarkably, the macrostructure of wood treated with Yakisugi remained intact despite a thicker charred layer compared to the alternative charring techniques. However, further investigations are required to assess the weather stability of the alternative charring method for a comprehensive understanding.

Cytosine epigenetic modifications and conformational changes in G‐quadruplex DNA: An ultraviolet resonance Raman spectroscopy study

Epigenetic modifications of DNA are known to play important regulatory roles in biological systems, especially in regulation of gene expression, and are associated with many types of human diseases, including cancer. Alternative DNA secondary structures, such as G‐quadruplexes, can also influence gene transcription, thus suggesting that such structures may represent a distinctive layer of epigenetic information. G‐quadruplex structures and DNA epigenetic modifications often go side by side, and recent evidence reveals that cytosine modifications within loops of G‐quadruplexes can play a role in modulating their stability and structural polymorphism. Therefore, the development and validation of experimental techniques that can easily and reliably analyse G‐quadruplex structures are highly desirable. In the present study, we propose to exploit the advantages of UV resonance Raman (UVRR) spectroscopy to investigate cytosine epigenetic modifications along with conformational changes in G‐quadruplex-forming DNA. Our findings show that clear and specific spectral changes occur when there is a change in a G‐quadruplex structure. Moreover, UVRR spectral analysis can indirectly distinguish the spectral variations occurring because of modifications in the guanine glycosidic conformations, as well as detect changes in the loops induced by H-bond formation or hydration of nitrogenous bases. The results further underscore the utility of UVRR spectroscopy for G‐quadruplex structure elucidation under biologically relevant solution conditions.

Insights into wavelength-mediated excited state intramolecular proton transfer in solution: UV resonance Raman spectroscopy and theoretical calculation

The excited-state intramolecular proton transfer (ESIPT) has been increasingly applied in the fields of chemistry, biology, materials science and so on. Herein, we proposed the efficiency and applicability of Raman spectroscopy (RS) toward the direct observation and characterization of transient species and monitoring of excited-state proton transfer reaction mediated by different excitation wavelength. We hope this help to understand the photochemical reactivity of the organic compounds containing CS and SH groups.

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA.

UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.

Evaluation of the Irradiation Treatment Effects on Ancient Parchment Samples

In this work, the effect of X-ray irradiation as a disinfection treatment in original ancient parchment samples, belonging to a discarded book cover of a 16th-century archival register, has been evaluated. Specifically, the bacterial and fungal species isolated from the book cover have been characterized and then irradiated with increasing doses of X-rays with the aim to evaluate the effectiveness of the antimicrobial protocol on the isolated microorganisms. The deterioration effects induced by the X-ray treatment as well as the natural aging on the collagen matrix of the parchment sample have been tested by employing several techniques, namely, Light Transmission Analysis, Fiber Optic Reflectance Spectroscopy, Attenuated Total Reflectance-Fourier Transformed Infrared spectroscopy, UV Resonant Raman spectroscopy and Atomic Force Microscopy. The results reveal that the irradiation treatment applied to our ancient parchment samples deteriorated by biological attack and other naturally occurring phenomena, possibly associated with inappropriate conservation conditions, does not seem to induce further damage factors even when large doses of irradiation are employed. The X-rays-based disinfection treatment effects are limited on the collagen support and this confirms the potential of this method in mass disinfection of library and archival materials.

Excitonic quenching of the oxygen-chain phonon in the photoinduced metal-to-insulator transition of photoexcited Sr0.95NbO3.37 studied by ultraviolet-resonance Raman scattering

The quasi-one-dimensional metal ${\mathrm{Sr}}_{0.95}{\mathrm{NbO}}_{3.37}$ shows a metal-to-insulator transition upon laser-induced pumping of the d-d exciton at 1.1 eV. The oxygen-chain-related phonon modes are highly susceptible to this metal-to-insulator transition due to their sensitivity to structural and electronic changes. We employ angle-dependent UV-resonance Raman spectroscopy to probe the nonequilibrium oxygen-chain-related phonon dynamics and the concomitant changes in the angle-dependent midinfrared reflectance. The latter shows the expected reduction of charge carrier density upon pumping, whereas the central chain mode at 680 $\mathrm{cm}{}^{\ensuremath{-}1}$ can be selectively quenched upon pumping the d-d excitons. We find that the underlying quenching mechanism for this phonon is electronically driven and related to the photo-induced bleaching of the charge-transfer transition. First-principles calculations show the connection between phonon dispersion and electronic band structure leading to the selective quenching of the oxygen-chain mode. Our results contribute to a deeper understanding of the interplay between lattice and charge degrees of freedom for exciton-based optoelectronics.

Picosecond UV Kerr‐gated Raman spectroscopy with 280 nm laser excitation

AbstractRaman spectra obtained by UV laser excitation above 260 nm are contaminated by spectrally overlapping UV‐excited fluorescence. Here, we demonstrate a picosecond UV Kerr‐gated Raman spectroscopy setup to suppress the fluorescence in Raman spectra excited by 280 nm laser pulses. Specifically, we use a model sample that consists of acetonitrile contaminated by a small amount of toluene for generating UV‐excited fluorescence. We were able to acquire a Raman spectrum of acetonitrile by suppressing the UV‐excited fluorescence of toluene by the action of a 1‐mm thick fused silica‐based UV Kerr gate operated by 1030 nm, ~1 ps gating pulses. These results also indicate the challenges that must be overcome in the future for realizing UV‐fluorescence‐free UV resonance Raman (UVRR) spectroscopy studies of molecules exhibiting electronic resonances around 280 nm using laser excitation wavelengths right at or close to this resonance.

TEMPO-oxidized cellulose nanofibril/polyvalent cations hydrogels: a multifaceted view of network interactions and inner structure

In the last years, hydrogels from renewable biopolymers and low-cost row materials are a hot topic for biomedical applications. In this context, cellulose nanofibrils are considered suitable building blocks for the synthesis of many biocompatible products, with a variety of chemical-physical properties. Herein we report a multi-technique and multi-scale study, from the molecular to the nanometric length scale, of the sol–gel transition observed in aqueous solutions of TEMPO-oxidized nano-sized cellulose fibrils (TOCNFs), when in the presence of polyvalent cations (Mg2+ and Ca2+). We combine the data from Small Angle Neutron Scattering (SANS), which provide information about the inner structure of the nanofibril, with those from UV Resonant Raman (UVRR) spectroscopy, which is a sensitive probe of the intra- and inter-molecular interactions in the gel and the liquid state. The transition between the gel and the liquid phases is investigated as a function of the concentration of both TOCNFs and cations, the nature of the latter, and the pH at which the phenomenon is observed. SANS analysis reveals that ion concentration induces an anisotropic swelling in the nanofibrils which, at the same time, become more and more flexible. The nanofibrils flexibility is also dependent on TOCNF concentration and pH value. UVRR allows us to elucidate the structural organization and hydrogen-bonding properties of water in aqueous TOCNF dispersions and gels, showing how water molecules partially lose their typical bulk-like tetrahedral organization when ions are added, and the gel phase is formed.Graphical abstract

New penta- and hexa-coordinated titanium sites in titanium silicalite-1 catalyst for propylene epoxidation

Creating and identifying catalytically active titanium sites is vital to further enhance performance of titanium-containing zeolites, particularly for environmentally friendly titanium silicalite-1 catalyst (TS-1). Herein, we prepared a typical TS-1 with two new Ti-sites including the penta-coordinated Ti(OH)2(OSi)3 and hexa-coordinated Ti(OH)4(OSi)2. They are identified by UV resonance Raman spectroscopy and their coordination structures delineated by density functional theory calculations. Evaluated by propylene epoxidation to propylene oxide, Ti(OH)4(OSi)2 is more active than Ti(OH)2(OSi)3. Furthermore, Ti(OH)4(OSi)2 delivers the catalytic activity about 8.7 times the activity of known tetra-coordinated framework Ti(OSi)4 sites. Thus, Ti(OH)4(OSi)2 is found to be highly active in this reaction.

Towards therapeutic drug monitoring of antibiotic levels - analyzing the pharmacokinetics of levofloxacin using DUV-resonance Raman spectroscopy.

Therapeutic drug monitoring (TDM) plays an important role in clinical practice. Here, pharmacokinetics has a decisive influence on the effective antibiotic concentration during treatment. Moreover, different kinetics exist for different administration forms. Accordingly, adjusting the correct concentration depends, in addition to gender, age, weight, clinical picture, etc., on the dosage form of the antibiotic. This study investigates the capability of deep UV resonance Raman spectroscopy (DUV-RRS) to simulate the pharmacokinetics of fluoroquinolone levofloxacin after two different administration forms (intravenous and oral). Three different pre-processing methods were applied, and the best agreement with the simulation was achieved using the extended multiplicative scatter correction. The resulting spectra were used for partial least squares (PLS) regression and ordinary least squares (OLS) regression. The kinetic parameters were compared with the simulated data, with PLS showing the best performance for intravenous administration and a comparable result to OLS for oral administration, while the errors are smaller. The acquired results show the potential of DUV-RRS in combination with PLS regression as a promising supportive method for TDM.

Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale.

Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.

Electrochemical and Structural Study of the Buried Tryptophan in Azurin: Effects of Hydration and Polarity on the Redox Potential of W48.

Tryptophan serves as an important redox-active amino acid in mediating electron transfer and mitigating oxidative damage in proteins. We previously showed a difference in electrochemical potentials for two tryptophan residues in azurin with distinct hydrogen-bonding environments. Here, we test whether reducing the side chain bulk at position Phe110 to Leu, Ser, or Ala impacts the electrochemical potentials (E°) for tryptophan at position 48. X-ray diffraction confirmed the influx of crystallographically resolved water molecules for both the F110A and F110L tyrosine free azurin mutants. The local environments of W48 in all azurin mutants were further evaluated by UV resonance Raman (UVRR) spectroscopy to probe the impact of mutations on hydrogen bonding and polarity. A correlation between the frequency of the ω17 mode─considered a vibrational marker for hydrogen bonding─and E° is proposed. However, the trend is opposite to the expectation from a previous study on small molecules. Density functional theory calculations suggest that the ω17 mode reflects hydrogen bonding as well as local polarity. Further, the UVRR data reveal different intensity/frequency shifts of the ω9/ω10 vibrational modes that characterize the local H-bonding environments of tryptophan. The cumulative data support that the presence of water increases E° and reveal properties of the protein microenvironment surrounding tryptophan.

Stoichiometry of reactions of ozone and hypochlorous acid with lignin and hexenuronic acid and its chlorination

The stoichiometry of ozone and hypochlorous acid reactions with lignin and hexenuronic acid (HexA) was measured in bleaching experiments of Eucalyptus sp. kraft pulp. The progress of the reactions was followed by UV Resonance Raman spectroscopy that can quantify lignin and HexA based on the Raman scattering intensities of the carbon–carbon double bond in HexA and the aromatic ring in lignin. Here, one mol of ozone converted 0.16 mol of lignin (C9 monomer units) and 0.28 mol of HexA, whereas 1 mol of hypochlorous acid converted 0.09 mol of lignin and 0.23 mol of HexA. The use of a tertiary amine catalyst with the hypochlorous acid treatments did not affect these stoichiometries. The stoichiometric ratios showed that ozone was more efficient in oxidizing lignin than hypochlorous acid, while both electrophiles reacted with HexA to a similar extent. HexA reaction by hypochlorous acid was concluded to involve initial electrophilic chlorination of the carbon–carbon double bond, contributing to significant organochlorine (OX) formation in the pulp. Evidence on this was the linear correlation between the initial HexA content and OX (0.59 mol OX per mol HexA) and the high OX content in the xylan extracted from the bleached pulp. The 2D NMR HSQC and TOCSY spectra of the isolated xylans showed the disappearance of HexA signals after the treatment with hypochlorous acid and the appearance of a new spin system, yet to be fully identified.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin.

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

Electron-phonon coupling and vibrational properties of size-selected linear carbon chains by resonance Raman scattering

UV resonance Raman spectroscopy of size-selected linear sp-carbon chains unveils vibrational overtones and combinations up to the fifth order. Thanks to the tunability of the synchrotron source, we excited each H-terminated polyyne (HCnH with n = 8,10,12) to the maxima of its vibronic absorption spectrum allowing us to precisely determine the electronic and vibrational structure of the ground and excited states for the main observed vibrational mode. Selected transitions are shown to enhance specific overtone orders in the Raman spectrum in a specific way that can be explained by a simple analytical model based on Albrecht’s theory of resonance Raman scattering. The determined Huang–Rhys factors indicate a strong and size-dependent electron-phonon coupling increasing with the sp-carbon chain length.

Gaining Insights on the Interactions of a Class of Decorated (2-([2,2'-Bipyridin]-6-yl)phenyl)platinum Compounds with c-Myc Oncogene Promoter G-Quadruplex and Other DNA Structures.

Organometallic molecules offer some of the most promising scaffolds for interaction with G-quadruplex nucleic acids. We report the efficient synthesis of a family of organoplatinum(II) complexes, featuring a 2-([2,2'-bipyridin]-6-yl)phenyl tridentate (N∧ N∧ C) ligand, that incorporates peripheral side-chains aiming at enhancing and diversifying its interaction capabilities. These include a di-isopropyl carbamoyl amide, a morpholine ethylenamide, two enantiomeric proline imides and an oxazole. The binding affinities of the Pt-complexes were evaluated via UV-vis and fluorescence titrations, against 5 topologically-distinct DNA structures, including c-myc G-quadruplex, two telomeric (22AG) G-quadruplexes, a duplex (ds26) and a single-stranded (polyT) DNA. All compounds exhibited binding selectivity in favour of c-myc, with association constants (Ka ) in the range of 2-5×105 M-1 , lower affinity for both folds of 22AG and for ds26 and negligible affinity for polyT. Remarkable emission enhancements (up to 200-fold) upon addition of excess DNA were demonstrated by a subset of the compounds with c-myc, providing a basis for optical selectivity, since optical response to all other tested DNAs was low. A c-myc DNA-melting experiment showed significant stabilizing abilities for all compounds, with the most potent binder, the morpholine-Pt-complex, exhibiting a ΔTm >30 °C, at 1 : 5 DNA-to-ligand molar ratio. The same study implied contributions of the diverse side-chains to helix stabilization. To gain direct evidence of the nature of the interactions, mixtures of c-myc with the four most promising compounds were studied via UV Resonance Raman (UVRR) spectroscopy, which revealed end-stacking binding mode, combined with interactions of side-chains with loop nucleobase residues. Docking simulations were conducted to provide insights into the binding modes for the same four Pt-compounds, suggesting that the binding preference for two alternative orientations of the c-myc G-quadruplex thymine 'cap' ('open' vs. 'closed'), as well as the relative contributions to affinity from end-stacking and H-bonding, are highly dependent on the nature of the interacting Pt-complex side-chain.