Steady-state and transient ultraviolet resonance Raman spectrometer for the 193-270 nm spectral region

Toward SERS based localized thermometry of Polymer-Supported silver and gold nanostructures

In order to accurately account for the contribution of different plasmon mediated phenomena when developing materials for applications in photothermal therapy, photovoltaics, or photocatalysis reliable, precise, and localized temperature measurements are required. In this work we applied two surface-enhanced Raman scattering (SERS) spectroscopy based methods to measure the local temperature increase due to the thermoplasmonic effect in gold and silver nanoparticles on thin polystyrene films. The first method relies on the temperature dependence of the anti-Stokes to Stokes Raman bands intensity ratio for a label Rhodamine 6G deposited on the nanostructures. We found that the method enables good measurements in the 20-60 °C temperature range but becomes less reliable at higher temperatures when the system undergoes transformations and the plasmonic response of the nanoparticles changes with heating. The second method makes use of the temperature dependent adsorption geometry of phenyl isocyanide (PIC) and a corresponding shift of ν(C≡N) vibration. The method demonstrates greater temperature sensitivity of gold nanoparticles than silver. The difference in sensing capability is related to the difference in molecular adsorption geometry of PIC on Au compared to Ag. We conclude that for universal thermometry of the nanoparticle/ thin film composite a combination of the two methods provides more precise localized temperature measurements.

Standoff Detection System Using Raman Spectroscopy in the Deep-Ultraviolet Wavelength Region for the Detection of Hazardous Gas

This study developed a standoff detection system for Raman spectra in the deep-ultraviolet region to facilitate remote detection of various hazardous materials. Although Raman spectroscopy can distinguish various materials, the measurement of Raman spectra through standoff detection is challenging because of the low scattering cross-section of Raman scattering. The resonance Raman scattering effect in the deep-ultraviolet wavelength region is promising in terms of enhancing the spectral intensity of Raman scattering. A catoptric light receiver system was developed to effectively collect deep-ultraviolet light via a change in the distance from the primary to secondary mirror of the telescope. The experimental results for the standoff detection indicate that the system enables the measurement of the Raman spectrum of SO₂ gas, which was locally present 20 m from the system with a wavelength resolution of 0.15 nm. The gas used in this remote measurement has a relatively simple molecular structure among chemical, biological, radiological, nuclear, and explosive gases. However, the high wavelength resolution of Raman spectroscopy will enable measurement of substances with complex molecular structures, such as bacteria and explosives, without losing the detailed structure of their spectra.

Ultraviolet resonance Raman spectroscopy with a continuously tunable picosecond laser: Application to the supramolecular ligand guanidiniocarbonyl pyrrole (GCP)

We present a UVRR spectroscopy setup which is equipped with a picosecond pulsed laser excitation source continuously tunable in the 210-2600 nm wavelength range. This laser source is based on a three-stage optical parametric amplifier (OPA) pumped by a bandwidth-compressed second harmonic output of an amplified Yb:KGW laser. It provides <15 cm^-1 linewidth pulses below 270 nm, which is sufficient for resolving Raman lines of samples in condensed phase studies. For demonstrating the capability of this tunable setup for UVRR spectroscopy we present its application to the artificial ligand guanidiniocarbonyl pyrrole (GCP), a carboxylate binder used in peptide and protein recognition. A UVRR excitation study in the range 244-310 nm was performed for identifying the optimum laser excitation wavelength for UVRR spectroscopy of this ligand (λ_max = 298 nm) at submillimolar concentrations (400 µM) in aqueous solution. The optimum UVRR spectrum is observed for laser excitation with λ_exc = 266 nm. Only in the relatively narrow range of λ_exc = 266-275 nm UVRR spectra with a sufficiently high signal-to-noise ratio and without severe interference from autofluorescence (AF) were detectable. At longer excitation wavelengths the UVRR signal is masked by AF. At shorter excitation wavelengths the UVRR spectrum is sufficiently separated from the AF, but the resonance enhancement is not sufficient. The presented tunable UVRR setup provides the flexibility to also identify optimum conditions for other supramolecular ligands for peptide/protein recognition.

New advances in using Raman spectroscopy for the characterization of catalysts and catalytic reactions

Gaining insight into the mode of operation of heterogeneous catalysts is of great scientific and economic interest. Raman spectroscopy has proven its potential as a powerful vibrational spectroscopic technique for a fundamental and molecular-level characterization of catalysts and catalytic reactions. Raman spectra provide important insight into reaction mechanisms by revealing specific information on the catalysts' (defect) structure in the bulk and at the surface, as well as the presence of adsorbates and reaction intermediates. Modern Raman instrumentation based on single-stage spectrometers allows high throughput and versatility in design of in situ/operando cells to study working catalysts. This review highlights major advances in the use of Raman spectroscopy for the characterization of heterogeneous catalysts made during the past decade, including the development of new methods and potential directions of research for applying Raman spectroscopy to working catalysts. The main focus will be on gas-solid catalytic reactions, but (photo)catalytic reactions in the liquid phase will be touched on if it appears appropriate. The discussion begins with the main instrumentation now available for applying vibrational Raman spectroscopy to catalysis research, including in situ/operando cells for studying gas-solid catalytic processes. The focus then moves to the different types of information available from Raman spectra in the bulk and on the surface of solid catalysts, including adsorbates and surface depositions, as well as the use of theoretical calculations to facilitate band assignments and to describe (resonance) Raman effects. This is followed by a presentation of major developments in enhancing the Raman signal of heterogeneous catalysts by use of UV resonance Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS), and shell-isolated nanoparticle surface-enhanced Raman spectroscopy (SHINERS). The application of time-resolved Raman studies to structural and kinetic characterization is then discussed. Finally, recent developments in spatially resolved Raman analysis of catalysts and catalytic processes are presented, including the use of coherent anti-Stokes Raman spectroscopy (CARS) and tip-enhanced Raman spectroscopy (TERS). The review concludes with an outlook on potential future developments and applications of Raman spectroscopy in heterogeneous catalysis.

Highly efficient tunable picosecond deep ultraviolet laser system for Raman spectroscopy

We present a narrowband laser system tunable from 219 to 236 nm for deep ultraviolet (DUV) Raman spectroscopy. The demonstrated laser system produces 6.7 ps nearly transform-limited pulses with energy up to 0.36 µJ at 100 kHz repetition rate. The system consists of a two-stage optical parametric amplifier (OPA) of a narrowband continuous wave diode laser and subsequent frequency conversion to the DUV radiation. We achieve more than 300 mW in the signal wave using ${{\rm LiB}_3}{{\rm O}_5}$LiB3O5 (LBO) and ${{\rm BaB}_2}{{\rm O}_4}$BaB2O4 (BBO) crystals, with the total 2.7 W pump after the two-stage OPA. We reach 12% conversion efficiency of the OPA signal wave into the DUV radiation using type-I phase matching in the BBO crystal. Finally, we demonstrate the applicability of the system for DUV Raman spectroscopy by collecting a high dynamic range, high spectral resolution spontaneous Raman spectrum of air.

Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent

Expanded polyglutamine (polyQ) tracts in proteins, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D₂Q₁₅K₂ (Q15) and D₂Q₂₀K₂ (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D₂Q₁₀K₂ (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that is thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.

UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide

Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D₂Q₂₀K₂ (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.

Detection of Ozone and Nitric Oxide in Decomposition Products of Air-Insulated Switchgear Using Ultraviolet Differential Optical Absorption Spectroscopy (UV-DOAS)

Air-insulated switchgear cabinets play a role in the protection and control of the modern power grid, and partial discharge (PD) switchgear is a long-term process in the non-normal operation of one of the situations; thus, condition monitoring of the switchgear is important. The air-insulated switchgear during PD enables the decomposition of air components, namely, O₃ and NO. A set of experimental platforms was designed on the basis of the principle of ultraviolet differential optical absorption spectroscopy (UV-DOAS) to detect O₃ and NO concentrations in air-insulated switchgear. Differential absorption algorithm and wavelet transform were used to extract effective absorption spectra; a linear relationship between O₃ and NO concentrations and absorption spectrum data were established. O₃ detection linearity was up to 0.9992 and the detection limit was at 3.76 ppm. NO detection linearity was up to 0.9990 and the detection limit was at 0.64 ppm. Results indicate that detection platform is suitable for detecting trace O₃ and NO gases produced by PD of the air-insulated switchgear.

Photonic crystal protein hydrogel sensor materials enabled by conformationally induced volume phase transition

Hydrogels that change volume in response to specific molecular stimuli can serve as platforms for sensors, actuators and drug delivery devices. There is great interest in designing intelligent hydrogels for tissue engineering, drug delivery, and microfluidics that utilize protein binding specificities and conformational changes. Protein conformational change induced by ligand binding can cause volume phase transitions (VPTs). Here, we develop a highly selective glucose sensing protein photonic crystal (PC) hydrogel that is fabricated from genetically engineered E. coli glucose/galactose binding protein (GGBP). The resulting 2-D PC-GGBP hydrogel undergoes a VPT in response to glucose. The volume change causes the 2-D PC array particle spacing to decrease, leading to a blue-shifted diffraction which enables our sensors to report on glucose concentrations. This 2-D PC-GGBP responsive hydrogel functions as a selective and sensitive sensor that easily monitors glucose concentrations from ∼0.2 μM to ∼10 mM. This work demonstrates a proof-of-concept for developing responsive, "smart" protein hydrogel materials with VPTs that utilize ligand binding induced protein conformational changes. This innovation may enable the development of other novel chemical sensors and high-throughput screening devices that can monitor protein-drug binding interactions.

Polyglutamine Fibrils: New Insights into Antiparallel β-Sheet Conformational Preference and Side Chain Structure

Understanding the structure of polyglutamine (polyQ) amyloid-like fibril aggregates is crucial to gaining insights into the etiology of at least ten neurodegenerative disorders, including Huntington's disease. Here, we determine the structure of D2Q10K2 (Q10) fibrils using ultraviolet resonance Raman (UVRR) spectroscopy and molecular dynamics (MD). Using UVRR, we determine the fibril peptide backbone Ψ and glutamine (Gln) side chain χ3 dihedral angles. We find that most of the fibril peptide bonds adopt antiparallel β-sheet conformations; however, a small population of peptide bonds exist in parallel β-sheet structures. Using MD, we simulate three different potential fibril structural models that consist of either β-strands or β-hairpins. Comparing the experimentally measured Ψ and χ3 angle distributions to those obtained from the MD simulated models, we conclude that the basic structural motif of Q10 fibrils is an extended β-strand structure. Importantly, we determine from our MD simulations that Q10 fibril antiparallel β-sheets are thermodynamically more stable than parallel β-sheets. This accounts for why polyQ fibrils preferentially adopt antiparallel β-sheet conformations instead of in-register parallel β-sheets like most amyloidogenic peptides. In addition, we directly determine, for the first time, the structures of Gln side chains. Our structural data give new insights into the role that the Gln side chains play in the stabilization of polyQ fibrils. Finally, our work demonstrates the synergistic power and utility of combining UVRR measurements and MD modeling to determine the structure of amyloid-like fibrils.

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations

We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.

Compact Solid-State 213 nm Laser Enables Standoff Deep Ultraviolet Raman Spectrometer: Measurements of Nitrate Photochemistry

We describe a new compact acousto-optically Q-switched diode-pumped solid-state (DPSS) intracavity frequency-tripled neodymium-doped yttrium vanadate laser capable of producing ~100 mW of 213 nm power quasi-continuous wave as 15 ns pulses at a 30 kHz repetition rate. We use this new laser in a prototype of a deep ultraviolet (UV) Raman standoff spectrometer. We use a novel high-throughput, high-resolution Echelle Raman spectrograph. We measure the deep UV resonance Raman (UVRR) spectra of solid and solution sodium nitrate (NaNO3) and ammonium nitrate (NH4NO3) at a standoff distance of ~2.2 m. For this 2.2 m standoff distance and a 1 min spectral accumulation time, where we only monitor the symmetric stretching band, we find a solid state NaNO3 detection limit of ~100 μg/cm(2). We easily detect ~20 μM nitrate water solutions in 1 cm path length cells. As expected, the aqueous solutions UVRR spectra of NaNO3 and NH4NO3 are similar, showing selective resonance enhancement of the nitrate (NO3(-)) vibrations. The aqueous solution photochemistry is also similar, showing facile conversion of NO3(-) to nitrite (NO2(-)). In contrast, the observed UVRR spectra of NaNO3 and NH4NO3 powders significantly differ, because their solid-state photochemistries differ. Whereas solid NaNO3 photoconverts with a very low quantum yield to NaNO2, the NH4NO3 degrades with an apparent quantum yield of ~0.2 to gaseous species.

Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy

Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.

Solution and Solid Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) Ultraviolet (UV) 229 nm Photochemistry

We measured the 229 nm deep-ultraviolet resonance Raman (DUVRR) spectra of solution and solid-state hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). We also examined the photochemistry of RDX both in solution and solid states. RDX quickly photodegrades with a solution quantum yield of φ ~ 0.35 as measured by high-performance liquid chromatography (HPLC). New spectral features form over time during the photolysis of RDX, indicating photoproduct formation. The photoproduct(s) show stable DUVRR spectra at later irradiation times that allow standoff detection. In the solution-state photolysis, nitrate is a photoproduct that can be used as a signature for detection of RDX even after photolysis. We used high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS) and gas chromatography mass spectrometry (GCMS) to determine some of the major solution-state photoproducts. X-ray photoelectron spectroscopy (XPS) was also used to determine photoproducts formed during solid-state RDX photolysis.

UV resonance Raman investigation of the aqueous solvation dependence of primary amide vibrations

We investigated the normal mode composition and the aqueous solvation dependence of the primary amide vibrations of propanamide. Infrared, normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied in conjunction with density functional theory (DFT) to assign the vibrations of crystalline propanamide. We examined the aqueous solvation dependence of the primary amide UVRR bands by measuring spectra in different acetonitrile/water mixtures. As previously observed in the UVRR spectra of N-methylacetamide, all of the resonance enhanced primary amide bands, except for the Amide I (AmI), show increased UVRR cross sections as the solvent becomes water-rich. These spectral trends are rationalized by a model wherein the hydrogen bonding and the high dielectric constant of water stabilizes the ground state dipolar (-)O-C═NH2(+) resonance structure over the neutral O═C-NH2 resonance structure. Thus, vibrations with large C-N stretching show increased UVRR cross sections because the C-N displacement between the electronic ground and excited state increases along the C-N bond. In contrast, vibrations dominated by C═O stretching, such as the AmI, show a decreased displacement between the electronic ground and excited state, which result in a decreased UVRR cross section upon aqueous solvation. The UVRR primary amide vibrations can be used as sensitive spectroscopic markers to study the local dielectric constant and hydrogen bonding environments of the primary amide side chains of glutamine (Gln) and asparagine (Asn).

Sodium dodecyl sulfate monomers induce XAO peptide polyproline II to α-helix transition

XAO peptide (Ac–X₂A₇O₂–NH₂; X: diaminobutyric acid side chain, −CH₂CH₂NH₃⁺; O: ornithine side chain, −CH₂CH₂CH₂NH₃⁺) in aqueous solution shows a predominantly polyproline II (PPII) conformation without any detectable α-helix-like conformations. Here we demonstrate by using circular dichroism (CD), ultraviolet resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce formation of α-helix-like conformations. The stoichiometry and the association constants of SDS and XAO were determined from the XAO–SDS diffusion coefficients measured by pulsed field gradient NMR. We developed a model for the formation of XAO–SDS aggregate α-helix-like conformations. Using UVRR spectroscopy, we calculated the Ramachandran ψ angle distributions of aggregated XAO peptides. We resolved α-, π- and 3₁₀- helical conformations and a turn conformation. XAO nucleates SDS aggregation at SDS concentrations below the SDS critical micelle concentration. The XAO₄–SDS₁₆ aggregates have four SDS molecules bound to each XAO to neutralize the four side chain cationic charges. We propose that the SDS alkyl chains partition into a hydrophobic core to minimize the hydrophobic area exposed to water. Neutralization of the flanking XAO charges enables α-helix formation. Four XAO–SDS₄ aggregates form a complex with an SDS alkyl chain-dominated hydrophobic core and a more hydrophilic shell where one face of the α-helix peptide contacts the water environment.

Stray light suppression in spectroscopy using periodic shadowing

It is well known that spectroscopic measurements suffer from an interference known as stray light, causing spectral distortion that reduces measurement accuracy. In severe situations, stray light may even obscure the existence of spectral lines. Here a novel general method is presented, named Periodic Shadowing, that enables effective stray light elimination in spectroscopy and experimental results are provided to demonstrate its capabilities and versatility. Besides its efficiency, implementing it in a spectroscopic arrangement comes at virtually no added experimental complexity.

Note: deep ultraviolet Raman spectrograph with the laser excitation line down to 177.3 nm and its application

Deep UV Raman spectrograph with the laser excitation line down to 177.3 nm was developed in this laboratory. An ellipsoidal mirror and a dispersed-subtractive triple monochromator were used to collect and disperse Raman light, respectively. The triple monochromator was arranged in a triangular configuration with only six mirrors used. 177.3 nm laser excited Raman spectrum with cut-off wavenumber down to 200 cm(-1) and spectral resolution of 8.0 cm(-1) can be obtained under the condition of high purity N2 purging. With the C-C σ bond in Teflon selectively excited by the 177.3 nm laser, resonance Raman spectrum of Teflon with good quality was recorded on the home-built instrument and the σ-σ(*) transition of C-C bond was studied. The result demonstrates that deep UV Raman spectrograph is powerful for studying the systems with electronic transition located in the deep UV region.

Solution and solid trinitrotoluene (TNT) photochemistry: persistence of TNT-like ultraviolet (UV) resonance Raman bands

We examined the 229 nm deep-ultraviolet resonance Raman (DUVRR) spectra of solution and solid-state trinitrotoluene (TNT) and its solution and solid-state photochemistry. Although TNT photodegrades with a solution quantum yield of ϕ ∼ 0.015, the initial photoproducts show DUVRR spectra extraordinarily similar to pure TNT, due to the similar photoproduct enhancement of the -NO2 stretching vibrations. This results in TNT-like DUVRR spectra even after complete TNT photolysis. These ultraviolet resonance Raman spectral bands enable DUVRR of trace as well as DUVRR standoff TNT detection. We determined the structure of various initial TNT photoproducts by using liquid chromatography-mass spectrometry and tandem mass spectrometry. Similar TNT DUVRR spectra and photoproducts are observed in the solution and solid states.

High-throughput, high-resolution Echelle deep-UV Raman spectrometer

We constructed an ultrahigh-throughput, high-resolution ultraviolet (UV) Raman spectrograph that utilizes a high-efficiency filter-stage monochromator and a high-dispersion Echelle spectrograph. The spectrograph utilizes a total of six mirrors and two gratings, with an overall efficiency at 229 nm of ~18%. The limiting resolution of our spectrometer is 0.6 cm⁻¹ full width half-maximum (FWHM), as measured for 229 nm Rayleigh scattering. Use of a 1 mm-wide entrance slit gives rise to an approximately 10 cm⁻¹ FWHM resolution at 229 nm. The ultrahigh spectrograph throughput enables ultrahigh signal-to-noise ratio, deep UV Raman spectra that allow us to monitor <1% changes in peptide bond composition. The throughput is measured to be 35-fold greater than conventional deep UV Raman spectrometers.

UV resonance Raman and DFT studies of arginine side chains in peptides: insights into arginine hydration

We examined the UV resonance Raman (UVRR) spectra of four models of the Arg side chain, guanidinium (Gdn), ethylguanidinium (EG), arginine (Arg), and Ac-Arg-OMe (AAO) in H2O and D2O, in order to identify spectral markers that report on the environment of the Arg side chain. To elucidate the resonance Raman enhancement mechanism of the Arg side chain, we used density functional theory (DFT) to calculate the equilibrium geometries of the electronic ground state and the first excited state. We determined the vibrational mode frequencies of the ground state and the first derivative of the first electronic excited state potential energy with respect to each vibrational normal mode of the electronic ground state at the electronic ground state equilibrium geometry. The DFT calculations and the potential energy distributions reveal that, in addition to the Gdn group C-N stretching vibrations, the C-N bond stretching vibration of the Gdn group-methylene linkage is also strongly resonance-enhanced in EG, Arg, and AAO. From the UVRR spectra, we find that the Raman cross section and frequency of the ~1170 cm(-1) vibration of the Arg side chain depends on its hydration state and can be used to determine the hydration state of the Arg side chain in peptides and proteins. We examined the hydration of the Arg side chain in two polyAla peptides and found that in the α-helical conformation the Arg side chain in the AEP peptide (sequence: A9RA3EA4RA2) is less hydrated than that in the AP peptide (sequence: A8RA4RA4RA2).

Deep-ultraviolet (UV) resonance raman spectroscopy as a tool for quality control of formulated therapeutic proteins

A deep-ultraviolet (UV) Raman spectrometer with excitation source tunable from 193 to 210 nm has been built and characterized. The dispersion of the spectrometer over the entire range was measured and described theoretically. The relative sensitivity of the spectrometer was estimated using the integrated intensity ratio of two Raman bands of cyclohexane. Resonance Raman spectra of three formulated insulin products were measured and compared. A band-targeted entropy minimization algorithm was applied to the collected spectra for mixture analysis of insulin products. We conclude that it is feasible to develop robust qualitative methods for quality control of protein-based formulated drug using DUVRR spectroscopy.

UV resonance Raman spectroscopy monitors polyglutamine backbone and side chain hydrogen bonding and fibrillization

We utilize 198 and 204 nm excited UV resonance Raman spectroscopy (UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone conformation and the Gln side chain hydrogen bonding (HB) of a short, mainly polyGln peptide with a D(2)Q(10)K(2) sequence (Q10). We measured the UVRR spectra of valeramide to determine the dependence of the primary amide vibrations on amide HB. We observe that a nondisaggregated Q10 (NDQ10) solution (prepared by directly dissolving the original synthesized peptide in pure water) exists in a β-sheet conformation, where the Gln side chains form hydrogen bonds to either the backbone or other Gln side chains. At 60 °C, these solutions readily form amyloid fibrils. We used the polyGln disaggregation protocol of Wetzel et al. [Wetzel, R., et al. (2006) Methods Enzymol.413, 34-74] to dissolve the Q10 β-sheet aggregates. We observe that the disaggregated Q10 (DQ10) solutions adopt PPII-like and 2.5(1)-helix conformations where the Gln side chains form hydrogen bonds with water. In contrast, these samples do not form fibrils. The NDQ10 β-sheet solution structure is essentially identical to that found in the NDQ10 solid formed upon evaporation of the solution. The DQ10 PPII and 2.5(1)-helix solution structure is essentially identical to that in the DQ10 solid. Although the NDQ10 solution readily forms fibrils when heated, the DQ10 solution does not form fibrils unless seeded with the NDQ10 solution. This result demonstrates very high activation barriers between these solution conformations. The NDQ10 fibril secondary structure is essentially identical to that of the NDQ10 solution, except that the NDQ10 fibril backbone conformational distribution is narrower than in the dissolved species. The NDQ10 fibril Gln side chain geometry is more constrained than when NDQ10 is in solution. The NDQ10 fibril structure is identical to that of the DQ10 fibril seeded by the NDQ10 solution.

Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics

We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO(4)(-) binding to the Lys side chain -NH(3)(+) groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO(4)(-) binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process.

A technique for contactless measurement of water temperature using Stokes and anti-Stokes comparative Raman spectroscopy

Contactless measurements of water temperature are utilized in a number of sciences, such as oceanography, climatology, and biology. Previously reported Raman spectroscopy techniques exploited the changes in the shapes of water Raman bands. Interpretation of these changes is difficult since these bands are composed of multiple lines, each influenced not only by temperature but also by pressure and salinity. This paper presents a proof-of-principal demonstration of a contactless technique which determines water temperature from the ratio of Stokes and anti-Stokes intensities of the water 180 cm(-1) Raman band. This ratio is not sensitive to pressure and salinity, allowing reliable determination of water temperature.

UV resonance Raman studies of the NaClO4 dependence of poly-L-lysine conformation and hydrogen exchange kinetics

We used 204 nm excitation UV Resonance Raman (UVRR) spectroscopy to examine the effects of NaClO(4) on the conformation of poly-L-lysine (PLL). The presence of NaClO(4) induces the formation of α-helix, π-helix/bulge, and turn conformations. The dependence of the AmIII(3) frequency on the peptide Ψ Ramachandran angle allows us to experimentally determine the conformational population distributions and the energy landscape of PLL along the Ramachandran Ψ angle. We also used UVRR to measure the NaClO(4) concentration dependence of PLL amide hydrogen exchange kinetics. Exchange rates were determined by fitting the D(2)O exchanging PLL UVRR AmII' band time evolution. Hydrogen exchange is slowed at high NaClO(4) concentrations. The PLL AmII' band exchange kinetics at 0.0, 0.2, and 0.35 M NaClO(4) can be fit by single exponentials, but the AmII' band kinetics of PLL at 0.8 M NaClO(4) requires a double exponential fit. The exchange rates for the extended conformations were monitored by measuring the C(α)-H band kinetics. These kinetics are identical to those of the AmII' band until 0.8 M NaClO(4) whereupon the extended conformation exchange becomes clearly faster than that of the α-helix-like conformations. Our results indicate that ClO(4)(-) binds to the PLL backbone to protect it from OH(-) exchange catalysis. In addition, ClO(4)(-) binding also slows the conformational exchange between the extended and α-helix-like conformations, probably by increasing the activation barriers for conformational interchanges.

UV resonance Raman finds peptide bond-Arg side chain electronic interactions

We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)(3)A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions. The Arg Raman bands in AP exhibit Raman excitation profiles similar to those of the amide bands in AP which are conformation specific. These Arg excitation profiles distinctly differ from the Arg monomer. The Raman depolarization ratios of Arg in monomeric solution are quite simple with ρ = 0.33 indicating enhancement by a single electronic transition. In contrast, we see very complex depolarization ratios of Arg in AP that indicate that the Arg residues are resonance enhanced by multiple electronic transitions.

Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations

We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection.

Circular dichroism and ultraviolet resonance Raman indicate little Arg-Glu side chain α-helix peptide stabilization

Electrostatic interactions between side chains can control the conformation and folding of peptides and proteins. We used circular dichroism (CD) and ultraviolet (UV) resonance Raman spectroscopy (UVRR) to examine the impact of side chain charge on the conformations of two 21 residue mainly polyala peptides with a few Arg and Glu residues. We expected that attractions between Arg-10 and Glu-14 side chains would stabilize the α-helix conformation compared to a peptide with an Arg-14. Surprisingly, CD suggests that the peptide with the Glu-14 is less helical. In contrast, the UVRR show that these two peptides have similar α-helix content. We conclude that the peptide with Glu-14 has the same net α-helix content as the peptide with the Arg but has two α-helices of shorter length. Thus, side chain interactions between Arg-10 and Glu-14 have a minor impact on α-helix stability. The thermal melting of these two peptides is similar. However the Glu-14 peptide pH induced melting forms type III turn structures that form α-helix-turn-α-helix conformations.

Ultraviolet resonance Raman study of side chain electrostatic control of poly-L-lysine conformation

We used 204 nm excitation UV resonance Raman (UVRR) spectroscopy to examine the role of side chain electrostatic interactions in determining the conformation of poly-L-lysine (PLL). We examined the pH and ionic strength dependence of the UVRR. The pH dependence of PLL UVRR spectra between pH 7.1 and 11.7 cannot be described by a two-state model but requires at least one additional state. The AmIII(3) region fitting with pH 7.1 and 11.7 basis spectra reveals a small pH-induced decrease in the relative fraction of the 2.5(1)-helix conformation compared to the PPII conformation. We performed a 2D general correlation analysis on the PLL pH dependence UVRR spectra. The asynchronous spectrum shows enhanced spectral resolution. The 2D asynchronous spectrum reveals multiple components in the C(α)-H b band and the AmII band whose origins are unclear. The cross peaks in the 2D asynchronous spectrum between the AmIII band and the other bands reveals that increasing pH induces three new structures: π-helix, α-helix, and some turn structure. We find that 2.5 M NaCl does not change the equilibrium between the PPII and 2.5(1)-helix conformations by screening side chain electrostatic repulsion. The result indicates that NaCl does not penetrate the region between the side chain and the peptide backbone. We also compared PLL conformations induced by high pH to that induced by 0.8 M ClO(4)(-). Both conditions induce α-helix-like conformations. ClO(4)(-) (0.8 M) induces 6% more α-helix-like conformations than at pH 12.4. Higher pH gives rise to longer α-helices and less turn structures.

Deep UV Resonance Raman Spectroscopy with a Tunable 4 kHz Nanosecond Solid-State Laser and a 1 mL Circulating Free-Flow System

Deep UVRR spectra of the aromatic amino acids Phe and Tyr in the wavenumber range 800–1800 cm−1 with λ exc=195–208 nm exhibit a selective enhancement of signals arising from vibrations localized in the aromatic ring. For λ exc>198 nm, the UVRR spectra of Phe and Tyr are dominated by contributions from the in-plane ring stretching modes ν 8a and ν 8b at ∼1600 cm−1. For λ exc≤198 nm, intense signals from the symmetric ring stretching, in-plane C–H bending and phenyl–C stretching vibrations below 1400 cm−1 are observed. Excellent stray light rejection is achieved by a triple monochromator, which can be used either in the additive or subtractive mode for high-resolution and low-wavenumber measurements, respectively. A home-built circulating free-flow system allows the investigation of sample volumes as small as 1 mL.

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III(3) band and the C(α)-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 3(10)- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures.

UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines

Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (3(1)-helices and β-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 3(1)-helix Ramachandran angles.

Lowest energy electronic transition in aqueous Cl(-) salts: Cl(-) → (H2O)6 charge transfer transition

We use UV resonance Raman spectroscopy to probe the lowest energy allowed electronic transitions of aqueous solutions containing Cl(-) salts. We show that the waters hydrating the Cl(-) are involved in charge transfer transitions that transfer electron density from Cl(-) to the water molecules. These charge transfer transitions cause significant change in the H-O-H bond angle in the excited state, which results in a strong enhancement of the preresonance Raman intensity of the water bending modes. Our work gives the first insight into the lowest allowed electronic transition of hydrated Cl(-).

UV resonance Raman investigation of the conformations and lowest energy allowed electronic excited states of tri- and tetraalanine: charge transfer transitions

UV resonance Raman excitation profiles and Raman depolarization ratios were measured for trialanine and tetraalanine between 198 and 210 nm. Excitation within the pi --> pi* electronic transitions of the peptide bond results in UVRR spectra dominated by amide peptide bond vibrations. In addition to the resonance enhancement of the normal amide vibrations, we find enhancement of the symmetric terminal COO(-) vibration. The Ala(3) UVRR AmIII(3) band frequencies indicate that poly-proline II and 2.5(1) helix conformations and type II turns are present in solution. We also find that the conformation of the interior peptide bond of Ala(4) is predominantly poly-proline-II-like. The Raman excitation profiles of both Ala(3) and Ala(4) reveal a charge transfer electronic transition at 202 nm, where electron transfer occurs from the terminal nonbonding carboxylate orbital to the adjacent peptide bond pi* orbital. Raman depolarization ratio measurements support this assignment. An additional electronic transition is found in Ala(4) at 206 nm.

Raman studies of solution polyglycine conformations

Polyglycine (polygly) is an important model system for understanding the structural preferences of unfolded polypeptides in solution. We utilized UV resonance and visible Raman spectroscopy to investigate the conformational preferences of polygly peptides of different lengths in water containing LiCl and LiClO(4). Lithium salts increase the solubility of polygly. Our study indicates that in solution the conformational ensemble of polygly, as well as central peptide bonds of gly(5) and gly(6), are dominated by the 3(1) extended helix, also known as the polyglycine II conformation (PGII). This preference of the polygly backbone for the PGII conformation in solution is likely a result of favorable interactions between carbonyl dipoles in these extended helices. We found that high concentrations of Li(+) stabilize the PGII conformation in solution, most likely by polarizing the peptide bond carbonyls that makes PGII-stabilizing carbonyl-carbonyl electrostatic interactions more favorable. This ability of Li(+) to stabilize 3(1)-helix conformations in solution gives use to the denaturing ability of lithium salts.

Circular dichroism and UV resonance raman study of the impact of alcohols on the Gibbs free energy landscape of an alpha-helical peptide

We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramachandran Psi-coordinate of a mainly poly-Ala peptide, AP with an AAAAA(AAARA)(3)A sequence. 2,2,2-Trifluoroethanol (TFE) most stabilizes the alpha-helix-like conformations, followed by ethanol, methanol, and pure water. The pi-bulge conformation is stabilized more than the alpha-helix, while the 3(10)-helix is destabilized due to the alcohol-increased hydrophobicity. Turns are also stabilized by alcohols. We also found that while TFE induces more alpha-helices, it favors multiple, shorter helix segments.

Deep ultraviolet resonance Raman excitation enables explosives detection

We measured the 229 nm absolute ultraviolet (UV) Raman cross-sections of the explosives trinitrotoluene (TNT), pentaerythritol tetranitrate (PETN), cyclotrimethylene-trinitramine (RDX), the chemically related nitroamine explosive HMX, and ammonium nitrate in solution. The 229 nm Raman cross-sections are 1000-fold greater than those excited in the near-infrared and visible spectral regions. Deep UV resonance Raman spectroscopy enables detection of explosives at parts-per-billion (ppb) concentrations and may prove useful for stand-off spectroscopic detection of explosives.

Hydrogen bonding and solvent polarity markers in the uv resonance raman spectrum of tryptophan: application to membrane proteins

Ultraviolet resonance Raman (UVRR) spectra of tryptophan compounds in various solvents and a model peptide are presented and reveal systematic changes that reflect solvent polarity, hydrogen bond strength, and cation-pi interaction. The commonly utilized UVRR spectral marker for environment polarity that has been based on off-resonance Raman data, the tryptophan Fermi doublet ratio I1360/I1340, exhibits different values in on- and off-resonance Raman spectra as well as for different tryptophan derivatives. Specifically, the UVRR Fermi doublet ratio for indole ranges from 0.3 in polar solvents to 0.8 in nonpolar solvents, whereas the respective values reported here and previously for off-resonance Raman spectra are 0.5-1.3. UVRR Fermi doublet ratios for the more biologically relevant molecule, N-acetyl tryptophan ethyl ester (NATEE), are in a smaller range of 1.1 (polar solvent) to 1.7 (nonpolar solvent) and correlate to the solvent polarity/polarization parameters pi* and ETN. As has been reported previously, several UVRR modes are also sensitive to the hydrogen bond strength of the indole N-H moiety. Here, we report a new unambiguous marker for H-bonding: the ratio of the W10 (approximately 1237 cm-1) intensity to that of the W9 (approximately 1254 cm-1) mode (RW10). This ratio is 0.7 for NATEE in the absence of hydrogen bond acceptors and increases to 3.1 in the presence of strong hydrogen bond acceptors, with a value of 2.3 in water. The W8 and W17 modes shift more than +10 and approximately -5 cm-1 upon increase in hydrogen bond strength; this range for W17 is smaller than that reported previously and reflects a more realistic range for proteins and peptides in solution. Finally, our data provide evidence for change in the W18 and W16 relative intensity in the presence of cation-pi interactions. These UVRR markers are utilized to interpret spectra of model membrane-bound systems tryptophan octyl ester and the peptide toxin melittin. These spectra reveal the importance of intra- and intermolecular hydrogen bonding and cation-pi interactions that likely influence the partitioning of membrane-associated biomolecules to lipid bilayers or self-associated soluble oligomers. The UVRR analysis presented here modifies and augments prior reports and provides an unambiguous set of spectral makers that can be applied to elucidate the molecular microenvironment and structure of a wide range of complex systems, including anchoring tryptophan residues in membrane proteins and peptides.

Salt dependence of an alpha-helical peptide folding energy landscapes

We used CD, UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Psi angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine alpha-helical peptide, AP of sequence AAAAA(AAARA)(3)A. NaClO(4) stabilizes alpha-helical-like conformations more than does NaCl, which stabilizes more than Na(2)SO(4) at identical ionic strengths. This alpha-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding. Much of the NaClO(4) alpha-helix stabilization results from ClO(4)(-) association with the AP terminal -NH(3)(+) groups and Arg side chains. ClO(4)(-) stabilizes 3(10)-helix conformations but destabilizes turn conformations. The decreased Cl(-) and SO(4)(2-) AP alpha-helix stabilization probably results from a decreased association with the Arg and terminal -NH(3)(+) groups. Cl(-) is expected to have a smaller binding affinity and thus stabilizes alpha-helical conformations intermediately between NaClO(4) and Na(2)SO(4). Electrostatic screening stabilizes pi-bulge conformations.