Calibration of Raman Bandwidths on the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) Deep Ultraviolet Raman and Fluorescence Instrument Aboard the Perseverance Rover.

In this work, we derive a simple method for calibrating Raman bandwidths for the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument onboard NASA's Perseverance rover. Raman bandwidths and shapes reported by an instrument contain contributions from both the intrinsic Raman band (IRB) and instrumental artifacts. To directly correlate bandwidth to sample properties and to compare bandwidths across instruments, the IRB width needs to be separated from instrumental effects. Here, we use the ubiquitous bandwidth calibration method of modeling the observed Raman bands as a convolution of a Lorentzian IRB and a Gaussian instrument slit function. Using calibration target data, we calculate that SHERLOC has a slit function width of 34.1 cm-1. With a measure of the instrument slit function, we can deconvolve the IRB from the observed band, providing the width of the Raman band unobscured by instrumental artifact. We present the correlation between observed Raman bandwidth and intrinsic Raman bandwidth in table form for the quick estimation of SHERLOC Raman intrinsic bandwidths. We discuss the limitations of using this model to calibrate Raman bandwidth and derive a quantitative method for calculating the errors associated with the calibration. We demonstrate the utility of this method of bandwidth calibration by examining the intrinsic bandwidths of SHERLOC sulfate spectra and by modeling the SHERLOC spectrum of olivine.

Diverse organic-mineral associations in Jezero crater, Mars.

The presence and distribution of preserved organic matter on the surface of Mars can provide key information about the Martian carbon cycle and the potential of the planet to host life throughout its history. Several types of organic molecules have been previously detected in Martian meteorites1 and at Gale crater, Mars2-4. Evaluating the diversity and detectability of organic matter elsewhere on Mars is important for understanding the extent and diversity of Martian surface processes and the potential availability of carbon sources1,5,6. Here we report the detection of Raman and fluorescence spectra consistent with several species of aromatic organic molecules in the Máaz and Séítah formations within the Crater Floor sequences of Jezero crater, Mars. We report specific fluorescence-mineral associations consistent with many classes of organic molecules occurring in different spatial patterns within these compositionally distinct formations, potentially indicating different fates of carbon across environments. Our findings suggest there may be a diversity of aromatic molecules prevalent on the Martian surface, and these materials persist despite exposure to surface conditions. These potential organic molecules are largely found within minerals linked to aqueous processes, indicating that these processes may have had a key role in organic synthesis, transport or preservation.

A Model for Inhomogeneously Broadened Raman Bands.

Detailed information on the physics and chemistry of a sample can be derived from Raman band parameters. However, the Raman band observed by the detector contains artifacts from the instrument, complicating analysis of these details. To obtain Raman data that can be directly correlated to sample properties and to compare Raman spectra across instrumentation, instrumental effects must be accounted for. This is commonly performed for homogeneously broadened bands by determining the contribution of the slit function to the spectrum. However, there is currently no method for understanding instrumental effects on inhomogeneously broadened bands or a method to account for these effects when examining data and comparing data across instruments, though these analyses are commonplace. This shortfall injects an unknown error into the analyses and comparisons of inhomogeneously broadened Raman bands. This work derives a method of modeling inhomogeneous Raman bands as a continuum of homogeneous Raman bands spanning the width of the stochastic fluctuation energy well that causes inhomogeneous broadening. This model is combined with previous work to examine the effects of the slit function, intrinsic Raman band, stochastic energy well, homogeneously broadened Raman band, and slit width band parameters on the inhomogeneously broadened Raman band parameters. This model, for the first time, provides a quantitative description of the experimental parameters that effect the inhomogeneous Raman bands.

Aqueous alteration processes in Jezero crater, Mars-implications for organic geochemistry.

The Perseverance rover landed in Jezero crater, Mars, in February 2021. We used the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument to perform deep-ultraviolet Raman and fluorescence spectroscopy of three rocks within the crater. We identify evidence for two distinct ancient aqueous environments at different times. Reactions with liquid water formed carbonates in an olivine-rich igneous rock. A sulfate-perchlorate mixture is present in the rocks, which probably formed by later modifications of the rocks by brine. Fluorescence signatures consistent with aromatic organic compounds occur throughout these rocks and are preserved in minerals related to both aqueous environments.

Raman spectroscopy provides insight into carbonate rock fabric based on calcite and dolomite crystal orientation.

Carbonate rocks record the oldest forms of life on Earth, and their geologic reconstruction requires multiple methods to determine physical and chemical processes before conclusions of ancient biosignatures are made. Since crystal orientation within rock fabric may be used to infer geologic settings, we present here a complementary Raman method to study the orientation of calcite (CaCO3) and dolomite [CaMg (CO3)2] minerals. The relative peak intensity ratio of the carbonate lattice Eg modes T and L reveals the crystallographic orientation of calcite and dolomite with respect to the incident light polarization. Our results for calcite show that when the incident laser light propagates down the crystallographic a/b axis: (1) the L mode is always greater in intensity than the T mode (I T < I L), and (2) the spectra are most intense at 45° and least intense at 90° polarization angles measured from around the c axis. Our results for dolomite show that (1) I T > I L when the incident light propagation is down the crystallographic c axis and (2) I T < I L when the incident light propagation is down the crystallographic a/b axis. This study reveals mineral orientation variation related to deposition and paragenesis within limestone and dolostone samples. The method presented yields information related to growth and deformation during diagenetic and metamorphic alteration and may be used in research seeking to identify the fabric parameters of any calcite or dolomite containing rock. The compositional and structural data obtained from Raman mapping is useful in structural geology, materials science, and biosignature research.

Calibration of the SHERLOC Deep Ultraviolet Fluorescence-Raman Spectrometer on the Perseverance Rover.

We describe the wavelength calibration of the spectrometer for the scanning of habitable environments with Raman and luminescence for organics and chemicals (SHERLOC) instrument onboard NASA's Perseverance Rover. SHERLOC utilizes deep ultraviolet Raman and fluorescence (DUV R/F) spectroscopy to enable analysis of samples from the Martian surface. SHERLOC employs a 248.6 nm deep ultraviolet laser to generate Raman-scattered photons and native fluorescence emission photons from near-surface material to detect and classify chemical and mineralogical compositions. The collected photons are focused on a charge-coupled device and the data are returned to Earth for analysis. The compact DUV R/F spectrometer has a spectral range from 249.9 nm to 353.6 nm (∼200 cm-1 to 12 000 cm-1) (with a spectral resolution of 0.296 nm (∼40 cm-1)). The compact spectrometer uses a custom design to project a high-resolution Raman spectrum and a low-resolution fluorescence spectrum on a single charge-coupled device. The natural spectral separation enabled by deep ultraviolet excitation enables wavelength separation of the Raman/fluorescence spectra. The SHERLOC spectrometer was designed to optimize the resolution of the Raman spectral region and the wavelength range of the fluorescence region. The resulting illumination on the charge-coupled device is curved, requiring a segmented, nonlinear wavelength calibration in order to understand the mineralogy and chemistry of Martian materials.

Impact shock origin of diamonds in ureilite meteorites.

The origin of diamonds in ureilite meteorites is a timely topic in planetary geology as recent studies have proposed their formation at static pressures >20 GPa in a large planetary body, like diamonds formed deep within Earth's mantle. We investigated fragments of three diamond-bearing ureilites (two from the Almahata Sitta polymict ureilite and one from the NWA 7983 main group ureilite). In NWA 7983 we found an intimate association of large monocrystalline diamonds (up to at least 100 µm), nanodiamonds, nanographite, and nanometric grains of metallic iron, cohenite, troilite, and likely schreibersite. The diamonds show a striking texture pseudomorphing inferred original graphite laths. The silicates in NWA 7983 record a high degree of shock metamorphism. The coexistence of large monocrystalline diamonds and nanodiamonds in a highly shocked ureilite can be explained by catalyzed transformation from graphite during an impact shock event characterized by peak pressures possibly as low as 15 GPa for relatively long duration (on the order of 4 to 5 s). The formation of "large" (as opposed to nano) diamond crystals could have been enhanced by the catalytic effect of metallic Fe-Ni-C liquid coexisting with graphite during this shock event. We found no evidence that formation of micrometer(s)-sized diamonds or associated Fe-S-P phases in ureilites require high static pressures and long growth times, which makes it unlikely that any of the diamonds in ureilites formed in bodies as large as Mars or Mercury.

Mechanisms by Which Organic Solvent Exchange Transforms Responsive Pure Protein Hydrogels into Responsive Organogels.

Responsive pure protein organogel sensors and catalysts are fabricated by replacing the aqueous mobile phase of protein hydrogels with pure ethylene glycol (EG). Exchanging water for EG causes irreversible volume phase transitions (VPT) in bovine serum albumin (BSA) polymers; however, BSA hydrogel and organogel sensors show similar volume responses to protein-ligand binding. This work elucidates the mechanisms involved in this enabling irreversible VPT by examining the protein secondary structure, hydration, and protein polymer morphology. Organogel proteins retain their native activity because their secondary structure and hydration shell are relatively unperturbed by the EG exchange. Conversely, the decreasing solvent quality initiates polymer phase separation to minimize the BSA polymer surface area exposed to EG, thus decreasing distances between BSA polymer strands. These protein polymer morphology changes promote interprotein interactions between BSA polymer strands, which increase the effective polymer cross-link density and prevent organogel swelling as the mobile phase is exchanged back to water.

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 ß-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone ß-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 ß-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.

Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils.

We determined an empirical correlation that relates the amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base interactions of its primary amide carbonyl. We used this correlation to determine the Q side chain carbonyl interaction enthalpy (Δ Hint) in monomeric and amyloid-like fibril conformations of D2Q10K2 (Q10). We independently verified these Δ Hint values through molecular dynamics simulations that showed excellent agreement with experiments. We found that side chain-side chain and side chain-peptide backbone interactions in fibrils and monomers are more enthalpically favorable than are Q side chain-water interactions. Q10 fibrils also showed a more favorable Δ Hint for side chain-side chain interactions compared to backbone-backbone interactions. This work experimentally demonstrates that interamide side chain interactions are important in the formation and stabilization of polyQ fibrils.

Hydrophobic Collapse Initiates the Poly( N-isopropylacrylamide) Volume Phase Transition Reaction Coordinate.

The best-known examples of smart, responsive hydrogels derive from poly( N-isopropylacrylamide) (PNIPAM) cross-linked polymer networks. These hydrogels undergo volume phase transitions (VPTs) triggered by temperature, chemical, and/or environmental changes. PNIPAM hydrogels can undergo more than 50-fold volume changes within ∼1 µs intervals. Studies have tried to elucidate the molecular mechanism of these extraordinarily large responses. Nevertheless, the molecular reaction coordinates that drive the VPT remain unclear. Using visible nonresonance Raman temperature-jump spectroscopy, we determined the molecular ordering of this VPT. The PNIPAM hydrophobic isopropyl and methylene groups dehydrate with time constants of 109 ± 64 and 104 ± 44 ns, initiating the volume collapse of PNIPAM. The subsequent dehydration of the PNIPAM amide groups is significantly slower, as our group previously discovered (360 ± 85 ns). This determination of the ordering of the molecular reaction coordinate of the PNIPAM VPT enables the development of the next generation of super-responsive materials.

Ultraviolet Resonance Raman Spectroscopic Markers for Protein Structure and Dynamics.

UV resonance Raman (UVRR) spectroscopy is a powerful tool for investigating the structure of biological molecules, such as proteins. Numerous UVRR spectroscopic markers that provide information on the structure and environment of the protein backbone and of amino acid side chains have recently been discovered. Combining these UVRR markers with hydrogen-deuterium exchange and advanced statistics is a powerful tool for studying protein systems, including the structure and formation mechanism of protein aggregates and amyloid fibrils. These techniques allow crucial new insights into the structure and dynamics of proteins, such as polyglutamine peptides, which are associated with 10 different neurodegenerative diseases. Here we summarize the spectroscopic structural markers recently developed and the important insights they provide.

Monomeric Polyglutamine Structures That Evolve into Fibrils.

We investigate the solution and fibril conformations and structural transitions of the polyglutamine (polyQ) peptide, D2Q10K2 (Q10), by synergistically using UV resonance Raman (UVRR) spectroscopy and molecular dynamics (MD) simulations. We show that Q10 adopts two distinct, monomeric solution conformational states: a collapsed ß-strand and a PPII-like structure that do not readily interconvert. This clearly indicates a high activation barrier in solution that prevents equilibration between these structures. Using metadynamics, we explore the conformational energy landscape of Q10 to investigate the physical origins of this high activation barrier. We develop new insights into the conformations and hydrogen bonding environments of the glutamine side chains in the PPII and ß-strand-like conformations in solution. We also use the secondary structure-inducing cosolvent, acetonitrile, to investigate the conformations present in low dielectric constant solutions with decreased solvent-peptide hydrogen bonding. As the mole fraction of acetonitrile increases, Q10 converts from PPII-like structures into α-helix-like structures and ß-sheet aggregates. Electron microscopy indicates that the aggregates prepared from these acetonitrile-rich solutions show morphologies similar to our previously observed polyQ fibrils. These aggregates redissolve upon the addition of water! These are the first examples of reversible fibril formation. Our monomeric Q10 peptides clearly sample broad regions of their available conformational energy landscape. The work here develops molecular-level insight into monomeric Q10 conformations and investigates the activation barriers between different monomer states and their evolution into 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) Cß-Cγ (Cα-Cß) stretching component of the vibration. The Cß-Cγ (Cα-Cß) bond length inversely correlates with the AmIII(P) band frequency. As the Cß-Cγ (Cα-Cß) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cß-Cγ (Cα-Cß) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cß-Cγ (Cα-Cß) 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.

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).