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.

Aptamer-functionalized 2D photonic crystal hydrogels for detection of adenosine.

Aptamer-functionalized two-dimensional photonic crystal (2DPC) hydrogels are reported for the detection of adenosine (AD). As a molecular recognition group, an AD-binding aptamer was covalently attached to 2DPC hydrogels. This aptamer selectively and sensitively binds AD, changing the conformation of the aptamer from a long single-stranded structure (AD-free conformation) to a short hairpin loop structure (AD-bound conformation). The AD-binding-induced changes of aptamer conformation reduced the volume of the 2DPC hydrogels and decreased the interparticle spacing of the 2DPC embedded in the hydrogel network. The particle spacing changes being dependent on AD concentration were determined by measuring 2DPC light diffraction using a simple laser pointer. The 2DPC hydrogel sensor showed a large particle spacing decrease of ~ 110 nm in response to 1 mM AD in phosphate-buffered saline (PBS). The linear range of determination of AD was 0.1 nM to 1 mM and the limit of detection was 0.09 nM. The hydrogel sensor response for real samples was then validated in diluted fetal bovine serum (FBS) and human urine. The average % difference in particle spacing changes measured between diluted FBS and pure PBS was only 3.99%. In diluted human urine, the recoveries for the detection of AD were 95-101% and the relative standard deviations were 4.9-7.8%. The results demonstrate the potential applicability of the hydrogel sensor for real samples. This sensing concept, using the aptamer-functionalized 2DPC hydrogels, allows for a simple, sensitive, selective, and reversible detection of AD. It may enable sensor development for a wide variety of analytes by simply changing the aptamer recognition group.

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.

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.

UV Resonance Raman Investigation of Pentaerythritol Tetranitrate Solution Photochemistry and Photoproduct Hydrolysis.

Ultraviolet resonance Raman spectroscopy (UVRR) is being developed for standoff trace explosives detection. To accomplish this, it is important to develop a deep understanding of the accompanying UV excited photochemistry of explosives, as well as the impact of reactions on the resulting photoproducts. In the work here we used 229 nm excited UVRR spectroscopy to monitor the photochemistry of pentaerythritol tetranitrate (PETN) in acetonitrile. We find that solutions of PETN in CD3CN photodegrade with a quantum yield of 0.08 ± 0.02, as measured by high performance liquid chromatography (HPLC). The initial step in the 229 nm UV photolysis of PETN in CD3CN is cleavage of an O-NO2 bond to form NO2. The accompanying photoproduct is pentaerythritol trinitrate (PETriN), (CH2ONO2)3CCH2OH formed by photolysis of a single O-NO2. The resulting UVRR spectra show a dominant photoproduct band at ∼1308 cm-1, which derives from the symmetric stretch of dissolved NO2. This photoproduct NO2 is hydrolyzed by trace amounts of water, which downshifts this 1308 cm-1 NO2 Raman band due to the formation of molecular HNO3. The dissociation of HNO3 to NO3- in the presence of additional water results in an intense NO3- symmetric stretching UVRR band at 1044 cm-1.

Aluminum Film-Over-Nanosphere Substrates for Deep-UV Surface-Enhanced Resonance Raman Spectroscopy.

We report here the first fabrication of aluminum film-over nanosphere (AlFON) substrates for UV surface-enhanced resonance Raman scattering (UVSERRS) at the deepest UV wavelength used to date (λex = 229 nm). We characterize the AlFONs fabricated with two different support microsphere sizes using localized surface plasmon resonance spectroscopy, electron microscopy, SERRS of adenine, tris(bipyridine)ruthenium(II), and trans-1,2-bis(4-pyridyl)-ethylene, SERS of 6-mercapto-1-hexanol (as a nonresonant molecule), and dielectric function analysis. We find that AlFONs fabricated with the 210 nm microspheres generate an enhancement factor of approximately 104-5, which combined with resonance enhancement of the adsorbates provides enhancement factors greater than 106. These experimental results are supported by theoretical analysis of the dielectric function. Hence our results demonstrate the advantages of using AlFON substrates for deep UVSERRS enhancement and contribute to broadening the SERS application range with tunable and affordable substrates.

Two-dimensional photonic crystal chemical and biomolecular sensors.

We review recent progress in the development of two-dimensional (2-D) photonic crystal (PC) materials for chemical and biological sensing applications. Self-assembly methods were developed in our laboratory to fabricate 2-D particle array monolayers on mercury and water surfaces. These hexagonal arrays strongly forward Bragg diffract light to report on their array spacings. By embedding these 2-D arrays onto responsive hydrogel surfaces, 2-D PC sensing materials can be fabricated. The 2-D PC sensors utilize responsive polymer hydrogels that are chemically functionalized to show volume phase transitions in selective response to particular chemical species. Novel hydrogels were also developed in our laboratory by cross-linking proteins while preserving their native structures to maintain their selective binding affinities. The volume phase transitions swell or shrink the hydrogels, which alter their 2-D array spacings, and shift their diffraction wavelengths. These shifts can be visually detected or spectrally measured. These 2-D PC sensing materials have been used for the detection of many analytes, such as pH, surfactants, metal ions, proteins, anionic drugs, and ammonia. We are exploring the use of organogels that use low vapor pressure ionic liquids as their mobile phases for sensing atmospheric analytes.

Removable interpenetrating network enables highly-responsive 2-D photonic crystal hydrogel sensors.

Responsive hydrogels functionalized with molecular recognition agents can undergo large volume changes upon interactions with specific chemical species. These responsive hydrogels can function as chemical sensing materials if the hydrogel volumes are monitored by using devices such as photonic crystals (PhC). An important criterion of merit is the responsiveness of these sensing hydrogels. Generally, hydrogel responsiveness is inversely proportional to the hydrogel crosslink density because the elastic constants scale with the crosslink density. The responsivities of these hydrogel sensors dramatically increase as their hydrogel crosslinker concentrations decrease. Unfortunately, the resulting highly responsive hydrogels become fragile at low crosslink densities, and are hard to fabricate and utilize. To temporarily increase the mechanical strengths of these highly responsive hydrogels we developed a method to incorporate a removable reinforcing interpenetrating hydrogel network. We demonstrate the utility of this approach by incorporating an interpenetrating PVA hydrogel within a weak, low crosslinked pH sensitive hydrogel through a freeze-thaw process. These interpenetrating PVA hydrogels are indefinitely stable at room temperature, but easily dissolved on transient heating to 70 °C. The pH sensing hydrogel response is unaffected by this incorporation and subsequent dissolution of the interpenetrating PVA hydrogel. These sacrificial hydrogels enable the fabrication and utilization of highly responsive hydrogel sensing materials.

A Photonic Crystal Protein Hydrogel Sensor for Candida albicans.

We report two-dimensional (2D) photonic crystal (PC) sensing materials that selectively detect Candida albicans (C. albicans). These sensors utilize Concanavalin A (Con A) protein hydrogels with a 2D PC embedded on the Con A protein hydrogel surface, that multivalently and selectively bind to mannan on the C. albicans cell surface to form crosslinks. The resulting crosslinks shrink the Con A protein hydrogel, reduce the 2D PC particle spacing, and blue-shift the light diffracted from the PC. The diffraction shifts can be visually monitored, measured with a spectrometer, or determined from the Debye diffraction ring diameter. Our unoptimized hydrogel sensor has a detection limit of around 32 CFU/mL for C. albicans. This sensor distinguishes between C. albicans and those microbes devoid of cell-surface mannan such as the gram-negative bacterium E. coli. This sensor provides a proof-of-concept for utilizing recognition between lectins and microbial cell surface carbohydrates to detect microorganisms in aqueous environments.

Two-dimensional photonic crystal sensors for visual detection of lectin concanavalin A.

We fabricated a two-dimensional (2-D) photonic crystal lectin sensing material that utilizes light diffraction from a 2-D colloidal array attached to the surface of a hydrogel that contains mannose carbohydrate groups. Lectin-carbohydrate interactions create hydrogel cross-links that shrink the hydrogel volume and decrease the 2-D particle spacing. This mannose containing 2-D photonic crystal sensor detects Concanavalin A (Con A) through shifts in the 2-D diffraction wavelength. Con A concentrations can be determined by measuring the diffracted wavelength or visually determined from the change in the sensor diffraction color. The concentrations are easily monitored by measuring the 2-D array Debye ring diameter. Our observed detection limit for Con A is 0.02 mg/mL (0.7 µM). The 2-D photonic crystal sensors are completely reversible and can monitor Con A solution concentration changes.

2D photonic crystal protein hydrogel coulometer for sensing serum albumin ligand binding.

Bovine and human serum albumin (BSA and HSA) are globular proteins that function as bloodstream carriers of hydrophobes such as fatty acids and drugs. We fabricated novel photonic crystal protein hydrogels by attaching 2D colloidal arrays onto pure BSA and HSA hydrogels. The wavelengths of the diffracted light sensitively report on the protein hydrogel surface area. The binding of charged species to the protein hydrogel gives rise to Donnan potentials that change the hydrogel volume causing shifts in the diffraction. These photonic crystal protein hydrogels act as sensitive Coulometers that monitor the hydrogel charge state. We find multiple high-affinity BSA and HSA binding sites for salicylate, ibuprofen and picosulfate by using these sensors to monitor binding of charged drugs. We demonstrate proof-of-concept for utilizing protein hydrogel sensors to monitor protein-ionic species binding.

Responsive ionic liquid-polymer 2D photonic crystal gas sensors.

We developed novel air-stable 2D polymerized photonic crystal (2DPC) sensing materials for visual detection of gas phase analytes such as water and ammonia by utilizing a new ionic liquid, ethylguanidine perchlorate (EGP) as the mobile phase. Because of the negligible ionic liquid vapor pressure these 2DPC sensors are indefinitely air stable and, therefore, can be used to sense atmospheric analytes. 2D arrays of ~640 nm polystyrene nanospheres were attached to the surface of crosslinked poly(hydroxyethyl methacrylate) (pHEMA)-based polymer networks dispersed in EGP. The wavelength of the bright 2D photonic crystal diffraction depends sensitively on the 2D array particle spacing. The volume phase transition response of the EGP-pHEMA system to water vapor or gaseous ammonia changes the 2DPC particle spacing, enabling the visual determination of the analyte concentration. Water absorbed by EGP increases the Flory-Huggins interaction parameter, which shrinks the polymer network and causes a blue shift in the diffracted light. Ammonia absorbed by the EGP deprotonates the pHEMA-co-acrylic acid carboxyl groups, swelling the polymer which red shifts the diffracted light.

Standoff Deep Ultraviolet Raman Spectrometer for Trace Detection.

We developed a state-of-the-art, high-sensitivity, low-stray-light standoff deep-ultraviolet (DUV) Raman spectrometer for the trace detection of resonance Raman-enhanced chemical species. As an excitation source for Raman measurements, we utilized our recently developed, second-generation, miniaturized, diode-pumped, solid-state neodymium-doped gadolinium orthovanadate (Nd:GdVO4) laser that generates quasi-continuous wave 228 nm light. This 228 nm excitation enhances the Raman intensities of vibrations of NOx groups in explosive molecules, aromatic groups in biological molecules, and various aromatic hydrocarbons. Our DUV Raman spectrograph utilizes a custom DUV f/8 Cassegrain telescope with an ∼200 mm diameter primary mirror, high-efficiency DUV transmission gratings, custom DUV mirrors, and a custom 228 nm Rayleigh rejection filter. We utilized our new standoff DUV Raman spectrometer to measure high signal-to-noise ratio spectra of ∼50 µg/cm2 drop-cast explosives: ammonium nitrate (AN), trinitrotoluene, pentaerythritol tetranitrate as well as aromatic biological molecules: lysozyme, tryptophan, tyrosine, deoxycytidine monophosphate, deoxyadenosine monophosphate at an ∼3 m distance within 10-30 s accumulation times. We roughly estimate the average ultraviolet resonance Raman (UVRR) detection limits for the relatively homogeneous drop-cast films of explosives and biological molecules to be ∼1 µg/cm2 when utilizing a continuous raster scanning that averages Raman signal over ∼1 cm2 sample area to avoid quick analyte depletion due to ultraviolet (UV) photolysis. We determined 3 m standoff UVRR detection limits for drop-cast AN films and identified factors impacting UVRR detection limits such as analyte photochemistry and analyte morphology. We found a detection limit of ∼0.5 µg/cm2 for drop-cast AN films on glass substrates when the Raman signal is averaged over ∼0.5 cm2 of sample surface using a continuous raster scan. For a step raster scan, when the probed sample area is limited to the laser spot size, the detection limit is approximately tenfold higher (∼5 µg/cm2) due to the impact of UV photochemistry.

Asymmetric free-standing 2-D photonic crystal films and their Janus particles.

We report the fabrication of large area, thin asymmetric free-standing two-dimensional (2-D) photonic crystals. We fabricate large area 2-D close-packed monodisperse polystyrene (PS) particle monolayers at air/water interfaces by using our needle tip flow method. We then layer tetraethyl orthosilicate (TEOS) onto the 2-D array to form a thin TEOS layer on the 2-D particle array on water. The hemispheres of PS particles located within the TEOS phase swell such that the adjacent particle hemispheres fuse. After TEOS evaporation, we obtain a free-standing connected photonic crystal film of hemispheres that efficiently diffracts light. The other side of the photonic crystal film consists of a fused connecting thin, flat sheet. Reactive ion etching (RIE) of the asymmetric films forms unusual, rough particle 2-D arrays and 2-D flower-like arrays. Mechanical abrasion allows one to separate the resulting novel Janus particles.

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.

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 ß-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 ß-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 ß-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.

Two-dimensional photonic crystal surfactant detection.

We developed a novel two-dimensional (2-D) crystalline colloidal array photonic crystal sensing material for the visual detection of amphiphilic molecules in water. A close-packed polystyrene 2-D array monolayer was embedded in a poly(N-isopropylacrylamide) (PNIPAAm)-based hydrogel film. These 2-D photonic crystals placed on a mirror show intense diffraction that enables them to be used for visual determination of analytes. Binding of surfactant molecules attaches ions to the sensor that swells the PNIPAAm-based hydrogel. The resulting increase in particle spacing red shifts the 2-D diffracted light. Incorporation of more hydrophobic monomers increases the sensitivity to surfactants.

Resonance Raman spectra of TNT and RDX using vibronic theory, excited-state gradient, and complex polarizability approximations.

Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.

DNA-Crosslinked 2D Photonic Crystal Hydrogels for Detection of Adenosine Actuated by an Adenosine-Binding Aptamer.

There is a need to develop versatile sensing motifs that can be used to detect a variety of chemical targets in resource-limited settings, for example, at the point of care. While numerous sensing technologies have been developed toward this effort, these technologies can be overly complex and require a skilled technician, extensive sample preparation, or sophisticated instrumentation to use, limiting their generalizability and application in resource-limited settings. Here, we report a novel sensing motif that utilizes DNA-crosslinked two-dimensional photonic crystal (2DPC) hydrogels. These hydrogel sensors contain a DNA aptamer recognition group that binds a target analyte. As proof of concept, we fabricated 2DPC hydrogels using a well-studied adenosine-binding aptamer. This adenosine aptamer is duplexed with a partially complementary strand and forms responsive crosslinks in the hydrogel polymer network. When adenosine is introduced, aptamer-adenosine binding occurs, breaking the DNA crosslinks and causing the hydrogel to swell. This in turn increases the particle spacing of an embedded 2DPC array, shifting the 2DPC Bragg diffraction. Thus, adenosine concentration can be monitored through 2DPC Bragg diffraction measurements. A linear range of 20 µM to 2 mM was observed. The detection limits were calculated to be 13.9 µM in adenosine-binding buffer and 26.7 µM in fetal bovine serum. This reported sensing motif has a readout that is simple and rapid and requires minimal equipment. We hypothesize that this sensing motif is generalizable and that other sensors can be easily fabricated by simply exchanging the aptamer that serves as a molecular recognition group.

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.