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1. Raman spectroscopy study of manganese oxides: Layer structures

   https://doi.org/10.2138/am-2021-7666  

   Post, Jeffrey E. ; McKeown, David A. ; Heaney, Peter J. ( March 2021 , American Mineralogist)

   null (Ed.)

   Abstract Raman spectra were collected for an extensive set of well-characterized layer-structure Mn oxide mineral species (phyllomanganates) employing a range of data collection conditions. We show that the application of various laser wavelengths, such as 785, 633, and 532 nm, at low power levels (30–500 μW) in conjunction with the comprehensive database of standard spectra presented here, makes it possible to distinguish and identify the various phyllomanganate minerals. The Raman mode relative intensities can vary significantly as a function of crystal orientation relative to the incident laser light polarization direction as well as incident laser light wavelength. Consequently, phase identification success is enhanced when using a standards database that includes multiple spectra collected for different crystal orientations and with different laser light wavelengths. The position of the highest frequency Raman mode near 630–665 cm–1 shows a strong linear correlation with the fraction of Mn3+ in the octahedral Mn sites. With the comprehensive Raman database of well-characterized Mn oxide standards provided here (and available online as Online Material1), and use of appropriate data collection conditions, micro-Raman is a powerful tool for identification and characterization of biotic and abiotic Mn oxide phases from diverse natural settings, including on other planets, as well as for laboratory and industrial materials. 

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2. Equation of State of TiN at High Pressures and Temperatures: A Possible Host for Nitrogen in Planetary Mantles

   https://doi.org/10.1029/2020JB020074  

   Daviau, Kierstin ; Fischer, Rebecca A. ; Brennan, Matthew C. ; Dong, Junjie ; Suer, Terry‐Ann ; Couper, Samantha ; Meng, Yue ; Prakapenka, Vitali B. ( January 2021 , Journal of Geophysical Research: Solid Earth)

   Nitrogen, the most abundant element in Earth's atmosphere, is also a primary component of solid nitride minerals found in meteorites and on Earth's surface. If they remain stable to high pressures and temperatures, these nitrides may also be important reservoirs of nitrogen in planetary interiors. We used synchrotron X‐ray diffraction to measure the thermal equation of state and phase stability of titanium nitride (TiN) in a laser‐heated diamond anvil cell at pressures up to ∼70 GPa and temperatures up to ∼2,500 K. TiN maintains the cubic B1 (NaCl‐type) crystal structure over the entire pressure and temperature range explored. It hasK₀ = 274 (4) GPa,K₀′ = 3.9 (2), andγ₀ = 1.39 (4) for a fixedV₀ = 76.516 (30) ų(based on experimental measurements),q = 1, andθ₀ = 579 K. Additionally, we collected Raman spectra of TiN up to ∼60 GPa, where we find that the transverse acoustic (TA), longitudinal acoustic (LA), and transverse optical phonon modes exhibit mode Grüneisen parameters of 1.66(17), 0.54(15), and 0.93 (4), respectively. Based on our equation of state, TiN has a density of ∼5.6–6.4 g/cm³at Earth's lower mantle conditions, significantly more dense than both the mantle of the Earth and the estimated densities of the mantles of other terrestrial planets, but less dense than planetary cores. We find that TiN remains stable against physical decomposition at the pressures and temperatures found within Earth's mantle, making it a plausible reservoir for deep planetary nitrogen if chemical conditions allow its formation.

    

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3. In vivo imaging using surface enhanced spatially offset raman spectroscopy (SESORS): balancing sampling frequency to improve overall image acquisition

   https://doi.org/10.1038/s44303-024-00011-9  

   Nicolson, Fay ; Andreiuk, Bohdan ; Lee, Eunah ; O’Donnell, Bridget ; Whitley, Andrew ; Riepl, Nicole ; Burkhart, Deborah L. ; Cameron, Amy ; Protti, Andrea ; Rudder, Scott ; et al ( April 2024 , npj Imaging)

   In the field of optical imaging, the ability to image tumors at depth with high selectivity and specificity remains a challenge. Surface enhanced resonance Raman scattering (SERRS) nanoparticles (NPs) can be employed as image contrast agents to specifically target cells in vivo; however, this technique typically requires time-intensive point-by-point acquisition of Raman spectra. Here, we combine the use of “spatially offset Raman spectroscopy” (SORS) with that of SERRS in a technique known as “surface enhanced spatially offset resonance Raman spectroscopy” (SESORRS) to image deep-seated tumors in vivo. Additionally, by accounting for the laser spot size, we report an experimental approach for detecting both the bulk tumor, subsequent delineation of tumor margins at high speed, and the identification of a deeper secondary region of interest with fewer measurements than are typically applied. To enhance light collection efficiency, four modifications were made to a previously described custom-built SORS system. Specifically, the following parameters were increased: (i) the numerical aperture (NA) of the lens, from 0.2 to 0.34; (ii) the working distance of the probe, from 9 mm to 40 mm; (iii) the NA of the fiber, from 0.2 to 0.34; and (iv) the fiber diameter, from 100 µm to 400 µm. To calculate the sampling frequency, which refers to the number of data point spectra obtained for each image, we considered the laser spot size of the elliptical beam (6 × 4 mm). Using SERRS contrast agents, we performed in vivo SESORRS imaging on a GL261-Luc mouse model of glioblastoma at four distinct sampling frequencies: par-sampling frequency (12 data points collected), and over-frequency sampling by factors of 2 (35 data points collected), 5 (176 data points collected), and 10 (651 data points collected). In comparison to the previously reported SORS system, the modified SORS instrument showed a 300% improvement in signal-to-noise ratios (SNR). The results demonstrate the ability to acquire distinct Raman spectra from deep-seated glioblastomas in mice through the skull using a low power density (6.5 mW/mm²) and 30-times shorter integration times than a previous report (0.5 s versus 15 s). The ability to map the whole head of the mouse and determine a specific region of interest using as few as 12 spectra (6 s total acquisition time) is achieved. Subsequent use of a higher sampling frequency demonstrates it is possible to delineate the tumor margins in the region of interest with greater certainty. In addition, SESORRS images indicate the emergence of a secondary tumor region deeper within the brain in agreement with MRI and H&E staining. In comparison to traditional Raman imaging approaches, this approach enables improvements in the detection of deep-seated tumors in vivo through depths of several millimeters due to improvements in SNR, spectral resolution, and depth acquisition. This approach offers an opportunity to navigate larger areas of tissues in shorter time frames than previously reported, identify regions of interest, and then image the same area with greater resolution using a higher sampling frequency. Moreover, using a SESORRS approach, we demonstrate that it is possible to detect secondary, deeper-seated lesions through the intact skull.

    

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4. Optimizing Raman spectral collection for quartz and zircon crystals for elastic thermobarometry

   https://doi.org/10.2138/am-2022-8423  

   Cizina, Mayara F. ; Mikesell, T. Dylan ; Kohn, Matthew J. ( May 2023 , American Mineralogist: Journal of Earth and Planetary Materials)

   Abstract Raman spectroscopy is widely used to identify mineral and fluid inclusions in host crystals, as well as to calculate pressure-temperature (P-T) conditions with mineral inclusion elastic thermobarometry, for example quartz-in-garnet barometry (QuiG) and zircon-in-garnet thermometry (ZiG). For thermobarometric applications, P-T precision and accuracy depend crucially on the reproducibility of Raman peak position measurements. In this study, we monitored long-term instrument stability and varied analytical parameters to quantify peak position reproducibility for Raman spectra from quartz and zircon inclusions and reference crystals. Our ultimate goal was to determine the reproducibility of calculated inclusion pressures (“Pinc”) and entrapment pressures (“Ptrap”) or temperatures (“Ttrap”) by quantifying diverse analytical errors, as well as to identify optimal measurement conditions and provide a baseline for interlaboratory comparisons. Most tests emphasized 442 nm (blue) and 532 nm (green) laser sources, although repeated analysis of a quartz inclusion in garnet additionally used a 632.8 nm (red) laser. Power density was varied from <1 to >100 mW and acquisition time from 3 to 270s. A correction is proposed to suppress interference on the ~206 cm–1 peak in quartz spectra by a broad nearby (~220 cm–1) peak in garnet spectra. Rapid peak drift up to 1 cm–1/h occurred after powering the laser source, followed by minimal drift (<0.2 cm–1/h) for several hours thereafter. However, abrupt shifts in peak positions as large as 2–3 cm–1 sometimes occurred within periods of minutes, commonly either positively or negatively correlated to changes in room temperature. An external Hg-emission line (fluorescent light) can be observed in spectra collected with the green laser and shows highly correlated but attenuated directional shifts compared to quartz and zircon peaks. Varying power density and acquisition time did not affect Raman peak positions of either quartz or zircon grains, possibly because power densities at the levels of inclusions were low. However, some zircon inclusions were damaged at higher power levels of the blue laser source, likely because of laser-induced heating. Using a combination of 1, 2, or 3 peak positions for the ~128, ~206, and ~464 cm–1 peaks in quartz to calculate Pinc and Ptrap showed that use of the blue laser source results in the most reproducible Ptrap values for all methods (0.59 to 0.68 GPa at an assumed temperature of 450 °C), with precisions for a single method as small as ±0.03 GPa (2σ). Using the green and red lasers, some methods of calculating Ptrap produce nearly identical estimates as the blue laser with similarly good precision (±0.02 GPa for green laser, ±0.03 GPa for red laser). However, using 1- and 2-peak methods to calculate Ptrap can yield values that range from 0.52 ± 0.06 to 0.93 ± 0.16 GPa for the green laser, and 0.53 ± 0.08 GPa to 1.00 ± 0.45 GPa for the red laser. Semiquantitative calculations for zircon, assuming a typical error of ±0.25 cm–1 in the position of the ~1008 cm–1 peak, imply reproducibility in temperature (at an assumed pressure) of approximately ±65 °C. For optimal applications to elastic thermobarometry, analysts should: (1) delay data collection approximately one hour after laser startup, or leave lasers on; (2) collect a Hg-emission line simultaneously with Raman spectra when using a green laser to correct for externally induced shifts in peak positions; (3) correct for garnet interference on the quartz 206 cm–1 peak; and either (4a) use a short wavelength (blue) laser for quartz and zircon crystals for P-T calculations, but use very low-laser power (<12 mW) to avoid overheating and damage or (4b) use either the intermediate wavelength (green; quartz and zircon) or long wavelength (red; zircon) laser for P-T calculations, but restrict calculations to specific methods. Implementation of our recommendations should optimize reproducibility for elastic geothermobarometry, especially QuiG barometry and ZiG thermometry. 

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5. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

   https://doi.org/10.1107/S2052252522006418  

   Moreno-Chicano, Tadeo ; Carey, Leiah M. ; Axford, Danny ; Beale, John H. ; Doak, R. Bruce ; Duyvesteyn, Helen M. ; Ebrahim, Ali ; Henning, Robert W. ; Monteiro, Diana C. ; Myles, Dean A. ; et al ( September 2022 , IUCrJ)

   Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B. 

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