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At least 163 records · Page 9

In situ temperature synthesis and characterization of ferroelectric PZN-4.5PT nanoparticles’ thin films using synchrotron light source

Despite the excellent properties of Pb(Zn 1/3 Nb 2/3 )O 3 -4.5PbTiO 3 (PZN-4.5PT) single crystals, the greatest difficulty for their application on electronic devices is to make them to thin layers related to the difficulty to make them as ceramic materials. In this paper, we use the combined USAXS/SAXS/WAXS instrument at 9ID beamline at APS-ANL for in situ characterization of PZN-4.5PT inorganic perovskite nanoparticles thin films deposited on nanotextured silicon to understand the phase transitions and determine the observed microcrystals' structure. Here, the sample was annealed from ambient to 1000°C. The results revealed structure changes in the nanoparticles' thin films which could be explained by the new phase that can be assigned to the Pb 3 (PO 4 )2-based component. The peak at 31° indicates the presence of the rhombohedral phase perovskites assigned to the nanoparticles. WAXS characterization permitted to identification of many transitions during thermal annealing like dehydration or dihydroxylation of phosphorus gel -OH bonds and internal water.

36 MATERIALS SCIENCE↗

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Fungal Trl1 is an essential tRNA splicing enzyme composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that convert the 2′,3′-cyclic-PO 4 and 5′-OH ends of tRNA exons into the 3′-OH,2′-PO 4 and 5′-PO 4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trifunctional Trl1 enzymes are present in most human fungal pathogens and are untapped targets for antifungal drug discovery. Mucorales species, deemed high-priority human pathogens by WHO, elaborate a noncanonical tRNA splicing apparatus in which a stand-alone monofunctional RNA ligase enzyme joins 3′-OH,2′-PO 4 and 5′-PO 4 termini. Here we identify a stand-aloneMucor circinelloidespolynucleotide kinase (MciKIN) and affirm its biological activity in tRNA splicing by genetic complementation in yeast. Recombinant MciKIN catalyzes magnesium-dependent phosphorylation of 5′-OH RNA and DNA ends in vitro. MciKIN displays a strong preference for GTP as the phosphate donor in the kinase reaction, a trait shared with the stand-alone RNA kinase homologs from Mucorales speciesRhizopus azygosporus(RazKIN) andLichtheimia corymbifera(LcoKIN) and with the kinase domains of fungal Trl1 enzymes. We report a 1.65 Å crystal structure of RazKIN in complex with GDP•Mg 2+ that illuminates the basis for guanosine nucleotide specificity.

Biochemistry & Molecular Biology↗

Zoology of Multiple- Q Spin Textures in a Centrosymmetric Tetragonal Magnet with Itinerant Electrons

Magnetic skyrmion is a topologically stable particle-like swirling spin texture potentially suitable for high-density information bit, which was first observed in noncentrosymmetric magnets with Dzyaloshinskii–Moriya interaction. Recently, nanometric skyrmion has also been discovered in centrosymmetric rare-earth compounds, and the identification of their skyrmion formation mechanism and further search of nontrivial spin textures are highly demanded. Here, magnetic structures in a prototypical skyrmion-hosting centrosymmetric tetragonal magnet GdRu2Si2 is exhaustively studied by performing the resonant X-ray scattering experiments. A rich variety of double-Q magnetic structures, including the antiferroic order of meron(half-skyrmion)/anti-meron-like textures with fractional local topological charges are identified. The observed intricate magnetic phase diagram is successfully reproduced by the theoretical framework considering the four-spin interaction mediated by itinerant electrons and magnetic anisotropy. The present results will contribute to the better understanding of the novel skyrmion formation mechanism in this centrosymmetric rare-earth compound, and suggest that itinerant electrons can ubiquitously host a variety of unique multiple-Q spin orders in a simple crystal lattice system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analysis of Phase Separation in Czochralski Grown Single Crystal Ilmenite

Ilmenite (FeTiOs) is a wide bandgap semiconductor with an energy gap of 2.58 eV. Ilmenite has properties suited for radiation tolerant applications, as well as a variety of other electronic applications. Single crystal ilmenite has been grown from the melt using the Czochralski method. Growth conditions have a profound effect on the microstructure of the samples. Here we present data from a variety of analytical techniques which indicate that some grown crystals exhibit distinct phase separation during growth. This phase separation is apparent for both post-growth annealed and unannealed samples. Under optical microscopy, there appear two distinct areas forming a matrix with an array of dots on order of 5 pm diameter. While appearing bright in the optical micrograph, atomic force microscope (AFM) shows the dots to be shallow pits on the surface. Magnetic force microscope (MFM) shows the dots to be magnetic. Phase identification via electron microprobe analysis (EMPA) indicates two major phases in the unannealed samples and four in the annealed samples, where the dots appear to be almost pure iron. This is consistent with micrographs taken with a scanning probe microscope used in the magnetic force mode. Samples that do not exhibit the phase separation have little or no discernible magnetic structure detectable by the MFM.

Wilkins, R.↗

Cryo-electron Microscopy of Adeno-associated Virus

Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.

59 BASIC BIOLOGICAL SCIENCES↗

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗

Anisotropic Phonon Response of Few-Layer PdSe 2 under Uniaxial Strain

PdSe 2 , an emerging 2D material with a novel anisotropic puckered pentagonal structure, has attracted growing interest due to its layer-dependent electronic bandgap, high carrier mobility, and good air stability. In this work, a detailed Raman spectroscopic study of few-layer PdSe 2 (two to five layers) under the in-plane uniaxial tensile strain up to 3.33% is performed. Two of the prominent PdSe 2 Raman peaks are influenced differently depending on the direction of strain application. Additionally, the A g 1 mode redshifts more than the A g 3 mode when the strain is applied along the a -axis of the crystal, while the A g 3 mode redshifts more than the A g 1 mode when the strain is applied along the b -axis. Such an anisotropic phonon response to strain indicates directionally dependent mechanical and thermal properties of PdSe 2 and also allows the identification of the crystal axes. The results are further supported using first-principles density-functional theory. Interestingly, the near-zero Poisson’s ratios for few-layer PdSe 2 are found, suggesting that the uniaxial tensile strain can easily be applied to few-layer PdSe 2 without significantly altering their dimensions at the perpendicular directions, which is a major contributing factor to the observed distinct phonon behavior. The findings pave the way for further development of 2D PdSe 2 -based flexible electronics.

36 MATERIALS SCIENCE↗

Optimization of the first CUPID detector module

CUPID will be a next generation experiment searching for the neutrinoless double β decay, whose discovery would establish the Majorana nature of the neutrino. Based on the experience achieved with the CUORE experiment, presently taking data at LNGS, CUPID aims to reach a background free environment by means of scintillating Li 2 100 MoO 4 crystals coupled to light detectors. Indeed, the simultaneous heat and light detection allows us to reject the dominant background of α particles, as proven by the CUPID-0 and CUPID-Mo demonstrators. In this work we present the results of the first test of the CUPID baseline module. In particular, we propose a new optimized detector structure and light sensors design to enhance the engineering and the light collection, respectively. We characterized the heat detectors, achieving an energy resolution of (5.9 ± 0.2) keV FWHM at the Q-value of 100 Mo (about 3034 keV). We studied the light collection of the baseline CUPID design with respect to an alternative configuration which features gravity-assisted light detectors’ mounting. In both cases we obtained an improvement in the light collection with respect to past measures and we validated the particle identification capability of the detector, which ensures an α particle rejection higher than 99.9%, fully satisfying the requirements for CUPID.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Direct Analysis of Early Solar System Aqueous Fluids

We lack fundamental information on early solar system aqueous fluids. Fluid inclusions are present in carbonates, sulfides and halides in astro materials, whose characterization is finally becoming feasible. The ordinary chondrite regolith breccias Monahans 1998 (H5) and Zag (H3-6)contain fluid inclusion-bearing halite (NaCl) crystals dated at~4.5 billion years old. Freezing studies to measure the eutectic temperature demonstrated that the brines likely contain divalent cations(Ca, Mg, Fe). Halite is effective at preservation (at least 250 MY) of organic phases and structures. Thus, compositional data on fluid inclusions in halite will reveal unique information on the origin and activity of aqueous fluids in the early solar system, and interactions with organics. To measure fluid compositions from individual fluid inclusions we performed TOF-SIMS depth profiling a tultra-high vacuum at ~110 Kusing a 30 kVBi+analysis ion beam and a1 kVO2+sputtering ion beam. Halite fluid inclusion FI1 contains H2O, K,Na,Cl and NaCl•2H2O.FI2 contains H2O, K, Na, Cl, Al, Fe,Ca,NaCl•2H2O and C-N-O-H species originating from organic molecules. Mass overlap with NaOH species prevented definitive identification of Cain FI1.

M. E Zolensky↗

CEGANN: CRYSTAL EDGE GRAPH ATTENTION NEURAL NETWORK

SF-22-156 Machine learning (ML) models and applications in materials design and discovery typically involve the use of feature representations or descriptors followed by a learning algorithm that maps them to user desired properties of interest. Most popular mathematical formulation-based descriptors are not unique across atomic environments and suffer from transferability issues across different application domains and/or material classes. The CEGANN code provides a unified interface to facilitate material characterization across materials across multiple scales (from atomic to mesoscale) and diverse classes of materials ranging from metals oxides, non-metals, and even hierarchical materials such as zeolites and semi ordered materials such as mesophases. CEGANN implements a Graph Attention Network (GAT) type convolution architecture. The details of network architecture can be found in the paper https://doi.org/10.48550/arXiv.2207.10168. The software comes with pretrained examples and dataset for the classification of the following representative systems: (1) Structure-level representation such as space group (2) Structural dimensionality (e.g., bulk, 2D, clusters etc.) (3) Grain boundary identification (4) Nucleation and growth of a zeolite polymorph (5) Characterization of binary mesophases and their phase transitions (6) Growth of ice. The code is written in python programming language.

CHAN, HENRYT↗

Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho

Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, the FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, burosumab. Small-molecule drugs that disrupt protein/protein interactions necessary for the ternary complex formation offer an alternative to disrupting FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein/protein interaction inhibitors since it was computationally predicted to have a large fraction of hot spots and two druggable residues on α-Klotho. We further identified Tyr433 on the KL1 domain of α-Klotho as a promising hot spot and α-Klotho as an appropriate drug-binding target at this interface. Subsequently, we performed in silico docking of ~5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 24 and 20 compounds were in the final list based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, respectively. Herein, five compounds were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities in vitro, and two of these reduced activities significantly. Both these compounds were predicted to have favorable binding affinities to α-Klotho but not have a large number of contacts with the hot spot Tyr433. ZINC12409120 was found experimentally to disrupt FGF23:α-Klotho interaction to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC50) of 5.0 ± 0.23 μM. Molecular dynamics (MD) simulations of the ZINC12409120:α-Klotho complex starting from in silico docking poses reveal that the ligand exhibits contacts with residues on the KL1 domain, the KL1–KL2 linker, and the KL2 domain of α-Klotho simultaneously, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23:α-Klotho interaction. ZINC12409120 is a candidate for lead optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗

Roadmap for Photonics with 2D Materials

Triggered by advances in atomic-layer exfoliation and growth techniques, along with the identification of a wide range of extraordinary physical properties in self-standing films consisting of one or a few atomic layers, two-dimensional (2D) materials such as graphene, transition metal dichalcogenides (TMDs), and other van der Waals (vdW) crystals now constitute a broad research field expanding in multiple directions through the combination of layer stacking and twisting, nanofabrication, surface-science methods, and integration into nanostructured environments. Photonics encompasses a multidisciplinary subset of those directions, where 2D materials contribute remarkable nonlinearities, long-lived and ultraconfined polaritons, strong excitons, topological and chiral effects, susceptibility to external stimuli, accessibility, robustness, and a completely new range of photonic materials based on layer stacking, gating, and the formation of moiré patterns. These properties are being leveraged to develop applications in electro-optical modulation, light emission and detection, imaging and metasurfaces, integrated optics, sensing, and quantum physics across a broad spectral range extending from the far-infrared to the ultraviolet, as well as enabling hybridization with spin and momentum textures of electronic band structures and magnetic degrees of freedom. The rapid expansion of photonics with 2D materials as a dynamic research arena is yielding breakthroughs, which this Roadmap summarizes while identifying challenges and opportunities for future goals and how to meet them through a wide collection of topical sections prepared by leading practitioners.

2D materials↗

A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1

The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM (“SAR by X-ray Poses Quickly”) platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or “undruggable” targets, allows for (i) hit generation; (ii) the mapping of protein–ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.

59 BASIC BIOLOGICAL SCIENCES↗

DC-8 Scanning Lidar Characterization of Aircraft Contrails and Cirrus Clouds

An angular-scanning large-aperture (36 cm) backscatter lidar was developed and deployed on the NASA DC-8 research aircraft as part of the SUCCESS (Subsonic Aircraft: Contrail and Cloud Effects Special Study) program. The lidar viewing direction could be scanned continuously during aircraft flight from vertically upward to forward to vertically downward, or the viewing could be at fixed angles. Real-time pictorial displays generated from the lidar signatures were broadcast on the DC-8 video network and used to locate clouds and contrails above, ahead of, and below the DC-8 to depict their spatial structure and to help select DC-8 altitudes for achieving optimum sampling by onboard in situ sensors. Several lidar receiver systems and real-time data displays were evaluated to help extend in situ data into vertical dimensions and to help establish possible lidar configurations and applications on future missions. Digital lidar signatures were recorded on 8 mm Exabyte tape and generated real-time displays were recorded on 8mm video tape. The digital records were transcribed in a common format to compact disks to facilitate data analysis and delivery to SUCCESS participants. Data selected from the real-time display video recordings were processed for publication-quality displays incorporating several standard lidar data corrections. Data examples are presented that illustrate: (1) correlation with particulate, gas, and radiometric measurements made by onboard sensors, (2) discrimination and identification between contrails observed by onboard sensors, (3) high-altitude (13 km) scattering layer that exhibits greatly enhanced vertical backscatter relative to off-vertical backscatter, and (4) mapping of vertical distributions of individual precipitating ice crystals and their capture by cloud layers. An angular scan plotting program was developed that accounts for DC-8 pitch and velocity.

Uthe, Edward E.↗

Resolving atomistic structure and oxygen evolution activity in nickel antimonates

The oxygen evolution reaction (OER) requires electrodes that are not only catalytically active, but also stable under harsh electrochemical environments to enable efficient, durable technologies. Our recent report of a stable amorphous Ni 0.5 Sb 0.5 O z OER photoanode established Ni–Sb–O as an important system for computational understanding of both the structural and catalytic behavior of these complex oxides. In the present work we show that Ni x Sb 1-x O z with x > 0.33 crystallizes into a previously unknown phase. Guided by experimental X-ray diffraction, here, we use density functional theory calculations to perform a prototype phase search to identify a broad family of stable and metastable mixed rutile and hexagonal-like phases for x = 0.33, 0.50, and 0.66 compositions. For the identified phases, we predict favorable oxygen vacancy formation energies for Ni-rich compositions under the reducing synthesis conditions which match measured Ni K-edge X-ray absorption spectra. The calculated overpotential for the most active site decreases with increasing Ni content, from 0.91 V (x = 0.33) to 0.49 V (x = 0.66), which captures the experimentally observed trend. We find the active site changes from the Ni–O–Sb bridge to a Ni–O–Ni bridge at increasing Ni concentrations, rather than the commonly studied singly under-coordinated sites. Finally, detailed Pourbaix analysis of the identified phases show excellent electrochemical stability, consistent with experimentally measured low metal ion concentrations in the electrolyte of photoelectrochemical cells. Collectively, our consideration of an ensemble of structures enables identification of the most catalytically prolific structural motifs, aiding the understanding of crystalline and amorphous catalysts and elucidating the co-optimization of activity and durability in nickel antimonates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗