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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Tuning the Coordination Environment of Rh Single Atoms on Highly Dispersed Reducible Oxides for Enhanced Reverse Water-Gas Shift Performance

Controlling the dynamic mobility of catalyst surface active sites and their interactions with the surrounding environment is critical in generating active surfaces that directly influence the catalytic activity and selectivity. Here, we report a strategy for tailoring the dispersion and electronic environment of single atom Rh catalysts by decorating the alumina support with highly dispersed (HD) cerium and molybdenum oxides. The resulting catalysts exhibit markedly different behavior in the Reverse Water Gas Shift (RWGS) reaction. In particular, Rh/MoOx(HD)/Al2O3 maintains atomically dispersed Rh even at elevated temperatures (up to 400 °C), achieving CO selectivity of up to 100% and resists sintering via the formation of a newly developed structure featuring Rh single atoms embedded in MoOx clusters. In situ spectroscopy and microscopy analyses confirm the stabilization of Rh and the dynamic evolution of Rh–Mo coordination under reaction conditions. Our findings highlight the power of support modification in steering active site structure and activity, offering a pathway toward enhanced and tunable single atom catalysts for CO2 valorization.

CO selectivity↗
DOE OSTI2024

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solvent Effects on Catalytic Reactions and Related Phenomena at Liquid-Solid Interfaces

Catalytic reactions involve the direct interaction of reactants, intermediates and products with the catalyst surface. We not only need to control the atomic structure and electronic properties of the active site, but also explore the multiple molecular interactions that occur beyond the active site; they play an essential role in altering the binding and reactivity of surface species. In liquid-phase catalysis, solvents provide additional degrees of freedom in the design of the catalytic process for desirable activity and selectivity. Here, the multi-faceted effects of solvents have a profound impact on the catalyst performance by restricting the mass transfer to the site, tuning the chemical potential of the surface species, competing for active sites, stabilizing the initial and transition states, and causing mechanistic changes by participating in the kinetically relevant elementary steps. This review addresses the different aspects of solvent effects, using a few prototype solid-liquid interfaces to illustrate these fundamental features. Recent experimental and computational studies that provide new insight at the molecular level are examined. Solvent structures in the proximity of the catalyst surface are discussed along with their influence in molecular binding and reaction at the solid-liquid interfaces. Furthermore, opportunities to alter such a solid-liquid interaction by tuning the wettability of the catalyst surfaces are explored.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cage effects control the mechanism of methane hydroxylation in zeolites

Catalytic conversion of methane to methanol remains an economically tantalizing but fundamentally challenging goal. Current technologies based on zeolites deactivate too rapidly for practical application. Here, we found that similar active sites hosted in different zeolite lattices can exhibit markedly different reactivity with methane, depending on the size of the zeolite pore apertures. Whereas zeolite with large pore apertures deactivates completely after a single turnover, 40% of active sites in zeolite with small pore apertures are regenerated, enabling a catalytic cycle. Detailed spectroscopic characterization of reaction intermediates and density functional theory calculations show that hindered diffusion through small pore apertures disfavors premature release of CH 3 radicals from the active site after C-H activation, thereby promoting radical recombination to form methanol rather than deactivated Fe-OCH 3 centers elsewhere in the lattice.

36 MATERIALS SCIENCE↗
DOE OSTI2024

N and OH-Immobilized Cu 3 Clusters In Situ Reconstructed from Single-Metal Sites for Efficient CO 2 Electromethanation in Bicontinuous Mesochannels

Cu-based catalysts hold promise for electrifying CO 2 to produce methane, an extensively used fuel. However, the activity and selectivity remain insufficient due to the lack of catalyst design principles to steer complex CO 2 reduction pathways. Herein, we develop a concept to design carbon-supported Cu catalysts by regulating Cu active sites’ atomic-scale structures and engineering the carbon support’s mesoscale architecture. This aims to provide a favorable local reaction microenvironment for a selective CO 2 reduction pathway to methane. In situ X-ray absorption and Raman spectroscopy analyses reveal the dynamic reconstruction of nitrogen and hydroxyl-immobilized Cu 3 (N,OH-Cu 3 ) clusters derived from atomically dispersed Cu–N 3 sites under realistic CO 2 reduction conditions. The N,OH-Cu 3 sites possess moderate *CO adsorption affinity and a low barrier for *CO hydrogenation, enabling intrinsically selective CO 2 -to-CH 4 reduction compared to the C–C coupling with a high energy barrier. Importantly, a block copolymer-derived carbon fiber support with interconnected mesopores is constructed. The unique long-range mesochannels offer an H 2 O-deficient microenvironment and prolong the transport path for the CO intermediate, which could suppress the hydrogen evolution reaction and favor deep CO 2 reduction toward methane formation. Thus, the newly developed catalyst consisting of in situ constructed N,OH-Cu 3 active sites embedded into bicontinuous carbon mesochannels achieved an unprecedented Faradaic efficiency of 74.2% for the CO 2 reduction to methane at an industry-level current density of 300 mA cm –2 . In conclusion, this work explores effective concepts for steering desirable reaction pathways in complex interfacial catalytic systems via modulating active site structures at the atomic level and engineering pore architectures of supports on the mesoscale to create favorable microenvironments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural and mechanistic basis for protein glutamylation by the kinase fold

The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here, in this work, we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Highly Oxidized Oxide Surface toward Optimum Oxygen Evolution Reaction by Termination Engineering

The oxygen evolution reaction (OER) is a critical step for sustainable fuel production through electrochemistry process. Maximizing active sites of nanocatalyst with enhanced intrinsic activity, especially the activation of lattice oxygen, is gradually recognized as the primary incentive. Since the surface reconfiguration to oxyhydroxide is unavoidable for oxygen-activated transition metal oxides, developing a surface termination like oxyhydroxide in oxides is highly desirable. In this work, we demonstrate an unusual surface termination of (111)-facet Co 3 O 4 nanosheet that is exclusively containing edge-sharing octahedral Co 3+ similar to CoOOH that can perform at approximately 40 times higher current density at 1.63 V (vs RHE) than commercial RuO 2 . It is found that this surface termination has an oxidized oxygen state in contrast to standard Co-O systems, which can serve as active site independently, breaking the scaling relationship limit. Finally, this work forwards the applications of oxide electrocatalysts in the energy conversion field by surface termination engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Nature of Zirconia on a Copper Inverse Catalyst Under CO 2 Hydrogenation Conditions

The growing concern over the escalating levels of anthropogenic CO 2 emissions necessitates effective strategies for its conversion to valuable chemicals and fuels. In this research, we embark on a comprehensive investigation of the nature of zirconia on a copper inverse catalyst under the conditions of CO 2 hydrogenation to methanol. We employ density functional theory calculations in combination with the Grand Canonical Basin Hopping method, enabling an exploration of the free energy surface including a variable amount of adsorbates within the relevant reaction conditions. Our focus centers on a model three-atom Zr cluster on a Cu(111) surface decorated with various OH, O, and formate ligands, noted Zr 3 O x (OH) y (HCOO) z /Cu(111), revealing major changes in the active site induced by various reaction parameters such as the gas pressure, temperature, conversion levels, and CO 2 /H 2 feed ratios. Further, through our analysis, we have unveiled insights into the dynamic behavior of the catalyst. Specifically, under reaction conditions, we observe a large number of composition and structures with similar free energy for the catalyst, with respect to changing the type, number, and binding sites of adsorbates, suggesting that the active site should be regarded as a statistical ensemble of diverse structures that interconvert.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Adsorbate-induced adatom formation on Au-Cu bimetallic alloys and its possible consequences for CO 2 electroreduction

The adsorbate-induced formation of sub-nanometer clusters on transition-metal single crystals observed in previous high-pressure microscopic studies hinted at the in-situ formation of unique active sites even on large nanoparticle catalysts. We propose that the adatom formation energy can be used as an energetic descriptor for the initial step toward the adsorbate-induced metal-cluster formation process. This descriptor can be efficiently computed using density functional theory (DFT) calculations and applied for screening and identification of metal catalysts where this phenomenon may play an important role in generating active sites in-situ. As a proof of concept, here, we construct an adatom formation energy database for three Au x Cu y alloys (x:y = 3:1, 1:1, or 1:3) and eighteen adsorbates (H, C, N, O, F, S, Cl, Br, I, CH x , NH x (x = 1 – 3), CO, NO, and OH) commonly involved in catalytic reactions. The energetics of adatom formation were examined in all cases where the (111) terrace, (211) step-edge, and (874) kink were the sources of the adatom. We demonstrate that the presence of an adsorbate could alter not only the energetics for adatom formation but also the elemental nature of the preferred adatom being formed. Using our database, we identified promising systems which favor adsorbate-induced adatom formation under near-ambient conditions. Specifically, CO-induced adatom formation on all three Au-Cu alloy surfaces could occur under CO 2 electroreduction (CO 2 RR) conditions. This phenomenon offers a qualitative explanation for the experimentally observed CO 2 RR activity on Au-Cu alloy catalysts. As a result, our methodology offers an easily expandable and efficient approach for large-scale catalyst screening with regards to adatom/cluster formation under reaction conditions and provides insight into the possible nature of active sites on alloy catalysts from a novel perspective.

Active site↗
DOE OSTI2022

Role of Molecular Simulations in the Design of Metal–Organic Frameworks for Gas-Phase Thermocatalysis: A Perspective

Here, metal organic frameworks (MOFs) are highly tunable porous crystalline solids with spatially and electronically isolated catalytically active sites that have been demonstrated for a variety of thermo-, redox-, and photocatalytic reactions. Their tunable natures and relatively well-defined active sites make them advantageous for catalyst design, and molecular simulations have proven highly valuable in this endeavor. However, complexities in the MOF structure require advanced simulation strategies that accurately capture quantum chemistry at the strongly correlated transition metal cation active sites, compositional and structural changes caused by finite temperature and pressure reaction conditions, and transport effects in variously sized pore environments. Luckily, several groups have started using such simulation strategies, paving the way for rich opportunities to design MOF catalysts. Herein, we highlight such examples and provide a perspective on the needs for molecular simulations in the design of MOF catalysts moving forward.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Mechanistic Studies of Continuous Partial Methane Oxidation on Cu−Zeolites Using Kinetic and Spectroscopic Methods

Abstract Over the past few decades, a significant amount of research effort has focused on investigating the active site requirements and reaction mechanisms for partial methane oxidation (PMO) to methanol over copper–exchanged zeolites during stoichiometric and stepwise chemical looping routes. More recently, research efforts have expanded to include investigating the PMO reaction in a continuous catalytic regime, primarily focusing on determining the influence of catalyst composition on Cu speciation and structure and, in turn, on PMO rate and selectivity. The structures of candidate Cu active sites are commonly studied using a combination of ex situ and in situ spectroscopic approaches. In this perspective, we critically examine the prior literature on catalytic PMO over Cu–zeolites to identify key knowledge gaps that remain in our understanding as motivation for future research efforts. We identify opportunities for future research to address these gaps by adapting analogous interrogation techniques that have been successfully used to elucidate the active site requirements and mechanistic details of another catalytic redox reaction cycle on Cu–zeolites, the selective catalytic reduction (SCR) of nitrogen oxides (NO x ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity

Immune checkpoint blockade is effective for some patients with cancer, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour cells or immune cells promotes anti-tumour immunity. However, phosphatases are challenging drug targets; in particular, the active site has been considered undruggable. Here we present the discovery and characterization of ABBV-CLS-484 (AC484), a first-in-class, orally bioavailable, potent PTPN2 and PTPN1 active-site inhibitor. AC484 treatment in vitro amplifies the response to interferon and promotes the activation and function of several immune cell subsets. In mouse models of cancer resistant to PD-1 blockade, AC484 monotherapy generates potent anti-tumour immunity. We show that AC484 inflames the tumour microenvironment and promotes natural killer cell and CD8 + T cell function by enhancing JAK–STAT signalling and reducing T cell dysfunction. Inhibitors of PTPN2 and PTPN1 offer a promising new strategy for cancer immunotherapy and are currently being evaluated in patients with advanced solid tumours (ClinicalTrials.gov identifier NCT04777994). More broadly, our study shows that small-molecule inhibitors of key intracellular immune regulators can achieve efficacy comparable to or exceeding that of antibody-based immune checkpoint blockade in preclinical models. Finally, to our knowledge, AC484 represents the first active-site phosphatase inhibitor to enter clinical evaluation for cancer immunotherapy and may pave the way for additional therapeutics that target this important class of enzymes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Unraveling Dimensional Tuning: From 2D to 3D in Covalent Organic Frameworks for Enhanced 2e – Oxygen Reduction Reaction

Covalent organic frameworks (COFs) with a two-dimensional (2D) topology have recently emerged as promising catalyst systems for the electrosynthesis of hydrogen peroxide (H 2 O 2 ) from oxygen (O 2 ). However, designing 2D catalysts to achieve higher H 2 O 2 selectivity presents a significant challenge because of the extensive layer stacking and the aggregated active sites located in the basal planes. It results in lower atom utilization, which requires attention. In this study, we present two functionally similar COFs: one with a 2D rhombus topology (2D@BT_TPA-COF) and another with a three-dimensional (3D) noninterpenetrated pts topology (3D@BT_TPA-COF). Both COFs were utilized for the 2e – oxygen reduction reaction (2e – ORR). Tunning the dimensionality from 2D to 3D resulted in an increase in H 2 O 2 selectivity from approximately ~56% to approximately ~96% (at 0.4 V) and a rise in the turnover frequency (TOF) from 0.05 to 0.08 s –1 at 0.3 V. Nonaggregated active site distribution over 3D topology, featuring higher active site exposure, provides better access to the O 2 /electrolyte and facilitates electron transfer leading to higher 2e – ORR activity and selectivity compared to the 2D counterpart.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa

Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp 215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.

Science & Technology - Other Topics↗
DOE OSTI2020

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Atomically dispersed metal–nitrogen–carbon catalysts for fuel cells: advances in catalyst design, electrode performance, and durability improvement

The urgent need to address the high-cost issue of proton-exchange membrane fuel cell (PEMFC) technologies, particularly for transportation applications, drives the development of simultaneously highly active and durable platinum group metal-free (PGM-free) catalysts and electrodes. The past decade has witnessed remarkable progress in exploring PGM-free cathode catalysts for the oxygen reduction reaction (ORR) to overcome sluggish kinetics and catalyst instability in acids. Among others, scientists have identified the newly emerging atomically dispersed transition metal (M: Fe, Co, or/and Mn) and nitrogen co-doped carbon (M–N–C) catalysts as the most promising alternative to PGM catalysts. Here, we provide a comprehensive review of significant breakthroughs, remaining challenges, and perspectives regarding the M–N–C catalysts in terms of catalyst activity, stability, and membrane electrode assembly (MEA) performance. A variety of novel synthetic strategies demonstrated effectiveness in improving intrinsic activity, increasing active site density, and attaining optimal porous structures of catalysts. Rationally designing and engineering the coordination environment of single metal MN x sites and their local structures are crucial for enhancing intrinsic activity. Increasing the site density relies on the innovative strategies of restricting the migration and agglomeration of single metal sites into metallic clusters. Relevant understandings provide the correlations among the nature of active sites, nanostructures, and catalytic activity of M–N–C catalysts at the atomic scale through a combination of experimentation and theory. Current knowledge of the transferring catalytic properties of M–N–C catalysts to MEA performance is limited. Rationally designing morphologic features of M–N–C catalysts play a vital role in boosting electrode performance through exposing more accessible active sites, realizing uniform ionomer distribution, and facilitating mass/proton transports. We outline future research directions concerning the comprehensive evaluation of M–N–C catalysts in MEAs. The most considerable challenge of current M–N–C catalysts is the unsatisfied stability and rapid performance degradation in MEAs. Therefore, we further discuss practical methods and strategies to mitigate catalyst and electrode degradation, which is fundamentally essential to make M–N–C catalysts viable in PEMFC technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗