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At least 235 records · Page 13

Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary Flexibility and Rigidity in the Bacterial Methylerythritol Phosphate (Mep) Pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

Bailey Marshall↗

USc 2 C 2 and USc 2 NC Clusters with U–C Triple Bond Character Stabilized Inside Fullerene Cages

The chemistry of f-block metal–carbon multiple bonds is underdeveloped compared to well-established carbene complexes of the d-block transition metals. Herein, we report two new actinide-rare earth mixed metal carbides and nitrogen carbide cluster fullerenes, USc 2 C 2 @D 5h (6)-C 80 and USc 2 NC@D 5h (6)-C 80 , which contain U–C bonds with triple bond character and were successfully synthesized and characterized by mass spectrometry, UV–vis–NIR spectroscopy, Fourier transform infrared spectroscopy, single crystal X-ray diffraction, and DFT calculations. Crystallographic studies show that the two previously unreported clusters, USc 2 C 2 and USc 2 NC, are stabilized in the D 5h (6)-C 80 carbon cage and adopt unique trifoliate configurations, in which C 2 /NC units are almost vertically inserted into the plane defined by the U and two Sc atoms. Combined experimental and theoretical studies further reveal the bonding structure of USc 2 C 2 and USc 2 NC, which contain C=U(VI)=C and C=U(V)=N bonding motifs. The electronic structures of the two compounds are determined as U 6+ (Sc 2 ) 6+ (C 4– ) 2 @D 5h (6)-C 80 4– and U 5+ (Sc 2 ) 6+ (N) 3– (C) 4– @D 5h (6)-C 80 4– , respectively. Quantum-chemical studies confirm that the U–C bonds in both molecules show unprecedented multicenter triple-bond character. Furthermore, the discovery of this unique U–C multiple bond offers a deeper understanding of the fundamentals of uranium chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pertechnetate/perrhenate–capped Zr/Hf–Dihydroxide Dimers: Elucidating Zr–TcO 4 Co–Mobility in the Nuclear Fuel Cycle

Spent nuclear fuel contains heavy element fission products that must be separated for effective reprocessing for a safe and sustainable nuclear fuel cycle. 93 Zr and 99 Tc are high-yield fission products that co-transport in liquid-liquid extraction processes. Here we seek atomic-level information of this co-extraction process, as well as fundamental knowledge about Zr IV (and Hf IV ) aqueous speciation in the presence of topology-directing ligands such as pertechnetate (TcO 4 – ) and non-radioactive surrogate perrhenate (ReO 4 – ). In this context, we show that the flat tetrameric oxyhydroxyl-cluster [M IV 4 (OH) 8 (H 2 O) 16 ] 8+ (and related polymers) is dissociated by perrhenate/pertechnetate to yield isostructural dimers, M 2 (OH) 2 (XO 4 – ) 6 (H 2 O) 6 • 3H 2 O (M=Zr/Hf IV ; X=Re/Tc VII ), elucidated by single-crystal X-ray diffraction. We used these model compounds to understand the pervasive 93 Zr- 99 Tc coextraction with further speciation studies in water, nitric acid, and tetrabutylphosphate (TBP) -kerosene; where the latter two media are relevant to nuclear fuel reprocessing. SAXS (small angle X-ray scattering), compositional evaluation, and where experimentally feasible, ESI-MS (electrospray ionization mass spectrometry) showed that perrhenate/pertechnetate influence Zr/Hf IV -speciation in water. Here, in Zr-XO 4 solvent extraction studies to simulate fuel reprocessing, we provide evidence that TcO 4 – enhances extraction of Zr IV , and compositional analysis of the extracted metal-complexes (Zr-ReO 4 study) is consistent with the crystallized Zr IV 2 (OH) 2 (Re VII O 4 – ) 6 (H 2 O) 6 •dimer.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Irradiation damage reduces alloy corrosion rate via oxide space charge compensation effects

Radiation effects in materials often compound and accelerate other detrimental phenomena such as embrittlement, oxidation and creep. However, irradiation can also decrease the oxidation rate, for instance with ZrNb alloys nuclear fuel cladding. In this study, we rationalize this observation on Zr-0.5Nb alloy by introducing a mechanism based on oxide space charge modification, resulting from irradiation enhanced Nb clustering. Here, this mechanism is investigated using a multiscale approach: from the macroscale, to determine post-irradiation oxidation kinetics, to the atomic scale, using in-situ atom probe tomography sample oxidation, to observe elemental solute redistribution across the oxide/metal interface. The mechanism is further supported by high resolution transmission electron microscopy characterization and density functional theory calculations. A point defect model is proposed to account for oxide space charge effects and their changes under irradiation. This integrated, multiscale experimental and modeling approach challenges the current paradigm on irradiation effects and how they can potentially improve materials performance in extreme environments.

36 MATERIALS SCIENCE↗

Formation of carbon homonuclear bonds in β-SiC under neutron irradiation at various temperatures and neutron doses

To elucidate radiation defect processes in SiC, Raman spectroscopy was systematically applied to high-purity, polycrystalline β-SiC that was neutron irradiated at a range of temperature and dose conditions. The analysis specifically focused on formation of carbon homonuclear bonds by irradiation; these bonds were indicated by D and G bands and amorphous carbon peaks. Intensity of the carbon peaks relative to SiC peaks significantly decreased in the case of high temperature and/or high neutron dose of 500 °C to 29 displacements per atom (dpa) and about 800 °C to 1.38 and 29 dpa. The absence of carbon bond peaks under those conditions was explained by growth of stoichiometric defect clusters, consistent with previous atomistic simulations on SiC defect stability. The lack of Raman bands associated with carbon clusters under high-temperature and high-dose radiation conditions accounts for the resistance of SiC to phase separation under irradiation. The findings further suggest that material compositions and chemical properties that are inherently resistant to chemical disordering under high-dose radiation conditions are indicative of the long-term durability of ceramic compounds in radiation environments.

36 MATERIALS SCIENCE↗

Beyond Simple Dilution: Superior Conductivities from Cosolvation of Acetonitrile/LiTFSI Concentrated Solution with Acetone

Concentrated solutions of Li salts in acetonitrile are promising alternative electrolytes for the next generation of Li batteries as they may exhibit superior electrochemical properties. However, the reduced mobility of the chemical species is a barrier yet to be overcome, and for this, we explore the utilization of acetone as a cosolvent. Although acetone is a polar compound, we find that its addition to the LiTFSI/acetonitrile solution does not follow the trends expected for a simple dilution process. At a low concentration, acetone subtly shifts acetonitrile from the first to extended solvation sheaths of the ions. Still, most of the original structure of the solution is preserved, and mobile high-concentration clusters are formed in the solution. At higher concentrations, the cosolvation promotes cation–anion interactions but with a different nature from those in the original solution and still allows for a further increase in conductivity. Additionally, the non-coordinating fraction of acetonitrile acquires features resembling the pure solvent, which is a possible additional facilitating factor for ionic diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. Finally, the expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.

59 BASIC BIOLOGICAL SCIENCES↗

Thiohalorhabdus methylotropha sp. nov., an extremely halophilic autotrophic methylotiotroph from hypersaline lakes

So far, there have been no reports of trimethylamine (TMA)-utilizing extremely halophilic microorganisms in hypersaline habitats. Our aerobic enrichments at 4 M total Na + with 5 mM TMA inoculated with surface sediments from hypersaline soda (at pH 9.5) or chloride-sulfate (at pH 7) lakes in southwestern Siberia were successful only for the latter. The initial enrichment included both bacteria and haloarchaea but only the bacterial component was able to grow as a pure culture with TMA. Strain Cl-TMA forms a new-species lineage within the genus Thiohalorhabdus which includes extremely halophilic and obligate lithoautotrophic sulfur-oxidizing gammaproteobacteria. Cl-TMA can grow methyloautotrophically utilizing TMA, dimethylamine (DMA) and methanol (MeOH) as the electron donors or chemolithoautotrophically with thiosulfate. Mixotrophic growth was also observed with the three methyl compounds and thiosulfate. Carbon is assimilated autotrophically via the Calvin-Benson-Basham pathway. Unlike the type species of Thiohalorhabdus, T. denitrificans , Cl-TMA was incapable of anaerobic growth via denitrification. The isolate belongs to extreme halophiles growing between 2.5 and 5 M NaCl with an optimum at 3–3.5 M. Genome analysis identified two gene clusters coding for PQQ-dependent methanol dehydrogenases (MxaFI and XoxF), four homologues of the formaldehyde activating enzymes (Faes), a TMA/DMA oxidation locus, and two cluster of genes encoding an N-methylglutamate dehydrogenase pathway (NMGP) for methylamine oxidation. The first steps of C 1 -subtrate conversions are followed by the tetrahydrofolate (THF)-linked and tetrahydromethanopterin (H4MPT)-linked formaldehyde oxidation pathways and two formate dehydrogenases. All of those signatures of methylotrophy were absent in T. denitrificans . In contrast, genes for two key sulfur oxidation enzymes, thiosulfate dehydrogenase TsdAB and sulfide dehydrogenase FccAB, that are present in the type species are missing in Cl-TMA. Thiosulfate is oxidized to sulfate by a combination of an incomplete Sox cycle and an sHdr system. Strain Cl-TMA T (JCM 35977 = UQM 41915) is proposed to be classified as Thiohalorhabdus methylotrophus sp. nov.

59 BASIC BIOLOGICAL SCIENCES↗

Unraveling the Formation Mechanism of a Hybrid Zr-Based Chemical Conversion Coating with Organic and Copper Compounds for Corrosion Inhibition

Environmental-friendly chromate-free, zirconium (Zr)-based conversion coating is a promising green technology for corrosion protection. Additives in the surface treatment provides critical functionalities and performance improvements; however, mechanistic understanding as of how the additives influence the coatings remains unclear. In this study, a new organic-inorganic hybrid Zrbased conversion coating which combines copper (Cu) compounds and polyamidoamine (PAMAM), taking advantages of a complementary nature of organic and inorganic additives. Here, a multimodal approach combining electron and X-ray characterization is applied to study the interaction of Cu 2+ and PAMAM and the resulting impacts on the coating formation. Adding PAMAM changed the surface morphology, thickness, distribution of Cu in the cluster and void formation of the coatings. High PAMAM (100-200 pm) leads to little conversion coating formation, and low PAMAM (0-25 ppm) shows voids formation under the coatings. Moreover, PAMAM incorporates in the coating in a form of PAMAM-Cu complex with a higher concentration towards the surface, provides an organic layer at the surface of the coating. X-ray absorption near-edge structure (XANES) spectroscopy shows a difference between the conventional and hybrid coating treatments in an alkaline solution to simulate the E-coat process, suggesting the contribution of PAMAM in the enhanced chemical stability in an alkaline environment. Therefore, an intermediate range of addition of PAMAM (50 ppm) is optimal to 1) avoid excessive voids formation, 2) promote some Cu cluster formation and thus enhancing the Zr-based coating formation and 3) incorporate organic components into the coating to improve the adhesion of the subsequent coatings. Overall, this work furthers our knowledge on the formation mechanism of an effective and environmentally friendly hybrid conversion coating for corrosion inhibition, demonstrating a critical processing-structureproperty relationship. This study will benefit future development of green and effective surface treatment technology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Probing U 5f Covalency in Uranium Compounds through Oxidant 2p Bonding

Oxidant K (1s) X-ray Emission Spectroscopy (XES) was used to investigate covalency in the Oxidant 2p – Uranium 5f bonds of Uranium Dioxide (UO 2 ) and Uranium Tetrafluoride (UF 4 ). It will be shown that the width of the 2p Occupied Density of States (ODOS), determined from the XES measurements, correlates with the increased 5f covalency of UO 2 and the increased ionicity of UF 4 . Analysis of the XES results includes comparison to spectral simulations, cluster calculations and peak fitting, demonstrating the potential of the oxidant XES measurements as a probe of 5f covalency.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont’s genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.

59 BASIC BIOLOGICAL SCIENCES↗

Detection of trace quantities of dimethylacetamide during the curing process of a polyimide film

An experimental study of positive ion clustering of dimethylacetamide (DMAC) with water molecules using high pressure mass spectrometry techniques is reported. The possibilities of using these techniques to determine the concentration levels of DMAC evolved from a polyimide film during the curing process, are examined. The test sample of gas contained DMAC of the order of a few micrograms, water, nitrogen, oxygen, and other compounds that might evolve during the curing cycle of a polyimide film. It is found that PPM concentrations such as DMAC lost from polyimide during curing stages can be detected with this technique. Improvement of the detection of lower concentrations (50 picograms) can be made by using electron multipliers with a gain in the 10 to the 8th power range and pulse counting techniques.

Smith, A. C.↗

Crystallographic Evidence for Formation of M 6 O 8 /M 6 O 9 f-Element Clusters in Hydrolysis Reactions

In this contribution, we have conducted an examination of crystallographic data which includes 184 4f- and 5f-structures containing the M 6 O 8 or M 6 O 9 moiety. Since much of the work in this field has actually been done to explore the formation and properties of metal organic frameworks (MOFs), we hope that this collection can be used by actinide scientists to further investigate structural and mechanistic trends and gain insight into the formation of these compounds. Here we discuss the general trends in coordination, ligands used, and bonding within the M 6 O 8 or M 6 O 9 core in the hope that further computational work can benefit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bridging the Transuranics with Uranium(IV) Sulfate Aqueous Species and Solid Phases

Isolating isomorphic compounds of tetravalent actinides (i.e., Th IV , U IV , Np IV , and Pu IV ) improve our understanding of the bonding behavior across the series, in addition to their relationship with tetravalent transition metals (Zr and Hf) and lanthanides (Ce). Similarities between these tetravalent metals are particularly illuminated in their hydrolysis and condensation behavior in aqueous systems, leading to polynuclear clusters typified by the hexamer [M IV 6 O 4 (OH) 4 ] 12+ building block. Prior studies have shown the predominance and coexistence of smaller species for Th IV (monomers, dimers, and hexamers) and larger species for U IV , Np IV , and Pu IV (including 38-mers and 70-mers). We show here that aqueous uranium(IV) sulfate also displays behavior similar to that of Th IV (and Zr IV ) in its isolated solidphase and solution speciation. Two single-crystal X-ray structures are described: a dihydroxide-bridged dimer (U 2 ) formulated as U 2 (OH) 2 (SO 4 ) 3 (H 2 O) 4 and a monomer-linked hexamer framework (U-U 6 ) as (U(H 2 O) 3.5 ) 2 U 6 O 4 (OH) 4 (SO 4 ) 10 (H 2 O) 9 . These structures are similar to those previously described for ThIV. Moreover, cocrystallization of monomer and dimer and of dimer and monomer–hexamer phases for both Th IV (prior) and U IV (current) indicates the coexistence of these species in solution. Because it was not possible to effectively study the sulfate-rich solutions via X-ray scattering from which U 2 and U-U 6 crystallized, we provide a parallel solution speciation study in low sulfate conditions, as a function of the pH. Raman spectroscopy, UV–vis spectroscopy, and small-angle X-ray scattering of these show decreasing sulfate binding, increased hydrolysis, increased species size, and increased complexity, with increasing pH. Furthermore, this study describes a bridge across the first half the actinide series, highlighting U IV similarities to Th IV , in addition to the previously known similarities to the transuranic elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Localized Active Space Method with Unitary Selective Coupled Cluster

Here, we introduce a hybrid quantum-classical algorithm, the localized active space unitary selective coupled cluster singles and doubles (LAS-USCCSD) method. Derived from the localized active space unitary coupled cluster (LAS-UCCSD) method, LAS-USCCSD first performs a classical LASSCF calculation, then selectively identifies the most important parameters (cluster amplitudes used to build the multireference UCC ansatz) for restoring interfragment interaction energy using this reduced set of parameters with the variational quantum eigensolver method. We benchmark LAS-USCCSD against LAS-UCCSD by calculating the total energies of (H 2 ) 2 , (H 2 ) 4 , and trans-butadiene, and the magnetic coupling constant for a bimetallic compound [Cr 2 (OH) 3 (NH 3 ) 6 ] 3+ . For these systems, we find that LAS-USCCSD reduces the number of required parameters and thus the circuit depth by at least 1 order of magnitude, an aspect which is important for the practical implementation of multireference hybrid quantum-classical algorithms like LAS-UCCSD on near-term quantum computers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization, Structure, and Reactivity of Hydroxyl Groups on Metal‐Oxide Cluster Nodes of Metal–Organic Frameworks: Structural Diversity and Keys to Reactivity and Catalysis

Among the most stable metal–organic frameworks (MOFs) are those incorporating nodes that are metal oxide clusters with frames such as Zr 6 O 8 . This review is a summary of the structure, bonding, and reactivity of MOF node hydroxyl groups, emphasizing those bonded to nodes containing aluminum and zirconium ions. Hydroxyl groups are often present on these nodes, sometimes balancing the charges of the metal ions. They arise during MOF syntheses in aqueous media or in post-synthesis treatments. They are identified with infrared and 1 H nuclear magnetic resonance spectroscopies and characterized by their reactivities with polar compounds such as alcohols. Terminal OH, paired µ 2 -OH, and aqua groups on nodes are catalytic sites in numerous reactions. Relatively unreactive hydroxyl groups (such as isolated µ 2 -OH groups) may replace reactive groups and inhibit catalysis; some node hydroxyl groups (e.g., µ 3 -OH) are mere spectators in catalysis. There are similarities between MOF node hydroxyl groups and those on the surfaces of bulk metal oxides, zeolites, and enzymes, but the comparisons are mostly inexact, and much remains to be understood about MOF node hydroxyl group chemistry. It is posited that understanding and controlling this chemistry will lead to tailored MOFs and improved adsorbents and catalysts.

36 MATERIALS SCIENCE↗

GronOR: Scalable and Accelerated Nonorthogonal Configuration Interaction for Molecular Fragment Wave Functions

GronOR is a program package for nonorthogonal configuration interaction calculations. Electronic wave functions are constructed in terms of antisymmetrized products of multiconfiguration molecular fragment wave functions. The computational complexity of the nonorthogonal methodologies implemented in GronOR applied to large molecular assemblies requires a design that takes full advantage of massively parallel supercomputer architectures and accelerator technologies. This work describes the implementation strategy and resulting performance characteristics. In addition to parallelization and acceleration, the software development strategy includes aspects of fault resiliency and heterogeneous computing. The program was designed for large-scale supercomputers but also runs effectively on small clusters and workstations for small molecular systems. GronOR is available as open source to the scientific community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗