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At least 307 records · Page 17

Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

Lucina pectinata live in high concentrations of hydrogen sulfide (H 2 S) and contains one hemoglobin, Hemoglobin I (HbI), transporting H 2 S and two hemoglobins, Hemoglobin II (HbII) and Hemoglobin (HbIII), transferring dioxygen to symbionts. HbII and HbIII contain B10 tyrosine (Tyr) and E7 glutamine (Gln) in the heme pocket generating an efficient hydrogen bonding network with the (HbII-HbIII)-O 2 species, leading to very low ligand dissociation rates. The results indicate that the oxy-hemeprotein is susceptible to pH from 4 to 9, at acidic conditions, and as a function of the potassium ferricyanide concentration, 100% of the met-aquo derivative is produced. Without a strong oxidant, pH 5 generates a small concentration of the met-aquo complex. The process is accelerated by the presence of salts, as indicated by the crystallization structures and UV–Vis spectra. The results suggest that acidic pH generates conformational changes associated with B10 and E7 heme pocket amino acids, weakening the (HbII-HbIII)-O 2 hydrogen bond network. The observation is supported by X-ray crystallography, since at pH 4 and 5, the heme-Fe tends to oxidize, while at pH 7, the oxy-heterodimer is present. Additionally, conformational changes are observed at higher pH by the presence of a 605 nm transition associated with the iron heme-Tyr interaction. Therefore, pH is one crucial factor regulating the (HbII-HbIII)-O 2 complex hydrogen-bonding network. Thus, it can be proposed that the hydrogen bonding adjustments between the heme bound O 2 and the Tyr and Gln amino acids contribute to oxygen dissociation from the (HbII-HbIII)-O 2 system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superhydrophilicity of $α$-alumina surfaces results from tight binding of interfacial waters to specific aluminols

Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Here, contact angles at the alumina (0001) and ($11\bar{2}0$) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials

Intermolecular interactions are critical to many chemical phenomena, but their accurate computation using ab initio methods is often limited by computational cost. The recent emergence of machine learning (ML) potentials may be a promising alternative. Useful ML models should not only estimate accurate interaction energies but also predict smooth and asymptotically correct potential energy surfaces. However, existing ML models are not guaranteed to obey these constraints. Indeed, systemic deficiencies are apparent in the predictions of our previous hydrogen-bond model as well as the popular ANI-1X model, which we attribute to the use of an atomic energy partition. As a solution, we propose an alternative atomic-pairwise framework specifically for intermolecular ML potentials, and we introduce AP-Net—a neural network model for interaction energies. The AP-Net model is developed using this physically motivated atomic-pairwise paradigm and also exploits the interpretability of symmetry adapted perturbation theory (SAPT). We show that in contrast to other models, AP-Net produces smooth, physically meaningful intermolecular potentials exhibiting correct asymptotic behavior. Initially trained on only a limited number of mostly hydrogen-bonded dimers, AP-Net makes accurate predictions across the chemically diverse S66x8 dataset, demonstrating significant transferability. On a test set including experimental hydrogen-bonded dimers, AP-Net predicts total interaction energies with a mean absolute error of 0.37 kcal mol−1, reducing errors by a factor of 2–5 across SAPT components from previous neural network potentials. The pairwise interaction energies of the model are physically interpretable, and an investigation of predicted electrostatic energies suggests that the model “learns” the physics of hydrogen-bonded interactions.

Glick, Zachary L. (ORCID:0000000309002849)↗

Crystal structure of oxibendazole, C 12 H 15 N 3 O 3

The crystal structure of oxibendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxibendazole crystallizes in space group C2/c (#15) with a = 23.18673(22), b = 5.35136(5), c = 19.88932(13) Å, β = 97.0876(9)°, V = 2449.018(17) Å 3 , and Z = 8. The structure consists of hydrogen-bonded layers of planar molecules parallel to the bc-plane. Strong N–H∙∙∙N hydrogen bonds link the molecules into dimers, with a graph set R2,2(8). N–H∙∙∙O hydrogen bonds further link these dimers into layers parallel to the bc-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of elvitegravir Form II, C 23 H 23 ClFNO 5

The crystal structure of elvitegravir Form II has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Elvitegravir Form II crystallizes in space group P2 1 (#4) with a = 11.54842(7), b = 14.04367(5), c = 13.33333(8) Å, β = 90.0330(6)°, V = 2162.427(14) Å 3 , and Z = 4. The crystal structure consists of alternating layers of parallel molecules perpendicular to the b-axis. The mean planes of the oxoquinoline ring systems in molecules 1 and 2 are 1(22)-1 and -1(22)1. Between the stacks are layers of the halogenated phenyl rings. These exhibit herringbone stacking. In each molecule, the carboxylic acid group forms a strong intramolecular O–H∙∙∙O hydrogen bond to the nearby carbonyl group. The hydroxyl group of each molecule forms a strong hydrogen bond to the carbonyl group of the carboxylic acid of the other molecule. These O–H∙∙∙O hydrogen bonds link the molecules into dimers, with a graph set R2,2(18) > a > c. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Constructing Water‐Stable Porous Organic Salts via Suppressed Proton Integration Using Fluorinated Tetrazole Tectons

Porous organic salts (POSs) are an emerging class of materials with ordered ionic architectures, offering excellent proton transfer and water uptake properties. However, conventional POS synthesis via strong acid–base neutralization (e.g., ─SO₃H and ─NH₂) leads to extensive hydrogen bonding with water, compromising stability in aqueous and water-lean environments. Here, we address this challenge by designing POSs with hydrophobic porous channels and minimal hydrogen bonding formation. Our key innovation is the use of fluorinated tetrazole as a weak acid tecton and a tetra-substituted imidazole precursor devoid of active protons as the base. Single-crystal analysis and computational modeling reveal that the structural integrity of the synthesized POSs arises primarily from cation–anion interactions, with water confined as clusters in the pores, independent of hydrogen bonding with the scaffold. Robustness of the POS structure under aqueous and water-lean conditions is confirmed by X-ray and neutron scattering, as well as computational modeling, confirming preserved packing and crystal structures. The stability of POS is further demonstrated in aqueous iodine capture, with imidazolium cations and C–F functionalizations serving as strong adsorption sites. As a result, the approach developed herein further pushes the boundary of POS materials to withstand both aqueous and water-lean conditions.

Fluorinated tecton↗

Formation of Water Networks on Anionic Perylene

We present infrared photodissociation spectra of hydrated perylene anion clusters with up to four water molecules, as well as electronic structure calculations based on density functional theory. Water molecules form weak hydrogen bonds to the π system of the perylene anion. For clusters with more than one water molecule, water−water hydrogen bonds are formed, which generally appear to be stronger than water−π hydrogen bonds, especially for the trihydrate and tetrahydrate. The resulting water networks exist as water subclusters on the surface of the carbon frame of perylene. Here, we observe temperature-dependent dynamic effects, which highlight large amplitude motions of the water network and the shallowness of the potential energy surfaces governing the structures of these clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Self‐Healing Chemistry‐Enabled Organic Cathode for Sustainable and Stable Sodium‐Ion Batteries

Sodium‐on batteries (SIBs) are promising alternatives to lithium‐ion batteries (LIBs) because of the low cost, abundance, and high sustainability of sodium resources. Analogous to LIBs, the high‐capacity electrodes in SIBs always suffer from rapid capacity decay upon long‐term cycling due to the particle pulverization induced by a large volume change. Circumventing particle pulverization plays a critical role in developing high‐energy and long‐life SIBs. Herein, tetrahydroxy‐1,4‐benzoquinone disodium salt (TBDS) that can self‐heal the cracks by hydrogen bonding between hydroxyl group and carbonyl group is employed as a cathode for sustainable and stable SIBs. The self‐healing TBDS exhibits long cycle life of 1000 cycles with a high rate capability up to 2 A g −1 due to the fast Na‐ion diffusion reaction in the TBDS cathode. The intermolecular hydrogen bonding has been comprehensively characterized to understand the self‐healing mechanism. The hydrogen bonding‐enabled self‐healing organic materials are promising for developing high‐energy and long‐cycle‐life SIBs.

25 ENERGY STORAGE↗

Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Epoxide Alcoholysis over M-BEA Zeolites: Effects of Alcohol Chain Length on Rates and Regioselectivities

The structures of nucleophilic reactants affect their coordination behavior among solvent molecules and kinetics of reactions with surface intermediates within the confines of fluidfilled pores of zeolites and other microporous materials. Consequently, rates and regioselectivities of diverse chemistries may depend sensitively on nucleophile identity in manners not observed for classic fluid phase reactions. Here, we examine the impact of varying the primary alcohol (ROH) chain length on the kinetics of 1,2-epoxybutane (C 4 H 8 O) ring-opening within Brønsted (Al-BEA) and Lewis acid (Zr-BEA) zeolites. Turnover rates increase by factors of ∼6 (Al-BEA) and 4-fold (Zr-BEA) between methanol and 1-hexanol, yet the reaction mechanisms remain comparable. Despite modest rate differences, apparent activation enthalpies calculated from rates and activities of solvated reactants decrease linearly by 12 (Al-BEA) to 33 kJ mol −1 (Zr- BEA) with increased proton affinity, which suggests bond formation energies for the nucleophile strongly influence rate increases. The molecular interpretation of these trends demonstrates, however, that the solvation of ring-opening transition states by zeolite pore structures and solvent molecules also governs rates. The impact of local solvating interactions appears most directly as changes in regioselectivities, which tend to enhance terminal alcohol formation with increasing ROH chain length. Regioselectivities largely do not vary with differences in fluid composition for a given ROH. The addition of H 2 O increases the number of hydrogen bonds among reactive species, and trends in regioselectivities imply that the decreased hydrogen bonding ability of longer chain ROH, and not the nucleophile strength or steric bulk, determines the regioselectivities of the resulting products. This work provides direct experimental evidence that nucleophilicity and hydrogen bonding influence reaction barriers and regioselectivities in zeolitecatalyzed epoxide ring-opening, offering pathways to better control reaction kinetics.

acidic zeolites↗

Nacre-like MXene/Polyacrylic Acid Layer-by-Layer Multilayers as Hydrogen Gas Barriers

MXenes are a promising class of 2D nanomaterials and are of particular interest for gas barrier applications due to their high aspect ratio. However, MXene nanosheets naturally bear a negative charge, which prevents assembly with negatively charged polymers, such as polyacrylic acid (PAA), into gas barrier coatings. Here, we present MXene- and PAA-based layer-by-layer (MXene/ PAA LbL) multilayers formed by leveraging hydrogen bonding interactions. When assembled in acidic conditions, MXene/PAA LbL multilayers exhibit conformal, pinhole-free, nacre-like structures. The MXene/PAA LbL multilayers yield high blocking capability and low permeability (0.14 ± 0.01 cc·mm·m −2 ·day −1 · MPa −1 ) for hydrogen gas which is over 9000 times lower than uncoated niobium (Nb) substrate. These nacre-like structures are also electronically conductive (σ DC , up to 370 ± 30 S cm −1 ). Because these multilayers utilize hydrogen bonding, their properties are highly sensitive to the pH of the assembly and its external environment. Specifically, the reversible deconstruction of these multilayers under basic conditions is experimentally verified. This study shows that hydrogen bonding interactions can be leveraged to form MXene LbL multilayers as gas barriers, electronically conductive coatings, and deconstructable thin films via pH control.

36 MATERIALS SCIENCE↗

Effect of the Segmental Structure of Thermoplastic Polyurethane (Hardness) on the Interfacial Adhesion of Textile-Grade Carbon Fiber Composites

In polymer composites, the fiber–matrix interface is primarily influenced by the surface treatment of the fibers and polymer morphology. Previous studies have investigated the effect of surface treatment of carbon fiber on the mechanical properties of the resulting composites. However, very few studies have explored the chemical structural modification of polymer effect on the fiber–matrix adhesion. In this work, the interfaces of soft thermoplastic polyurethane (S-TPU) and hard-segmented TPU (H-TPU) were investigated through surface, thermal, and mechanical characterization. A textile-grade carbon fiber (TCF) with 1% concentration of epoxy sizing (an emerging material for nonaerospace applications with 450 K filament tows) was used as a reinforcement to investigate the structure–property relationship at the interface. Atomic force microscopy results showed 39% higher surface roughness for S-TPU than for H-TPU. X-ray photoelectron spectroscopy results revealed a 550% increase in C=O content, which can provide multiple hydrogen bonding networks in H-TPU, and these C=O bonds can produce a strong chemical bond at the fiber–matrix interface. Additionally, dynamic mechanical analysis and differential scanning calorimetry results confirmed the presence of hydrogen bonding that enhances the cross-linked density by 232% in H-TPU compared to S-TPU. The improved mechanical properties of H-TPU composites, such as flexural, impact and tensile by 30, 50, and 130% compared to S-TPU composites, prove that the crystallinity and hydrogen bonding significantly increase the load bearing capacity due to the strong interface. The mechanical properties of TCF–TPU composites validate the formation of chemical bonds through a nucleophilic addition reaction at the interface and improve the bond strength of the composites. Thus, tailoring the polyurethane structure broadens the performance of segmented TPU in conjunction with TCF reinforcement, which has implications for cost-effective, high-strength composites.

36 MATERIALS SCIENCE↗

Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo 3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o 3 , and Cu B ), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71 I . In both structures, residue H98 I occupies two conformations. In conformation 1, H98 I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 I has flipped to form a hydrogen bond with E14 I at the N-terminal end of TM0. We propose that H98 I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98 I .

bioenergetics↗

Analysis of persistent contaminants and personal care products by dispersive liquid-liquid microextraction using hydrophobic magnetic deep eutectic solvents

Here, in this work, hydrophobic magnetic deep eutectic solvents (HMDESs) were used in the development of a simple and rapid dispersive liquid-liquid microextraction (DLLME) approach coupled to high performance liquid chromatography with UV detection (HPLC-UV) for the determination of ten organic contaminants including five polycyclic aromatic hydrocarbons, four UV filters, and a pesticide from water at trace levels. The HMDESs were prepared by mixing a hydrogen bond acceptor, metal halide salt, and hydrogen bond donor in suitable molar ratios. Two HMDESs, 2 tetraoctylammonium bromide ([N 8888 + ][Br - ]): cobalt chloride (CoCl 2 ): 4 octanoic acid (OA) and 3 trioctylphosphine oxide (TOPO): neodymium chloride (NdCl 3 ): 3 OA, offered the highest analyte extraction efficiency overall and were chosen as suitable solvents for validation of the microextraction method. Under optimized extraction conditions, the method required 30 µL of HMDES as extraction solvent, acetone (87.5 µL) as disperser solvent, a NaCl concentration of 30% (w/v), and an extraction time of 120 s at 20°C. Enrichment factors of the analytes ranged from 44.6 for 3-(4-methylbenzylindene) camphor to 66.0 for 2-ethylhexyl-4-(dimethyl)aminobenzoate. The method provided low limits of detection (LODs) ranging from 0.5 to 4.5 µg L -1 , and acceptable precision, with RSD values lower than 9.6%. Furthermore, the validated method was successfully applied for tap and lake water analysis, resulting in relative recoveries of spiked samples ranging between 94.7 and 119.2%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Liquid Structure and Transport Properties of the Deep Eutectic Solvent Ethaline

A range of techniques including physical property measurements, neutron scattering experiments, ab initio molecular dynamics, and classical molecular dynamics simulations are used to probe the structural, thermodynamic, and transport properties of a deep eutectic solvent comprised of a 1:2 molar ratio of choline chloride and ethylene glycol. This mixture, known as Ethaline, has many desirable properties for use in a range of applications, and therefore, understanding its liquid structure and transport properties is of interest. Simulation results are able to capture experimental densities, diffusivities, viscosities, and structure factors extremely well. Here, the solvation environment is dynamic and dominated by different hydrogen bonding interactions. Dynamic heterogeneities resulting from hydrogen bonding interactions are quantified. Rotational dynamics of molecular dipole moments of choline and ethylene glycol are computed and found to exhibit a fast and slow mode.

25 ENERGY STORAGE↗

60 Years of Betaine 30–From Solvatochromic Discovery to Future Frontiers

Betaine-30 (B30) was reported by Karl Dimroth and Christian Reichardt et al. in 1963 as a solvatochromic probe that can be easily synthesized, shows good solubility, and remains stable in various organic solvents and solutions. Its strongly negatively solvatochromic behavior arises from differential solvation between its electronic ground and excited states, making it a valuable tool for assessing solvent polarity using the E T (30) polarity scale, also devised by Dimroth and Reichardt. In addition, advancements in femtosecond laser spectroscopy in the 1990s greatly improved the understanding of B30’s relaxation dynamics following photoexcitation. In solvents capable of hydrogen bonding, such as alcohols, intermolecular hydrogen-bond rearrangement contributes to the multiple relaxation components observed. Since the 1990s, the applications of B30 have expanded beyond simple organic solvents to include complex solvent mixtures, such as electrolyte solutions for battery technologies and eutectic solvent mixtures. Furthermore, given the growing importance of these complex solvent mixtures, B30 is becoming an increasingly valuable tool for studying previously unexplored solvation properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proton-Coupled Electron Transfer in a Ruthenium(II) Bipyrimidine Complex in Its Ground and Excited Electronic States

In this work, proton-coupled electron transfer (PCET) was studied for the ground and excited electronic states of a [Ru(terpy)(bpm)(OH 2 )(PF 6 ) 2 ] complex, Ru-bpm. Cyclic voltammetry measurements show that the Ru(II)-aqua moiety undergoes PCET to form a Ru(IV)-oxo moiety in the anodic region, while the bpm ligand undergoes PCET to form bpmH 2 in the cathodic region. The photophysical behavior of Ru-bpm was studied using steady-state and femtosecond transient UV–vis absorption spectroscopy, coupled with density functional theory (DFT) calculations. The lowest-lying excited state of Ru-bpm is described as a (Ru → bpm) metal-to-ligand charge-transfer (MLCT) state, while the metal-centered (MC) excited state was found computationally to be close in energy to the lowest-energy bright MLCT state (MC state was 0.16 eV above the MLCT state). The excited-state kinetics of Ru-bpm were found via transient absorption spectroscopy to be short-lived and were fit well to a biexponential function with lifetimes $τ_1$ = 4 ps and $τ_2$ = 65 ps in aqueous solution. Kinetic isotope effects of 1.75 ($τ_1$) and 1.61 ($τ_2$) were observed for both decay components, indicating that the solvent plays an important role in the excited-state dynamics of Ru-bpm. Based on the pH-dependent studies and the results from prior studies of similar Ru-complexes, we hypothesize that the 3 MLCT state forms an excited-state hydrogen-bond adduct with the solvent molecules and that this process occurs with a 4 ps lifetime. The formation of such a hydrogen-bond complex is consistent with the electronic density accumulation at the peripheral N atoms of the bpm moiety in the 3 MLCT state. The hydrogen-bonded state 3 MLCT decays to the ground state with a 65 ps lifetime. Such a short lifetime is likely associated with the efficient vibrational energy transfer from the 3 MLCT state to the solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep Eutectic Solvents: A Review of Fundamentals and Applications

Deep eutectic solvents (DESs) are an emerging class of mixtures characterized by significant depressions in melting points compared to those of the neat constituent components. These green materials are promising for applications as inexpensive ’designer’ solvents exhibiting a host of tunable physicochemical properties. Here, a detailed review of the current literature reveals the lack of predictive understanding of the microscopic mechanisms that govern the structure-property relationships in this class of solvents. Complex hydrogen bonding behavior is postulated as the root cause of their melt-ing point depressions and physicochemical properties; to understand these hydrogen bonded networks, it is imperative to study these systems as dynamic entities using both simulations and experiments. This review emphasizes recent research efforts in order to elucidate the next steps needed to develop a fundamental framework for understanding DESs. It covers recent developments in DES research, frames outstanding scientific questions, and identifies gainful research thrusts that would advance the field towards predictive models and fundamental understanding of these solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗