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At least 559 records · Page 31

Nonadiabatic Force Matching for Alchemical Free-Energy Estimation

We propose a method to compute free-energy differences from nonadiabatic alchemical transformations by using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical switching process in terms of a nonadiabatic force field that can be learned through stochastic flow matching. The learned field can be used in conjunction with short-time trajectory data to evaluate upper and lower bounds on the alchemical free energy that variationally converge to the exact value if the field is optimal. Applying the method to evaluate the alchemical free energy of atomistic models shows that it can substantially reduce the simulation cost of a free-energy estimate at a negligible loss of accuracy when compared with thermodynamic integration.

Computational chemistry↗

Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks

We report that the ability to accurately and efficiently compute quantum-mechanical partial atomistic charges has many practical applications, such as calculations of IR spectra, analysis of chemical bonding, and classical force field parametrization. Machine learning (ML) techniques provide a possible avenue for the efficient prediction of atomic partial charges. Modern ML advances in the prediction of molecular energies [i.e., the hierarchical interacting particle neural network (HIP-NN)] has provided the necessary model framework and architecture to predict transferable, extensible, and conformationally dynamic atomic partial charges based on reference density functional theory (DFT) simulations. Utilizing HIP-NN, we show that ML charge prediction can be highly accurate over a wide range of molecules (both small and large) across a variety of charge partitioning schemes such as the Hirshfeld, CM5, MSK, and NBO methods. To demonstrate transferability and size extensibility, we compare ML results with reference DFT calculations on the COMP6 benchmark, achieving errors of 0.004e – (elementary charge). This is remarkable since this benchmark contains two proteins that are multiple times larger than the largest molecules in the training set. An application of our atomic charge predictions on nonequilibrium geometries is the generation of IR spectra for organic molecules from dynamical trajectories on a variety of organic molecules, which show good agreement with calculated IR spectra with reference method. Critically, HIP-NN charge predictions are many orders of magnitude faster than direct DFT calculations. Lastly, these combined results provide further evidence that ML (specifically HIP-NN) provides a pathway to greatly increase the range of feasible simulations while retaining quantum-level accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled Φ/ψ parameters using 2D Φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, we have performed a total of ~5 milliseconds MD simulations in explicit solvent. Here, our results show that after amino-acid specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino acid specific Protein Data Bank (PDB) Ramachandran maps better, but also shows significantly improved capability to differentiate amino acid dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Energy-Screened Many-Body Expansion: A Practical Yet Accurate Fragmentation Method for Quantum Chemistry

We introduce an implementation of the truncated many-body expansion, MBE(n), in which the n-body corrections are screened using the effective fragment potential force field, and only those that exceed a specified energy threshold are computed at a quantum-mechanical level of theory. This energy-screened MBE(n) approach is tested at the n = 3 level for a sequence of water clusters, (H2O) N=6–34 . A threshold of 0.25 kJ/mol eliminates more than 80% of the subsystem electronic structure calculations and is even more efficacious in that respect than is distance-based screening. Even so, the energy-screened MBE(3) method is faithful to a full-system quantum chemistry calculation to within 1–2 kJ/mol/monomer, even in good quality basis sets such as aug-cc-pVTZ. These errors can be reduced by means of a two-layer approach that involves a Hartree–Fock calculation for the entire cluster. Such a correction proves to be necessary in order to obtain accurate relative energies for conformational isomers of (H2O)20, but the cost of a full-system Hartree–Fock calculation remains smaller than the cost of three-body subsystem calculations at correlated levels of theory. At the level of second-order Møller–Plesset perturbation theory (MP2), a screened MBE(3) calculation plus a full-system Hartree–Fock calculation is less expensive than a full-system MP2 calculation starting at N = 12 water molecules. This is true even if all MBE(3) subsystem calculations are performed on a single 40-core compute node, i.e., without significant parallelization. Energy-screened MBE(n) thus provides a fragment-based method that is accurate, stable in large basis sets, and low in cost, even when the latter is measured in aggregate computer time.

74 ATOMIC AND MOLECULAR PHYSICS↗

Nitromethane Decomposition via Automated Reaction Discovery and an Ab Initio Corrected Kinetic Model

In the explore the systematic construction of kinetic models from in silico reaction data for the decomposition of nitromethane. Our models are constructed in a computationally affordable manner by using reactions discovered through accelerated molecular dynamics simulations using the ReaxFF reactive force field. The reaction paths are then optimized to determine reaction rate parameters. We introduce a reaction barrier correction scheme that combines accurate thermochemical data from density functional theory with ReaxFF minimal energy paths. We validate our models across different thermodynamic regimes, showing predictions of gas phase CO and NO concentrations and high-pressure induction times that are similar to experimental data. The kinetic models are analyzed to find fundamental decomposition reactions in different thermodynamic regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicted Reaction Mechanisms, Product Speciation, Kinetics, and Detonation Properties of the Insensitive Explosive 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105)

2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a relatively new and promising insensitive high-explosive (IHE) material that remains only partially characterized. IHEs are of interest for a range of applications and from a fundamental science standpoint, as the root causes behind insensitivity are poorly understood. In this work, we adopt a multitheory approach based on reactive molecular dynamic simulations performed with density functional theory, density functional tight-binding, and reactive force fields to characterize the reaction pathways, product speciation, reaction kinetics, and detonation performance of LLM-105. We compare and contrast these predictions to 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a prototypical IHE, and 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), a more sensitive and higher performance material. The combination of different predictive models allows access to processes operative on progressively longer timescales while providing benchmarks for assessing uncertainties in the predictions. We find that the early reaction pathways of LLM-105 decomposition are extremely similar to TATB; they involve intra- and intermolecular hydrogen transfer. Additionally, the detonation performance of LLM-105 falls between that of TATB and HMX. We find agreement between predictive models for first-step reaction pathways but significant differences in final product formations. Predictions of detonation performance result in a wide range of values, and one-step kinetic parameters show the similar reaction rates at high temperatures for three out of four models considered.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quasi-Classical Trajectory Calculation of Rate Constants Using an Ab Initio Trained Machine Learning Model (aML-MD) with Multifidelity Data

Machine learning (ML) provides a great opportunity for the construction of models with improved accuracy in classical molecular dynamics (MD). However, the accuracy of a ML trained model is limited by the quality and quantity of the training data. Generating large sets of accurate ab initio training data can require significant computational resources. Furthermore, inconsistent or incompatible data with different accuracies obtained using different methods may lead to biased or unreliable ML models that do not accurately represent the underlying physics. Recently, transfer learning showed its potential for avoiding these problems as well as for improving the accuracy, efficiency, and generalization of ML models using multifidelity data. In this work, ab initio trained ML-based MD (aML-MD) models are developed through transfer learning using DFT and multireference data from multiple sources with varying accuracy within the Deep Potential MD framework. Further, the accuracy of the force field is demonstrated by calculating rate constants for the H + HO 2 → H 2 + 3 O 2 reaction using quasi-classical trajectories. We show that the aML-MD model with transfer learning can accurately predict the rate constants while reducing the computational cost by more than five times compared to the use of more expensive quantum chemistry training data sets. Hence, the aML-MD model with transfer learning shows great potential in using multifidelity data to reduce the computational cost involved in generating the training set for these potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparison of Machine Learning Approaches for Prediction of the Equivalent Alkane Carbon Number for Microemulsions Based on Molecular Properties

The chemical properties of oils are vital in the design of microemulsion systems. The hydrophilic–lipophilic difference equation used to predict microemulsions’ phase behavior expresses the oils’ physiochemical properties as the equivalent alkane carbon number (EACN). The experimental determination of EACN requires knowledge of the temperature dependence of the microemulsion system and the effects of different surfactant concentrations. Thus, the experimental determination is time-intensive and tedious, requiring days to months for proper separations. Furthermore, the experiments require high purity of chemicals because microemulsions are sensitive to impurities. Our work focuses on the quick and reliable predictions of the EACN with machine learning (ML) models. Due to the immaturity of ML chemical predictions, we compare three graph neural networks (GNNs) and a gradient-boosted tree algorithm, known as XGBoost. The GNNs use the molecular structures represented as simplified molecular-input line-entry system (SMILES) codes for the initial input, which allows us to assess whether geometry optimization is necessary for reliable results. The XGBoost model also begins with the SMILES representations of the molecules but uses molecular descriptors instead of geometry optimizations. As a result, the best model tested (crystal graph convolutional neural network with Merck molecular force field-94) has an error of 1.15 EACN units of the true EACN for unknown data with the errors skewed toward zero and an R² score of 0.9

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. Part 5: Computational Study of Ethane Dissociation and Recombination Reactions C 2 H 6 ⇌ CH 3 + CH 3

Fossil fuel oxy-combustion is an emerging technology where the habitual nitrogen diluent is replaced by high-pressure supercritical CO 2 (sCO 2 ), which increases the efficiency of energy conversion. In this study, the chemical kinetics of the combustion reaction C 2 H 6 ⇌ CH 3 + CH 3 in the sCO 2 environment is predicted at 30–1000 atm and 1000–2000 K. We adopt a multiscale approach, where the reactive complex is treated quantum mechanically in rigid rotor/harmonic oscillator approximation, while environment effects at different densities are taken into account by the potential of mean force, produced with classical molecular dynamics (MD). Here, we used boxed MD, where enhanced sampling of infrequent events of barrier crossing is accomplished without application of the bias potential. The multistate empirical valence bond model is applied to describe free radical formation accurately at the cost of the classical force field. Predicted rates at low densities agree well with the literature data. In conclusion, rate constants at 300 atm are 2.41 × 10 14 T –0.20 exp(–77.03 kcal/mol/RT) 1/s for ethane dissociation and 8.44 × 10 –19 T 1.42 exp(19.89 kcal/mol/RT) cm 3 /molecule/s for methyl–methyl recombination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulations of the Biodegradation of Citrate Based Polymers for Artificial Scaffolds Using Accelerated Reactive Molecular Dynamics

Here, we explore the reactivity and mechanical properties of poly(1,6-hexanediol-co-Citric acid) via ReaxFF molecular dynamics simulations. We implement an accelerated scheme within the ReaxFF framework to study the hydrolysis reaction of the polymer which is provided with sufficient amount of energy known as the restrain energy after a suitable pre-transition state configuration is obtained to overcome the activation energy barrier and the desired product is obtained. The validity of the ReaxFF force field is established by comparing the ReaxFF energy barriers of ester and ether hydrolysis with benchmark DFT values in literature. We perform chemical and mechanical degradation of polymer chain bundles at 300 K. We find that ester hydrolyzes faster than ether due to lower activation energy barrier of the reaction. The selectivity of the bond-boost scheme has been demonstrated by lowering the boost parameters of the accelerated simulation which almost stops the ether hydrolysis. Mechanical degradation of pre-hydrolyzed and intermittent hydrolyzed polymer bundles is performed along the longitudinal direction at two different strain rates. We find that the tensile modulus of the polymers are increases with increase in strain rates which shows that polymers show a strain dependent behavior. The tensile modulus of the Polyester-ether is higher than Polyester yet reaches yield-stress faster than Polyester. This makes Polyester more ductile than Polyester-ether.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the Network Topology of Cross-Linked Acrylate Photopolymers: A Molecular Dynamics Case Study

A reactive molecular dynamics approach is used to simulate cross-linking of acrylate polymer networks. By employing the same force field and reactive scheme and studying three representative multifunctional acrylate monomers, we isolate the importance of the nonreactive moieties within these model monomers. Analyses of reactive trajectories benchmark the estimated gel points, cyclomatic character, and spatially resolved cross-linking tendencies of the acrylates as a function of conversion. The insights into the similarities and differences of the polymerization and resulting networks presented here suggest molecular mechanics as a useful tool in the rational design of photopolymerization resins.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Comparative Studies of the Structural and Transport Properties of Molten Salt FLiNaK Using the Machine-Learned Neural Network and Reparametrized Classical Forcefields

Despite surging interest in molten salt reactors and thermal storage systems, knowledge of the physicochemical properties of molten salts are still inadequate due to demanding experiments that require high temperature, impurity control, and corrosion mitigation. Therefore, the ability to predict these properties for molten salts from first-principles computations is urgently needed. Herein, we developed and compared a machine-learned neural network force field (NNFF) and a reparametrized rigid ion model (RIM) for a prototypical molten salt LiF–NaF–KF (FLiNaK). We found that NNFF was able to reproduce both the structural and transport properties of the molten salt with first-principles accuracy and classical-MD computational efficiency. Furthermore, the correlation between the local atomic structures and the dynamics was identified by comparing with RIMs, suggesting the significance of polarization of anions implicitly embedded in the NNFF. Furthermore, this work demonstrated a computational framework that can facilitate the screening of molten salts with different chemical compositions, impurities, and additives, and at different thermodynamic conditions suitable for the next-generation nuclear reactors and thermal energy storage facilities.

36 MATERIALS SCIENCE↗

Using Computationally-Determined Properties for Machine Learning Prediction of Self-Diffusion Coefficients in Pure Liquids

The ability to predict transport properties of liquids quickly and accurately will greatly improve our understanding of fluid properties both in bulk and complex mixtures, as well as in confined environments. Such information could then be used in the design of materials and processes for applications ranging from energy production and storage to manufacturing processes. As a first step, we consider the use of machine learning (ML) methods to predict the diffusion properties of pure liquids. Recent results have shown that Artificial Neural Networks (ANNs) can effectively predict the diffusion of pure compounds based on the use of experimental properties as the model inputs. In the current study, a similar ANN approach is applied to modeling diffusion of pure liquids using fluid properties obtained exclusively from molecular simulations. A diverse set of 102 pure liquids is considered, ranging from small polar molecules (e.g., water) to large nonpolar molecules (e.g., octane). Self-diffusion coefficients were obtained from classical molecular dynamics (MD) simulations. Since nearly all the molecules are organic compounds, a general set of force field parameters for organic molecules was used. The MD methods are validated by comparing physical and thermodynamic properties with experiment. Computational input features for the ANN include physical properties obtained from the MD simulations as well as molecular properties from quantum calculations of individual molecules. Furthermore, fluid properties describing the local liquid structure were obtained from center of mass radial distribution functions (COM-RDFs). Feature sensitivity analysis revealed that isothermal compressibility, heat of vaporization, and the thermal expansion coefficient were the most impactful properties used as input for the ANN model to predict the MD simulated self-diffusion coefficients. The MD-based ANN successfully predicts the MD self-diffusion coefficients with only a subset (2 to 3) of the available computationally determined input features required. A separate ANN model was developed using literature experimental self-diffusion coefficients as model targets. Although this second ML model was not as successful due to a limited number of data points, a good correlation is still observed between experimental and ML predicted self-diffusion coefficients.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonane and Hexanol Adsorption in the Lamellar Phase of a Nonionic Surfactant: Molecular Simulations and Comparison to Ideal Adsorbed Solution Theory

Adsorption of n-nonane/1-hexanol (C9/C6OH) mixtures into the lamellar phase formed by a 50/50 w/w triethylene glycol mono-n-decyl ether (C10E3)/water system was studied using configurational-bias Monte Carlo simulations in the osmotic Gibbs ensemble. The interactions were described by the Shinoda–Devane–Klein coarse-grained force field. Prior simulations probing single-component adsorption indicated that C9 molecules preferentially load near the center of the bilayer increasing the bilayer thickness, whereas C6OH molecules are more likely to be found near the interface of the polar and non-polar moieties swelling the bilayer in the lateral dimension. Here, we extend this work to binary C9/C6OH adsorption to probe whether the difference in the spatial preferences may lead to a synergistic effect and enhanced loadings for the mixture. Comparing loading trends and the thermodynamics of binary adsorption to unary adsorption reveals that C9–C9 interactions lead to the largest enhancement, whereas C9–C6OH and C6OH–C6OH interactions are less favorable for this bilayer system. As a result, ideal adsorbed solution theory yields satisfactory predictions of the binary loading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Water–Hydrocarbon Interactions in Anionic Pyrene Monohydrate

Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond timescales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the linewidth and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Furthermore, our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. Furthermore, the strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CO 2 Capture Characteristics of Hyperbranched Poly(alkylene imine): A Molecular Dynamics Simulation Approach

This study explores the CO 2 capture characteristics of hyperbranched poly(ethylenimine) (HB-PEI) and poly- (propyleneimine) (HB-PPI) through molecular dynamics simulations using density functional theory-calibrated force fields. Key features such as density, free volume, glass transition temperature, CO 2 /H 2 O distribution, and molecular diffusion are systematically investigated to elucidate structure−function relationships under dry and hydrated conditions. HB-PEI demonstrates a slightly higher density and lower free volume compared to HB-PPI yet shows superior CO 2 capture due to the high amine concentration. Glass transition analysis indicates a higher thermal mobility in HBPEI, enhancing the CO 2 diffusivity. Pair correlation and coordination analyses confirm a stronger affinity of CO 2 with primary and secondary amines, particularly in hydrated environments where water competes with CO 2 for binding sites. Despite its more compact structure, HB-PEI outperformed HB-PPI in CO 2 and H 2 O transport, as confirmed by higher diffusion coefficients across all hydration levels. These findings highlight a critical balance among polymer architecture, amine accessibility, and hydration in designing next-generation solid amine sorbents for efficient direct air capture applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗