Understanding the shape of chemistry data-Applications with persistent homology.

Chemical data often have complex and nonlinear patterns in how data points relate to one another. Concurrently, there are many situations where chemical data are of high dimensionality (e.g.

A Thermal [2+2] Cycloaddition/Retro-4π-Electrocyclization Reaction of -Quinone Methides with Alkyne and a Mechanistic Investigation: Ingress of a Vinyl Fuchsone Pharmacophore.

Herein, we demonstrate a [2+2] cycloaddition/electrocyclic ring-opening reaction between quinone methide and electronically unbiased terminal alkynes under strictly thermal conditions. The present investigation is a unique example that demonstrates the effect of extended conjugation and cross-conjugation on the energy of the lowest unoccupied molecular orbital. As supported by density functional theory calculations, the reaction proceeds through the biradical pathway, accommodating both electron-deficient and electron-rich alkyne partners.

Isotropic ↔ anisotropic surface geometry transitions induced by adsorbed surfactants at water/vapor interfaces.

Adsorbates at a water/vapor interface change the surface geometry through altered surface tension, yet detailed theoretical studies are relatively sparse, and many applications focus on ensemble average characteristics. Here, we demonstrate that different interpretations of surface geometry emerge when considering the distributions of surface curvature and orientation as a function of adsorbed surfactant concentration and sterics. At low surface densities, the tributyl phosphate (TBP) sorbed water/vapor surface has an increased presence of ridges that are defined by principal curvatures κ1 and κ2 of opposite signs yet close in magnitude.

Tracking nitrite's deviation from Stokes-Einstein predictions with pulsed field gradient N NMR spectroscopy.

Predicting the behavior of oxyanions in radioactive waste stored at the Department of Energy legacy nuclear sites requires the development of novel analytical methods. This work demonstrates N pulsed field gradient nuclear magnetic resonance spectroscopy to quantify the diffusivity of nitrite. Experimental results, supported by molecular dynamics simulations, indicate that the diffusivity of free hydrated nitrite exceeds that of free hydrated sodium despite the greater hydrodynamic radius of nitrite.

Predicting Outcomes of Nanoparticle Attachment by Connecting Atomistic, Interfacial, Particle, and Aggregate Scales.

Predicting nanoparticle aggregation and attachment phenomena requires a rigorous understanding of the interplay among crystal structure, particle morphology, surface chemistry, solution conditions, and interparticle forces, yet no comprehensive picture exists. We used an integrated suite of experimental, theoretical, and simulation methods to resolve the effect of solution pH on the aggregation of boehmite nanoplatelets, a case study with important implications for the environmental management of legacy nuclear waste. Real-time observations showed that the particles attach preferentially along the (010) planes at pH 8.

Cation coordination polyhedra lead to multiple lengthscale organization in aqueous electrolytes.

Understanding multiple lengthscale correlations in the pair distribution functions (PDFs) of aq. electrolytes is a persistent challenge. Here, the coordination chemistry of polyoxoanions supports an ion-network of cation-coordination polyhedra in NaNO and NaNO that induce long-range solution structure.

An Efficient Reactive Force Field without Explicit Coordination Dependence for Studying Caustic Aluminum Chemistry.

Reactive force fields (RFFs) are an expedient approach to sample chemical reaction paths in complex systems, relative to density functional theory. However, there is continued need to improve efficiencies, specifically in systems that have slow transverse degrees of freedom, as in highly viscous and superconcentrated solutions. Here, we present an RFF that is differentiated from current models (e.

Adsorbate Organization Characterized by Sublevelset Persistent Homology.

Interfacial adsorbate organization influences a variety physicochemical properties and reactivity. Surfaces that are rough, defect laden, or have large fluctuations (as in soft matter interfaces) can lead to complex adsorbate structures. This is amplified if adsorbate-adsorbate interactions lead to self-assembly.

Additive energy functions have predictable landscape topologies.

Recent work [Mirth et al., J. Chem.

Disordered interfaces of alkaline aluminate salt hydrates provide glimpses of Al coordination changes.

Hypothesis: The precipitation and dissolution of aluminum-bearing mineral phases in aqueous systems often proceed via changes in both aluminum coordination number and connectivity, complicating molecular-scale interpretation of the transformation mechanism. Here, the thermally induced transformation of crystalline sodium aluminum salt hydrate, a phase comprised of monomeric octahedrally coordinated aluminate which is of relevance to industrial aluminum processing, has been studied. Because intermediate aluminum coordination states during melting have not previously been detected, it is hypothesized that the transition to lower coordinated aluminum ions occurs within ahighly disordered quasi-two-dimensional phase at the solid-solution interface.

Modulating Aggregation in Microemulsions: The Dispersion by Competitive Intermolecular Interaction Model.

A phenomenological model has been developed for the mechanism of action of phase modifiers as additives that control aggregation phenomena within water-in-oil emulsions. The "Dispersion by Competitive Intermolecular Interaction" model (DCI) explicitly considers the strength and prevalence of different that influence the molecular association of amphiphiles, the resulting distribution of aggregate size, and interaggregate interactions that influence phase phenomena. The existing "cosolvent" and "cosurfactant" association models, which describe the distribution of these amphiphiles within the solution, are re-examined in the context of intermolecular interactions.

Dynamic Community Detection Decouples Multiple Time Scale Behavior of Complex Chemical Systems.

Although community or cluster identification is becoming a standard tool within the simulation community, traditional algorithms are challenging to adapt to time-dependent data. Here, we introduce temporal community identification using the Δ-screening algorithm, which has the flexibility to account for varying community compositions, merging and splitting behaviors within dynamically evolving chemical networks. When applied to a complex chemical system whose varying chemical environments cause multiple time scale behavior, Δ-screening is able to resolve the multiple time scales of temporal communities.

pH dependent reactivity of boehmite surfaces from first principles molecular dynamics.

pH dependent interfacial chemistry depends upon the distribution and respective p values of different surface active sites. This is highly relevant to the chemistry of nanoparticle morphologies that expose faces with varying surface termination. Recent synthetic advances for nanoparticles of various minerals, including AlO(OH) (boehmite), present an excellent opportunity to compare and contrast predicted surface p on low Miller index planes so as to reinterpret reported interfacial properties (, point of zero charge - PZC) and reactivity.

Behavior of Linear and Nonlinear Dimensionality Reduction for Collective Variable Identification of Small Molecule Solution-Phase Reactions.

Identifying collective variables (CVs) for chemical reactions is essential to reduce the 3-dimensional energy landscape into lower dimensional basins and barriers of interest. However, in condensed phase processes, the nonmeaningful motions of bulk solvent often overpower the ability of dimensionality reduction methods to identify correlated motions that underpin collective variables. Yet solvent can play important indirect or direct roles in reactivity, and much can be lost through treatments that remove or dampen solvent motion.

Unexpected inverse correlations and cooperativity in ion-pair phase transfer.

Liquid/liquid extraction is one of the most widely used separation and purification methods, where a forefront of research is the study of transport mechanisms for solute partitioning and the relationships that these have to solution structure at the phase boundary. To date, organized surface features that include protrusions, water-fingers, and molecular hinges have been reported. Many of these equilibrium studies have focused upon small-molecule transport - yet the extent to which the complexity of the solute, and the competition between different solutes, influence transport mechanisms have not been explored.

Theory-Guided Inelastic Neutron Scattering of Crystalline Alkaline Aluminate Salts Bearing Principal Motifs of Solution-State Species.

Aluminate salts precipitated from caustic alkaline solutions exhibit a correlation between the anionic speciation and the identity of the alkali cation in the precipitate, with the aluminate ions occurring either in monomeric (Al(OH)) or dimeric (AlO(OH)) forms. The origin of this correlation is poorly understood as are the roles that oligomeric aluminate species play in determining the solution structure, prenucleation clusters, and precipitation pathways. Characterization of aluminate solution speciation with vibrational spectroscopy results in spectra that are difficult to interpret because the ions access a diverse and dynamic configurational space.

The Middle Science: Traversing Scale In Complex Many-Body Systems.

A roadmap is developed that integrates simulation methodology and data science methods to target new theories that traverse the multiple length- and time-scale features of many-body phenomena.

Shear stress dependence of force networks in 3D dense suspensions.

The geometric organization and force networks of 3D dense suspensions that exhibit both shear thinning and thickening have been examined as a function of varying strength of interparticle attractive interactions using lubrication flow discrete element simulations. Significant rearrangement of the geometric topology does not occur at either the local or global scale as these systems transition across the shear thinning and shear thickening regimes. In contrast, massive rearrangements in the balance of attractive, lubrication, and contact forces are observed with interesting behavior of network growth and competition.

An octanol hinge opens the door to water transport.

Despite their prevalent use as a surrogate for partitioning of pharmacologically active solutes across lipid membranes, the mechanism of transport across water/octanol phase boundaries has remained unexplored. Using molecular dynamics, graph theoretical, cluster analysis, and Langevin dynamics, we reveal an elegant mechanism for the simplest solute, water. Self-assembled octanol at the interface reversibly binds water and swings like the hinge of a door to bring water into a semi-organized second interfacial layer (a "bilayer island").

Ensemble effects on allylic oxidation within explicit solvation environments.

Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene using a Cu(ii) 7-amino-6-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile to create cyclohexenone and H2O as products. After the initial H-atom abstraction step, two different reaction pathways have been identified that are distinguished by the participation of alkyl hydroperoxide (referred to as the "open" cycle) versus the methanol side-product (referred to as the "closed" cycle) within the catalyst recovery process. Importantly, both pathways involve dehydrogenation and re-hydrogenation of the -NH2 group bound to the Cu-site - a feature that is revealed from the ensemble sampling of configurations of the reactive species that are stabilized within the explicit solvent environment of the simulation.

Cluster Identification Using Modularity Optimization to Uncover Chemical Heterogeneity in Complex Solutions.

Structural heterogeneity is commonly manifested in solutions and liquids that feature competition of different interparticle forces. Identifying and characterizing heterogeneity across different length scales requires multimodal experimental measurement and/or the application of new techniques for the interrogation of atomistic simulation data. Within the latter, the parsing of networks of interparticle interactions (chemical networks) has been demonstrated to be a valuable tool for identifying subensembles of chemical environments.

Origins of Clustering of Metalate-Extractant Complexes in Liquid-Liquid Extraction.

Effective and energy-efficient separation of precious and rare metals is very important for a variety of advanced technologies. Liquid-liquid extraction (LLE) is a relatively less energy intensive separation technique, widely used in separation of lanthanides, actinides, and platinum group metals (PGMs). In LLE, the distribution of an ion between an aqueous phase and an organic phase is determined by enthalpic (coordination interactions) and entropic (fluid reorganization) contributions.

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics.

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a "ring polymer" whose spread is related to the quantum mechanical uncertainty in the particle's position, i.e.