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At least 91 records · Page 5

Finding predictive models for singlet fission by machine learning

Singlet fission (SF), the conversion of one singlet exciton into two triplet excitons, could significantly enhance solar cell efficiency. Molecular crystals that undergo SF are scarce. Computational exploration may accelerate the discovery of SF materials. However, many-body perturbation theory (MBPT) calculations of the excitonic properties of molecular crystals are impractical for large-scale materials screening. We use the sure-independence-screening-and-sparsifying-operator (SISSO) machine-learning algorithm to generate computationally efficient models that can predict the MBPT thermodynamic driving force for SF for a dataset of 101 polycyclic aromatic hydrocarbons (PAH101). SISSO generates models by iteratively combining physical primary features. The best models are selected by linear regression with cross-validation. The SISSO models successfully predict the SF driving force with errors below 0.2 eV. Based on the cost, accuracy, and classification performance of SISSO models, we propose a hierarchical materials screening workflow. Three potential SF candidates are found in the PAH101 set.

36 MATERIALS SCIENCE↗

Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

Abstract Background Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4′ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4′ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4′ ether bond cleavage, 27.0% C α -C 1 carbon bond cleavage, and 3.6% C α -oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4′ bonds. Conclusion These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.

09 BIOMASS FUELS↗

Artificial intelligence in computational materials science

In this themed collection we aim to broadly review some of the critical, recent progress in the application of AI/ML to various aspects of computational materials science and materials science more broadly. In this collection spread across two issues, we have assembled a collection of articles from leaders in the broad domain of applying AI/ML, which we collectively refer to as ML, in computational materials science. Together these articles curate the critical, recent progress in the application of ML to various aspects of materials science. Furthermore, these include ML approaches for understanding and driving electron microscopy, designing energy materials and the discovery of principles and materials relevant to the design of materials for the future, studying crystal nucleation and growth, the use of ML to describe force fields governing material and molecular behavior, and other topics.

36 MATERIALS SCIENCE↗

Fragment-based drug nanoaggregation reveals drivers of self-assembly

Drug nanoaggregates are particles that can deleteriously cause false positive results during drug screening efforts, but alternatively, they may be used to improve pharmacokinetics when developed for drug delivery purposes. The structural features of molecules that drive nanoaggregate formation remain elusive, however, and the prediction of intracellular aggregation and rational design of nanoaggregate-based carriers are still challenging. We investigate nanoaggregate self-assembly mechanisms using small molecule fragments to identify the critical molecular forces that contribute to self-assembly. We find that aromatic groups and hydrogen bond acceptors/donors are essential for nanoaggregate formation, suggesting that both π-π stacking and hydrogen bonding are drivers of nanoaggregation. We apply structure-assembly-relationship analysis to the drug sorafenib and discover that nanoaggregate formation can be predicted entirely using drug fragment substructures. We also find that drug nanoaggregates are stabilized in an amorphous core-shell structure. These findings demonstrate that rational design can address intracellular aggregation and pharmacologic/delivery challenges in conventional and fragment-based drug development processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes

Conspectus Given the universal importance of electrolyte solutions, it is natural to expect that we have a nearly complete understanding of the fundamental properties of these solutions (e.g., the chemical potential) and that we can therefore explain, predict, and control the phenomena occurring in them. In fact, reality falls short of these expectations. But, recent advances in the simulation and modeling of electrolyte solutions indicate that it should soon be possible to make progress toward these goals. In this Account, we will discuss the use of first-principles interaction potentials based in quantum mechanics (QM) to enhance our understanding of electrolyte solutions. Specifically, we will focus on the use of quantum density functional theory (DFT) combined with molecular dynamics simulation (DFT-MD) as the foundation for our approach. The overarching concept is to understand and accurately reproduce the balance between local or short-ranged (SR) structural details and long-range (LR) correlations, allowing the prediction of the thermodynamics of both single ions in solution as well as the collective interactions characterized by activity/osmotic coefficients. In doing so, relevant collective motions and driving forces characterized by chemical potentials can be determined. Here, in this Account, we will make the case that understanding electrolyte solutions requires a faithful QM representation of the SR nature of the ion–ion, ion–water, and water–water interactions. However, the number of molecules that is required for collective behavior makes the direct application of high-level QM methods that contain the best SR physics untenable, making methods that balance accuracy and efficiency a practical goal. Alternatives such as continuum solvent models (CSMs) and empirically based classical molecular dynamics have been extensively employed to resolve this problem but without yet overcoming the fundamental issue of SR accuracy. We will demonstrate that accurately describing the SR interaction is imperative for predicting both intrinsic properties, namely, at infinite dilution, and collective properties of electrolyte solutions. DFT has played an important role in our understanding of condensed phase systems, e.g., bulk liquid water, the air–water interface, ions in bulk, and at the air–water interface. This approach holds huge promise to provide benchmark calculations of electrolyte solution properties that will allow for the development and improvement of more efficient methods, as well as an enhanced understanding of fundamental phenomena. However, the standard protocol using the generalized gradient approximation with van der Waals (vdW) correction requires improvement in order to achieve a high level of quantitative accuracy. Simply simulating with higher level DFT functionals may not be the best route considering the significant computational cost. Alternative methods of incorporating information from higher levels of QM should be explored; e.g., using force matching techniques on small clusters, where high level benchmark calculations are possible, to develop ideal correction terms to the DFT functional is a promising possibility. We argue that DFT with statistical mechanics is becoming an increasingly useful framework enabling the prediction of collective electrolyte properties.

Duignan, Timothy T.↗

Interface-modulated kinetic differentials in electron and hole transfer rates as a key design principle for redox photocatalysis by Sb2VO5/QD heterostructures

The efficient conversion of solar energy to chemical energy represents a critical bottleneck to the energy transition. Photocatalytic splitting of water to generate solar fuels is a promising solution. Semiconductor quantum dots (QDs) are prime candidates for light-harvesting components of photocatalytic heterostructures, given their size-dependent photophysical properties and band-edge energies. A promising series of heterostructured photocatalysts interface QDs with transition-metal oxides which embed midgap electronic states derived from the stereochemically active electron lone pairs of p-block cations. Here, we examine the thermodynamic driving forces and dynamics of charge separation in Sb2VO5/CdSe QD heterostructures, wherein a high density of Sb 5s2-derived midgap states are prospective acceptors for photogenerated holes. Hard-x-ray valence band photoemission spectroscopy measurements of Sb2VO5/CdSe QD heterostructures were used to deduce thermodynamic driving forces for charge separation. Interfacial charge transfer dynamics in the heterostructures were examined as a function of the mode of interfacial connectivity, contrasting heterostructures with direct interfaces assembled by successive ion layer adsorption and reaction (SILAR) and interfaces comprising molecular bridges assembled by linker-assisted assembly (LAA). Transient absorption spectroscopy measurements indicate ultrafast (<2 ps) electron and hole transfer in SILAR-derived heterostructures, whereas LAA-derived heterostructures show orders of magnitude differentials in the kinetics of hole (<100 ps) and electron (∼1 ns) transfer. The interface-modulated kinetic differentials in electron and hole transfer rates underpin the more effective charge separation, reduced charge recombination, and greater photocatalytic efficiency observed for the LAA-derived Sb2VO5/CdSe QD heterostructures.

Chemistry↗

Driving force and pathway in polyelectrolyte complex coacervation

There is notable discrepancy between experiments and coarse-grained model studies regarding the thermodynamic driving force in polyelectrolyte complex coacervation: experiments find the free energy change to be dominated by entropy, while simulations using coarse-grained models with implicit solvent usually report a large, even dominant energetic contribution in systems with weak to intermediate electrostatic strength. Here, using coarse-grained, implicit-solvent molecular dynamics simulation combined with thermodynamic analysis, we study the potential of mean force (PMF) in the two key stages on the coacervation pathway for symmetric polyelectrolyte mixtures: polycation–polyanion complexation and polyion pair–pair condensation. We show that the temperature dependence in the dielectric constant of water gives rise to a substantial entropic contribution in the electrostatic interaction. By accounting for this electrostatic entropy, which is due to solvent reorganization, we find that under common conditions (monovalent ions, room temperature) for aqueous systems, both stages are strongly entropy-driven with negligible or even unfavorable energetic contributions, consistent with experimental results. Furthermore, for weak to intermediate electrostatic strengths, this electrostatic entropy, rather than the counterion-release entropy, is the primary entropy contribution. From the calculated PMF, we find that the supernatant phase consists predominantly of polyion pairs with vanishingly small concentration of bare polyelectrolytes, and we provide an estimate of the spinodal of the supernatant phase. Finally, we show that prior to contact, two neutral polyion pairs weakly attract each other by mutually induced polarization, providing the initial driving force for the fusion of the pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Homogeneous ice nucleation in an ab initio machine-learning model of water

Molecular simulations have provided valuable insight into the microscopic mechanisms underlying homogeneous ice nucleation. While empirical models have been used extensively to study this phenomenon, simulations based on first-principles calculations have so far proven prohibitively expensive. Here, we circumvent this difficulty by using an efficient machine-learning model trained on density-functional theory energies and forces. We compute nucleation rates at atmospheric pressure, over a broad range of supercoolings, using the seeding technique and systems of up to hundreds of thousands of atoms simulated with ab initio accuracy. The key quantity provided by the seeding technique is the size of the critical cluster (i.e., a size such that the cluster has equal probabilities of growing or melting at the given supersaturation), which is used together with the equations of classical nucleation theory to compute nucleation rates. We find that nucleation rates for our model at moderate supercoolings are in good agreement with experimental measurements within the error of our calculation. We also study the impact of properties such as the thermodynamic driving force, interfacial free energy, and stacking disorder on the calculated rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tradeoff between Intermolecular Interaction and Backbone Disorder by High Molecular Dipole Block for Improving Blend Morphology of Polymer Solar Cells

Constructing terpolymer has attracted increasing attention as a strategy to improve the performance of polymer solar cell. Terpolymer usually offers an opportunity to lower the frontier molecular orbital energy level, introduces additional absorption band and sometimes optimizes the morphology of the active blend. Generally, the additional segment in terpolymer backbone inevitably introduces backbone disorder, which causes entropy rises. However, selecting a suitable dipole unit introduces extra driving forces for crystallization by enhancing intermolecular interactions. This provides a handy knob for tradeoff between intermolecular interaction and backbone disorder, thus regulating the blend morphology. In this study, a high dipole and electron-deficient group of pyrrolo[3,4-f ]benzotriazole-5,7(6H)-dione (TzBI) is incorporated into the high-performance donor polymer and a series of terpolymers with different content of TzBI are designed. As expected, the morphology is optimized gradually for improving charge generation and charge transport, also suppressing charge recombination. The champion device with 10% TzBI exhibited a power conversion efficiency (PCE) of 18.36%, which is 5% increase compared to the controlled device. This study presents a charming terpolymer strategy by highly electron-deficient and high dipole segment to realize a tradeoff between intermolecular interaction and backbone disorder, facilitating the optimization of morphology and elevation of fill factor and device efficiency.

36 MATERIALS SCIENCE↗

Molecular Dynamics Simulation and Cryo-Electron Microscopy Investigation of AOT Surfactant Structure at the Hydrated Mica Surface

Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.

58 GEOSCIENCES↗

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Electron Injection from Singlet Fission-Borne Triplets into Mesoporous Transparent Conducting Oxides

Photoinduced electron transfer from a molecular chromophore into mesoporous metal oxide substrates occurs efficiently from both singlet and triplet excited states for traditional metal-to-ligand charge transfer (MLCT) dyes. All organic molecules that undergo singlet fission (SF), the process of generating two triplet excitons with photoexcitation of one singlet exciton, offers a promising method of generating two charges per one absorbed photon. However, the singlet-triplet energy balance required to drive SF often places the driving force for triplet electron injection into metal oxides too low. As such, the dynamics of singlet vs. triplet electron transfer for SF in dye-sensitized solar cell configurations has not been elucidated. Here, we use applied bias transient absorption spectroscopy to modulate the driving force for triplet electron transfer from an anthradithiophene-based SF chromophore (ADT-COOH) adsorbed to mesoporous indium tin oxide (nanoITO).

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗

A Hybrid Quantum–Classical Study of Ion Adsorption at the Copper Electrode

Here, we present a set of computational studies that surveys the molecular structure and thermodynamics of simple ions at the electrode–electrolyte interface. A hybrid quantum–classical approach is used to obtain free energy profiles and solvent structure as a function of the ion’s position relative to the electrochemical liquid/solid interface and system potential. Model systems consist of a copper electrode and single halide or alkali metal ion in contact with an implicit solvent and reveal new insights into the interplay of forces that drive or resist ion absorption at the electrode/ electrolyte interface. We also expand on subtleties of absorption site preference and describe the complex relationship between the energetic barrier to absorption and the ion–electrode binding energy as a function of electrode potential.

36 MATERIALS SCIENCE↗

Corrigendum and Addendum: Helium flux effects on bubble growth and surface morphology in plasma-facing tungsten from large-scale molecular dynamics simulations (2019 Nucl. Fusion 59 066035)

Two of the simulations discussed in a prior article (Hammond et al 2019 Nucl. Fusion 59 066035) were affected by a simulation glitch. We repeated the affected calculations and discuss them here. Here, the overall conclusions are essentially unchanged, though the details are different. In particular, observations that we referred to as ‘concerted bursting’ were caused primarily by non-physical heating and cooling applied by the thermostat after most atoms’ velocities were deleted (for reasons that are not known for certain). The phenomenon of one bubble bursting and causing another nearby bubble to burst does exist, though its effects are much less spectacular in the absence of non-physical driving forces. The observation of an interconnected network of sub-surface cavities formed by burst bubbles is real, and the observation of holes on the surface 1–2 nm in diameter is also confirmed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗

Pathways for Nucleation and Growth in Confined Spaces and at Interfaces

Mineral crystallization is central to myriad natural processes from the formation of snowflakes to stalagmites, but the molecular-scale mechanisms are often far more complex than models reflect. Feedbacks between the hydro-, bio-, and geo-spheres drive complex crystallization processes that challenge our ability to observe and quantify them, motivating an expansion of crystallization theories. Here, in this article, we discuss how the driving forces and timescales of nucleation are influenced by factors ranging from simple geometric confinement to distinct interfacial solution structures involving solvent organization, electrical double layers, and surface charging effects. Taken together, these ubiquitous natural phenomena can preserve metastable intermediates, drive precipitation of undersaturated phases, and modulate crystallization in time and space.

biosphere↗

Local conformations and heterogeneities in structures and dynamics of isotactic polypropylene adsorbed onto carbon fiber

Carbon fiber (CF) reinforced polymers (CFRPs) have experienced widespread use in various industries. One of the most important parameters that controls the macroscopic property of CFRPs is the interface between a polymer matrix and CF. There is growing evidence to suggest the formation of a bound polymer layer (BPL), i.e., polymer chains that physically adsorb on a filler surface. However, this interface is always in contact with the thicker part of a polymer matrix, rendering its understanding a difficult task. Therein, we use CF-reinforced isotactic polypropylene (iPP) as a rational CFRP. To characterize the BPL on the CF surface, we extracted it from the CFRP using solvent-rinsing with p-xylene. The physical and thermal properties of the BPL were characterized by differential scanning calorimetry and thermogravimetric analysis, while its microscopic structures and dynamics were probed by small-angle neutron scattering and quasi-elastic neutron scattering (QENS) techniques. Subsequently, we employed atomistic molecular dynamics (MD) simulations to complement the QENS results above the bulk melting temperature and reveal details that were experimentally inaccessible. In this work, we observed that the degree of crystallinity of the BPL was quite lower than the bulk, while the melting temperature of the BPL remained the same as the bulks. Within the given length and time scales probed by QENS and MD, we also observed that most of the bound chains were mobile, with the formation of a high-density region (less than 1 nm in thickness) near the CF surface. The segmental dynamics of the bound chains probed by both QENS and MD were also much faster than those of the free chains, possibly due to the presence of a free surface region at the topmost surface of the BPL. Furthermore, the MD results demonstrated that the backbone chains and side groups lie nearly flat on the CF surface, which is the driving force for the flattening process of the iPP BPL to overcome the conformational entropy loss in the total free energy.

36 MATERIALS SCIENCE↗

Cyclopropenylidenes as Strong Carbene Anchoring Groups on Au Surfaces

The creation of stable molecular monolayers on metallic surfaces is a fundamental challenge of surface chemistry. N-Heterocyclic carbenes (NHCs) were recently shown to form self-assembled monolayers that are significantly more stable than the traditional thiols on Au system. In this study, we theoretically and experimentally demonstrate that the smallest cyclic carbene, cyclopropenylidene, binds even more strongly than NHCs to Au surfaces without altering the surface structure. We deposit bis(diisopropylamino)cyclopropenylidene (BAC) on Au(111) using the molecular adduct BAC–CO 2 as a precursor and determine the structure, geometry, and behavior of the surface-bound molecules through high-resolution X-ray photoelectron spectroscopy, atomic force microscopy, and scanning tunneling microscopy. Our experiments are supported by density functional theory calculations of the molecular binding energy of BAC on Au(111) and its electronic structure. Our work is the first demonstration of surface modification with a stable carbene other than NHC; more broadly, it drives further exploration of various carbenes on metal surfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗