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At least 73 records · Page 4

Energetics of high temperature degradation of fentanyl into primary and secondary products

Fentanyl is a synthetic opioid used for managing chronic pain. Due to its higher potency (50–100×) than morphine, fentanyl is also an abused drug. A sensor that could detect illicit fentanyl by identifying its thermally degraded fragments would be helpful to law enforcement. While experimental studies have probed the thermal degradation of fentanyl, little theoretical work has been done to understand the mechanism. Here, we studied the thermal degradation pathways of fentanyl using extensive ab initio molecular dynamics simulations combined with enhanced sampling via multiple-walker metadynamics. We calculated the free energy profile for each bond suggested earlier as a potential degradation point to map the thermodynamic driving forces. In conclusion, we also estimated the forward attempt rate of each bond degradation reaction to gain information about degradation kinetics.

Poudel, Bharat↗

Specific Ion Solvation and Pairing Effects in Glycerol Carbonate

Identifying the driving forces behind the solvation of inorganic salts by nonaqueous solvents is an important step in the development of green solvents. Here we focus on one promising solvent: glycerol carbonate (GC). Using ab initio molecular dynamics simulations, we build upon our previous work by detailing glycerol carbonate’s interactions with a series of anions, a lithium ion, and the LiF ion pair. Through these investigations, we highlight the changes in solvation behavior as the anion size increases, the competition of binding shown by lithium for the oxygens of GC, and the behavior of the LiF ion pair in a GC solution. These results in this work indicate the importance of the cation’s identity in ion-pairing structure and dynamics and lend insight into the key factors behind the specific ion effects seen in GC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystals of Benzamide, the First Polymorphous Molecular Compound, Are Helicoidal

Abstract The growth of spontaneously twisted crystals is a common but poorly understood phenomenon. An analysis of the formation of twisted crystals of a metastable benzamide polymorph (form II ) crystallizing from highly supersaturated aqueous and ethanol solutions is given here. Benzamide, the first polymorphic molecular crystal reported (1832), would have been the first helicoidal crystal observed had the original authors undertaken an analysis by light microscopy. Polymorphism and twisting frequently concur as they are both associated with high thermodynamic driving forces for crystallization. Optical and electron microscopies as well as electron and powder X‐ray diffraction reveal a complex lamellar structure of benzamide form II needle‐like crystals. The internal stress produced by the overgrowth of lamellae is shown to be able to create a twist moment that is responsible for the observed non‐classical morphologies.

Shtukenberg, Alexander G.↗

Atomistic simulations of dislocation mobility in refractory high-entropy alloys and the effect of chemical short-range order

Abstract Refractory high-entropy alloys (RHEAs) are designed for high elevated-temperature strength, with both edge and screw dislocations playing an important role for plastic deformation. However, they can also display a significant energetic driving force for chemical short-range ordering (SRO). Here, we investigate mechanisms underlying the mobilities of screw and edge dislocations in the body-centered cubic MoNbTaW RHEA over a wide temperature range using extensive molecular dynamics simulations based on a highly-accurate machine-learning interatomic potential. Further, we specifically evaluate how these mechanisms are affected by the presence of SRO. The mobility of edge dislocations is found to be enhanced by the presence of SRO, whereas the rate of double-kink nucleation in the motion of screw dislocations is reduced, although this influence of SRO appears to be attenuated at increasing temperature. Independent of the presence of SRO, a cross-slip locking mechanism is observed for the motion of screws, which provides for extra strengthening for refractory high-entropy alloy system.

36 MATERIALS SCIENCE↗

Determination of Thermal Expansion, Defect Formation Energy, and Defect-Induced Strain of α-U Via ab Initio Molecular Dynamics

Uranium (U) is often alloyed with molybdenum (Mo) or zirconium (Zr) in order to stabilize its high-temperature body-centered cubic phase for use in nuclear reactors. However, in all metallic fuel forms, the α phase of U remains in some fraction. This phase decomposition due to temperature or compositional variance can play an outsized role on fuel performance and microstructural evolution. Relatively little is known about fundamental point defect properties in α -U at non-zero temperatures, from either computational or experimental studies. This work performs the first thorough evaluation of the α phase of U via ab initio molecular dynamics (AIMD). A number of thermophysical properties are calculated as a function of temperature, including equilibrium lattice parameters, thermal expansion, and heat capacity. These results indicate a two-region behavior, with the transition at 400 K. The thermal expansion/contraction in the a / b direction occurs rapidly from 100 up to 400 K, after which a more linear and gradual change in the lattice constant takes place. The volumetric expansion matches experiments quantitatively, but the individual lattice constant expansion only matches experiments qualitatively. Point defect formation energies and induced lattice strains are also determined as a function of temperature, providing insight on defect populations and the fundamentals of irradiation growth in α -U. Interstitials induce significantly more strain than vacancies, and the nature of that strain is highly dependent on the individual lattice directions. The direction of point defect-induced lattice strain is contrary to the irradiation growth behavior of α -U. This work shows that isolated point defects cannot be the primary driving force responsible for the significant irradiation-induced growth of α -U observed experimentally.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

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↗