Crystallization of trans-stilbene derivatives via bound-sphere kinetic Monte Carlo in SPPARKS (Stochastic Parallel PARticle Kinetic Simulator)
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Janicki, Tesia Danielle↗
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Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity
1,3-Dimethyl-2,3-dihydrobenzo[ d ]imidazoles, 1H , and 1,1',3,3'-tetramethyl-2,2',3,3'-tetrahydro-2,2'-bibenzo[ d ]imidazoles, 1 2 , are of interest as n-dopants for organic electron-transport materials. Salts of 2-(4-(dimethylamino)phenyl)-4,7-dimethoxy-, 2-cyclohexyl-4,7-dimethoxy-, and 2-(5-(dimethylamino)thiophen-2-yl)benzo[ d ]imidazolium ( 1g–i + , respectively) have been synthesized and reduced with NaBH 4 to 1gH , 1hH , and 1iH , and with Na:Hg to 1g 2 and 1h 2 . Their electrochemistry and reactivity were compared to those derived from 2-(4-(dimethylamino)phenyl)- ( 1b + ) and 2-cyclohexylbenzo[ d ]imidazolium ( 1e + ) salts. E ( 1 + / 1 • ) values for 2-aryl species are less reducing than for 2-alkyl analogues, i.e., the radicals are stabilized more by aryl groups than the cations, while 4,7-dimethoxy substitution leads to more reducing E ( 1 + / 1 • ) values, as well as cathodic shifts in E ( 1 2 •+ / 1 2 ) and E ( 1H •+ / 1H ) values. Both the use of 3,4-dimethoxy and 2-aryl substituents accelerates the reaction of the 1H species with PC 61 BM. Because 2-aryl groups stabilize radicals, 1b 2 and 1g 2 exhibit weaker bonds than 1e 2 and 1h 2 and thus react with 6,13-bis(triisopropylsilylethynyl)pentacene ( VII ) via a “cleavage-first” pathway, while 1e 2 and 1h 2 react only via “electron-transfer-first”. 1h 2 exhibits the most cathodic E ( 1 2 •+ / 1 2 ) value of the dimers considered here and, therefore, reacts more rapidly than any of the other dimers with VII via “electron-transfer-first”. Crystal structures show rather long central C–C bonds for 1b 2 (1.5899(11) and 1.6194(8) Å) and 1h 2 (1.6299(13) Å).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Chapmanite [Fe 2 Sb(Si 2 O 5 )O 3 (OH)]: thermodynamic properties and formation in low-temperature environments
Abstract. of synthetic Sb 2 O 5 , MgSb 2 O 6 (analogue of the mineral byströmite), Mg[Sb(OH) 6 ] 2 ∙6H 2 O (brandholzite), and natural chapmanite [(Fe 1.88 Al 0.12 )Sb(Si 2 O 5 )O 3 (OH)]. Enthalpies of reactions, including formation enthalpies, were evaluated using reference compounds Sb, Sb 2 O 3 , Sb 2 O 5 , and other phases, with high-temperature oxide melt solution calorimetry in lead borate and sodium molybdate solvents. Heat capacity and entropy were determined by relaxation and differential scanning calorimetry. The best set of Δ f H o (kJ mol -1 ) and S o (J mol -1 K -1 ) is byströmite -1733.0±3.6, 139.3±1.0; brandholzite -5243.1±3.6, 571.0±4.0; and chapmanite -3164.9±4.7, 305.1±2.1. The data for chapmanite give Δ f G o of -2973.6±4.7 kJ mol -1 and log K=-17.10 for the dissolution reaction (Fe 1.88 Al 0.12 )Sb(Si 2 O 5 )O 3 (OH) + 6H + → 1.88Fe 3+ + 0.12Al 3+ + 2SiO$_2^0$ + Sb(OH)$_3^0$ + 2H 2 O. Analysis of the data showed that chapmanite is finely balanced in terms of its stability with schafarzikite (FeSb 2 O 4 ) and tripuhyite (FeSbO 4 ) under a specific, narrow range of conditions when both aqueous Fe(III) and Sb(III) are abundant. In such a model, chapmanite is metastable by a narrow margin but could be stabilized by high SiO$_2^0$(aq) activities. Natural assemblages of chapmanite commonly contain abundant amorphous silica, suggesting that this mechanism may be indeed responsible for the formation of chapmanite. Chapmanite probably forms during low-temperature hydrothermal overprint of pre-existing Sb ores under moderately reducing conditions; the slightly elevated temperatures may help to overcome the kinetic barrier for its crystallization. During weathering, sheet silicates may adsorb Sb 3+ in tridentate hexanuclear fashion, thus exposing their chapmanite-like surfaces to the surrounding aqueous environment. Formation of chapmanite, as many other sheet silicates, under ambient conditions, is unlikely.
58 GEOSCIENCES↗
Mapping Interfacial Solution Forces that Drive Fluorescent Nanoparticle Incorporation into Crystals
Interfacial solution structure governs processes ranging from catalytic and electrochemical reactions to particle aggregation and crystallization. Here, we design bio-inspired nanocomposites by mapping interfacial forces and controlling nanoparticle incorporation during crystal growth. Our analytical model contains measured kinetic barriers for surface approaches and equilibrium binding constants with the crystal surface. We validate this model using fluorescent silica nanoparticles and calcite. Our results show that surface chemistry dictates incorporation pathways: methoxy groups are least favorable, hydroxyls reduce kinetic barriers by interacting favorably with hydration layers, carboxylates bind strongly but must overcome a kinetic barrier, and amines outperform all kinetically and thermodynamically. This framework resolves the interplay between interfacial solution structures, particle forces and dynamics, and growth kinetics, enabling predicative control of nanocomposite formation and multiplexed mixed-particle systems.
Zhang, Mingyi [Pacific Northwest National Laborato↗
Decoding Zeolite Crystallization and Stage III in Nuclear Waste Glasses by Coupled Modeling and Experiments
Under specific conditions of pH and temperature, nuclear waste immobilization borosilicate glasses may exhibit a sudden acceleration in their corrosion kinetics (stage III)—a behavior that has been associated with the formation of zeolite crystals. Such accelerated dissolution may compromise the integrity of nuclear wasteforms placed in geological depositories. However, thus far, none of the available models is able to predict the thermodynamic propensity and kinetics of zeolite precipitation as a function of the solution conditions due to (i) a lack of fundamental knowledge regarding the nucleation & growth mechanisms of zeolitic phases, (ii) uncertainty regarding the compositions (types) of zeolites that may form and the rate-limiting step in their precipitation as a function of the solution conditions, and (iii) the complexities that arise due to the vast parametric space (i.e., solution chemistry, temperature, number of secondary phases, etc.) that encompass these systems under conditions of environmental exposure. To resolve these challenges, this project aimed to unambiguously identify the thermodynamic propensity for zeolite precipitation and the kinetics thereof as a function of the solution conditions (composition, pH, and temperature). To achieve this goal: 1) We identified the solution conditions and zeolite phases relevant to nuclear glass dissolution. 2) We performed a series of ab initio molecular dynamics (AIMD) simulations to compute the thermodynamic properties of a group of characteristic zeolites that features a large range of compositions, various hydration levels, a wide range of framework structures, and partial atomic site occupancies. 3) We released a first-of-a-kind self-consistent thermodynamic database that can be used to assess the kinetics and the stability fields of zeolitic phases within a Gibbs energy minimization (GEM) framework. 4) We developed a robust geochemical modeling method allowing us to predict the stability of secondary phases (including zeolites, calcium–silicate–hydrate gels, and clays) upon the dissolution of nuclear waste immobilization glasses. 5) We introduced a model that predicts the dissolution kinetics of a series of borosilicate nuclear waste immobilization glasses in terms of the topology of their atomic network. 6) We investigated the roles of the solution composition on the crystallization kinetics of phillipsite zeolites and tobermorite silicate hydrates. Via PNNL’s collaboration and engagement, this project directly supports DOE’s nuclear waste immobilization activities by offering a technical, science-based foundation that will (i) facilitate predictions of the long-term corrosion rates and extents of existing nuclear waste immobilization glasses to help ensure safe and successful vitrification operations, (ii) inform the development of advanced glass formulations with enhanced durability, and, (iii) enable cost-savings that result from making more decisive and hence less conservative predictions while offering higher levels of nuclear waste embedment in smaller, more compact glass volumes.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
In situ TEM study of crystallization and chemical changes in an oxidized uncapped Ge 2 Sb 2 Te 5 film
Ge 2 Sb 2 Te 5 (GST-225) has been the most used active material in nonvolatile phase-change memory devices. Understanding the kinetics and dynamics involved in crystallization is critical for the optimization of materials and devices. A GST-225 thin film of 20 nm thickness was prepared by sputtering directly onto a Protochip and left uncapped and exposed to atmosphere for approximately 1 year. Here, early stages of crystallization and growth of the film have been studied inside the TEM from room temperature to 140 °C. The morphological and structural transformations have been studied by a C s -corrected environmental TEM, and images have been recorded using a high-speed low electron dose camera (Gatan K3 IS). The amorphous to crystalline transformation has been observed at ~35 °C. From the large field, high-resolution images obtained using the Gatan K3 IS camera early crystallization can be detected and nucleation rates and growth velocities can be obtained.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Citation for the 2019 Victor M. Goldschmidt award to Donald J. DePaolo
Perhaps the comments most commonly heard when a colleague receives professional recognition are “well-deserved” and “long-overdue”. As such, it is my pleasure to introduce Donald DePaolo as the recipient of this year’s Goldschmidt Award as it is both long-overdue and so well-deserved. While Don has received many honors over the course of his career, the Goldschmidt best recognizes his broad impact on geochemistry. There are few who have contributed as much to geochemistry as Don DePaolo. Finally, his scientific contributions are voluminous and broad, ranging from pioneering efforts to establish the Sm/Nd isotopic system, and its applications to mantle evolution and basalt petrogenesis, to studies of magma mixing, assimilation and crystal fractionation, to evolution of the lower crust and granite petrogenesis, to chemical oceanography, diagenesis and seafloor alteration, to reactive transport accompanying rock-water interaction, and to kinetic isotopic fractionation associated with crystal growth, diffusion and evaporation.
58 GEOSCIENCES↗
Single-Crystallization of O3-Type Layered Oxide Cathode for Na-Ion Battery
The development of high-energy-density Na-ion batteries places significant demands on single-crystal layered oxide cathodes, especially for further high-voltage, solid-state battery scenarios. In the O3-type structure, due to the original sluggish Na ion diffusion kinetics (approximately 1 order of magnitude lower than that of Li-ion), and further hindrance against diffusion kinetics caused by single-crystal architecture, these inherent defects lead to the decline in the electrochemical performance. Herein, we demonstrated that the single crystallization of O3-type NaNi 1/3 Fe 1/3 Mn 1/3 O 2 cathode (d 50 = 5.04 μm) aggravates surface-to-bulk phase inhomogeneity distribution, which is attributed to the uneven Na ions extraction. Moreover, the Na-depletion of the surface/shell region not only aggravates Na ion diffusion resistance but also leads to a higher valence state of transition-metal elements (e.g., Ni/Fe) near the surface of the single-crystal particle, which further compromises the cathode-electrolyte interface stability. Furthermore, not limited to revealing the challenges, tuning the particle size and moderating quasi-single-crystal strategies have been proven to effectively mitigate the negative uneven distributions of Na ions, phases, and valence/oxidative states, resulting in efficient modification for single crystallization of Na-layered oxide cathodes.
36 MATERIALS SCIENCE↗
Luminescence relaxation dynamics for planar and rolled-up CdSe nanocrystals in a photonic-crystal matrix
Samples of inverted photonic-crystal films, containing planar and rolled-up (in the form of scrolls) CdSe nanocrystals, are studied. The transmission spectra of these structures are recorded. These spectra (along with the change in colour) confirm the incorporation of nanocrystals into the films. The photoluminescence decay dynamics is investigated. It is shown that the photonic-crystal matrix affects significantly the luminescence kinetics of nanostructures. The differences in the decay curves measured for nanocrystals in a photonic-crystal matrix and for their ensemble on a glass substrate are explained by the influence of the photonic-crystal stop band and the orientational effect of crystalline matrix, which orients anisotropic nanocrystals and prevents them from aggregation. The results obtained may be important for potential applications in optoelectronic devices. (paper)
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Controlled Placement of Trivalent Heteroatoms in MFI Zeolite Frameworks Using Structure-Directing Agents
MFI zeolites contain distinct confining pore environments, either smaller (∼0.55 nm) channels or larger (∼0.70 nm) intersections. The substitution of trivalent heteroatoms generates Brønsted acid sites of varying acid strength, which, together with their location within different pore environments, dictates the stability of transition states via electrostatic (ion-pair) and van der Waals interactions. Here, we report that structure-directing agents (SDAs) that control Al 3+ substitutional patterns during MFI crystallization analogously position other trivalent heteroatoms (Ga 3+ , Fe 3+ , B 3+ ), altering the distribution of acid sites between channels and intersections, as probed by low-temperature (403 K) toluene methylation kinetics. Heteroatom-substituted MFI crystallized with tetrapropylammonium result in low selectivity toward p-xylene (<30%), while those crystallized using (co-)SDAs containing peripheral hydrogen-bonding groups (e.g., ethylenediamine) show high p-xylene selectivity (∼80%). These selectivities are consistent with DFT-calculated Gibbs free energy barriers for intersection-dominant and channel-dominant active site distributions, respectively. Transition states to form each xylene isomer are similar in size and charge; thus, their rate constants decrease with acid strength similarly, causing isomer selectivity to depend strongly on confinement but not on acid strength. These generalizable synthetic strategies enable independently controlling acid site strength and location in MFI zeolites and, in turn, catalytic rates and selectivities.
36 MATERIALS SCIENCE↗
Numerical simulations of three-dimensional ion crystal dynamics in a Penning trap using the fast multipole method
We simulate the dynamics, including laser cooling, of three-dimensional (3-D) ion crystals confined in a Penning trap using a newly developed molecular dynamics-like code. The numerical integration of the ions’ equations of motion is accelerated using the fast multipole method to calculate the Coulomb interaction between ions, which allows us to efficiently study large ion crystals with thousands of ions. In particular, we show that the simulation time scales linearly with ion number, rather than with the square of the ion number. By treating the ions’ absorption of photons as a Poisson process, we simulate individual photon scattering events to study laser cooling of 3-D ellipsoidal ion crystals. Initial simulations suggest that these crystals can be efficiently cooled to ultracold temperatures, aided by the mixing of the easily cooled axial motional modes with the low frequency planar modes. In our simulations of a spherical crystal of 1000 ions, the planar kinetic energy is cooled to several millikelvin in a few milliseconds while the axial kinetic energy and total potential energy are cooled even further. This suggests that 3-D ion crystals could be well suited as platforms for future quantum science experiments.
Zaris, John (ORCID:0009000196476323)↗
A Novel Glutathione S-Transferase Gtt2 Class (VpGSTT2) Is Found in the Genome of the AHPND/EMS Vibrio parahaemolyticus Shrimp Pathogen
Glutathione S-transferases are a family of detoxifying enzymes that catalyze the conjugation of reduced glutathione (GSH) with different xenobiotic compounds using either Ser, Tyr, or Cys as a primary catalytic residue. We identified a novel GST in the genome of the shrimp pathogen V. parahaemolyticus FIM- S1708+, a bacterial strain associated with Acute Hepatopancreatic Necrosis Disease (AHPND)/Early Mortality Syndrome (EMS) in cultured shrimp. This new GST class was named Gtt2. It has an atypical catalytic mechanism in which a water molecule instead of Ser, Tyr, or Cys activates the sulfhydryl group of GSH. The biochemical properties of Gtt2 from Vibrio parahaemolyticus (VpGSTT2) were characterized using kinetic and crystallographic methods. Recombinant VpGSTT2 was enzymatically active using GSH and CDNB as substrates, with a specific activity of 5.7 units/mg. Low affinity for substrates was demonstrated using both Michaelis–Menten kinetics and isothermal titration calorimetry. The crystal structure showed a canonical two-domain structure comprising a glutathione binding G-domain and a hydrophobic ligand H domain. A water molecule was hydrogen-bonded to residues Thr9 and Ser 11, as reported for the yeast Gtt2, suggesting a primary role in the reaction. Molecular docking showed that GSH could bind at the G-site in the vicinity of Ser11. G-site mutationsT9A and S11A were analyzed. S11A retained 30% activity, while T9A/S11A showed no detectable activity. VpGSTT2 was the first bacterial Gtt2 characterized, in which residues Ser11 and Thr9 coordinated a water molecule as part of a catalytic mechanism that was characteristic of yeast GTT2. The GTT2 family has been shown to provide protection against metal toxicity; in some cases, excess heavy metals appear in shrimp ponds presenting AHPND/EMS. Further studies may address whether GTT2 in V. parahaemolyticus pathogenic strains may provide a competitive advantage as a novel detoxification mechanism.
59 BASIC BIOLOGICAL SCIENCES↗
Interplay of molten salt and dopants in tuning the performance of single-crystalline LiNiO 2
Single-crystalline layered oxide cathodes have seen great research interest in recent years. Adoption of single-crystal morphology improves mechanical robustness and eliminates intergranular boundaries, improving the chemical stability of the cathode. Furthermore, single-crystal cathodes also suffer from worsened lithium-diffusion kinetics stemming from the significantly increased diffusion path lengths. Sluggish lithiation kinetics induce concentration gradients within the cathode particle during cell operation, resulting in the accumulation of lattice strain, which deteriorates cell performance. Foreign dopants have been shown to greatly improve ion diffusion in many high-Ni layered oxide cathode systems. In particular, we identify Ti and Te as promising dopants to ameliorate the slow diffusion kinetics. We find that doping 1 mol.% Te into single crystal LiNiO 2 greatly improves Li + diffusivity, as determined through galvanostatic intermittent titration technique. Further incorporating 2 mol.% Al and pairing with lithium-metal anode in a localized high concentration electrolyte (LHCE) delivers 206 mA h g -1 at C/3 rate and retains 94% capacity after 100 cycles in Li metal half cells. By addressing kinetically mediated degradation with Te doping, and surface-based degradation with Al and LHCE, the cathode experiences very little polarization and overpotential growth, enabling stable cycling with high accessible capacity.
25 ENERGY STORAGE↗
Crystallization by Amorphous Particle Attachment: On the Evolution of Texture
Abstract Crystallization by particle attachment (CPA) is a gradual process where each step has its own thermodynamic and kinetic constrains defining a unique pathway of crystal growth. An important example is biomineralization of calcium carbonate through amorphous precursors that are morphed into shapes and textural patterns that cannot be envisioned by the classical monomer‐by‐monomer approach. Here, a mechanistic link between the collective kinetics of mineral deposition and the emergence of crystallographic texture is established. Using the prismatic ultrastructure in bivalve shells as a model, a fundamental leap is made in the ability to analytically describe the evolution of form and texture of biological mineralized tissues and to design the structure and crystallographic properties of synthetic materials formed by CPA.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA
Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. Here, when targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Kinetic and structural evidence for specific DMSO interference with reversible binding of uncharged bis-oximes to hAChE and their reactivation kinetics of OP-hAChE
The structural basis of inhibitory effect of organic solvent dimethyl sulfoxide (DMSO) on human acetylcholinesterase (EC 3.1.1.7; hAChE) was inferred from the effect of DMSO on kinetics of reversible inhibition of uncharged, heterocyclic bis-oximes to hAChE, from DMSO effect on rates of reactivation of inactive organophosphate (OP)-hAChE conjugates by bis-oximes and by X-ray structures of bis-oxime and DMSO binding to hAChE. Here, the reversible inhibition constant of DMSO for hAChE in 0.1 M phosphate buffer pH 7.4 at 22 °C, was K i = (0.32 ± 0.04) % (or 45 ± 5 mM). The K i of the bis-oxime LG-703 for hAChE was 3.2-fold larger in 1 % DMSO, consistent with direct competition between LG-703 and DMSO. The X-ray structure of the LG-703∗hAChE complex (PDB ID: 6U3P) shows DMSO and LG-703 bound to individual hAChE monomers, LG-703 in the chain A and DMSO in the chain B. In the co-crystallization both small molecules were present at a similar excess over their corresponding K i values for hAChE (7.8-fold for DMSO and 6.5-fold for LG-703) and formation of two different complexes (DMSO∗hAChE and LG-703∗hAChE), in the same crystal, appears consistent with inhibition kinetics. Furthermore, rates of reactivation of paraoxon-inhibited hAChE (POX-hAChE) and of VX-hAChE by LG-703 and by a novel heterocyclic bis-oxime LG-1922 were reduced 2 – 3-fold in DMSO, consistent with observation of the active-center-bound DMSO molecules in the newly solved structure of the LG-1922∗POX-hAChE complex presented here and in our POX-hAChE structure (PDB ID: 8DT2) showing obstruction of the reactivator access to the conjugated P atom.
Acetylcholinesterase inhibition↗
Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity
Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE–CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants kon and koff, respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates (koff) and reduced effective adsorption rates (nkon), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
59 BASIC BIOLOGICAL SCIENCES↗