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At least 289 records · Page 16

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

Reducing Thermal Degradation of Perovskite Solar Cells during Vacuum Lamination by Internal Diffusion Barriers

Current photovoltaic (PV) panels typically contain interconnected solar cells that are vacuum laminated with a polymer encapsulant between two pieces of glass or glass with a polymer backsheet. This packaging approach is ubiquitous in conventional photovoltaic technologies such as silicon and thinfilm solar modules, contributing to thermal management, mechanical reinforcement, and environmental protection to enable the long lifetimes necessary to become financially acceptable. Commercial vacuum lamination processes typically occur at 150 °C to ensure cross-linking and/or glass bonding of the encapsulant to the glass and PV cells. Perovskite solar cells (PSCs) have emerged as a promising next-generation PV technology that is known to degrade under thermal stresses, especially at temperatures above 100 °C. In this study, we determine degradation modes during lamination and engineer internal diffusion barriers within the PSC to withstand the harsh thermal conditions of vacuum lamination. PSCs with self-assembled monolayers at the ITO interface and SnO X layers deposited by atomic layer deposition at the electron extraction side of the device endured vacuum lamination at conditions typical of commercial PV processes (150 °C) without degradation. This work demonstrates that perovskite PV can be integrated into the existing module lamination process, enabling future single- and multijunction modules utilizing perovskite absorbers.

14 SOLAR ENERGY↗

Activation of Low-Valent, Multiply M–M Bonded Group VI Dimers toward Catalytic Olefin Metathesis via Surface Organometallic Chemistry

Olefin metathesis is a broadly employed reaction with applications that range from fine chemicals to materials and petrochemicals. The design and investigation of olefin metathesis catalysts have been ongoing for over half a century, with advancements made in terms of activity, stability, and selectivity. Immobilization of organometallic complexes onto solid supports such as silica or alumina is a promising strategy for catalyst heterogenization, often resulting in increased activity and stability. Consequently, a broad range of early transition metal catalysts bearing alkyl, oxide/alkoxide, and amide ligands have been grafted onto silica and their reactivities investigated. In this paper, we report a series of silica-supported tungsten and molybdenum dimers (X 3 M≡MX 3, where M = W and Mo; X = neopentyl, tert-butoxide, and dimethyl amide) and their reactivities toward catalytic olefin metathesis. Dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (SSNMR), diffuse reflectance infrared Fourier transform (DRIFT), UV resonance Raman, and X-ray absorption (XAS) spectroscopies suggest that upon heterogenization the dimers bind to the surface in a monopodal fashion, with the M≡M triple bond remaining intact. These structural assignments were further corroborated by density functional theory (DFT) calculations. While the homogeneous dimer counterparts are inert, the supported low-valent alkyl W and Mo dimers become active for the disproportionative self-metathesis of propylene to ethylene and butenes and 4-nonene to 4-octene and 5-decene under mild conditions. The lack of activity observed for the free and supported tert-butoxide and dimethyl amide dimers likely suggests that the neopentyl groups are necessary for the formation of a putative alkylidene active species. The difference in reactivity between the free and supported dimers could be explained either by the lowering of the activation barrier of the complex through the electronic effects of the surface or by site isolation of catalytically relevant reactive intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanochemical synthesis of hydraulically reactive calcium silicate minerals via thermally-assisted mechanical grinding

This study explores a thermally assisted mechanochemical approach alternative to conventional cement synthesis as a potential to produce hydraulically reactive calcium silicate phases. Ball milling of mixed CaO/SiO 2 feedstocks at temperature ranges 100-300 °C increases the formation of the Ca-O-Si bonds and precursor reactivity. Spectroscopic analyses (FTIR, MAS-NMR, UV-Vis DRS) indicate increasing amorphization with milling temperature, attributed to improved mixing and thermally assisted diffusion. Upon hydration, all treated samples exhibit exothermic heat release, with the sample prepared at 300 °C showing the most pronounced reactivity. Thermal analysis reveals weight loss consistent with C-S-H formation, confirming cement-like behavior. In summary, moderate thermal input during milling promotes structural activation and enhances downstream hydraulic reactivity, providing a proof-of-concept for energy-reduced cement precursor processing.

Alite↗

Enabling hydrogen chemisorption on charged graphene

Two-dimensional (2D) materials, including graphitic derivatives, have long been of interest for hydrogen storage applications, due to their high theoretical storage capacity, low weight, and other useful properties. However, poor kinetics for hydrogen adsorption and surface diffusion as part of the proposed spillover process for hydrogenation have limited their technological potential. Here, we use first-principles calculations to study electronic doping as a means to improve hydrogen chemisorption on graphene, which we use here as a proxy for graphitic derivatives more broadly. We find that positively charged graphene sheets have vastly improved kinetics for hydrogen diffusion and adsorption, while they limit unwanted hydrogen desorption. This combination of effects should favor hydrogen chemisorption via spillover. We connect these trends to the C–H bond, which introduces states near the Fermi level. These states are depopulated as electrons are removed, thereby lowering the bond energy and permitting more facile movement of hydrogen. Our results suggest that spillover mechanisms for hydrogen chemisorption should be revisited if strategies to apply a large charge to graphitic systems can be realized. Moreover, switchable application of the charge may lead to the reversible chemisorption of hydrogen. While the large magnitude of charging required suggests that graphene itself may not be suitable for reversible hydrogen chemisorption, the factors we identify and discuss could significantly boost the prospects of graphitic derivatives and other 2D or layered materials for hydrogen storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional

We investigate the temperature dependence of nuclear quantum effects (NQEs) on structural and dynamic properties of liquid water by training a neural network force field using first-principles molecular dynamics (FPMD) based on the strongly constrained and appropriately normed meta-generalized gradient approximation exchange-correlation approximation. The FPMD simulation based on density functional theory has become a powerful computational approach for studying a wide range of condensed phase systems. However, its large computational cost makes it difficult to incorporate NQEs in the simulation and investigate temperature dependence of various properties. To circumvent this difficulty, we use an artificial neural network model and employ the thermostatted ring polymer MD approach for studying the temperature dependence of NQEs on various properties. The NQEs generally bring the radial distribution functions closer to the experimental measurements. Translational diffusivity and rotational dynamics of water molecules are both slowed down by the NQEs. The competing inter-molecular and intra-molecular quantum effects on hydrogen bonds, as discussed by Habershon, Markland, and Manolopoulos [J. Chem. Phys. 131(2), 024501 (2019)], can explain the observed temperature dependence of the NQEs on the dynamical properties in our simulation.

Yao, Yi (ORCID:0000000299576979)↗

Modeling Coupled Chemo-Mechanical Behavior of Randomly Oriented NMC811 Polycrystalline Li-Ion Battery Cathodes

This paper develops a three-dimensional, transient, chemo-mechanical model that predicts the performance of single secondary particle Li-ion battery cathodes. The secondary particles are composed of numerous (approximately 60) randomly oriented single-crystal primary particles. The model incorporates concentration-dependent and anisotropic material properties. As much as possible, electrochemical, transport, and structural properties for crystalline NMC811 (Li x Ni 0.8 Mn 0.1 Co 0.1 O 2 ) are taken from prior publications. Weak Van der Waals bonding between primary particles is modeled empirically using a spring analogy, which enables local primary-particle separations (disintegration) and subsequent reattachments. The model fully couples Li diffusion and the mechanical response. Results include predictions of local Li-concentrations and stresses. High stresses are found near grain boundaries, especially when the lattice orientations are greatly misaligned. Particle separations are characterized in terms of a damage parameter. The model is used to predict the effects of design and operating conditions, including charge/discharge rates, cycling scenarios, and particle sizes.

25 ENERGY STORAGE↗

Removal of deuterium retained in boron powder by oxygen or high-temperature bakeout

Fuel retention in dust accumulated in fusion devices is a potential operational hazard. Boronization is one of the leading wall-conditioning candidates for future fusion devices. Fuel retention characteristics of boron dust must be studied to accurately understand the potential hazards of boron dust in fusion devices. We evaluated the retention of deuterium (D) in commercially available boron powder as a proxy for tritium retention in boron dust. Diffuse reflectance infrared Fourier transform spectroscopy revealed that boron powder between 300 and 500 K exposed to neutral hydrogen (H 2 ) gas retains H via B-H bonding. We utilized D 2 exposures of 17,400 L on the boron powder, which led to retention on the order of 0.5 g D per 100 kg B or 1.2 g D per m 2 B, as estimated from temperature programmed desorption measurements. We evaluated how powder bakeouts under ultra-high vacuum (UHV), or in an oxygen (O 2 ) or H 2 gas backfilled environment can remove the retained fuel. Bakeouts below 523 K under UHV exhibited poor D removal, promoting recapture of D 2 present as background gas in the chamber. Higher temperature bakeouts led to the removal of over 80% of the retained D within 3 days (623 K) or 1 h (723 K). Bakeouts at 423 K under an O 2 gas environment removed ∼150% more retained D from the boron powder, when compared to bakeouts conducted under UHV. These results suggest that efficient fuel removal from boron dust can be achieved by high-temperature bakeout (>623 K) or by bakeouts at lower temperature (423 K) under an O 2 environment.

Bakeout↗

From Salt in Solution to Solely Ions: Solvation of Methyl Viologen in Deep Eutectic Solvents and Ionic Liquids

Solvation and transport properties of methlyviologen dichloride in mixtures of choline chloride (ChCl) and ethylene glycol (EG) including the deep eutectic solvent (DES) ethaline were studied through physical property measurements, cyclic voltammetry, and Raman spectroscopy. The transport properties of the solvate structures in ethaline and ChCl:EG mixtures were compared to a well-studied ionic liquid (IL), 1-methyl-1-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [PYR 13 ][TFSI] through the lens of hole theory. Here by exchanging the chloride anion of ethaline with bis(trifuoromethylsufonyl)imide) anion, [TFSI], is found to increase the fluidity of the solvent and promoted stronger solute-solvent interactions. Raman spectroscopy shows that methylviologen is solvated by EG in solutions with ChTFSI but interstitially accommodated in void spaces in both ChCl solutions and [PYR 13 ][TFSI]. Here, complex solvents such as DESs are regarded as “designer solvents” and we demonstrate that the physical properties and solvation characteristics of these fluids can be varied by anion exchange of hydrogen bond acceptors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Isolating the Contributions of Specific Network Sites to the Diffuse Vibrational Spectrum of Interfacial Water with Isotopomer-Selective Spectroscopy of Cold Clusters

Decoding the structural information contained in the interfacial vibrational spectrum of water requires understanding how the spectral signatures of individual water molecules respond to their local hydrogen bonding environments. In this study, we isolated the contributions for the five classes of sites that differ according to the number of donor (D) and acceptor (A) hydrogen bonds that characterize each site. These patterns were measured by exploiting the unique properties of the water cluster cage structures formed in the gas phase upon hydration of a series of cations M+·(H2O)n (M = Li, Na, Cs, NH4, CH3NH3, H3O, and n = 5, 20-22). This selection of ions was chosen to systematically express the A, AD, AAD, ADD, and AADD hydrogen bonding motifs. The spectral signatures of each site were measured using two-color, IR-IR isotopomer-selective photofragmentation vibrational spectroscopy of the cryogenically cooled, mass selected cluster ions in which a single intact H2O is introduced without isotopic scrambling, an important advantage afforded by the cluster regime. The resulting patterns provide an unprecedented picture of the intrinsic line shapes and spectral complexities associated with excitation of the individual OH groups, as well as the correlation between the frequencies of the two OH groups on the same water molecule, as a function of network site. The properties of the surrounding water network that govern this frequency map are evaluated by dissecting electronic structure calculations that explore how changes in the nearby network structures, both within and beyond the first hydration shell, affect the local frequency of an OH oscillator. The qualitative trends are recovered with a simple model that correlates the OH frequency with the network-modulated local electron density in the center of the OH bond.

Yang, Nan↗

Chemical and Electronic Structure at the Interface between a Sputter-Deposited Zn(O,S) Buffer and a Cu(In,Ga)(S,Se) 2 Solar Cell Absorber

The chemical and electronic structure of the interface between a sputter-deposited Zn(O,S) buffer layer and an industrial Cu(In,Ga)(S,Se) 2 (CIGSSe) absorber for thin-film solar cells is investigated with X-ray and UV photoelectron spectroscopy, inverse photoemission spectroscopy, and X-ray emission spectroscopy. We find a CIGSSe absorber surface band gap of 1.61 (±0.14) eV, which is significantly increased as compared to the minimal value derived with bulk-sensitive methods (≈1.1 eV). We find no indication for diffusion of absorber elements into the buffer layer. Surface- and bulk-sensitive measurements of the buffer layer suggest the presence of S-Zn and S-O bonds in the Zn(O,S) layer. We find that the naturally existing downward band bending toward the CIGSSe absorber surface is increased by the formation of the interface, likely enhancing carrier separation under illumination. We also derive a flat conduction band alignment, in line with the reported high conversion efficiencies of corresponding large-area solar cells.

14 SOLAR ENERGY↗

Heterobinuclear Molecular Precursors Direct the Formation of Supported Subnanometer Cu–M Clusters with Tunable Catalytic Behavior

Subnanometer bimetallic clusters hold great promise for catalytic applications due to their unique electronic properties and high surface-to-volume ratios. However, precise control over their composition and size remains a major challenge, particularly for immiscible metal pairs. Here, we report a surface-anchored molecular approach for synthesizing ∼0.7–0.8 nm Cu–M (M = Ru, Mo, W, Fe) bimetallic clusters on mesoporous silica supports, using heterobinuclear N-heterocyclic carbene (NHC)-based complexes as precursors. The NHC ligand functionalized with an alkoxysilane anchor enables robust grafting to the silica interface. Controlled calcination and reduction lead to subnanometer clusters with tunable composition, dictated by the metal–metal bond stability in the precursor. In situ transmission electron microscopy reveals cluster growth proceeds via sintering of adjacent surface-bound units, while elevated temperatures above 300 °C triggering diffusion and phase separation. Catalytic testing in ethylene hydrogenation demonstrates composition-dependent activity and kinetics, with CuRu and CuW clusters exhibiting lower apparent activation energy barriers compared with monometallic Cu nanoparticles. This study establishes a generalizable strategy for the interfacial synthesis of alloyed clusters from molecular precursors and provides mechanistic insight into how precursor design governs nanostructure formation and catalytic behavior.

N-heterocyclic carbene↗

Constraining Interlayer Slipping in P2-Type Layered Oxides with Oxygen Redox by Constructing Strong Covalent Bonds

Lattice oxygen redox (LOR) in P2-type layered oxides is an effective strategy to break through the limit of energy density of conventional cathodes due to its high redox potential (>4 V vs. Na + /Na) as well as extra capacity. Nevertheless, LOR induced local structure distortion and irreversible phase transitions cause serious electrochemical performance degradation, hindering the practical applications. In this work, we propose that the generation of the OP4 phase can be replaced with the Z phase by introducing Sb element with higher ionic potential and strong covalent bonds within the TMO 6 octahedron. Z phase transition is realized by constraining interlayer slipping between adjacent TM layers compared to OP4, which reduces the strain in the layered structure, lowers the Na+ diffusion energy barrier and creates more efficient Na+ diffusion channels. Consequently, Sb-substituted oxides demonstrates excellent kinetics, rate capability (79 mAh g -1 at 1 A g -1 ) in half cell and a high energy density of 487 Wh kg -1 (on cathode) in full cell.

25 ENERGY STORAGE↗

NMR Relaxometry and Diffusometry Analysis of Dynamics in Ionic Liquids and Ionogels for Use in Lithium-Ion Batteries

Solvation and transport properties of methlyviologen dichloride in mixtures of choline chloride (ChCl) and ethylene glycol (EG) including the deep eutectic solvent (DES) ethaline were studied through physical property measurements, cyclic voltammetry, and Raman spectroscopy. The transport properties of the solvate structures in ethaline and ChCl:EG mixtures were compared to a well-studied ionic liquid (IL), 1-methyl-1-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [PYR13][TFSI] through the lens of hole theory. Exchanging the chloride anion of ethaline with bis(trifuoromethylsufonyl)imide) anion, [TFSI], is found to increase the fluidity of the solvent and promoted stronger solute-solvent interactions. Raman spectroscopy shows that methylviologen is solvated by EG in solutions with ChTFSI but interstitially accommodated in void spaces in both ChCl solutions and [PYR13][TFSI]. Complex solvents such as DESs are regarded as “designer solvents” and we demonstrate that the physical properties and solvation characteristics of these fluids can be varied by anion exchange of hydrogen bond acceptors.

25 ENERGY STORAGE↗

Impact of Site Identity, Location, and Accessibility on Polyethylene Conversion Rates and Product Selectivities over Metal-Free MFI Zeolites

Brønsted (BAS), Lewis (LAS), and surface Brønsted (SBAS) acid sites have been investigated for polyethylene (PE) upcycling by zeolite catalysts, but there is no clear consensus regarding their catalytic roles, partly due to the complexity of the catalysts used and varying reaction conditions across studies. This work systematically determined how these sites impact PE conversion rates and product distributions by utilizing a suite of microporous MFI catalysts with varying Si/Al ratios, acid site densities, and inherent mesoporosities. PE conversion rates did not trend with total BAS or LAS densities due to a combination of internal mass transfer limitation and the apparent inability of LAS alone to cleave C–C bonds, but a strong, statistically significant correlation was present with respect to SBAS density and mesopore surface area, jointly, owing to accelerated polymer activation on external surfaces to smaller diffusion-limited chains. However, ingress of these SBAS-derived fragments ultimately remained rate limiting, as demonstrated by solid conversion rates that increased with mesopore surface area at similar SBAS density and likewise increased with SBAS density at similar mesopore surface area. In batch PE cracking reactions, light gaseous product selectivities were most sensitive to total BAS, with higher densities generally exhibiting higher selectivity to C 3 and linear C 4 –C 7 products and higher alkane/alkene product ratios, consistent with increased β-scission turnovers. Insights from this work help systematically clarify the roles of BAS, LAS, SBAS, and mesopores in PE cracking reactions and inform the development of tailored zeolite catalysts for efficient polyolefin upcycling.

accessibility↗

Understanding geopolymer binder-aggregate interfacial characteristics at molecular level

The interfacial characteristics of geopolymer binder to aggregate composites are poorly understood, especially at molecular level. Herein, molecular models are developed to study, for the first time, the geopolymer-aggregate interface. Chemically, various forms of interfacial bonding are characterized, including Al-O-Si bonding through condensation reactions, NaO and H-bonding. An atomic-level interfacial transition zone (ITZ) is identified, attributed to the concentration of –OH groups. Increasing the Si/Al ratio of geopolymer is found to decrease the ITZ density, but have limited effect on the ITZ width. A heterogeneous diffusion characteristic occurs in geopolymer, due to the weak interfacial interaction. Mechanically, lowering the Si/Al ratio promotes the interfacial strength due to the stronger interfacial interaction and higher cross-linking degree in geopolymer. Under loading the interfacial fracture undergoes three stages: crack propagation, chain bridging (including aluminosilicate and ionic bridging) and breakage. The above atomic-level findings may facilitate a better design of geopolymer concrete in engineering.

36 MATERIALS SCIENCE↗

Dynamics of poly[n]catenane melts

Inspired by advances in the chemical synthesis of interlocking polymer architectures, extensive molecular dynamics simulations have been conducted to study the dynamical properties of poly[n]catenanes-polymers composed entirely of interlocking rings-in the melt state. Both the degree of polymerization (number of links) and the number of beads per ring are systematically varied, and the results are compared to linear and ring polymers. Herein, a simple Rouse-like model is presented, and its analytical solution suggests a decomposition of the dynamics into "ring-like" and "linear-like" regimes at short and long times, respectively. In agreement with this picture, multiple sub-diffusive regimes are observed in the monomer mean-squared-displacements even though interchain entanglement is not prevalent in the system. However, the Rouse-type model does not account for the topological effects of the mechanical bonds, which significantly alter the dynamics at intermediate length scales both within the rings and at the chain segment scales. The stress relaxation in the system is extremely rapid and may be conveniently separated into ring-like and linear-like contributions, again in agreement with the Rouse picture. However, the viscosity has a non-monotonic dependence on the ring size for long chains, which disagrees strongly with theoretical predictions. This unexpected observation cannot be explained in terms of chain disentanglement and is inconsistent with other measures of polymer relaxation. Possible mechanisms for this behavior are proposed and implications for materials design are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗