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At least 505 records · Page 28

Fluorophilic Sigma(σ)‐Lock Self‐Healable Copolymers

Although F-Containing molecules and macromolecules are often used in molecular biology to increase the binding with Lewis acidic groups by introducing favorable C−F dipoles, there is virtually no experimental evidence and limited understanding of the nature of these interactions, especially their role in synthetic polymeric materials. These studies elucidate the molecular origin of inter- and intra-Chain interactions responsible for self-healing of F-Containing copolymers composed of pentafluorostyrene and n-butyl acrylate units (p(PFS/nBA). Guided by dynamic surface oscillating force (SOF) and spectroscopic measurements supported by molecular dynamics (MD) simulations, these studies show that the reformation of σ-σ orbitals in −C−F of PFS and CH 3 CH 2 − of nBA units enables the recovery of entropic energy via fluorophilic-σ-lock van der Waals forces when PFS/nBA molar ratios are ~50/50. The strength of these interactions determined experimentally for self-healable PFS/nBA compositions is in the order ~0.3 kcal/mol which primarily comes from fluorophilic-σ-lock (~70 %) contributions. These interactions are significantly diminished for non-self-healable counterparts. Strongly polarized −C−F σ orbitals create lateral dipolar forces enhancing the affinity towards −C−H orbitals, facilitating energetically favorable interactions. Entropic recovery driven by non-Covalent bonding offers a valuable tool in designing materials with unique functionalities, particularly self-healable batteries and energy storage devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermal conductivity and resonant multipole interactions

The influence of multipole interactions on exchanges of rotational energy in molecular collisions was investigated by means of a simple two-state impact parameter approximation. The calculations are restricted to linear molecules and to dipole and quadrupole fields. The effects of such exchanges on the thermal conductivity of gases and of gaseous mixtures was investigated, after correcting the kinetic theory of mixtures to include exchanges between unlike molecules. It was found that dipole-quadrupole and quadrupole-quadrupole interactions may have a significant effect for molecules with low moments of inertia. In particular, quadrupole interactions are important in the hydrogen isotopes, and the calculated corrections for H2 are consistent with recent experimental work by Harris. The theory seems capable of accounting for the anomalies observed in HF + DF and HCl + DCl mixtures in terms of multipolar accidental resonances.

Nyeland, C.↗

Inverse Trans Influence and Uranium-Arene σ-Bonding Drive Molecular Geometry: Ligand Modification from Hard to Soft Flips the Oxide from Axial to Equatorial

A rare example of an equatorially bound terminal uranium(V) oxo complex in a chelating sulfur-based ligand environment, namely [(mes( Me,Ad ArS) 3 )U V (O eq )(THF)] (2), is presented. Octahedrally coordinated 2 is obtained by reaction of the mesitylene-anchored tris-thiophenolate-coordinated uranium(III) complex [U III ((SAr Ad,Me ) 3 mes)] (1) with the oxygen-atom transfer reagent N 2 O. The observed, equatorially bound oxo ligand in 2 is in stark contrast to its known tris-aryloxide analog, [(mes( Me,Ad ArO) 3 )U V (O ax )(THF)] (A), where the oxo ligand occupies the typically observed axial coordination site. Complexes 1 and 2 are characterized by single-crystal X-ray diffraction analyses and spectroscopic and magnetochemical methods, including 1 H NMR, UV/vis/NIR electronic absorption, as well as EPR spectroscopy and SQUID magnetometry, thus confirming the C S symmetry and the pentavalent oxidation state of 2. Encompassing quantum chemical calculations (DFT and CASPT2) on 2 and its tris-phenolate analog A, support and rationalize the structural and electronic differences. The molecular orbital pictures show that a stabilizing σ-bonding interaction arising from the U–O eq inverse trans influence (ITI) is present in 2 but missing in A. In 2, the sulfur 3p orbitals are closer in energy to the uranium 5f manifold than the arene π-system, leading to an ITI, while U–arene σ- or δ-bonding is not observed. Although the arene orbitals remain separated from the uranium 5f orbitals in A, the absence of an ITI allows the arene a 2u orbital to engage in a σ-type interaction with the metal. Thus, incorporating a tris-thiophenolate to an arene anchor introduces a new design concept in molecular f-element chemistry. This approach stabilizes an equatorially bound U(V) oxo center, contrasting with its tris-phenolate counterpart, where oxo coordination is axial. The observed geometric divergence, driven by competing ITI and U–arene interactions, not only tunes electronic structure but also leads to differentiated reactivity: only the phenolate analogs activate H 2 O, while the thiolates do not.

Hydrocarbons↗

General contraction of Gaussian basis sets. Part 2: Atomic natural orbitals and the calculation of atomic and molecular properties

A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.

Almloef, Jan↗

New insights in the photochemistry of grain mantles: The identification of the 4.62 and 6.87 micron bands

The mid-IR spectral region of molecular clouds is known to show the fingerprints of molecules frozen in the icy mantles of the interstellar grains. To study the complex chemical and physical interactions on the ice mantles accreted on grains in molecular clouds numerous UV irradiation and diffusion experiments were performed. The irradiation of binary ices was studied. Using isotopic labelling on NH3/CO and NH3/O2 ices numerous compounds were identified, of which OCN(-), NO2(-), NO3(-), and NH4(+) ions reveal a new type of chemical reactions. It appeared that these compounds were formed by proton transfer reactions induced by the interaction between an acid (HNCO, HNO2, HNO3) and a base (NH3) through a hydrogen bond. This mechanism was confirmed by a study of photolyzed diluted argon mixtures. The main astrophysically relevant data from the overall study are presented. The 4.62 micron band in W33A can be reproduced with NH3/CO containing irradiated ices and was identified with OCN(-). The 6.87 micron band in W33A and other photostellar objects is reproduced with NH3/O2 containing ices and is identified with NH4(+).

Grim, Ruud↗

Fermi Large Area Telescope Observations of the Supernova Remnant GS.7-0.1

We present a detailed analysis of the GeV gamma-ray emission toward the supernova remnant (SNR) G8.7-0.1 with the Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope. An investigation of the relationship among G8.7-0.l and the TeV unidentified source HESS J1804-216 provides us with an important clue on diffusion process of cosmic rays if particle acceleration operates in the SNR. The GeV gamma-ray emission is extended with most of the emission in positional coincidence with the SNR G8.7-0.l and a lesser part located outside the western boundary of G8.7-0.l. The region of the gamma-ray emission overlaps spatially-connected molecular clouds, implying a physical connection for the gamma-ray structure. The total gamma-ray spectrum measured with LAT from 200 MeV-100 GeV can be described by a broken power-law function with a break of 2.4 +/- 0.6 (stat) +/- 1.2 (sys) GeV, and photon indices of 2.10 +/- 0.06 (stat) +/- 0.10 (sys) below the break and 2.70 +/- 0.12 (stat) +/- 0.l4 (sys) above the break. Given the spatial association among the gamma rays, the radio emission of G8.7-0.1, and the molecular clouds, the decay of 1IoS produced by particles accelerated in the SNR and hitting the molecular clouds naturally explains the GeV gamma-ray spectrum. We also find that the GeV morphology is not well represented by the TeV emission from HESS J1804-216 and that the spectrum in the GeV band is not consistent with the extrapolation of the TeV gamma-ray spectrum. The spectral index of the TeV emission is consistent with the particle spectral index predicted by a theory that assumes energy-dependent diffusion of particles accelerated in an SNR. We discuss the possibility that the TeV spectrum originates from the interaction of particles accelerated in G8.7-0.1 with molecular clouds, and we constrain the diffusion coefficient of the particles.

Ajello, M.↗

Disentangling interlayer confinement and pore surface adsorption in functionalized smectites for tunable ethylene gas capture

Smectite-based adsorbents are increasingly being studied as sustainable packaging materials for scavenging ethylene, a plant hormone that accelerates fruit ripening. However, the mechanisms governing their uptake and retention remain poorly understood. Here, to tackle this question we systematically investigate ethylene gas-solid interactions in pristine, acid-activated, and choline-functionalized montmorillonites using a complementary combination of structural, gravimetric, and spectroscopic techniques, including inelastic neutron scattering. We experimentally distinguish ethylene populations associated with interlayer confinement, mesopore, and external surface adsorption. We show that chemical functionalization distinctly controls adsorption pathways: acid activation enhances total uptake by generating mesoporous adsorption sites and promoting partial interlayer intercalation, yielding capacities comparable to those of leading smectite-based adsorbents, while choline functionalization promotes preferential confinement and stabilization of guest molecules within the interlayer galleries. Advanced spectroscopic analysis provides molecular-level insight into confinement environments and interaction strengths. We also establish clear structure-property relationships by correlating uptake values derived from independent techniques, linking chemical modification, accessible adsorption domains, and retention behavior. These findings provide general design principles for tuning gas-solid interactions in functionalized layered silicates and highlight their potential as adaptable platforms for sustainable ethylene gas capture and selective adsorption technologies.

Ethylene adsorption mechanism↗

Fermi Large Area Telescope Observations of the Supernova Remnant GS.7-0.1

We present a detailed analysis of the GeV gamma-ray emission toward the supernova remnant (SNR) G8.7-0.1 with the Large Area Telescope (LAT) onboard the Fermi Gamma-ray Space Telescope. An investigation of the relationship among G8.7-0.1 and the TeV unidentified source HESS J1804-216 provides us with an important clue on diffusion process of cosmic rays if particle acceleration operates in the SNR. The GeV gamma-ray emission is extended with most of the emission in positional coincidence with the SNR G8.7-0.1 and a lesser part located outside the western boundary of G8.7-0.1. The region of the gamma-ray emission overlaps spatially-connected molecular clouds, implying a physical connection for the gamma-ray structure. The total gamma-ray spectrum measured with LAT from 200 MeV-100 GeV can be described by a broken power-law function with a break of 2.4 +/- 0.6 (stat) +/- 1.2 (sys) GeV, and photon indices of2.10 +/- 0.06 (stat) +/- 0.10 (sys) below the break and 2.70 +/- 0.12 (stat) +/- 0.14 (sys) above the break. Given the spatial association among the gamma rays, the radio emission ofG8.7-0.1, and the molecular clouds, the decay of pions produced by particles accelerated in the SNR and hitting the molecular clouds naturally explains the GeV gamma-ray spectrum. We also find that the GeV morphology is not well represented by the TeV emission from HESS Jl804-2l6 and that the spectrum in the Ge V band is not consistent with the extrapolation of the TeV gamma-ray spectrum. The spectral index of the TeV emission is consistent with the particle spectral index predicted by a theory that assumes energy-dependent diffusion of particles accelerated in an SNR. We discuss the possibility that the TeV-spectrum originates from the interaction of particles accelerated in G8.7-0.l with molecular clouds, and we constrain the diffusion coefficient of the particles.

Ferrara, E. C.↗

Breaking the mold: Overcoming the time constraints of molecular dynamics on general-purpose hardware

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of accuracy, atom count (spatial scale), and duration (temporal scale). Since the mid-2000s, computer platforms have, however, failed to provide strong scaling for MD, as scale-out central processing unit (CPU) and graphics processing unit (GPU) platforms that provide substantial increases to spatial scale do not lead to proportional increases in temporal scale. Important scientific problems therefore remained inaccessible to direct simulation, prompting the development of increasingly sophisticated algorithms that present significant complexity, accuracy, and efficiency challenges. While bespoke MD-only hardware solutions have provided a path to longer timescales for specific physical systems, their impact on the broader community has been mitigated by their limited adaptability to new methods and potentials. In this work, we show that a novel computing architecture, the Cerebras wafer scale engine, completely alters the scaling path by delivering unprecedentedly high simulation rates up to 1.144 M steps/s for 200 000 atoms whose interactions are described by an embedded atom method potential. This enables direct simulations of the evolution of materials using general-purpose programmable hardware over millisecond timescales, dramatically increasing the space of direct MD simulations that can be carried out. In this paper, we provide an overview of advances in MD over the last 60 years and present our recent result in the context of historical MD performance trends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perspective on Lewis Acid‐Base Interactions in Emerging Batteries

Lewis acid-base interactions are common in chemical processes presented in diverse applications, such as synthesis, catalysis, batteries, semiconductors, and solar cells. The Lewis acid-base interactions allow precise tuning of material properties from the molecular level to more aggregated and organized structures. This review will focus on the origin, development, and prospects of applying Lewis acid-base interactions for the materials design and mechanism understanding in the advancement of battery materials and chemistries. The covered topics relate to aqueous batteries, lithium-ion batteries, solid-state batteries, alkali metal-sulfur batteries, and alkali metal-oxygen batteries. In this review, the Lewis acid-base theories will be first introduced. Thereafter the application strategies for Lewis acid-base interactions in solid-state and liquid-based batteries will be introduced from the aspects of liquid electrolyte, solid polymer electrolyte, metal anodes, and high-capacity cathodes. The underlying mechanism is highlighted in regard to ion transport, electrochemical stability, mechanical property, reaction kinetics, dendrite growth, corrosion, and so on. Last but not least, perspectives on the future directions related to Lewis acid-base interactions for next-generation batteries are like to be shared.

Lewis acid-base interactions↗

Numerically Simulating an Expanding Continuum Jet into a Surrounding Non-Continuum Region

A numerical technique that simulates the interaction between a continuum jet and a free-molecular, rarefied or transitional flow field is presented and applied. The technique is based on selecting a boundary between the expanding jet plume and interacting flow field defined by the Bird breakdown parameter, P. By properly choosing the boundary, the jet plume computed by computational fluid dynamics (CFD) is uncoupled from the interaction region that is simulated by direct simulation Monte Carlo (DSMC). The mechanics of uncoupling the continuum and non-continuum regions is discussed first. Also, a discussion of expanding continuum plume breakdown and the formulation of the Bird breakdown parameter is presented. To show the usefulness, examples of applying the CFD-DSMC technique are given. Many of the examples were taken from projects worked by the staff of the Aerothermodynamics Branch at the NASA Langley Research Center. These examples show a variety of applications of the technique and allow those examples not previously documented to be formally presented.

Jet interaction↗

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗

Shear-Induced Conformations of Salt-Free Polyelectrolytes in Semidilute Solutions

Here, we present coarse-grained molecular dynamics simulations of salt-free polyelectrolyte chains in semidilute solutions under simple shear flow, with full hydrodynamic interactions and explicit dipolar solvent. At equilibrium, chain orientation statistics follow a pseudo-Voigt distribution, and the structural correlation length and chain end-to-end vector autocorrelation function exhibit scaling behavior consistent with theoretical predictions for polyelectrolytes. Under shear, chains transition from coiled to stretched states and the end-to-end vector autocorrelation function reveals oscillatory dynamics at high Weissenberg numbers. Analysis of the gyration tensor and shear strain distributions identified three distinct chain populations with directional alignment along and against the shear gradient. Compared with their neutral polymer counterparts, polyelectrolytes exhibit stronger shear thinning and enhanced chain alignment under the same Weissenberg number, which is attributed to electrostatic interactions and shear-induced counterion release. These findings provide molecular insight into the distinct flow response of charged polymers and have implications for tailoring the rheological properties of polyelectrolyte-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes

Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.

Chemical engineering↗

Interaction of a sodium ion with the water liquid-vapor interface

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

NASA Center ARC↗

Ultrafast exciton and trion dynamics in highly 𝑛-doped Mo⁢S 2 monolayers: Many-body effects

Understanding many-body interactions of excitons and charge carriers in monolayer semiconductors is crucial for tuning their unique optical properties and optimizing their performance in optoelectronic devices. However, the sensitivity of these atomically thin semiconductors to doping, defects, and strain–arising from synthesis, substrate, and environmental conditions–hinders consistent observation of many-body effects. In this work, we employed linear and ultrafast transient optical absorption spectroscopy to investigate the influence of background doping on exciton many-body interactions in Mo⁢S 2 monolayers. Using reversible molecular physisorption gating, we achieved a high background doping density of 4.9 × 10 13 c⁢m −2 in an argon environment, which is significantly higher than those attainable with conventional electrical gating. Our results reveal a photoinduced 𝐴-exciton resonance redshift, attributed to band-gap renormalization at a low background-doping density of 4.3 × 10 12 c⁢m −2 in an air environment, transitioning to a blueshift at a high background-doping density of 4.9 × 10 13 c⁢m −2 due to dominant Pauli blocking effects and vertical excitation shifts. We further observed transient energy splitting between free-exciton and -trion states up to 57 meV due to exciton-electron interactions. The ultrafast spectroscopy further revealed exciton and trion dynamics, including fast energy splitting of exciton and trion resonances within 1 picosecond (ps) followed by a rapid decay having a lifetime of ∼5.4 ps. Furthermore, our results demonstrate the critical role of background-doping conditions in tuning many-body interactions and quasiparticle dynamics in 2D semiconductors, providing valuable insights for future device design and material engineering.

Doped semiconductors↗

Quantum Light Imaging of the Plant Root─Rhizobacteria─System Using iLOV Fluorescence

It has been demonstrated recently that the use of specific quantum states of light for two-photon microscopy can lead to a substantial reduction of the intensity of light needed for the imaging of biological objects. This opens new ways to better understand the delicate mechanisms of the interactions of living organisms in the rhizosphere on an extended time scale without optical damage or alteration of their native behavior. Herein, we report a successful realization of entangled two-photon excited fluorescence microscopy of wheat plant roots and a set of biological samples, including purified iLOV protein, bacterial cells expressing iLOV, and combination of these under an extremely low excitation intensity. The entangled two-photon coupling strength of iLOV was modeled using electronic structure calculations which demonstrated that the FMN chromophore in the iLOV protein has an entangled two-photon absorption (ETPA) cross section that is large enough for imaging using weak quantum light for fluorescence excitation. Successful imaging of plant-associated Pantoea sp. YR343 cells expressing iLOV validates the feasibility of using iLOV as a molecular label for characterizing plant-microbe interactions based on entangled photon imaging. In conclusion, the results demonstrate the advantageous use of entangled photon imaging under noninvasive and nondestructive conditions.

Varnavksi, Oleg [Univ. of Michigan, Ann Arbor, MI ↗

Sulfonated polybenzimidazole membrane with graphene oxide additive for 2,3-butanediol/water separation: A molecular simulation

Membrane separation for 2,3-butanediol (2,3-BDO) recovery from fermentation broth is highly valued for sustainable and renewable processes, but it requires efficient membrane materials. Here, this work evaluates the sulfonated polybenzimidazole (sPBI) and its graphene oxide (GO) doped composite membrane for separating 2,3-BDO and water via atomistic simulations. Density functional theory calculations are applied to identify various forms of sPBI structures and quantify their binding interactions with 2,3-BDO and water. Classical molecular dynamic simulations are used to evaluate the structural changes, diffusivity, and selectivity of 2,3-BDO and water in different sPBI models, GO surfaces, and GO-doped sPBI composite models. Our results suggest that sPBI slightly increases the crystallinity of the membrane structures, enhances the adsorption strength for both 2,3-BDO and water, and improves the water/2,3-BDO selectivity by 2–3 times. The GO surfaces display a maximum selectivity at a surface coverage of 0.1–0.15 for both hydroxyl and epoxy surface groups. The addition of GO flakes to sPBI creates new interaction sites for 2,3-BDO and water at the interface of sPBI and GO, and the water/2,3-BDO selectivity of GO-doped sPBI models is further increased up to 3 times. This work illustrates how the integrated addition of sPBI and GO flakes offers a promising approach to selective separation of 2,3-BDO and water, providing theoretical guidance for polybenzimidazole-based membranes in the potential application of 2,3-BDO recovery.

2,3-butanediol↗