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At least 253 records · Page 14

The Structure, Anharmonic Vibrational Frequencies, and Intensities of NNHNN+

A semi-global potential energy surface (PES) and quartic force field (QFF) based on fitting high-level electronic structure energies are presented to describe the structures and spectroscopic properties of NNHNN+. The equilibrium structure of NNHNN+ is linear with the proton equidistant between the two nitrogen groups and thus of D(sub ∞h) symmetry. Vibrational second-order perturbation theory (VPT2) calculations based on the QFF fails to describe the proton “rattle” motion, i.e., the antisymmetric proton stretch, due to the very flat nature of PES around the global minimum, but performs properly for other modes with sharper potential wells. Vibrational self-consistent field/virtual state configuration interaction (VSCF/VCI) calculations using a version of MULTIMODE without angular momentum terms successfully describe this motion and predict the fundamental to be at 759 cm(exp -1). This is in good agreement with the value of 746 cm(exp -1) from a fixed-node diffusion Monte Carlo calculation and the experimental Ar-tagged result of 743 cm(exp -1). Other VSCF/VCI energies are in good agreement with other experimentally reported ones. Both double-harmonic intensity and rigorous MULTIMODE intensity calculations show the proton transfer fundamental has a very strong intensity.

Astrochemistry↗

Deep potential molecular dynamics simulations of low-temperature plasma-surface interactions

Machine learning approaches to potential generation for molecular dynamics (MD) simulations of low-temperature plasma-surface interactions could greatly extend the range of chemical systems that can be modeled. Empirical potentials are difficult to generalize to complex combinations of multiple elements with interactions that might include covalent, ionic, and metallic bonds. This work demonstrates that a specific machine learning approach, Deep Potential Molecular Dynamics (DeepMD), can generate potentials that provide a good model of plasma etching in the Si-Cl-Ar system. Comparisons are made between MD results using DeepMD models and empirical potentials, as well as experimental measurements. Pure Si properties predicted by the DeepMD model are in reasonable agreement with experimental results. Simulations of Si bombardment by Ar + ions demonstrate the ability of the DeepMD method to predict sputtering yields as well as the depth of the amorphous-crystalline interface. Etch yields as a function of flux ratio and ion energy for simultaneous Cl 2 and Ar + impacts are in good agreement with previous simulation results and experiment. Predictions of etch yields and etch products during plasma-assisted atomic layer etching of Si-Cl 2 -Ar are shown to be in good agreement with MD predictions using empirical potentials and with experiment. Finally, good agreement was also seen with measurements for the spontaneous etching of Si by Cl atoms at 300 K. Further, the demonstration that DeepMD can reproduce results from MD simulations using empirical potentials is a necessary condition to future efforts to extend the method to a much wider range of systems for which empirical potentials may be difficult or impossible to obtain.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancing Thermal Transport in Polymeric Composites Via Engineered Noncovalent Filler–Polymer Interactions

Understanding thermal transport mechanisms in polymeric composites allows us to expand the boundaries of thermal conductivity in them, either increasing it for more efficient heat dissipation or decreasing it for better thermal insulation. But, these mechanisms are not fully understood. Systematic experimental investigations remain limited. Practical strategies to tune the interfacial thermal resistance (ITR) between fillers and polymers and the thermal conductivity of composites remain elusive. Here, we studied the thermal transport in representative polymer composites, using polyethylene (PE) or polyaniline (PANI) as matrices and graphite as fillers. PANI, with aromatic rings in its backbone, interacts with graphite through strong noncovalent π–π stacking interactions, whereas PE lacks such interactions. We can then quantify how π–π stacking interactions between graphite and polymers enhance thermal transport in composites. PE/graphite and PANI/graphite composites with the same 1.5% filler volume fractions show a ∼22.82% and ∼34.85% enhancement in thermal conductivity compared to pure polymers, respectively. Calculated ITRs in PE/graphite and PANI/graphite are ~6 x 10 -8 m 2 KW -1 and ~1 x 10 -8 m 2 KW -1 , respectively, highlighting how π–π stacking interactions reduce ITR. Molecular dynamics (MD) simulations suggest that π–π stacking interactions between PANI chains and graphite surfaces enhance alignment of PANI's aromatic rings with graphite surfaces. This allows more carbon atoms from PANI chains to interact with graphite surfaces at a shorter distance compared to PE chains. Finally, our work indicates that tuning the π–π stacking interactions between polymers and fillers is an effective approach to reduce the ITR and enhance the thermal conductivity of composites.

atoms↗

Interactions of Polar and Nonpolar Groups of Alcohols in Zeolite Pores

Understanding the quantitative interactions among zeolite pore walls, Bro̷nsted acid sites, and molecules with both polar and nonpolar regions is essential for scoping out the potential of zeolites as sorbents and catalysts. Purely siliceous zeolites (MFI and Beta in the present study) are hydrophobic, whereas those containing aluminum are considered hydrophilic, preferentially adsorbing organic molecules even in aqueous environments. To characterize these interactions, we use primary alcohols of increasing molecular weight, quantifying their specific interactions in the confined pore space of the alkyl (CH x ) and OH groups. Three types of interactions were identified: (i) alkyl CH x groups interacting with the zeolite pore walls (approximately 10 kJ mol −1 per carbon), (ii) alcohol OH groups interacting with the pore walls (30−35 kJ mol −1 ), and (iii) alcohol OH groups interacting with Bro̷nsted acid sites (37 kJ mol −1 ). All three interactions were well mirrored by computational simulations. The contribution of the alkyl CH x groups was inferred from the incremental increase in sorption enthalpy with increasing molecular weight; the interaction strength of the OH groups was determined by extrapolating the global adsorption enthalpy of the alcohols to a hypothetical OH group without an alkyl group. This value was identical to the adsorption enthalpy of water. The experiments demonstrated that only water has an adsorption enthalpy on zeolite pore walls lower than its condensation enthalpy (30−35 kJ mol −1 vs 45 kJ mol −1 ), limiting the concentration of water that can be adsorbed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Examining astrophysical gas cloud collapse using an optical depth-scaled, x-ray-irradiated, carbon-foam sphere

When stellar radiation interacts with a molecular cloud, the cloud's fate depends on the strength of the incident radiation and the radiation's mean-free-path within the cloud [F. Bertoldi, Astrophys. J. 346, 735–755 (1989)]. Under the right conditions, the radiation compresses the cloud and a star formation may occur. Where and when the stellar formation occurs in the cloud's collapse are open questions. Direct observation of the complete star–cloud lifecycle is nearly impossible due to the immense timescales and distances over which the interaction occurs. Laboratory astrophysics offers a way to investigate such a system by scaling the important astrophysical parameters to the laboratory. This work describes laboratory experiments to study the radiation-driven implosion of clouds, using x rays from a laser-irradiated, thin, gold foil as a surrogate star and a carbon-foam sphere as a surrogate cloud. An optically thick system, theoretically corresponding to a star-forming regime, was selected by choice of the foam density. Gold foil and sphere motions were imaged by x-ray radiography. Radiographic images show the formation of an interface between rarefied gold and carbon plasmas, a shock moving into the sphere, and a blunting of the initial sphere's shape. Measurements show that the shock moved linearly around 64 μm/ns into the sphere, and the gold–carbon interface formed by 2 ns at the sphere edge remained stationary. The deformation of the sphere was driven by the incident radiation and not by mechanical pressures applied by gold plasma. The blunting of the sphere was likely due to the geometric reduction of flux near the sphere's poles. Higher x-ray flux near the sphere's equator caused high compression and a faster shock, which flattened the sphere. We will discuss the results and implications of our observations.

VanDervort, R. W. [University of Michigan 1 , Ann ↗

Tensegrity II. How structural networks influence cellular information processing networks

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Review↗

Reversible Physical Gelation of Thermotropic Liquid Crystals Driven by Nanoplate Self-Assembly

Physically gelled soft materials, driven by the self-assembly of low-molecular-mass gelators (LMGs), have emerged as a platform for designing advanced gels that exhibit reversible gelation and property tunability. Liquid crystal (LC) gels are of great interest due to their supramolecular orderings as gel hosts and their enhanced electro-optical properties. In this study, we demonstrate the physical gelation of a nematic LC driven by nanoplate self-assembly, expanding the concept of gelators from small molecules to nanoparticles. These nanoplates are functionalized with promesogenic ligands and form a fibrillar network in LCs with face-to-face interplate stacking, resembling LMGs. The critical gelation volume fraction in the tilt test is only 0.14 v %, comparable to values reported for LMGs. Rheological analyses confirm viscoelastic properties characteristic of gelation. In situ small-angle X-ray scattering (SAXS) characterizes the formation of nanoplate networks in the LC with decreasing temperature, wherein LC mesogens become trapped in pores. Molecular dynamics (MD) simulations reveal that the interaction between ligand-coated nanoplates and LC-forming mesogens induces a multidomain LC structure, increasing friction between LC domains and stabilizing the gel. This study establishes direct relationships among molecular interactions, nanostructures, and mechanical properties in physically gelled LCs. In conclusion, the findings inspire the future gelator design of both LMGs and nanoplates, with potential applicability in bioscaffold engineering and liquid crystalline nanocomposites.

36 MATERIALS SCIENCE↗

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.

36 MATERIALS SCIENCE↗

Data from "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions"

Data and input files related to the paper "Deep Potential Molecular Dynamics Simulations of Low-Temperature Plasma-Surface Interactions" (https://doi.org/10.1116/6.0004027). This includes the final DP model used in all simulations, training data set, example input files to run DeepMD (with LAMMPS), and data tables summarizing the results obtained from the simulations.

machine learning models↗

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of↗

Laser-enhanced dynamics in molecular rate processes

The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

George, T. F.↗

Quantum-mechanical calculation of three-dimensional atom-diatom collisions in the presence of intense laser radiation

A formalism is presented for describing the collision of fluorine with the hydrogen molecule in the presence of intense radiation. For a laser frequency on the order of the spin-orbit splitting of fluorine, the interaction of the molecular system with the radiation occurs at relatively long range where, for this system, the electric dipole is vanishingly small. Hence the interaction occurs due to the magnetic dipole coupling. Even so, at low collision energies a substantial enhancement of the quenching cross section is found for a radiation intensity of 10 to the 11th W/sq cm.

Devries, P. L.↗

Growth Mechanism of the (110) Face of Tetragonal Lysozyme Crystals

The measured macroscopic growth rates of the (110) face of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. In earlier studies it has been shown that an aggregate growth unit could account for experimental growth-rate trends. In particular molecular packing and interactions in the growth of the crystal were favored by completion of the helices along the 4, axes. In this study the molecular orientations of the possible growth units and the molecular growth mechanism were identified. This indicated that growth was a two-step process: aggregate growth units corresponding to the 4, helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds. A more comprehensive analysis of the measured (110) growth rates was also undertaken. They were compared with the predicted growth rates from several dislocation and two-dimensional nucleation growth models, employing tetramer and Octamer growth units in polydisperse solutions and monomer units in monodisperse solutions. The calculations consistently showed that the measured growth rates followed the expected model relations with octamer growth units, in agreement with the predictions from the molecular level analyses.

Nadarajah, Arunan↗

Does Orbital Angular Momentum Have Effect on Laser’s Scattering by Molecular Atmosphere?

Lasers with orbital angular momentum (OAM) have potential applications in communication technology, manipulation of particles, and remote sensing. Because of its unusual light-scattering properties, the OAM laser’s interaction with a molecular atmosphere must be studied to ensure that it is not lossy for communication or remote-sensing applications that involve its transmission through an atmospheric environment. In this study, the finite-difference time-domain (FDTD) method [21] is applied to calculate the light scattering of the purely azimuthal (the radial mode number is assumed to be zero) Laguerre-Gaussian (LG) beams with OAM by very small dielectric particles. Not like Lorentz-Mie solutions, the FDTD method can calculate for particles off the central axis of the LG beam. It is found that when the particles are very small, and the topological charge number of the OAM of a laser is not extremely large, the laser’s OAM has little effect on the scattering phase function. This suggests that Rayleigh theory can be applied directly to calculate the light scattering by atmospheric molecules. The transmission of a laser beam with OAM in a molecular atmosphere is not different from that of a regular Gaussian beam.

Molecular atmosphere↗

Microfluidic Extraction of Biomarkers using Water as Solvent

A proposed device, denoted a miniature microfluidic biomarker extractor (mu-EX), would extract trace amounts of chemicals of interest from samples, such as soils and rocks. Traditionally, such extractions are performed on a large scale with hazardous organic solvents; each solvent capable of dissolving only those molecules lying within narrow ranges of specific chemical and physical characteristics that notably include volatility, electric charge, and polarity. In contrast, in the mu-EX, extractions could be performed by use of small amounts (typically between 0.1 and 100 L) of water as a universal solvent. As a rule of thumb, in order to enable solvation and extraction of molecules, it is necessary to use solvents that have polarity sufficiently close to the polarity of the target molecules. The mu-EX would make selection of specific organic solvents unnecessary, because mu-EX would exploit a unique property of liquid water: the possibility of tuning its polarity to match the polarity of organic solvents appropriate for extraction of molecules of interest. The change of the permittivity of water would be achieved by exploiting interactions between the translational states of water molecules and an imposed electromagnetic field in the frequency range of 300 to 600 GHz. On a molecular level, these interactions would result in disruption of the three-dimensional hydrogen-bonding network among liquid-water molecules and subsequent solvation and hydrolysis of target molecules. The mu-EX is expected to be an efficient means of hydrolyzing chemical bonds in complex macromolecules as well and, thus, enabling analysis of the building blocks of these complex chemical systems. The mu-EX device would include a microfluidic channel, part of which would lie within a waveguide coupled to an electronically tuned source of broad-band electromagnetic radiation in the frequency range from 300 to 600 GHz (see figure). The part of the microfluidic channel lying in the waveguide would constitute an interaction volume. The dimensions of the interaction volume would be chosen in accordance with the anticipated amount of solid sample material needed to ensure extraction of sufficient amount of target molecules for detection and analysis. By means that were not specified at the time of reporting the information for this article, the solid sample material would be placed in the interaction volume. Then the electromagnetic field would be imposed within the waveguide and water would be pumped through the interaction volume to effect the extraction.

Amashukeli, Xenia↗