Results for “Bond angles” — Page 7

DOE OSTI2025

Investigation of the Effect of Framework Flexibility on CO 2 Adsorption in SIFSIX-3-Cu Using a Machine-Learned Force Field

Metal–organic frameworks (MOFs) offer promise as selective CO 2 sorbents, but successful MOF sorbent materials need high CO 2 binding affinity and selectivity for CO 2 over water. This work focuses on the use of machine-learned force fields (MLFFs) to model CO 2 adsorption in flexible MOFs, with a focus on SIFSIX-3-Cu, an anion-pillared MOF known for its high CO 2 affinity. A preliminary high-throughput screening of over 900 anion-pillared MOFs was performed using rigid UFF+DDEC6 force fields to predict zero-loading heats of adsorption for CO 2 and H 2 O. SIFSIX-3-Cu was selected for further computational study due to its predicted CO 2 heat of adsorption and experimental relevance. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies and forces, with an iterative sampling scheme combining molecular dynamics, geometry optimization, random geometric insertion, and NVT Monte Carlo-based configuration generation to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included, contrasting with previous models that approximated the MOF as rigid. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations with the MLFF produced CO 2 adsorption isotherms in good agreement with experimental data at direct air capture (DAC) pressures (e.g., 40 Pa), in contrast to previous overestimations of CO 2 sorption by models with rigid structures. Bond and angle histogram analysis showed that MOF flexibility increased the variance of fluorine–fluorine diagonal distances at adsorption sites, resulting in a lower predicted sorption for flexible, asymmetric SIFSIX-3-Cu pore geometries compared to the rigid, symmetric DFT-optimized SIFSIX-3-Cu pore geometry. A detailed description of flexibility afforded by the MLFF resulted in an accurately predicted CO 2 uptake (0.88 mmol/g) at low pressure (40 Pa) compared to the experimentally measured value (1.24 mmol/g). In conclusion, these results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low-pressure applications.

adsorption↗

DOE OSTI2024

Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials

A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot’s entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C–C–C angle, thereby allowing rupture at lower bond strains. Here, we extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick–slip phenomena upon tightening and similar points of failure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Gaussian approximation potential for amorphous Si : H

Hydrogenation of amorphous silicon (a–Si : H) is critical for reducing defect densities, passivating midgap states and surfaces, and improving photoconductivity in silicon-based electro-optical devices. Modeling the atomic-scale structure of this material is critical to understanding these processes, which in turn is needed to describe c–Si/a–Si : H heterojunctions that are at the heart of modern solar cells with world-record efficiency. Density functional theory (DFT) studies achieve the required high accuracy but are limited to moderate system sizes of 100 atoms or so by their high computational cost. Simulations of amorphous materials have been hindered by this high cost because large structural models are required to capture the medium-range order that is characteristic of such materials. Empirical potential models are much faster, but their accuracy is not sufficient to correctly describe the frustrated local structure. Data-driven, machine-learned interatomic potentials have broken this impasse and have been highly successful in describing a variety of amorphous materials in their elemental phase. Here, we extend the Gaussian approximation potential (GAP) for silicon by incorporating the interaction with hydrogen, thereby significantly improving the degree of realism with which amorphous silicon can be modeled. We show that our Si : H GAP enables the simulation of hydrogenated silicon with an accuracy very close to DFT but with computational expense and run times reduced by several orders of magnitude for large structures. Here, we demonstrate the capabilities of the Si : H GAP by creating models of hydrogenated liquid and amorphous silicon and showing that their energies, forces, and stresses are in excellent agreement with DFT results, and their structure as captured by bond and angle distributions are in agreement with both DFT and experiments.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Thermal Scattering Law Data Development for Paraffin Wax

Paraffin wax is often used as a nuclear moderator to slow down the fast neutrons in experimental critical assemblies [1]. It is a colorless and soft solid material that consists primarily of straight-chain alkanes (n-alkanes), which are hydrocarbons with the general formula CnH2n+2 [2-3]. The length of the hydrocarbon chain ranges from C20 to C30 and higher [2]. It is distinguished by its solid state at room temperature and begins to melt above approximately 310 K [4]. Paraffin wax is a commonly employed substance in the manufacture of shielding. One of its noteworthy characteristics is its ability to effectively absorb the neutrons. Also, it possesses a high macroscopic cross section, which enables it to efficiently moderate neutrons. As a result, paraffin wax is extensively utilized in various applications where moderation and shielding of neutrons are needed. For simulations, it is necessary to evaluate its thermal scattering law (TSL) and cross sections. Computationally, classical molecular dynamics (CMD) simulations provide the capability of simulating atomic details. For example, several unary, binary, and few multi component mixtures have been investigated of the paraffin model by using molecular dynamics simulations [5-12]. An assessment of thermal neutron scattering in a heavy paraffinic oil treated both as a solid and a viscous fluid containing 25% linear branched paraffin (C30H62), 35% one ring cycloalkane (C30H60), 15% two rings cycloalkane (C30H58), and 25% aromatic (C30H60) chains has been studied using CMD simulations for producing TSL data [13]. Nevertheless, there is lack of TSL and cross section data for paraffin wax as most of the reported analyses focus on the unary and binary mixture of n-alkanes, which is not consistent with actual paraffin wax [2]. In this work, we applied the equilibrium CMD simulations technique to explore the structure and dynamical properties of wax, which are fundamental input to calculate the TSL. A paraffin wax system was modeled using the CMD code LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) [14-15] with the semi-empirical COMPASS [16] force field. The density of state (DOS) was calculated from the normalized velocity autocorrelation function (VACF), which is the Fourier transform of the normalized VACF. The DOS was used for the calculation of the TSL and thermal scattering cross sections. The paraffin wax atomic system was constructed by using the MedeA material design platform [17], and was benchmarked using available properties (i.e., density, bond lengths, angles, diffusivity, and viscosity).

Nuclear Criticality Safety Program (NCSP)↗

NASA NTRS1988

Computer modeling of polymers

A Polymer Molecular Analysis Display System (p-MADS) was developed for computer modeling of polymers. This method of modeling allows for the theoretical calculation of molecular properties such as equilibrium geometries, conformational energies, heats of formations, crystal packing arrangements, and other properties. Furthermore, p-MADS has the following capabilities: constructing molecules from internal coordinates (bonds length, angles, and dihedral angles), Cartesian coordinates (such as X-ray structures), or from stick drawings; manipulating molecules using graphics and making hard copy representation of the molecules on a graphics printer; and performing geometry optimization calculations on molecules using the methods of molecular mechanics or molecular orbital theory.

Green, Terry J.↗

DOE OSTI2024

Optimizing Aluminum Bonding: Exploring Surface Roughness and Contact Angle Effects through Plasma and Acid Etching Contrasts

The use of adhesives to replace traditional techniques like welding and riveting has been on the rise in various industries as increasingly complex geometries and situations for bonding is required. It’s well known in the scientific community that an adhesive bond is only as efficient as the surface preparation used beforehand. Plasma treatments have been shown to gently clean the surface by only removing the top-most layer from the adherend and “charging” the surface instead of berating it. Whereas chemical treatments “etch” the surface in hopes of increasing surface area by increasing surface roughness. This method can be difficult to control quantitatively and can generate waste leading to serious environmental concerns. This study aims to address the encountered differences between plasma treatments and acid etching on aluminum substrates for adhesive bonding. Treating the surface of adherends plays a crucial role in promoting a good bond between adhesive and adherend. In this study, the effects of plasma and acid treatments are categorized using surface roughness measurements as well as contact angle which have been shown to correlate to mechanical strength. When evaluating different surface treatments, it is notable to mention that not only surface roughness and contact angle play a role in determining which method is most effective but also the consequences of the treatment itself. It was found that although chemical etching was the most effective in increasing roughness and decreasing contact angle, it generates a large amount of waste and is not sustainable compared to plasma work which uses a renewable process. The results from this work provide a deeper understanding of the relationship between surface treatments and surface roughness/contact angle and how this relates to a stronger adhesive bond.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Optimizing Aluminum Bonding: Exploring Surface Roughness and Contact Angle Effects through Plasma and Acid Etching Contrasts.

The use of adhesives to replace traditional techniques like welding and riveting has been on the rise in various industries as increasingly complex geometries and situations for bonding is required. It’s well known in the scientific community that an adhesive bond is only as efficient as the surface preparation used beforehand. Plasma treatments have been shown to gently clean the surface by only removing the top-most layer from the adherend and “charging” the surface instead of berating it. Whereas chemical treatments “etch” the surface in hopes of increasing surface area by increasing surface roughness. This method can be difficult to control quantitatively and can generate waste leading to serious environmental concerns. This study aims to address the encountered differences between plasma treatments and acid etching on aluminum substrates for adhesive bonding. Treating the surface of adherends plays a crucial role in promoting a good bond between adhesive and adherend. In this study, the effects of plasma and acid treatments are categorized using surface roughness measurements as well as contact angle which have been shown to correlate to mechanical strength. When evaluating different surface treatments, it is notable to mention that not only surface roughness and contact angle play a role in determining which method is most effective but also the consequences of the treatment itself. It was found that although chemical etching was the most effective in increasing roughness and decreasing contact angle, it generates a large amount of waste and is not sustainable compared to plasma work which uses a renewable process. The results from this work provide a deeper understanding of the relationship between surface treatments and surface roughness/contact angle and how this relates to a stronger adhesive bond

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Nonlinear deformation and elasticity of BCC refractory metals and alloys

Application of isotropic pressure or uniaxial strain alters the elastic properties of materials; sufficiently large strains can drive structural transformations. Linear elasticity describes stability against infinitesimal strains, while nonlinear elasticity describes the response to finite deformations. Here, it was previously shown that uniaxial strain along [100] drives refractory metals and alloys towards mechanical instabilities. These include an extensional instability, and a symmetry-breaking orthorhombic distortion caused by a Jahn-Teller-Peierls instability that splays the cubic lattice vectors. Here we analyze these transitions in depth. Eigenvalues and eigenvectors of the Wallace tensor identify and classify linear instabilities in the presence of strain. We show that both instabilities are discontinuous, leading to discrete jumps in the lattice parameters. We provide physical intuition for the instabilities by analyzing the changes in first-principles energy, stress, bond lengths, and angles upon application of strain. Electronic band structure calculations show differential occupation of bonding and antibonding orbitals, driven by the changing bond lengths and leading to the structural transformations. Strain thresholds for these instabilities depend on the valence electron count.

36 MATERIALS SCIENCE↗

NASA NTRS2016

Controlled Contamination of Epoxy Composites with PDMS and Removal by Laser Ablation

Surface preparation is critical to the performance of adhesively bonded composites. During manufacturing, minute quantities of mold release compounds are inevitably deposited on faying surfaces and may compromise bond performance. To ensure safety, mechanical fasteners and other crack arrest features must be installed in the bondlines of primary structures, which negates some advantages of adhesively bonded construction. Laser ablation is an automated, repeatable, and scalable process with high potential for the surface preparation of metals and composites in critical applications such as primary airframe structures. In this study, laser ablation is evaluated on composite surfaces for the removal of polydimethylsiloxane (PDMS), a common mold release material. Composite panels were contaminated uniformly with PDMS film thicknesses as low as 6.0 nm as measured by variable angle spectroscopic ellipsometry. Bond performance was assessed by mechanical testing using a 250 F cure, epoxy adhesive and compared with pre-bond surface inspection results. Water contact angle, optically stimulated electron emission, and laser induced breakdown spectroscopy were used to characterize contaminated and laser ablated surfaces. The failure mode obtained from double cantilever beam tests correlated well with surface characterization data. The test results indicated that even low levels of PDMS were not completely removed by laser ablation.

Palmieri, Frank↗

NASA NTRS1989

Strong, Low-Resistance Bonds For AMTEC Electrodes

Heat of operating cell helps form contacts. Strong, low-electrical-resistance contacts between elements of current-collection grid in alkali-metal thermoelectric converter (AMTEC) cell obtained by simple in-place thermocompression bonding. Bonds formed between porous electrode of molybdenum film, nickel or cobalt strips overlying film, and molybdenum tie wires running at right angles to strips. Bonding method also works on films of tungsten or tungsten/platinum.

Williams, Roger M.↗

DOE OSTI2024

Uranyl Naphthylsalophen and Pyrasal Complexes: Oxo Ligands Acting as Hydrogen Bond Acceptors in the Solid State

Uranium is most stable when it is exposed to oxygen or water in its +6 oxidation state as the uranyl (UO 2 2+ ) ion. This ion is subsequently particularly stable and very resistant to functionalization due to the inverse trans effect. Uranyl oxo ligands are typically not considered good hydrogen bond acceptors due to their weak Lewis basicity; however, the ligands bound in the equatorial plane greatly affect the strength of the oxo ligands’ hydrogen bonding. Here, in this work, new naphthylsalophen and pyrasal complexes of uranium were synthesized and crystallized for characterization in the solid state. The bond lengths and angles of the uranyl ion and the ligand conformation are compared. In the solid state, one of the pyrasal complexes showed a hydrogen bond directly from a water molecule to the uranyl oxo ligand, which resulted in an asymmetric lengthening of the U–O yl bonds from 1.789 to 1.862 Å and 1.784 to 1.844 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2013

Stability of Menisci in Detached Bridgman Growth

Detached growth, also referred to as dewetted growth, is a Bridgman crystal growth process in which the melt is in contact with the crucible wall but the crystal is not. A meniscus bridges the gap between the top of the crystal and the crucible wall. The meniscus shape depends on the contact angle of the melt with the crucible wall, the growth angle of the melt with respect to the solidifying crystal, the gas pressure differential, the Weber number describing the rotation rate of the crucible, and the Bond number. Only some of the meniscus shapes are stable and the stability criterion is the sign of the second variation of the potential energy upon admissible meniscus shape perturbations. The effects of confined gas volumes above and below the melt and crucible rotation are evaluated. The analysis is applicable to the non-stationary case where the crystal radius changes during growth. Static stability maps (crystal radius versus pressure differential) are obtained for a series of Bond numbers, growth angles and Weber numbers. Also, the specific cases of Ge and InSb, in both terrestrial and microgravity conditions, are analyzed. Stability was found to depend significantly on whether the interior surface was considered to be microscopically rough or smooth, corresponding to pinned or unpinned states. It was also found that all meniscus shapes are statically stable in a microgravity environment.

Mazuruk, K.↗

NASA NTRS2013

Stability of Menisci in Detached Bridgman Growth

Detached growth, also referred to as dewetted growth, is a Bridgman crystal growth process in which the melt is in contact with the crucible wall but the crystal is not. A meniscus bridges the gap between the top of the crystal and the crucible wall. The meniscus shape depends on the contact angle of the melt with the crucible wall, the growth angle of the melt with respect to the solidifying crystal, the gas pressure differential, the Weber number describing the rotation rate of the crucible, and the Bond number. Only some of the meniscus shapes are stable and the stability criterion is the sign of the second variation of the potential energy upon admissible meniscus shape perturbations. The effects of confined gas volumes above and below the melt and crucible rotation are evaluated. The analysis is applicable to the non-stationary case where the crystal radius changes during growth. Static stability maps (crystal radius versus pressure differential) are obtained for a series of Bond numbers, growth angles and Weber numbers. Also, the specific cases of Ge and InSb, in both terrestrial and microgravity conditions, are analyzed. Stability was found to depend significantly on whether the interior surface was considered to be microscopically rough or smooth, corresponding to pinned or unpinned states. It was also found that all meniscus shapes are statically stable in a microgravity environment.

Mazuruk, Konstantin↗

NASA NTRS1991

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

NASA Program Exobiology↗

DOE OSTI2023

Synchrotron X-ray diffraction of pyrolusite (MnO 2 ) and rutile (TiO 2 ) during heating to ~1000 °C

To compare thermal expansion behaviors in isomorphic structures with different redox behaviors, we separately heated pyrolusite (Mn 4+ O 2 ) and rutile (Ti 4+ O 2 ) powders from 25 to ~1000 °C at a rate of 0.05 °C/s at ambient pressure and analyzed them using synchrotron X-ray diffraction and Rietveld refinement. The pyrolusite exhibited two reduction-induced phase decompositions. Between 531 and 583 °C, pyrolusite decomposed to bixbyite (Mn 3+ 2 O 3 ), and between 972 and 998 °C, bixbyite decomposed to hausmannite (Mn 2+ Mn 3+ 2 O 4 ). The rutile experienced no phase decompositions or transitions over this same temperature interval. The refined bond lengths and angles for pyrolusite showed that the Mn 4+ coordination octahedron became more distorted near the phase decomposition to bixbyite due to the approach of two coordinating oxygen atoms. The 3d electrons of each Mn 4+ ion in pyrolusite make π bonds with the 2p electrons of the surrounding O 2- ions, whereas the Ti 4+ of rutile has no 3d electrons. Thus, π bonding between octahedral Mn 4+ and the surrounding O 2- anions increases the strength of the Mn–O bonds of pyrolusite relative to the Ti–O bonds of rutile. However, we observed a small decrease in O–O distances in pyrolusite before the decomposition, suggesting that at high temperature, increased π bonding between adjacent O anions precedes the release of O 2 and the reduction of Mn 4+ to Mn 3+ . Analogous behavior was observed for bixbyite before its reductive phase decomposition to hausmannite. In contrast, no anomalous changes in the O–O distances occurred for rutile. Our X-ray diffraction analyses provided accurate thermal expansion coefficients for these materials over a broader temperature range than reported in previous studies. The Mn–O bond lengths in pyrolusite were shorter and stronger than the Ti–O bonds of rutile; for example, at 60 °C, bond distances in pyrolusite refined to 1.8854(6) Å whereas the bond lengths of rutile were 1.9575(4) Å. Accordingly, the axial and volumetric thermal expansion coefficients refined for rutile were greater than those for pyrolusite. Further, the axial coefficients of thermal expansion (CTE) for pyrolusite were 96% (a-axis) and 69% (c-axis) of the corresponding values for rutile, and the volumetric CTE for pyrolusite was 85% of that for rutile.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2010

Laser Surface Preparation for Adhesive Bonding of Aerospace Structural Composites

Adhesive bonds are critical to the integrity of built-up structures. Disbonds can often be detected but the strength of adhesion between surfaces in contact is not obtainable without destructive testing. Typically the number one problem in a bonded structure is surface contamination, and by extension, surface preparation. Standard surface preparation techniques, including grit blasting, manual abrasion, and peel ply, are not ideal because of variations in their application. Etching of carbon fiber reinforced plastic (CFRP) panels using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser appears to be a highly precise and promising way to both clean a composite surface prior to bonding and provide a bond-promoting patterned surface akin to peel ply without the inherent drawbacks from the same (i.e., debris and curvature). CFRP surfaces prepared using laser patterns conducive to adhesive bonding were compared to typical pre-bonding surface treatments through optical microscopy, contact angle goniometry, and post-bonding mechanical testing.

Belcher, M. A.↗

DOE OSTI2022

Non‐Linear Optical Properties of the ( RE ) 3 CuGeS 7 Family of Compounds

Abstract Non‐linear optical materials must possess a balanced combination of laser‐induced damage threshold (LDT) and second‐harmonic generation (SHG) and be phase matchable. In our previous work, chiral and polar La 3 CuGeS 7 was identified as a promising non‐linear optical material. Herein, we report the optimization of non‐linear optical properties through replacement of La with smaller lanthanides. It is determined that Gd 3 CuGeS 7 exhibits the best combination of SHG (1.6× AgGaS 2 at 88–105 μm particle size) and LDT (3× AgGaS 2 , 89 MW/cm 2 ) and is phase matchable. Based on changes in metal‐sulfur bond lengths and angles, we further propose structural optimization through solid‐solution formation and doping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗