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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

Here mechanisms underlying the mechanically induced amorphization of metal-organic frameworks (MOFs) are of current interest, and both high-pressure experimentation and molecular dynamics simulations have been used to reveal the fundamentals of load bearing, deformation, and pressure-induced amorphization (PIA) in these highly porous materials. Unfortunately, MOFs are typically highly susceptibility to amorphization, which limits the conditions under which they can be processed and used. However, their flexible structures can be stabilized to high pressures by incorporating guest species into the framework matrix. In this study, a large molecule pressure transmitting medium (DAPHNE 7575 ) is used as a structure-fortifying guest species to stabilize the prototypical MOF -5 to ultra-high pressures ( >9 GPa) and enable the recovery of crystalline material upon decompression. Structural changes associated with the penetration of the pressure transmitting medium on compression are examined using a combination of high pressure synchrotron powder diffraction and molecular dynamics simulations. This work enhances the understanding of PIA in MOFs while showcasing a potential route for the stabilization of MOFs to surprisingly high-pressures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein

Ensembles of amino acid side chains often dominate the interfacial interactions of intrinsically disordered proteins; however, backbone contributions are far from negligible. Using a combination of nanoscale force measurements and molecular dynamics simulations, we demonstrated with analogous mussel-mimetic adhesive peptides and peptoids both 34 residues long that highly divergent adhesive/cohesive outcomes can be achieved on mica surfaces by altering backbone chemistry only. The Phe, Tyr, and Dopa containing peptoid variants used in this study deposited as dehydrated and incompressible films that facilitated analysis of peptoid side chain contributions to adhesion and cohesion. For example, whereas Phe and Dopa peptoids exhibited similar cohesion, Dopa peptoids were ~3 times more adhesive than Phe peptoids on mica. Compared with the peptides, Phe peptoid achieved only ~20% of Phe containing peptide adhesion, but the Dopa peptoids were >2-fold more adhesive than the Dopa peptides. Cation-π interactions accounted for some but not all of the cohesive interactions. Finally, our results were corroborated by molecular dynamics simulations and highlight the importance of backbone chemistry and the potential of peptoids or peptoid/peptide hybrids as wet adhesives and primers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces

Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current interest as antifoulant strategies. Furthermore, despite significant proofs-of-concept, we still lack a fundamental understanding of how the nanoscopic structure of this hydration layer translates to reduced fouling, how surface chemistry can be tuned to achieve antifouling through hydration water, and why, in particular, zwitterionic surfaces seem so promising. Here, we use molecular dynamics simulations and free energy calculations to investigate the molecular relationships among surface chemistry, hydration water structure, and surface–solute affinity across a variety of surface-decorated chemistries. Specifically, we consider polypeptoid-decorated surfaces that display well-known experimental antifouling capabilities and that can be synthesized sequence specifically, with precise backbone positioning of, e.g., charged groups. Through simulations, we calculate the affinities of a range of small solutes to polypeptoid brush surfaces of varied side-chain chemistries. We then demonstrate that measures of the structure of surface hydration water in response to a particular surface chemistry signal solute–surface affinity; specifically, we find that zwitterionic chemistries produce solute–surface repulsion through highly coordinated hydration water while suppressing tetrahedral structuring around the solute, in contrast to uncharged surfaces that show solute–surface affinity. Based on the relationship of this structural perturbation to the affinity of small-molecule solutes, we propose a molecular mechanism by which zwitterionic surface chemistries enhance solute repulsion, with broader implications for the design of antifouling surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Pivotal Roles of Triple Screening-Topological, Electrostatic, and Hydrodynamic-On Dynamics in Semidilute Polyelectrolyte Solutions

For semidilute polyelectrolyte solutions, it is generally assumed that topological, electrostatic, and hydrodynamic interactions are screened (called triple screening). Despite a large body of research focused on polyelectrolyte solutions, the concept of triple screening has never been rigorously verified. In this work, we test the concept by probing concentration fluctuations in aqueous solutions containing a well-studied polyelectrolyte, sodium poly(styrenesulfonate) (NaPSS) with neutron scattering, theory, and molecular dynamics simulations. Neutron spin–echo (NSE) and small-angle neutron scattering (SANS) data from semidilute solutions of NaPSS are presented at different polymer and salt (NaCl) concentrations. A combined theory for structure (J. Chem. Phys. 105, 5183 (1996)) and dynamics (J. Chem. Phys. 107, 2619 (1997)), which captures effects of hydrodynamic, topological, and electrostatic screening, is used to interpret the experimental results. Here, the theory quantitatively predicts the decay rate obtained from the NSE measurements while capturing the shape and concentration dependencies of the polyelectrolyte peak observed in the SANS spectra. Detailed comparisons of the theory and the experiments reveal that the wavevector-dependent decay rate of concentration fluctuations in semidilute solutions of polyelectrolytes is dictated by the screening of hydrodynamic, topological, and electrostatic interactions. This conclusion is corroborated by coarse-grained molecular dynamics simulations, executed without any hydrodynamic interactions, which fail to capture the correct wavevector dependence of the decay rate. These results highlight that the theories based on the concept of triple screening provide a quantitative framework for predicting a relation between the structure and dynamics of polyelectrolyte solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanical behavior of ultralight nickel metamaterial

The mechanical response of ultralight kagomé structures consisting of hollow nickel (Ni) nanotubes and solid Ni nanorods to compression is studied using molecular dynamics simulations. In both kagomé architectures, 16[112] Shockley partial dislocations and twin formation are observed under compression. The structure made from solid nanorods shows deformation near both the nodes and beams of the kagomé lattice. The hollow kagomé architecture has a higher yield point than the solid kagomé structure. The deformation in the hollow nanotube structure is mostly localized in the nodal region for strains less than 11%. At higher strains, the deformation sets in all the struts and nodes of the hollow kagomé lattice. Owing to this two-stage deformation mechanism, the hollow Ni nanotube kagomé structure shows less bending and greater toughness than the solid Ni nanorod kagomé architecture.

Rajak, Pankaj (ORCID:0000000263446056)↗
DOE OSTI2020

Tuning the melting point of selected ionic liquids through adjustment of the cation’s dipole moment.

In prior research with thermally robust salts [Cassity et al., PCCP, 2017, 19, 31560] it was noted that an increase in the dipole moment of the cation generally led to a decrease in the melting point. Molecular dynamics simulations of the liquid state revealed that an increased dipole moment reduces cation-cation repulsions through dipole-dipole alignment. This was believed to reduce the liquid phase enthalpy, which would tend to lower the melting point of the IL. Here, we also test this principle by replacing hydrogen atoms with fluorine atoms at selected positions within the cation. This allows us to alter the electrostatics of the cation without substantially affecting the sterics. Furthermore, the strength of the dipole moment can be controlled by choosing different positions within the cation for replacement. We studied variants of four different parent cations paired with bistriflimide and determined their melting points, and enthalpies and entropies of fusion through DSC experiments. The decreases in the melting point were determined to be enthalpically driven. We found that the dipole moment of the cation, as determined by quantum chemical calculations, is inversely correlated with the melting point of the given compound. Molecular dynamics simulations of the crystalline and solid states of two isomers showed differences in their enthalpies of fusion that closely matched those seen experimentally. Moreover, this reduction in the enthalpy of fusion was determined to be caused by an increase in the enthalpy of the crystalline state. We provide evidence that dipole-dipole interactions between cations leads to the formation of cationic domains in the crystalline state. These cationic associations partially block favourable cation–anion interactions, which are recovered upon melting. If, however, the dipole- dipole interactions between cations is too strong they have a tendency to form glasses. This study provides a design rule for lowering the melting point of structurally similar ILs by altering their dipole moment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Raman studies of hydrogen trapped in As 4 O 6 ·2H 2 at high pressure and low temperature

In this work, Raman spectroscopic measurements of the arsenolite–hydrogen inclusion compound As 4 O 6 ·2H 2 were performed in diamond anvil cells at high pressure and variable temperature down to 80 K. The experimental results were complemented by ab initio molecular dynamics simulations and phonon calculations. Observation of three hydrogen vibrons in As 4 O 6 ·2H 2 is reported in the entire temperature and pressure range studied (up to 24 GPa). While the experiments performed with protium and deuterium at variable temperatures allowed for the assignment of two vibrons as Q 1 (1) and Q 1 (0) transitions of ortho and para spin isomers of hydrogen trapped in the inclusion compound, the origin of the third vibron could not be unequivocally established. Low-temperature spectra revealed that the lowest-frequency vibron is actually composed of two overlapping bands of A g and T 2g symmetries dominated by H 2 stretching modes as predicted by our previous density functional theory calculations. We observed low-frequency modes of As 4 O 6 ·2H 2 vibrations dominated by H 2 “librations,” which were missed in a previous study. A low-temperature fine structure was observed for the J = 0 → 2 and J = 1 → 3 manifolds of hydrogen trapped in As 4 O 6 ·2H 2 , indicating the lifting of degeneracy due to an anisotropic environment. A non-spherical distribution was captured by molecular dynamics simulations, which revealed that the trajectory of H 2 molecules is skewed along the crystallographic $\langle$111$\rangle$ direction. Last but not least, low-temperature synchrotron powder x-ray diffraction measurements on As 4 O 6 ·2H 2 revealed that the bulk structure of the compound is preserved down to 5 K at 1.6 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Three-dimensional atomic packing in amorphous solids with liquid-like structure

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Shape-preserving amorphous-to-crystalline transformation of CaCO3 revealed by in situ TEM

Organisms use inorganic ions and macromolecules to regulate crystallization from amorphous- precursors, endowing natural biominerals with complex morphologies and enhanced properties. The mechanisms by which modifiers enable these shape preserving transformations are poorly understood. We used in situ liquid-phase transmission electron microscopy to follow the evolution from amorphous calcium carbonate to calcite in the presence of additives. A combination of contrast analysis and infrared spectroscopy shows that Mg ions, which are widely present in seawater and biological fluids, alter the transformation pathway in a concentration-dependent manner. The ions bring excess (structural) water into the amorphous bulk so that a direct transformation is triggered by dehydration in the absence of morphological changes. Molecular dynamics simulations suggest Mg-incorporated water induces structural fluctuations, allowing transformation without the need to nucleate a separate crystal. Thus, the obtained calcite retains the original morphology of the amorphous state, biomimetically achieving the morphological control of crystals seen in biominerals

crystallization, biomineralization, calcium carbon↗
DOE OSTI2020

Polyelectrolyte Complex Coacervate Assembly with Cellulose Nanofibers

Polyelectrolytes are used in paper manufacturing to increase flocculation and water drainage and improve mechanical properties. In this study, we examine the interaction between charged cellulosic nanomaterials and polyelectrolyte complex coacervates of weak polyelectrolytes, polyacrylic acid salt, and polyallylamine hydrochloride. We observe that by changing the order of addition of the polyelectrolytes to cellulose nanofibers (CNFs), we can tune the interactions between the materials, which in turn changes the degree of association of the coacervates to the CNFs and the rate at which they aggregate. Importantly for the papermaking process, when adding the polyelectrolytes sequentially to the CNFs, we found faster aggregation to the fibers and lower water retention values compared to those when preformed coacervates or CNFs by themselves were used. Coarse-grain molecular dynamic simulations further support the fundamental mechanism of aggregation by taking into consideration the interaction between cellulose and the complexes at the molecular level. The simulations corroborate the experimental observations by showing the importance of strong electrostatic interactions in aggregate formation.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Facile diamond synthesis from lower diamondoids

Carbon-based nanomaterials have exceptional properties that make them attractive for a variety of technological applications. Here, we report on the use of diamondoids (diamond-like, saturated hydrocarbons) as promising precursors for laser-induced high-pressure, high-temperature diamond synthesis. The lowest pressure and temperature $(P-T)$ conditions that yielded diamond were 12 GPa (at ~2000 K) and 900 K (at ~20 GPa), respectively. This represents a substantially reduced transformation barrier compared with diamond synthesis from conventional (hydro)carbon allotropes, owing to the similarities in the structure and full sp 3 hybridization of diamondoids and bulk diamond. At 20 GPa, diamondoid-to-diamond conversion occurs rapidly within <19 μs. Molecular dynamics simulations indicate that once dehydrogenated, the remaining diamondoid carbon cages reconstruct themselves into diamond-like structures at high $P-T$. This study is the first successful mapping of the $P-T$ conditions and onset timing of the diamondoid-to-diamond conversion and elucidates the physical and chemical factors that facilitate diamond synthesis.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Unseeded, spontaneous nucleation of spherulitic magnesium calcite

Most of the sedimentary carbonates deposited in the marine environments are composed of calcium carbonate minerals with varying amounts of incorporated Mg 2+ . However, understanding how interactions of impurities with carbonate and their incorporation affect sediments behavior remains a challenge. Here, a new insight is obtained by monitoring solution composition, morphology, and electrokinetic potential of carbonate particles formed in a spontaneous unseeded batch precipitation experiment using electrochemical and scanning electron microscopy methods. The solid composition and growth rate are extracted from changes in the bulk composition and fitted to chemical affinity rate law, revealing that the precipitation pathway consists of second-order dissolution and first-order precipitation. The molecular dynamics simulations show that the lattice strain induced by randomly substituting Ca 2+ by Mg 2+ stabilizes spherical nanoparticles and reduces their surface area and volume. Combining kinetics and thermodynamics insight, we conclude that variation in the carbonate bulk and interfacial energies, along with the solution supersaturation, lead to the dissolution-precipitation transformation pathway from Mg-rich to Mg-poor carbonate phase that preserves spherulitic morphology. Furthermore, our findings are relevant for long-standing questions of how impurities influence diagenesis of carbonate sediments and spherulitic carbonate particles' origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Conformation and dynamics of ring polymers under symmetric thin film confinement

Understanding the structure and dynamics of polymers under confinement has been of widespread interest, and one class of polymers that have received comparatively little attention under confinement is that of ring polymers. The properties of non-concatenated ring polymers can also be important in biological fields because ring polymers have been proven to be a good model to study DNA organization in the cell nucleus. From our previous study, linear polymers in a cylindrically confined polymer melt were found to segregate from each other as a result of the strong correlation hole effect that is enhanced by the confining surfaces. By comparison, our subsequent study of linear polymers in confined thin films at similar levels of confinements found only the onset of segregation. Here, we use molecular dynamics simulation to investigate the chain conformations and dynamics of ring polymers under planar (1D) confinement as a function of film thickness. Our results show that conformations of ring polymers are similar to the linear polymers under planar confinement, except that ring polymers are less compressed in the direction normal to the walls. While we find that the correlation hole effect is enhanced under confinement, it is not as pronounced as the linear polymers under 2D confinement. Finally, we show that chain dynamics far above Tg are primarily affected by the friction from walls based on the monomeric friction coefficient we get from the Rouse mode analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Unveiling the Mechanism of Mn Dissolution Through a Dynamic Cathode‐Electrolyte Interphase on LiMn2O4

Abstract Understanding the formation and evolution of the cathode‐electrolyte interphase (CEI), which forms at the interface between the cathode and electrolyte, is crucial for revealing degradation mechanisms in cathode materials, especially for developing strategies to stabilize the interphase in the strongly oxidizing conditions that evolve at high operating voltages in next‐generation Li‐ion batteries. However, The present understanding of the CEI is challenged by its complex and dynamic nature. In this work, near‐edge X‐ray absorption fine structure spectroscopy, electrochemical characterization, and reactive molecular dynamics simulations are combined to reveal a mechanism for CEI formation and evolution above model LiMn 2 O 4 (LMO) thin‐film electrodes in contact with conventional carbonate‐based electrolytes. It is found that Mn dissolution from LMO can be understood in terms of repetitive Mn 3 O 4 formation and dissolution behavior during cycling, which is closely connected to electrolyte decomposition and a key aspect of the CEI formation and growth. The behavior of the CEI in this model system offers detailed insight into the dynamic chemistry of the interphase, underscoring the important role of electrolyte composition and cathode surface structure in interphase degradation.

Ou, Wenhan↗
DOE OSTI2023

Data-driven prediction of α IIb β 3 integrin activation paths using manifold learning and deep generative modeling

The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αI I b β3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. Furthermore, this work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multi-scale technique to predict transition pathways for biomolecular systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Gaussian approximation potentials for accurate thermal properties of two-dimensional materials

Two-dimensional materials (2DMs) continue to attract a lot of attention, particularly for their extreme flexibility and superior thermal properties. Molecular dynamics simulations are among the most powerful methods for computing these properties, but their reliability depends on the accuracy of interatomic interactions. While first principles approaches provide the most accurate description of interatomic forces, they are computationally expensive. In contrast, classical force fields are computationally efficient, but have limited accuracy in interatomic force description. Machine learning interatomic potentials, such as Gaussian Approximation Potentials, trained on density functional theory (DFT) calculations offer a compromise by providing both accurate estimation and computational efficiency. Here, in this work, we present a systematic procedure to develop Gaussian approximation potentials for selected 2DMs, graphene, buckled silicene, and h-XN (X = B, Al, and Ga, as binary compounds) structures. We validate our approach through calculations that require various levels of accuracy in interatomic interactions. The calculated phonon dispersion curves and lattice thermal conductivity, obtained through harmonic and anharmonic force constants (including fourth order) are in excellent agreement with DFT results. HIPHIVE calculations, in which the generated GAP potentials were used to compute higher-order force constants instead of DFT, demonstrated the first-principles level accuracy of the potentials for interatomic force description. Molecular dynamics simulations based on phonon density of states calculations, which agree closely with DFT-based calculations, also show the success of the generated potentials in high-temperature simulations.

2D Materials↗