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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Nanocavitation Approach to Understanding Water Capture, Water Release, and Framework Physical Stability in Hierarchically Porous MOFs

Chemically stable metal–organic frameworks (MOFs) featuring interconnected hierarchical pores have proven to be promising for a remarkable variety of applications. Nevertheless, the framework’s susceptibility to capillary-force-induced pore collapse, especially during water evacuation, has often limited practical applications. Methodologies capable of predicting the relative magnitudes of these forces as functions of the pore size, chemical composition of the pore walls, and fluid loading would be valuable for resolution of the pore collapse problem. Here, we report that a molecular simulation approach centered on evacuation-induced nanocavitation within fluids occupying MOF pores can yield the desired physical-force information. Here, the computations can spatially pinpoint evacuation elements responsible for collapse and the chemical basis for mitigation of the collapse of modified pores. Experimental isotherms and difference-electron density measurements of the MOF NU-1000 and four chemical variants validate the computational approach and corroborate predictions regarding relative stability, anomalous sequence of pore-filling, and chemical basis for mitigation of destructive forces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Interzeolite Transformation through Cross-Nucleation: A Molecular Mechanism for Seed-Assisted Synthesis

Polymorph selection and efficient crystallization are central goals in zeolite synthesis. Crystalline seeds are used for both purposes. While it has been proposed that zeolite seeds induce interzeolite transformation by dissolving into structural units that promote nucleation of the daughter crystal, the seed’s structural elements do not always match those of the target zeolite. This discrepancy raises the question of how the seed promotes the daughter phase. Here, we present the first molecularly resolved investigation of seed-assisted zeolite synthesis. Using molecular simulations, we reproduce the experimental finding that a parent zeolite can promote the nucleation of a daughter zeolite even when it lacks common composite building units (CBUs) or crystal planes. Modeling the seed-assisted synthesis of an AFI-type zeolite using zeolite CHA, our simulations indicate that stand-alone CBUs from the parent seed do not facilitate daughter crystal formation. However, introducing the intact seed significantly reduces the synthesis time, supporting that seed integrity is key to increased efficiency. This reduction arises from the cross-nucleation of the AFI-type zeolite on the CHA (001) face. We find that parent and daughter zeolites are connected by an interfacial transition layer with an order distinct from that of both zeolites. Simulations reveal that cross-nucleation occurs over a broad range of synthesis conditions. We argue that cross-nucleation would be most favorable for zeolite pairs that share crystalline planes such as those forming intergrowths. In conclusion, our findings suggest that the prevalence of intergrowths with a common lattice plane in zeolite synthesis is likely a kinetic effect of accelerated cross-nucleation.

Crystallization↗
DOE OSTI2026

Mechanistic Insights into Defect-Mediated Crystallization Revealed by Lattice Strain Evolution

Structural defects and lattice strain are intrinsic to many crystalline materials, yet their roles in controlling chemical reaction mechanisms and directing crystallization pathways remain poorly understood. Here, in this study, we revealed the three-dimensional evolution of strain and dislocation defects at the nanoscale during the growth of heterogeneously nucleated barite (BaSO 4 ) and calcite (CaCO 3 ) crystals by using coherent X-ray scattering, electron microscopy, and molecular simulations. Unlike barite, which formed with minimal internal strain, calcite developed dislocation defects and exhibited spatially varying strain that increased during growth. During growth in Sr-rich solutions, calcite likely incorporates Sr 2+ into the defects, which further modulates the local lattice structure and increases both the compressive and tensile strain. These findings suggest that calcite crystallization was likely dominated by attachment of precursor phases, which gave rise to defect-enriched domain structures not predicted by classical growth models. By linking defect formation to ion incorporation and growth dynamics, this work provides fundamental insight into how lattice-level strain heterogeneity governs the chemical reactivity of ionic crystals.

Bragg coherent diffractive imaging↗
DOE OSTI2020

Molecular Insight into Fluorocarbon Adsorption in Pore Expanded Metal–Organic Framework Analogs

The rapid growth in the global energy demand for space cooling requires the development of more efficient environmental chillers for which adsorption-based cooling systems can be utilized. Here, in this contribution, we explore sorbents for chiller use via a pore-engineering concept to construct analogs of the 1-dimensional pore metal–organic framework MOF-74 by using elongated organic linkers and stereochemistry control. The prepared pore-engineered MOFs show remarkable equilibrium adsorption of the selected fluorocarbon refrigerant that is translated to a modeled adsorption-based refrigeration cycle. To probe molecular level interactions at the origin of these unique adsorption properties for this series of Ni-MOFs, we combined in situ synchrotron X-ray powder diffraction, neutron powder diffraction, X-ray absorption spectroscopy, calorimetry, Fourier transform infrared techniques, and molecular simulations. Our results reveal the coordination of fluorine (of CH2F in R134a) to the nickel(II) open metal centers at low pressures for each Ni-MOF analog and provide insight into the pore filling mechanism for the full range of the adsorption isotherms. The newly designed Ni-TPM demonstrates exceptional R134a adsorption uptake compared to its parent microporous Ni-MOF-74 due to larger engineered pore size/volume. The application of this adsorption performance toward established chiller conditions yields a working capacity increase for Ni-TPM of about 400% from that of Ni-MOF-74, which combined with kinetics directly correlates to both a higher coefficient of performance and a higher average cooling capacity generated in a modeled chiller.

Zheng, Jian↗
DOE OSTI2020

Retrieving functional pathways of biomolecules from single-particle snapshots

Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path

Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3'-5' exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states of E. coli replicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

How μ-opioid receptor recognizes fentanyl

Abstract Roughly half of the drug overdose-related deaths in the United States are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, X-ray crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like opioids remains lacking. Exploiting the X-ray structure of BU72-bound mOR and several molecular simulation techniques, we elucidated the detailed binding mechanism of fentanyl. Surprisingly, in addition to the salt-bridge binding mode common to morphinan opiates, fentanyl can move deeper and form a stable hydrogen bond with the conserved His297 6.52 , which has been suggested to modulate mOR’s ligand affinity and pH dependence by previous mutagenesis experiments. Intriguingly, this secondary binding mode is only accessible when His297 6.52 adopts a neutral HID tautomer. Alternative binding modes may represent a general mechanism in G protein-coupled receptor-ligand recognition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Bias free multiobjective active learning for materials design and discovery

The design rules for materials are clear for applications with a single objective. For most applications, however, there are often multiple, sometimes competing objectives where there is no single best material and the design rules change to finding the set of Pareto optimal materials. In this work, we leverage an active learning algorithm that directly uses the Pareto dominance relation to compute the set of Pareto optimal materials with desirable accuracy. We apply our algorithm to de novo polymer design with a prohibitively large search space. Using molecular simulations, we compute key descriptors for dispersant applications and drastically reduce the number of materials that need to be evaluated to reconstruct the Pareto front with a desired confidence. This work showcases how simulation and machine learning techniques can be coupled to discover materials within a design space that would be intractable using conventional screening approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Entropically engineered formation of fivefold and icosahedral twinned clusters of colloidal shapes

Fivefold and icosahedral symmetries induced by multiply twinned crystal structures have been studied extensively for their role in influencing the shape of synthetic nanoparticles, and solution chemistry or geometric confinement are widely considered to be essential. Here we report the purely entropy-driven formation of fivefold and icosahedral twinned clusters of particles in molecular simulation without geometric confinement or chemistry. Hard truncated tetrahedra self-assemble into cubic or hexagonal diamond colloidal crystals depending on the amount of edge and vertex truncation. By engineering particle shape to achieve a negligible entropy difference between the two diamond phases, we show that the formation of the multiply twinned clusters is easily induced. The twinned clusters are entropically stabilized within a dense fluid by a strong fluid-crystal interfacial tension arising from strong entropic bonding. Our findings provide a strategy for engineering twinning behavior in colloidal systems with and without explicit bonding elements between particles.

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

Solvent-derived defects suppress adsorption in MOF-74

Defects in metal-organic frameworks (MOFs) have great impact on their nano-scale structure and physiochemical properties. However, isolated defects are easily concealed when the frameworks are interrogated by typical characterization methods. In this work, we unveil the presence of solvent-derived formate defects in MOF-74, an important class of MOFs with open metal sites. With multi-dimensional solid-state nuclear magnetic resonance (NMR) investigations, we uncover the ligand substitution role of formate and its chemical origin from decomposed N,N-dimethylformamide (DMF) solvent. The placement and coordination structure of formate defects are determined by 13 C NMR and density functional theory (DFT) calculations. The extra metal-oxygen bonds with formates partially eliminate open metal sites and lead to a quantitative decrease of N 2 and CO 2 adsorption with respect to the defect concentration. In-situ NMR analysis and molecular simulations of CO 2 dynamics elaborate the adsorption mechanisms in defective MOF-74. Our study establishes comprehensive strategies to search, elucidate and manipulate defects in MOFs.

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

Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Accurate protein synthesis is determined by the two-subunit ribosome’s capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by antibiotics, remains incompletely understood. Using molecular simulations, we find that cognate and near-cognate tRNAs delivered to the ribosome by Elongation Factor Tu (EF-Tu) can follow divergent pathways of motion into the ribosome during both initial selection and proofreading. Consequently, cognate aa-tRNAs follow pathways aligned with the catalytic GTPase and peptidyltransferase centers of the large subunit, while near-cognate aa-tRNAs follow pathways that are misaligned. These findings suggest that differences in mRNA codon-tRNA anticodon interactions within the small subunit decoding center, where codon-anticodon interactions occur, are geometrically amplified over distance, as a result of this site’s physical separation from the large ribosomal subunit catalytic centers. These insights posit that the physical size of both tRNA and ribosome are key determinants of the tRNA selection fidelity mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Molecular model of TFIIH recruitment to the transcription-coupled repair machinery

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.

Paul, Tanmoy↗
DOE OSTI2025

Metastability and Ostwald step rule in the crystallisation of diamond and graphite from molten carbon

Abstract Experimental challenges in determining the phase diagram of carbon at temperatures and pressures near the graphite-diamond-liquid triple point are often related to the persistence of metastable crystalline or glassy phases, superheated crystals, or supercooled liquids. A deeper understanding of the crystallisation kinetics of diamond and graphite is crucial for effectively interpreting the outcomes of these experiments. Here, we reveal the microscopic mechanisms of diamond and graphite nucleation from liquid carbon through molecular simulations with first-principles machine learning potentials. Our simulations accurately reproduce the experimental phase diagram of carbon near the triple point and show that liquid carbon crystallises spontaneously upon cooling. Metastable graphite crystallises in the domain of diamond thermodynamic stability at pressures above the triple point. Furthermore, whereas diamond crystallises through a classical nucleation pathway, graphite follows a two-step process in which low-density fluctuations forego ordering. Calculations of the nucleation rates of the two competing phases confirm this result and reveal a manifestation of Ostwald’s step rule, where the strong metastability of graphite hinders the transformation to the stable diamond phase. Our results provide a key to interpreting melting and recrystallisation experiments and shed light on nucleation kinetics in polymorphic materials with deep metastable states.

Science & Technology - Other Topics↗
DOE OSTI2025

Phosphorylation toggles the SARS-CoV-2 nucleocapsid protein between two membrane-associated condensate states

Abstract The Nucleocapsid protein (N) of SARS-CoV-2 plays a critical role in the viral lifecycle by regulating RNA replication and by packaging the viral genome. N and RNA phase separate to form condensates that may be important for these functions. Both functions occur at membrane surfaces, but how N toggles between these two membrane-associated functional states is unclear. Here, we reveal that phosphorylation switches how N condensates interact with membranes, in part by modulating condensate material properties. Our studies also show that phosphorylation alters N’s interaction with viral membrane proteins. We gain mechanistic insight through structural analysis and molecular simulations, which suggest phosphorylation induces a conformational change in N that softens condensate material properties. Together, our findings identify membrane association as a key feature of N condensates and provide mechanistic insights into the regulatory role of phosphorylation. Understanding this mechanism suggests potential therapeutic targets for COVID infection.

Science & Technology - Other Topics↗
DOE OSTI2025

Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Abstract XPD is a key nucleotide excision repair (NER) protein whose function is vital for genome integrity. During NER, XPD serves as a 5′−3′ single-strand DNA translocase that enables lesion scanning and verification in genomic DNA. Yet, its translocation mechanism is incompletely understood. Here we use molecular simulations and chain-of-replicas path optimization methods to model the ATP-driven translocation mechanisms of XPD and its bacterial homolog DinG, revealing all on-path metastable intermediates and corresponding kinetic rates. We identify the XPD(DinG) global domain motions that modulate the strength of DNA association at the opposing ends of the DNA-binding groove. During the ATP hydrolysis cycle, alternating weak and strong interactions at two defined groove constrictions enable DNA reptation and forward displacement of the ATPase. Moreover, we show that DNA- or ATP-binding residues directly involved in translocation are hotspots for genetic disease mutations. Thus, our findings shed light on the etiology of XPD-associated genetic syndromes.

Paul, Tanmoy↗
DOE OSTI2024

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate

Metal carbonates, which are ubiquitous in the near-surface mineral record, are a major product of biomineralizing organisms and serve as important targets for capturing anthropogenic CO 2 emissions. However, pathways of carbonate mineralization typically diverge from classical predictions due to the involvement of disordered precursors, such as the dense liquid phase (DLP), yet little is known about DLP formation or solidification processes. Using in situ methods we report that a highly hydrated bicarbonate DLP forms via liquid–liquid phase separation and transforms into hollow hydrated amorphous CaCO 3 particles. Acidic proteins and polymers extend DLP lifetimes while leaving the pathway and chemistry unchanged. Molecular simulations suggest that the DLP forms via direct condensation of solvated Ca 2+ •(HCO 3 – ) 2 complexes that react due to proximity effects in the confined DLP droplets. Furthermore, our findings provide insight into CaCO 3 nucleation that is mediated by liquid–liquid phase separation, advancing the ability to direct carbonate mineralization and elucidating an often-proposed complex pathway of biomineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Forces that control self-organization of chemically-propelled Janus tori

Control of the individual and collective behavior of self-propelled synthetic micro-objects has immediate application for nanotechnology, robotics, and precision medicine. Despite significant progress in the synthesis and characterization of self-propelled Janus (two-faced) particles, predictive understanding of their behavior remains challenging, especially if the particles have anisotropic forms. Here, by using molecular simulation, we describe the interactions of chemically-propelled microtori near a wall. The results show that a torus hovers at a certain distance from the wall due to a combination of gravity and hydrodynamic flows generated by the chemical activity. Moreover, electrostatic dipolar interactions between the torus and the wall result in a spontaneous tilt and horizontal translation, in a qualitative agreement with experiment. Simulations of the dynamics of two and four tori near a wall provide evidence for the formation of stable self-propelled bound states. Our results illustrate that self-organization at the microscale occurs due to a combination of multiple factors, including hydrodynamic, chemical, electrostatic and steric interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗