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DOE OSTI2020

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Finally, such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Oligomerization of Pr55 Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55 Gag . However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55 Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18–33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles’ membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain’s 2D layers during assembly and budding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Molecular interactions↗

DOE OSTI2022

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance–decay relationship within the 200-m 2 field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Assembly of polyelectrolyte star block copolymers at the oil–water interface

To understand and resolve adsorption, reconfiguration, and equilibrium conformations of charged star copolymers, we carried out an integrated experimental and coarse-grained molecular dynamics simulation study of the assembly process at the oil–water interface. This is important to guide development of novel surfactants or amphiphiles for chemical transformations and separations. The star block copolymer consisted of arms that are comprised of hydrophilic–hydrophobic block copolymers that are covalently tethered via the hydrophobic blocks to one point. The hydrophobic core represents polystyrene (PS) chains, while the hydrophilic corona represents quaternized poly(2-vinylpyridine) (P2VP) chains. The P2VP is modeled to become protonated when in contact with an acidic aqueous phase, thereby massively increasing the hydrophilicity of this block, and changing the nature of the star at the oil–water interface. This results in a configurational change whereby the chains comprising the hydrophilic corona are significantly stretched into the aqueous phase, while the hydrophobic core remains solubilized in the oil phase. In the simulations, we followed the kinetics of the anchoring and assembly of the star block copolymer at the interface, monitoring the lateral assembly, and the subsequent reconfiguration of the star via changes in the interfacial tension that varies as the degree-of-protonation increases. At low fractions of protonation, the arm cannot fully partition into the aqueous side of the interface and instead interacts with other arms in the oil phase forming a network near the interface. These insights were used to interpret the non-monotonic dependence of pH with the asymptotic interfacial tension from pendant drop tensiometry experiments and spectral signatures of aromatic stretches seen in vibrational sum frequency generation (SFG) spectroscopy. We describe the relationship of interfacial tension to the star assembly via the Frumkin isotherm, which phenomenologically describes anti-cooperativity in adsorbing stars to the interface due to crowding. Although our model explicitly considers long-range electrostatics, the contribution of electrostatics to interfacial tension is small and brought about by strong counterion condensation at the interface. Finally, these results provide key insights into resolving the adsorption, reconfiguration, and equilibrium conformations of charged star block copolymers as surfactants.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Role of the Solvent–Surfactant Duality of Ionic Liquids in Directing Two-Dimensional Particle Assembly

Nanoparticle self-assembly plays a key role in formation of superlattices, which exhibit remarkable physical and chemical properties. However, controlling assembly remains a challenge partly due to a lack of understanding of the assembly dynamics and the difficulty in linking interfacial solution properties to interparticle forces. In this study, using liquid-cell transmission electron microscopy, self-assembly of gold nanoparticles (NPs) into superlattices in mixtures of water and ionic liquid (IL) was visualized, revealing a dual role of the IL in the assembly process. At intermediate concentrations, the IL acts as a surfactant stabilizing the particles at a well-defined equilibrium separation corresponding to the length of hydrogen bonded IL cations adsorbed onto neighboring NPs. Analysis of the interparticle forces reveals attractive long-range interactions of a van der Waals nature. At separations of 1-3 nm, interactions are dominated by attractive ion correlation and repulsive hydration forces giving rise to an energy minimum at 1.5 nm separation. The superlattice is further stabilized by hydrogen bonding, which shifts the equilibrium interparticle distance to 1.1 nm. In contrast, at higher concentrations, IL accumulates and forms a structured network in the gap between nanoparticles, where it acts as a solvent that eliminates the repulsive barrier and thus promotes particle coalescence. This solvent-surfactant duality of IL opens new opportunities for their use in directing particle assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

High Performance Computing to Quantify the Evolution of Microscopic Concentration Gradients During Flash Processing

During the Flash process, the cross section of a plain-carbon or a low-alloy steel is austenitized through rapid heating and transformed on rapid cooling to a predominantly martensite + bainite structure with small amounts of retained austenite. Unlike conventional heat treating, homogeneity is intentionally avoided during Flash processing of steels. The Flash process assembly consists of a pair of rolls that transfer the steel sheets through the heating and cooling stage of the thermal cycle. The initial microstructure of the steel consists of ferrite (body-centered cubic iron) + carbide ((Fe,X)mCn) mixture. The heating rate through the peak temperature is a function of temperature and reaches a peak of about 300-400°C/s and the cooling rate has a maximum value of 3,000-4,000°C/s. The on-heating phase transformations include carbide dissolution, austenite (face-centered cubic iron) nucleation and growth, and diffusion of carbon and other substitutional elements in the steel. The on-cooling phase transformations include formation of martensite (body-centered tetragonal phase containing supersaturated solute) and bainite (ferrite plates with or without fine carbides). In this project, the focus is on Fe-C-Cr steels that are currently Flash processed for armor applications. The modeling effort proposed here will help optimize the Flash thermal cycle for these low alloy steels to achieve the target performance, which is an ongoing effort at SFP Works. A significant feature of Flash processed Fe-C-Cr steels is the presence of scatter in the through-thickness in the sheet. The variability in hardness results from a variability in the bainite + martensite microstructure that is sensitive to the local chemical concentration of C and Cr. Such a chemical inhomogeneity is intentionally obtained in the Flash process. Although such a microstructural gradient is presumably responsible for the exceptional properties of the Flash processed steel, it is very important to quantify the gradients as a function of Flash variabilities in processing parameters and the input microstructure. Understanding the mechanistic pathway that leads to microstructural gradients could be ground-breaking and instrumental for achieving better process control and optimized microstructural state to meet application-specific strength-ductility requirements. Since the final microstructure depends on setting up precise solute concentration gradients through a rapid heating process, and transforming these regions into various phases, it is important to understand how small changes in steel chemistry, input microstructure (carbide size and distribution), and process variables (Flash thermal cycle) will impact the solute concentration gradients.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Observation of an Orientational Glass in a Superlattice of Elliptically-Faceted CdSe Nanocrystals

Extensive prior work has shown that colloidal inorganic nanocrystals coated with organic ligand shells can behave as artificial atoms and, as such, form superlattices with different crystal structures and packing densities. Although ordered superlattices present a high degree of long-range positional order, the relative crystallographic orientation of the inorganic nanocrystals with respect to each other tends to be random. Recent works have shown that superlattices can achieve orientational alignment through combinations of nanocrystal faceting and ligand modification, as well as selective metal particle attachment to particular facets. These studies have focused on the assembly of high-symmetry nanocrystals, such as cubes and cuboctahedra. In this work, we study the assembly of elliptically faceted CdSe/CdS core/shell nanocrystals with one distinctive crystallographic orientation along the major elliptical axis. We show that the nanocrystals form an unexpectedly well-ordered translational superlattice, with a degree of order comparable to that achieved with higher-symmetry nanocrystals. Additionally, we show that, due to the particles' faceted shape, the superlattice is characterized by an orientational glass phase in which only certain orientations are possible due to entropically frustrated crystallization. In this phase, the nanocrystals do not exhibit a local orientational ordering but rather have distinct orientations that emerge at different locations within the same domain. The distinct orientations are a result of a facet-to-facet lock-in mechanism that occurs during the self-assembly process. These facet-to-facet alignments force the nanocrystals to tilt on different lattice planes forming different projections that we termed apparent polydispersity. Our experimental realization of an orientational glass phase for multifaceted semiconducting nanocrystals can be used to investigate how this phase is formed and how it can be utilized for potential optical, electrical, and thermal transport applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Temperature-Controlled Reversible Formation and Phase Transformation of 3D Nanocrystal Superlattices Through In Situ Small-Angle X-ray Scattering

For decades, the spontaneous organization of nanocrystals into superlattices has captivated the scientific community. However, achieving direct control over the formation of the superlattice and its phase transformations has proven to be a grand challenge, often resulting in the generation of multiple symmetries under the same experimental conditions. Here, we achieve direct control over the formation of the superlattice and its phase transformations by modulating the thermal energy of a nanocrystal dispersion without relying on solvent evaporation. In this study, we follow the temperature-dependent dynamics of the self-assembly process using synchrotron-based small-angle X-ray scattering. When cooled below –24.5 °C, lead sulfide nanocrystals form micrometer-sized three-dimensional phase-pure body-centered cubic superlattices. When cooled below –35.1 °C, these superlattices undergo a collective diffusionless phase transformation that yields denser body-centered tetragonal phases. These structural changes can be reversed by increasing the temperature of the dispersion and may lead to the direct modulation of the optical properties of these artificial solids.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Controlled Assembly of Upconverting Nanoparticles for Low-Threshold Microlasers and Their Imaging in Scattering Media

Micron-sized lasers fabricated from upconverting nanoparticles (UCNP) coupled to whispering gallery mode (WGM) microresonators can exhibit continuous-wave anti-Stokes lasing useful for tracking cells, environmental sensing, and coherent stimulation of biological activity. The integration of these microlasers into organisms and microelectronics requires even smaller diameters, however, which raises threshold pump powers beyond practical limits for biological applications. To meet the need for low lasing thresholds and high fidelity fabrication methods, we use correlative optical and electron microscopy to uncover the nanoparticle assembly process and structural factors that determine efficient upconverted lasing. We show that 5 μm microspheres with controlled submonolayer UCNP coatings exhibit, on average, 25-fold lower laser thresholds (1.7 ± 0.7 kW/cm 2 ) compared to the mean values of the lowest threshold UCNP lasers, and variability is reduced 30-fold. WGMs are observed in the upconversion spectra for TiO 2 -coated microspheres as small as 3 μm, a size at which optical losses had previously prevented such observations. Finally, we demonstrate that the WGM signatures of these upconverting microlasers can be imaged and distinguished through tissue-mimicking phantoms. These advances will enable the fabrication of more efficient upconverting lasers for imaging, sensing, and actuation in optically complex environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Optimizing the use of pressurized bladders for the assembly of HL-LHC MQXFB magnets

The use of pressurized bladders for stress control of superconducting magnets was firstly proposed at Lawrence Berkeley National Laboratory in the early 2000s. Since then, the so-called ‘bladders and keys’ procedure has become one of the reference techniques for the assembly of high-field accelerator magnets and demonstrators. Exploiting the advantages of this method is today of critical importance for Nb$_{3}$Sn-based accelerator magnets, whose production requires the preservation of tight stress targets in the superconducting coils to limit the effects of the strain sensitivity and brittleness of the conductor. The present manuscript reports on the results of an experimental campaign focused on the optimization of the ‘bladders and keys’ assembly process in the MQXFB quadrupoles. These 7.2 m long magnets shall be among the first Nb$_{3}$Sn cryomagnets to be installed in a particle accelerator as a part of the High Luminosity upgrade of the LHC. One of the main practical implications of the bladders technique, especially important when applied to long magnets like MQXFB, is that to insert the loading keys, the opening of a certain clearance in the support structure is required. The procedure used so far for MQXF magnets involved an overstress in the coils during bladder inflation. The work presented here shows that such an overshoot can be eliminated thanks to additional bladders properly positioned in the structure. This optimized method was validated in a short model magnet and in a full-length mechanical model, becoming the new baseline for the series production at CERN. Furthermore, the results are supported by numerical predictions using finite element models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

High Temperature, Isothermal Growth Promotes Close Packing and Thermal Stability in DNA-Engineered Colloidal Crystals

Here, we report a strategy to accelerate the synthesis and increase the crystallinity of colloidal crystals engineered with DNA. Specifically, by holding the DNA-modified Au particle building blocks above the T m of the individual nanoparticle building blocks, but slightly below the T m of the anticipated colloidal crystal during the assembly process, crystallinity is increased, and enthalpically-favored phases with high degrees of facet registration are observed. We studied the utility of this approach with systems for which the commonly adopted slow-cooling approach yielded primarily amorphous aggregates. In particular, we used it to synthesize high-volume fraction colloidal crystals from large (80 nm) anisotropic nanoparticles (cubes and rhombic dodecahedra) with short (<14 nm) DNA designed to restrict the degrees of freedom for the DNA bonds and maintain the anisotropy of the particle building block. Small-angle X-ray scattering and electron microscopy studies show that the crystalline phases synthesized via this method are more thermally stable than their corresponding aggregate phases, likely due to an increased number of DNA-DNA bonds between particles. Crystal size tunability (between 0.5 and 15 µm edge lengths) and epitaxial growth were demonstrated using this strategy by modulating the NaCl concentration in tandem with previously synthesized colloidal crystal nuclei. Taken together, this isothermal strategy provides a route to deliberately crystallize a wide variety of anisotropic colloidal materials and expands the phase space accessible to nanoparticles modified with DNA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Isoreticular Tolerance and Phase Selection in the Synthesis of Multi‐Module Metal–Organic Frameworks for Gas Separation and Electrocatalytic OER

Abstract Although metal–organic frameworks are coordination‐driven assemblies, the structural prediction and design using metal‐ligand interactions can be unreliable due to other competing interactions. Leveraging non‐coordination interactions to develop porous assemblies could enable new materials and applications. Here, we use a multi‐module MOF system to explore important and pervasive impact of ligand‐ligand interactions on metal‐ligand as well as ligand‐ligand co‐assembly process. It is found that ligand‐ligand interactions play critical roles on the scope or breakdown of isoreticular chemistry. With cooperative di‐ and tri‐topic ligands, a family of Ni‐MOFs has been synthesized in various structure types including partitioned MIL‐88‐acs ( pacs ), interrupted pacs (i‐ pacs ), and UMCM‐1‐muo. A new type of isoreticular chemistry on the muo platform is established between two drastically different chemical systems. The gas sorption and electrocatalytic studies were performed that reveal excellent performance such as high C 2 H 2 /CO 2 selectivity of 21.8 and high C 2 H 2 uptake capacity of 114.5 cm 3 /g at 298 K and 1 bar.

Xiao, Yuchen [Department of Chemistry University o↗

DOE OSTI2025

Isoreticular Tolerance and Phase Selection in the Synthesis of Multi‐Module Metal–Organic Frameworks for Gas Separation and Electrocatalytic OER

Xiao, Yuchen [Department of Chemistry University o↗

DOE OSTI2020

Tunable Metal–Organic Frameworks Based on 8-Connected Metal Trimers for High Ethane Uptake

Metal trimers [M 3 (O/OH)](OOCR) 6 are among the most important structural building blocks. From these trimers, a great success has been achieved in the design of 6- or 9-connected framework materials with various topological features and outstanding gas-sorption properties. In comparison, 8-connected trimer-based MOFs are rare. Given multiple competitive pathways for the formation of 6- or 9-connected frameworks, it remains challenging to identify synthetic or structural parameters that can be used to direct self-assembly process towards trimer-based 8-connected materials. Here, we reveal a viable strategy called angle bending modulation for creating a prototypical MOF type based on 8-connected M 3 (OH)(OOCR) 5 (Py-R) 3 trimers, M = Zn, Co, Fe). As a proof of concept, we synthesized six members in this family using three types of ligands (CPM-80, -81, and -82). These materials do not possess open-metal sites and show excellent uptake capacity for various hydrocarbon gas molecules and inverse C 2 H 6 /C 2 H 4 selectivity. CPM-81-Co, made from 2,5-furandicarboxylate and isonicotinate, features selectivity of 1.80 with high uptake capacity for ethane (123 cm 3 /g -1 ) and ethylene (113 cm 3 /g -1 ) at 298 K and 1 bar.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Integrated Micro‐Scale Concentrating Photovoltaics: A Scalable Path Toward High‐Efficiency, Low‐Cost Solar Power

The global energy market is seeing increases in the electricity demand of a couple of percentage points annually. The photovoltaic (PV) industry is also growing rapidly every year. One of the PV technologies is concentrator photovoltaics (CPV). CPV uses high‐efficiency multijunction solar cells and optics to concentrate sunlight, thereby significantly reducing the amount of semiconductor material needed. Yet, due to the high upfont manufacturing cost of CPV, it currently does not offer a competitive price against silicon PV. With this a new branch is introduced to the industry, micro‐CPV, which can be broadly explained as the miniaturization of the solar cells and optical components. The motivation for micro‐CPV is lowering the cost by decreasing the material volume and enabling new system architectures and high‐throughput manufacturing methods, while still maintaining high electrical efficiencies, taking advantage of a lower thermal load, shorter optical paths, lower resistive losses, and lower material volumes. Herein, a comprehensive review of the technological advances is presented, key synergies between micro‐CPV and other industries sharing similar challenges are identified, exemplified by micro‐light emitting diodes display manufacturing. New assembly process development in these industries will facilitate commercial adoption of micro‐CPV with continued miniaturization while driving down the cost.

Jost, Norman↗

DOE OSTI2019

Boosting High-Rate Zinc-Storage Performance by the Rational Design of Mn 2 O 3 Nanoporous Architecture Cathode

Manganese oxides are regarded as one of the most promising cathode materials in rechargeable aqueous Zn-ion batteries (ZIBs) because of the low price and high security. However, the practical application of Mn 2 O 3 in ZIBs is still plagued by the low specific capacity and poor rate capability. Herein, highly crystalline Mn 2 O 3 materials with interconnected mesostructures and controllable pore sizes are obtained via a ligand-assisted self-assembly process and used as high-performance electrode materials for reversible aqueous ZIBs. The coordination degree between Mn 2+ and citric acid ligand plays a crucial role in the formation of the mesostructure, and the pore sizes can be easily tuned from 3.2 to 7.3 nm. Ascribed to the unique feature of nanoporous architectures, excellent zinc-storage performance can be achieved in ZIBs during charge/discharge processes. The Mn 2 O 3 electrode exhibits high reversible capacity (233 mAh g -1 at 0.3 A g -1 ), superior rate capability (162 mAh g -1 retains at 3.08 A g -1 ) and remarkable cycling durability over 3000 cycles at a high current rate of 3.08 A g -1 . Moreover, the corresponding electrode reaction mechanism is studied in depth according to a series of analytical methods. These results suggest that rational design of the nanoporous architecture for electrode materials can effectively improve the battery performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗