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DOE OSTI2023

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or “material voxels” and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies, but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. In conclusion, x-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Evidence of a Uranium‐Paddlewheel Node in a Catecholate‐Based Metal–Organic Framework

Abstract The interactions between uranium and non‐innocent organic species are an essential component of fundamental uranium redox chemistry. However, they have seldom been explored in the context of multidimensional, porous materials. Uranium‐based metal–organic frameworks (MOFs) offer a new angle to study these interactions, as these self‐assembled species stabilize uranium species through immobilization by organic linkers within a crystalline framework, while potentially providing a method for adjusting metal oxidation state through coordination of non‐innocent linkers. We report the synthesis of the MOF NU‐1700 , assembled from U 4+ ‐paddlewheel nodes and catecholate‐based linkers. We propose this highly unusual structure, which contains two U 4+ ions in a paddlewheel built from four linkers—a first among uranium materials—as a result of extensive characterization via powder X‐ray diffraction (PXRD), sorption, transmission electron microscopy (TEM), and thermogravimetric analysis (TGA), in addition to density functional theory (DFT) calculations.

Knapp, Julia G.↗

DOE OSTI2023

Evidence of a Uranium‐Paddlewheel Node in a Catecholate‐Based Metal–Organic Framework

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Designed and biologically active protein lattices

Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Tunable Solid‐State Properties and Anisotropic Charge Mobility in Hydrogen‐Bonded Diketopyrrolopyrrole Polymers via Automated Device Fabrication and Characterization

The optoelectronic properties of semiconducting polymers and device performance rely on a delicate interplay of design and processing conditions. However, screening and optimizing the relationships between these parameters for reliably fabricating organic electronics can be an arduous task requiring significant time and resources. To overcome this challenge, Polybot is developed—a robotic platform within a self‐driving lab that can efficiently produce organic field‐effect transistors (OFETs) from various semiconducting polymers via high‐throughput blade coating deposition. Polybot not only handles the fabrication process but also can conduct characterization tests on the devices and autonomously analyze the data gathered, thus facilitating the rapid acquisition of data on a large scale. This work leverages the capabilities of this platform to investigate the fabrication of OFETs using hydrogen bonding‐containing semiconducting polymers. Through high‐throughput fabrication and characterization, various data trends are analyzed, and large extents of anisotropic charge mobility are observed in devices. The materials are thoroughly characterized to understand the role of processing conditions in solid state and electronic properties of these organic semiconductors. The findings demonstrate the effectiveness of automated fabrication and characterization platforms in uncovering novel structure–property relationships, facilitating refinement of rational chemical design, and processing conditions, ultimately leading to new semiconducting materials.

automated fabrication and characterization↗

DOE OSTI2021

Protein Assembly by Design

Proteins are nature’s primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Furthermore, our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Understanding Metal–Organic Framework Nucleation from a Solution with Evolving Graphs

A mechanistic understanding of metal–organic framework (MOF) synthesis and scale-up remains underexplored due to the complex nature of the interactions of their building blocks. In this work, we investigate the collective assembly of building units at the early stages of MOF nucleation, using MIL-101(Cr) as a prototypical example. Using large-scale molecular dynamics simulations, we observe that the choice of solvent (water and N,N-dimethylformamide), the introduction of ions (Na+ and F–) and the relative populations of MIL-101(Cr) half-secondary building unit (half-SBU) isomers have a strong influence on the cluster formation process. Additionally, the shape, size, nucleation and growth rates, crystallinity, and short and long-range order largely vary depending on the synthesis conditions. We evaluate these properties as they naturally emerge when interpreting the self-assembly of MOF nuclei as the time evolution of an undirected graph. Solution-induced conformational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly. While pure solvents lead to the rapid formation of a small number of large clusters, the presence of ions in aqueous solutions results in smaller clusters and slower nucleation. This diversity is captured by the key features of the graph representation. Principle component analysis on graph properties reveals that only a small number of molecular descriptors is needed to deconvolute MOF self-assembly. Furthermore, descriptors such as the average coordination number between half-SBUs and fractal dimension are of particular interest as they can be can be followed experimentally by techniques like by time-resolved spectroscopy. Ultimately, graph theory emerges as an approach that can be used to understand complex processes revealing molecular descriptors accessible by both simulation and experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Closing the Gap Between Modeling and Experiments in the Self-assembly of Biomolecules at Interfaces and in Solution

Molecular self-assembly is a powerful tool in materials design, wherein non-covalent interactions like electrostatic, hydrophobic, hydrogen bonding, and van der Waals can be exploited to produce supramolecular nanostructures that are functional and highly tunable. Biomolecules are attractive building blocks, as they are biocompatible, biodegradable and adopt a wide array of higher order structures. Moreover, naturally occurring protein systems display a manifold of structures and interactions that can be replicated in synthetic biomolecules. In this perspective, we highlight advances in multiscale simulation techniques across broad spatiotemporal scales that can aid in characterizing self-assembly of hybrid and hierarchical bionanomaterial systems, with an emphasis on physics-based simulation approaches currently employed to study biomolecules at mineral interfaces. The power of these approaches is highlighted across a few recent areas where molecular simulations have advanced our understanding of self-assembly spanning peptides to protein self-assembly. Looking forward, we discuss how in the near future emerging methods in statistical and machine learning will advance this research field in all areas from expanding the capabilities of physics-based simulation methods to enabling new analyses of high throughput experiments. These advances will pave the way for understanding the molecular recognition patterns in systems that are dictated by self-assembly - biomineralizing peptides, hierarchical peptoids, and large protein assemblies, and will aid in the development of a new synthesis science for achieving precise molecular control in materials design

Sampath, Janani↗

DOE OSTI2022

Investigating Deposition Sequence During Synthesis of Pd/Al2O3 Catalysts Modified with Organic Monolayers

Modification of supported metal catalysts with self-assembled monolayers (SAMs) has been shown to improve selectivity and turnover frequencies (TOFs) for many catalytic reactions. However, these benefits are often accompanied by a decrease in overall mass activity due to partial blocking of active sites by the monolayers. Therefore, a potential method for increasing site accessibility is to deposit the active metal (e.g., Pd) after deposition of a SAM modifier on the support material. In this work, Pd/Al2O3 catalysts were synthesized using both a conventional, "metal-first" sequence in which the phosphonic acid (PA) SAM was deposited on Pd/Al2O3 and a "SAM-first" technique in which the ligands were deposited onto the support prior to deposition of the metal. Although metal-first catalysts showed a significant increase in TOF during benzyl alcohol HDO, they exhibited only a modest increase in overall mass activity due to a decrease in the number of active sites. Meanwhile, SAM-first catalysts showed similar improvements in TOF and toluene selectivity but exhibited significantly improved HDO rates compared to metal-first catalysts. The rate increase was attributed to reduced site blocking as evidenced by CO chemisorption measurements. Additionally, analysis of catalysts having high Pd loadings using transmission electron microscopy (TEM) showed that SAM-first catalysts generally resulted in lower average particle sizes than traditionally modified and unmodified catalysts, suggesting that precoating the support surface with PAs changes the way that Pd is deposited during incipient wetness, leading here to improved activity.

catalytic reactions↗

NASA NTRS2016

Neural Mechanisms to the Space Environment

Highly conserved neural systems have evolved to sense the inertial forces due to head translation and head tilt relative to gravitational vertical. These structures consist of ciliated mechanosensitive receptor cells inserted into a neuroepithelium surmounted by biomineral grains of calcium carbonate (CaCO3) called oto- (vertebrates) or stato-conia (invertebrates). Detection of these forces by receptor cells relies on the CaCO3 mass being weighted in Earths 1G. A change in gravity or orientation with respect to gravity has a profound effect on how an organism interacts with its environment, and it is evident that the nervous system responds to the new gravity state. This response might involve the peripheral receptors, the CaCO3 mass, the brain or any combination of these mechanisms based on the intensity and duration of the gravity change. Here, we examine the arguments supporting the different mechanisms of adaptation to the space environment. First, a pre- or post-synaptic alteration in the strength of synaptic transmission between the receptor cell and nerve afferent can adjust the system output. The number of synaptic ribbons in certain type II hair cells in rodent is labile, increasing following exposure to microgravity. An increase in number of synaptic ribbons in toadfish otolith hair cells following exposure to microgravity could potentially explain the observed afferent hypersensitivity to acceleration postflight. The physiological findings in the isolated statocyst in snails are in line with the vertebrate data, and conform to the proposition that G exposure leads to changes in gravireceptor function. At the same time this similarity in neural response to G exposure between the vertebrates and invertebrates is intriguing: the increased neural sensitivity in the vertebrate was detected in the nerve afferents, one synapse away from the receptor cell, whereas the increased neural sensitivity observed in the snail was detected directly at the receptor level. Second, the CaCO3 mass provides mechanical loading of receptor cell cilia, and their density alters sensitivity. A widely considered mechanism by which the animal responds to a chronic change in amplitude of gravity is a change in weight-lending CaCO3 mass. In G, it is argued, the organism counters the loss of gravity by increasing CaCO3 production, thereby increasing its mass, as a means to increase system gain. In hypergravity, the converse is argued. Earlier evidence in mollusks and recent results in mice suggest a remodeling might occur, especially after long-term space exposure. Lastly, we have to distinguish at least two kinds of neural feedbacks. One is connected with local mechanisms of self-regulation and specific for initial period of organ development when the neural connections are still absent. And the other feedback is related to neural self-regulation and specific for later stages of the organ development, and includes an efferent vestibular feedback. Complexity of the problem is enhanced by incompleteness of experiments, and consequently the experimental results have not led to a clear interpretation despite the numerous studies.

Boyle, Richard D.↗

NASA NTRS1997

The first living systems: a bioenergetic perspective

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

Review↗

DOE OSTI2020

Probing Self-Assembly in Arginine–Oleic Acid Solutions with Terahertz Spectroscopy and X-ray Scattering

A study of the formation of microstructures in the reaction of oleic acid with arginine elucidates dynamical self-assembly processes at the molecular level. Terahertz spectroscopy combined with density functional calculations reveals the initial hydrogen-bonding motifs in the assembly process, leading to the formation of micelles and vesicles. Small-angle X-ray scattering measurements allow for kinetic analysis of the growth processes of these nanostructures, revealing a prenucleation pathway of vesicles and micelles which lead to spongelike structures. This final stage of the assembly into spongelike aggregates is investigated with optical microscopy. The formed structures only occur at pH > 8 and are resistant to extreme acidic and basic conditions. Here, a mechanistic pathway to the formation of the spongelike aggregates is described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature’s own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and “smart” architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Furthermore, continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Self-Assembly of Metallo-Supramolecules with Dissymmetrical Ligands and Characterization by Scanning Tunneling Microscopy

Asymmetrical and dissymmetrical structures are widespread and play a critical role in nature and life systems. In the field of metallo-supramolecular assemblies, it is still in its infancy for constructing artificial architectures using dissymmetrical building blocks. Herein, we report the self-assembly of supramolecular systems based on two dissymmetrical double-layered ligands. With the aid of ultra-high-vacuum, low-temperature scanning tunneling microscopy (UHV-LT-STM), we were able to investigate four isomeric structures corresponding to four types of binding modes of ligand LA with two major conformations complexes A. The distribution of isomers measured by STM and total binding energy of each isomer obtained by density functional theory (DFT) calculations suggested that the most abundant isomer could be the most stable one with highest total binding energy. Lastly, through shortening the linker between inner and outer layers and the length of arms, the arrangement of dissymmetrical ligand LB could be controlled within one binding mode corresponding to the single conformation for complexes B.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Lyotropic Liquid Crystal Mediated Assembly of Donor Polymers Enhances Efficiency and Stability of Blade-Coated Organic Solar Cells

Conjugated polymers can undergo complex, concentration-dependent self-assembly during solution processing, yet little is known about its impact on film morphology and device performance of organic solar cells. Herein, lyotropic liquid crystal (LLC) mediated assembly across multiple conjugated polymers is reported, which generally gives rise to improved device performance of blade-coated non-fullerene bulk heterojunction solar cells. Using D18 as a model system, the formation mechanism of LLC is unveiled employing solution X-ray scattering and microscopic imaging tools: D18 first aggregates into semicrystalline nanofibers, then assemble into achiral nematic LLC which goes through symmetry breaking to yield a chiral twist-bent LLC. The assembly pathway is driven by increasing solution concentration – a common driving force during evaporative assembly relevant to scalable manufacturing. This assembly pathway can be largely modulated by coating regimes to give 1) lyotropic liquid crystalline assembly in the evaporation regime and 2) random fiber aggregation pathway in the Landau–Levich regime. The chiral liquid crystalline assembly pathway resulted in films with crystallinity 2.63 times that of films from the random fiber aggregation pathway, significantly enhancing the T80 lifetime by 50-fold. The generality of LLC-mediated assembly and enhanced device performance is further validated using polythiophene and quinoxaline-based donor polymers.

14 SOLAR ENERGY↗

DOE OSTI2025

Self-Assembly of Accumulated Sphingolipids into Cytotoxic Fibrils in Globoid Cell Leukodystrophy and Their Inhibition by Small Molecules In Vitro

Globoid cell leukodystrophy (GLD) is a rare hereditary inborn error of metabolism due to recessive mutations that cause loss of function of the enzyme galactosylceramidase (GALC). This results in the accumulation of the sphingolipids galactosylceramide (GalCer) and galactosylsphingosine (GalSph) in the lysosomes of neuronal cells. The accumulated GalCer and GalSph in cerebral macrophages of GLD patients are neurotoxic to oligodendrocytes and Schwann cells, leading to demyelination in the nervous system. The disease typically presents with infantile onset in the first six months of life and death by age 2. Here, we identified a supramolecular structure of GalCer and GalSph that may contribute to GLD pathology. Using biophysical assays commonly used for studying proteinaceous amyloids, e.g., amyloidspecific dyes, microscopical imaging, and a series of analytical methods (FTIR, PXRD, and SAXS), we demonstrate that both GalCer and GalSph can self-assemble in vitro into highly organized fibrils reminiscent of fibrils of amyloidogenic proteins. These fibrils exhibit significant cytotoxicity to both neuronal and oligodendroglial cells. Using an inhibitor of the GALC enzyme in cell culture to mimic the GLD pathophysiology, we could detect the accumulation of these fibrils in cells. We also observed that small molecules, which are bona fide inhibitors of proteinaceous amyloids, effectively mitigated the formation of the GalCer and GalSph fibrillar structures in vitro. Finally, the small molecule ameliorated the cytotoxic effects of the sphingolipid fibrils in SH-SY5Y cells, suggesting a potential avenue for therapeutic intervention in GLD orphan disease.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1993

Solar particle dose rate buildup and distribution in critical body organs

Human body organs have varying degrees of radiosensitivity as evidenced by radioepidemiologic tables. The major critical organs for both the male and female that have been identified include the lung, thyroid, stomach, and breast (female). Using computerized anatomical models of the 50th percentile United States Air Force male and female, we present the self-shielding effects of these various body organs and how the shielding effects change as the location (dose point) in the body varies. Several major solar proton events from previous solar cycles and several events from the current 22nd solar cycle have been analyzed. The solar particle event rise time, peak intensity, and decay time vary considerably from event to event. Absorbed dose and dose equivalent rate calculations and organ risk assessment data are presented for each critical body organ. These data are compared with the current NASA astronaut dose limits as recommended by the National Council on Radiation Protection and Measurements.

Atwell, William↗

NASA NTRS2003

Functional nanocomposites prepared by self-assembly and polymerization of diacetylene surfactants and silicic acid

Conjugated polymer/silica nanocomposites with hexagonal, cubic, or lamellar mesoscopic order were synthesized by self-assembly using polymerizable amphiphilic diacetylene molecules as both structure-directing agents and monomers. The self-assembly procedure is rapid and incorporates the organic monomers uniformly within a highly ordered, inorganic environment. By tailoring the size of the oligo(ethylene glycol) headgroup of the diacetylene-containing surfactant, we varied the resulting self-assembled mesophases of the composite material. The nanostructured inorganic host altered the diacetylene polymerization behavior, and the resulting nanocomposites show unique thermo-, mechano-, and solvatochromic properties. Polymerization of the incorporated surfactants resulted in polydiacetylene (PDA)/silica nanocomposites that were optically transparent and mechanically robust. Molecular modeling and quantum calculations and (13)C spin-lattice relaxation times (T(1)) of the PDA/silica nanocomposites indicated that the surfactant monomers can be uniformly organized into precise spatial arrangements prior to polymerization. Nanoindentation and gas transport experiments showed that these nanocomposite films have increased hardness and reduced permeability as compared to pure PDA. Our work demonstrates polymerizable surfactant/silica self-assembly to be an efficient, general approach to the formation of nanostructured conjugated polymers. The nanostructured inorganic framework serves to protect, stabilize, and orient the polymer, mediate its performance, and provide sufficient mechanical and chemical stability to enable integration of conjugated polymers into devices and microsystems.

NASA Discipline Life Support Systems↗