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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled–coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled–coil hydrogel design. Using Rosetta energy scores and Poisson–Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled–coil proteins while simultaneously exploring five new coiled–coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled–coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled–coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled–coil fiber formation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Investigation of design principles for metal-binding and conductive protein assemblies

Throughout the lifetime of this initiative, including renewals, we focused on understanding the fundamental principles of protein-protein interface design that enable predictable and modular spatial and kinetic control of multi-component protein self-assembly in 1D, 2D, and 3D, including the interface with inorganic materials, small molecules, and metal ions. We designed individual protein components that bind specific metal ions, including REEs and transport ions across lipid membranes. We created helical 1D filaments of repeating units with programmed periodicity, pitch, and multi-component environmentally responsive self-assembling protein fibers. We showed that these filaments reversibly assemble and disassemble under specific pH conditions and created end-specific caps that independently tune the balance of attachment and detachment rates at each terminus of the filament. Using similar filaments, we succeeded in binding arrays of heme and chlorophyll molecules and assembling patterned helical coatings around carbon nanotubes in efforts to create de novo conductive nanowires. By arraying REE binding sites in a large circular tandem array with a repeat protein-based cyclic oligomer, we created a molecular scaffold for superradiance and paramagnetic quantum sensing. We created a range of one-component and two-component self-assembling 2D arrays and showed that when designed to engage cell receptors, these arrays can control cell behavior from outside the cell signal to inside the cell. We designed helical repeat proteins with variable lengths displaying charged residues in a pattern matched to the cation lattice of mica. achieved a range of ordered states with an epitaxial match to the underlying crystal lattice. We further applied the learned principles of protein-induced biomineralization to design proteins with an interface lattice matching CaCO 3 and guide the formation of specific crystal forms of CaCO 3 from solution, a significant advance toward the global need to manage carbon. In all cases of mineral lattice matching and biomineralization, we followed assembly using molecularly resolved in situ AFM imaging and extracted information about assembly pathways and energetics, applying deep learning to quantify the dynamics of protein self-organization. We developed techniques for using dynamic metal-dependent interfaces on protein nanopores for discriminatively sensing dilute REEs in solution and demonstrated the use of strong metal-binding interfaces to drive nanocage disassembly for conditional nanocompartmentalization applications. This grant supported 11 people, including Asim Bera, Evans Brackenbrough, Andrew Borst, Nikita Hanikel, Timothy Huddy, Emily Joyce, Alex Young-Seug Kang, Ryan Kibler, Joshua Morris Lubner, Harley Pyles, and Shuai Zhang. The research effort culminated in the production of published papers and theses. Electronic Thesis/Dissertation are distributed by ProQuest/UMI Dissertation Publishing and made available on an open access basis through UW Libraries ResearchWorks Service.

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

Characterisation of nano-assemblies inside mesopores using neutron scattering

Adsorption of molecular and nanoscale matter in mesoporous materials is important in filtration and chromatography as well as membrane processes. However, the morphology and distribution of self-assembled structures of adsorbate formed within nanoconfined environments is largely unknown. Small Angle Neutron Scattering (SANS) with porous matrix matching the neutron scattering length density of the solvent has the potential to provide detailed information on the self-assemblies formed in pore spaces. However, analysis of such SANS profiles remains a challenge. In this study, we extend the SANS analysis method previously developed by Findenegg and co-workers to include interparticle correlations, providing a qualitative characterisation of the adsorption state of surfactants and nanoparticles in the cylindrical pores of silica nanomaterials. We find that the pore filling fraction and the self-assembled state of the adsorbate governs the scattering profile. We apply the model to two materials namely, triethyleneglycol monohexyl ether (C 6 E 3 ) surfactant and gold nanoparticles adsorbed in SBA-15 mesoporous silica. In contrast to the C 6 E 3 system, Bragg scattering dominates the diffuse scattering in gold nanoparticle system, which we attribute to the immobile internal structure of the nanoparticles. In conclusion, this new SANS analysis method has potential to elucidate structures of soft matter nanoassemblies inside mesopores.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons

Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine–glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine’s role in suppressing right-handed β-sheet formation. Furthermore, this study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗
DOE OSTI2022

Priming self-assembly pathways by stacking block copolymers

Abstract Block copolymers spontaneously self-assemble into well-defined nanoscale morphologies. Yet equilibrium assembly gives rise to a limited set of structures. Non-equilibrium strategies can, in principle, expand diversity by exploiting self-assembly’s responsive nature. In this vein, we developed a pathway priming strategy combining control of thin film initial configurations and ordering history. We sequentially coat distinct materials to form prescribed initial states, and use thermal annealing to evolve these manifestly non-equilibrium states through the assembly landscape, traversing normally inaccessible transient structures. We explore the enormous associated hyperspace, spanning processing (annealing temperature and time), material (composition and molecular weight), and layering (thickness and order) dimensions. We demonstrate a library of exotic non-native morphologies, including vertically-oriented perforated lamellae, aqueduct structures (vertical lamellar walls with substrate-pinned perforations), parapets (crenellated lamellae), and networks of crisscrossing lamellae. This enhanced structural control can be used to modify functional properties, including accessing regimes that surpass their equilibrium analogs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Ce IV 70 Oxosulfate Rings, Frameworks, Supramolecular Assembly, and Redox Activity**

Abstract M IV molecular oxo‐clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms‐up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel‐shaped oxo‐cluster, [Ce IV 70 (OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4− . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce‐monomer linkers. Eight crystal‐structures feature four framework types in which the Ce 70 ‐rings are linked as propellers, in offset‐stacks, in a tartan pattern, and as isolated rings. Small‐angle X‐ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion‐exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV ‐monomer linkers demonstrate both oxidation and reduction. This study opens the door to mixed‐metal, highly porous framework catalysts, and new clusters for metal‐organic framework design

Colliard, Ian↗
DOE OSTI2023

Quantitative evaluation of perfluorinated alkanethiol molecular order on gold surfaces

Self-assembled monolayers (SAMs) of perfluoroalkanethiols [CF3(CF2)xCH2CH2SH (x = 3, 5, 7, and 9)] on gold were characterized by x-ray photoelectron spectroscopy (XPS), near edge x-ray absorption fine structure (NEXAFS), and static time-of-flight secondary ion mass spectrometry (ToF-SIMS). Perfluoroalkanethiols of several chain lengths were synthesized using a known hydride reduction method for transforming commercially available perfluoroalkyliodides to corresponding perfluoroalkanethiols. This strategy provides improved product yields compared to other known routes based on hydrolysis from the common thioacetyl perfluoroalkyl intermediate. Angle-dependent XPS analysis revealed that CF3(CF2)xCH2CH2SH (x = 5, 7, and 9; F6, F8, and F10, respectively) SAMs on gold exhibited significant enrichment of the terminal CF3 group at the outer monolayer surface with the sulfur present as a metal-bound thiolate located at the monolayer-gold interface. XPS of the CF3(CF2)3CH2CH2SH (F4) monolayer revealed a thin film with a significant (>50%) amount of hydrocarbon contamination consistent with poorly organized monolayers, while the longest thiol (F10) showed XPS signals attributed to substantial ordering and anisotropy. ToF-SIMS spectra from all four SAMs contained molecular ions representative of the particular perfluorinated thiol used to prepare the monolayer. NEXAFS methods were used to determine degrees of ordering and average tilt for molecules comprising monolayers. The SAMs prepared from the longest (F10) thiols exhibited the highest degree of ordering with the molecular axis nearly perpendicular to the gold surface. The degree of ordering decreased significantly with decreasing length of the perfluorocarbon tail.

Biophysics↗
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 OSTI2022

Design and Preparation of Nematic Colloidal Particles

Colloidal systems are abundant in technology, in biomedical settings, and in our daily life. The so-called “colloidal atoms” paradigm exploits interparticle interactions to self-assemble colloidal analogs of atomic and molecular crystals, liquid crystal glasses, and other types of condensed matter from nanometer- or micrometer-sized colloidal building blocks. Nematic colloids, which comprise colloidal particles dispersed within an anisotropic nematic fluid host medium, provide a particularly rich variety of physical behaviors at the mesoscale, not only matching but even exceeding the diversity of structural and phase behavior in conventional atomic and molecular systems. This feature article, using primarily examples of works from our own group, highlights recent developments in the design, fabrication, and self-assembly of nematic colloidal particles, including the capabilities of preprogramming their behavior by controlling the particle’s surface boundary conditions for liquid crystal molecules at the colloidal surfaces as well as by defining the shape and topology of the colloidal particles. Here recent progress in defining particle-induced defects, elastic multipoles, self-assembly, and dynamics is discussed along with open issues and challenges within this research field.

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

Lipid vesicles induced ordered nanoassemblies of Janus nanoparticles

Since many advanced applications require specific assemblies of nanoparticles (NPs), considerable efforts have been made to fabricate nanoassemblies with specific geometries. Although nanoassemblies can be fabricated through top-down approaches, recent advances show that intricate nanoassemblies can also be obtained through self-assembly, mediated for example by DNA strands. Here, we show, through extensive molecular dynamics simulations, that highly ordered self-assemblies of NPs can be mediated by their adhesion to lipid vesicles (LVs). Specifically, Janus NPs are considered so that the amount by which they are wrapped by the LV is controlled. The specific geometry of the nanoassembly is the result of effective curvature-mediated repulsion between the NPs and the number of NPs adhering to the LV. Further, the NPs are arranged on the LV into polyhedra which satisfy the upper limit of Euler's polyhedral formula, including several deltahedra and three Platonic solids, corresponding to the tetrahedron, octahedron, and icosahedron.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Charge transport and antiferromagnetic ordering in nitroxide radical crystals

Nonconjugated radical polymers and small molecules are employed as functional materials in organic electronic devices. Furthermore, the unpaired electrons on these materials have permanent magnetic moments, making these materials promising candidates for organic magnets. Through molecular design, strong antiferromagnetic and ferromagnetic ordering have been achieved in conjugated materials. However, the magnetic properties of nonconjugated radical polymers have only shown weak magnetic interactions among the open-shell sites due to the large mean separation between radicals in typical materials. Here, we have designed, synthesized, and crystalized two open-shell molecules that used molecular engineering to control the assembly of the open-shell sites into a strong antiferromagnetically ordered network. The strong antiferromagnetic interaction is evidenced by a high paramagnetic-to-antiferromagnetic transition temperature of ~40 K. This high transition temperature was a result of a high spin exchange coupling constant J of about –20 cm –1 , which was suggested by both experimental and computed coupling parameters given by the energy difference between high-spin and low-spin broken-symmetry structures. In addition, a single-crystal electrical conductivity of ~10 –3 S m –1 was achieved, which indicated the potential of this material in electronic applications. As a result, this work provides an insight into a design strategy for radical-based electronic and magnetic materials through proper molecular structure modifications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach

Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The influence of molecular design on structure–property relationships of a supramolecular polymer prodrug

Supramolecular self-assemblies of hydrophilic macromolecules functionalized with hydrophobic, structure-directing components have long been used for drug delivery. In these systems, loading of poorly soluble compounds is typically achieved through physical encapsulation during or after formation of the supramolecular assembly, resulting in low encapsulation efficiencies and limited control over release kinetics, which are predominately governed by diffusion and carrier degradation. To overcome these limitations, amphiphilic prodrugs that leverage a hydrophobic drug as both the therapeutic and structure-directing component can be used to create supramolecular materials with higher loading and controlled-release kinetics using biodegradable or enzymatically cleavable linkers. Here, we report the design, synthesis, and characterization of a library of supramolecular polymer prodrugs based on poly(ethylene glycol) (PEG) and the proregenerative drug 1,4-dihydrophenonthrolin-4-one-3-carboxylic acid (DPCA). Structure–property relationships were elucidated through experimental characterization of prodrug behavior in both the wet and dry states using scattering techniques and electron microscopy and corroborated by coarse-grained modeling. Molecular architecture and the hydrophobic-to-hydrophilic ratio of PEG–DPCA conjugates strongly influenced their physical state in water, ranging from fully soluble to supramolecular spherical assemblies and nanofibers. Molecular design and supramolecular structure, in turn, were shown to dramatically alter hydrolytic and enzymatic release and cellular transport of DPCA. In addition to potentially expanding therapeutic options for DPCA through control of supramolecular assemblies, the design principles elaborated here may inform the development of other supramolecular prodrugs based on hydrophobic small-molecule compounds.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Valence-free open nanoparticle superlattices

A cornerstone of advanced materials design is establishing a framework for assembling nanoparticle superstructures with tailored symmetries. A longstanding challenge has been assembling diamond-like superstructures for photonic devices. Traditionally, such open superstructures require functionalized nanoparticles with directional or anisotropic interactions, reminiscent of valence bonding in a diamond. Here, we present a robust strategy for assembling valence-free nanoparticles into a broad array of cubic superstructures. By grafting nanoparticles with oppositely charged, end-functionalized water-soluble polymers of adjustable molecular weight, we gain control over electrostatic interactions and conformational constraints. This unified approach yields lattices analogous to rock salt, CsCl, zinc-blende, diamond, and the rare simple cubic phase, with tunable lattice constants. Theoretical models and simulations elucidate the underlying interactions, providing a framework for engineering valence-free nanoparticle superlattices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Peroxide-Templated Assembly of a Trimetal Neodymium Complex Single-Molecule Magnet

In this study, we present a tri-metal neodymium complex with two notable qualities. Firstly, the assembly of the complex is templated by peroxide derived from atmospheric oxygen. Secondly, the bulk material behaves as a super-paramagnet, implying that the individual complexes are molecular magnets. The peroxide-templated assembly is possible due to the confluence of the high oxophilicity of neodymium along with the use of an azeotropic distillation synthesis method, which excludes water but admits oxygen. SQUID magnetometer measurements show an extremely high magnetic susceptibility as well as a lack of remanence.

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

Self-assembly of aramid amphiphiles into ultra-stable nanoribbons and aligned nanoribbon threads

Small molecule self-assembly is an established route for producing high surface area nanostructures with readily customizable chemistries and precise molecular organization. However, these structures are fragile, exhibiting molecular exchange, migration, and rearrangement - among other dynamic instabilities - and ultimately disassociate upon drying. Here we show a small molecule platform, the aramid amphiphile (AA), that overcomes these dynamic instabilities by incorporating a Kevlar-inspired domain into the molecular structure. Strong, anisotropic interactions between AAs suppress molecular exchange and elicit spontaneous self-assembly in water to form nanoribbons with lengths of up to 20 microns. The nanoribbons have a Young’s modulus of 1.7 GPa and tensile strength of 1.9 GPa. Here, we exploit this stability to extend small molecule self-assembly to hierarchically ordered macroscopic materials outside of solvated environments. Through an aqueous shear alignment process, we organize AA nanoribbons into arbitrarily long flexible threads that support 200 times their weight when dried. Tensile tests of the threads provide a benchmark for Young’s moduli (between ~400 and 600 MPa) and extensibilities (between ~0.6 and 1.1%) that depend on the counterion chemistry in solution. This bottom-up approach to macroscopic materials could benefit solid-state applications, historically inaccessible by self-assembled nanomaterials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗