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Results for “molecular assembly”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A blueprint for biomolecular condensation driven by bacterial microcompartment encapsulation peptides

Bacterial microcompartments are protein organelles with diverse metabolic capabilities. Their functional diversity is determined by an enzymatic core that is sequestered within a structurally conserved protein shell architecture. Segregation of protein cargo into the bacterial microcompartment is enabled by encapsulation peptides, which are short helical domains fused to core proteins through a disordered linker. Here, we investigate how encapsulation peptides drive multicomponent cargo assembly into biomolecular condensates. In vitro experiments supported by molecular dynamics simulations demonstrate the importance of both conserved hydrophobic packing and electrostatic interactions in stabilizing trimeric encapsulation peptide bundles. Topological rearrangements of encapsulation peptide domains can drive programmable liquid- or gel-like partitioning in vitro and in vivo. This partitioning is found to be encapsulation peptide-specific, modular, and can co-assemble at least three fluorescent reporters. In summary, we describe the molecular features necessary to drive biomolecular condensation using a widespread peptide tag. This work can serve as a blueprint for implementing encapsulation peptide biotechnology across diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Complex pH-Dependent Interactions between Weak Polyelectrolyte Block Copolymer Micelles and Molecular Fluorophores

Amphiphilic block copolymers with weak polyelectrolyte blocks can assemble stimulus-responsive nanostructures and interfaces. Applications of these materials in drug delivery, biomimetics, and sensing largely rely on the well-understood swelling of polyelectrolyte chains upon deprotonation, often induced by changes in pH or ionic strength. This deprotonation can also tune interfacial interactions between the polyelectrolyte blocks and surrounding solution, an effect which is less studied than morphological swelling of polyelectrolytes but can be just as critical for intended function. Here, we investigate whether the pH-driven morphological response of polyelectrolyte-bearing nanostructures also affects the interactions of these nanostructures with molecules in solution, using micelles of a short-chain polybutadiene-block-poly(acrylic acid) (pBd–pAA) as a model system. Here we introduce a Förster resonance energy transfer (FRET) approach to probe interactions between micelles and fluorescent molecular solutes as a function of solution pH. As expected, the pAA corona of these pBd–pAA micelles increases in thickness monotonically as a function of pH. However, FRET efficiency, which provides a metric of the spatial proximity of fluorescently labeled micelles and freely diffusing fluorophores, exhibits complex nonmonotonic behavior as a function of pH, indicating that the average separation of micelles and acceptor fluorophores is not strictly correlated with micelle swelling. Dialysis experiments quantify the affinity of fluorophores for micelles as a function of pH, confirming that changes in FRET are driven almost entirely by the pH-dependent affinity of the pAA block for the investigated molecular fluorophores, not simply by a shape change of the pAA corona. This study provides key insights into the interfacial interactions between weak-polyelectrolyte-bearing nanostructures and molecular solutes, of importance for the development of their stimulus-responsive applications.

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

Correlating structure, self-assembly chemistry and conductivity of trithiocyanuric acid on Au(111)

The majority of candidates for simple model molecular-electronic components consist of a conductive π-conjugated hydrocarbon linker attached to at least two anchoring groups, such as thiols or isocyanides. It has been found that select molecules self-assemble on gold surfaces, creating one-dimensional conductive structures that act as “molecular wires”. Furthermore, these oligomers can form molecular bridges between gold nanoparticles, leading to the creation of simple molecular-electronic devices. This raises the question whether other π-conjugated molecular linkers could exhibit similar behavior that might offer a broader range of candidates for fabricating electronic devices. Trithiocyanuric acid (1,3,5-triazine-2,4,6-trithiol, TTCA) provides a possible candidate. TTCA (C3N3(SH)3) can exist as a trithiol or as a trithione in which hydrogens transfer to the sulfurs so that they are present with three C=N groups within the ring. TTCA exists naturally in the trithione form but converts into a trithiol when adsorbed onto an Ag(111) where it is vertically oriented. The structure of TTCA adsorbed on Au(111) is studied here using reflection-absorption infrared spectroscopy (RAIRS) where it is found to remain as the trithione isomer, but changes orientation as the coverage increases. Scanning-tunneling microscopy (STM) reveals that TTCA oligomerizes on Au(111) to form chains and triangular structures. The influence on molecular conductivity due to the differences in the adsorbate's isomeric structure was investigated using devices comprising either silver or gold nanoparticles deposited in the gap between gold nanoelectrodes. Both devices were found to conduct when dosed with TTCA, but the devices fabricated using silver were about 13 time more conductive than those made from gold nanoparticles, consistent with the π-conjugated structure formed on silver but not on gold. This implies that oligomers form both on silver and on gold and potentially increases the range of molecule-metal combinations that might be used to fabricate molecular-electronic devices.

Molecular electronics↗
DOE OSTI2021

Voltage-Dependent Barrier Height of Electron Transport through Iron Porphyrin Molecular Junctions

Electron transport through iron porphyrin (FeP) molecules self-assembled on a gold (Au) substrate was investigated using conductive atomic force microscopy (AFM) to measure current–voltage (I–V) characteristics. In the direct tunneling region (|V| ≤ 0.1 V), the Simmons model was used to characterize the electron transport. Furthermore, the energy barrier between the Fermi energy level of Au and the highest occupied molecular orbital (HOMO) level of the FeP molecule was determined to be between 0.3 and 0.6 eV; the range of the electron attenuation coefficient was 0.6–0.8 Å–1. Instead of a constant barrier height, a voltage-dependent barrier height was adapted to simulate the experimental I–V curves over the entire voltage range (|V| ≤ 2 V) using the Simmons model for the intermediate case. The voltage-dependent barrier height is supported by a previously predicted response of molecular-projected self-consistent Hamiltonian orbitals. The dependence showed that the HOMO level relative to the Fermi energy level of the Au electrode decreased as the bias voltage increased. To verify the deposition of the FeP on the Au substrate, Raman spectroscopy and AFM analysis were performed.

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

Ion-dependent protein–surface interactions from intrinsic solvent response

Significance Hard–soft interfaces between inorganic surfaces and biomolecules promote self-assembly processes with broad implications in biogeochemistry, energy sciences, nanomedicine, and origins of life. Yet, detailed molecular-scale understanding of inorganic–biomolecule interactions and their dependence on solution conditions is missing. We present a theory for the initial stages of inorganic–biomolecule assembly based on the far-field response of water, using experimentally characterized interactions between muscovite surfaces and mica-binding proteins as model systems. Our work connects molecular details of the solution to assembly outcomes and suggests the initial driving forces for assembly are dominated by long-range, ion-specific interactions. The connections made between interfacial structure and long-range surface–biomolecule interactions provide insights toward a predictive understanding of biomolecular self-assembly on mineral surfaces.

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

Substituent Effects on Transient, Carbodiimide-Induced Geometry Changes in Diphenic Acids

Nucleotide-induced conformational changes in motor proteins are key to many important cell functions. Inspired by this biological behavior, we report a simple chemically fueled system that exhibits carbodiimide-induced geometry changes. Bridging via transient anhydride formation leads to a significant reduction of the twist about the biaryl bond of substituted diphenic acids, giving a simple molecular clamp. The kinetics are well-described by a simple mechanism, allowing structure–property effects to be determined. The kinetic parameters can be used to derive important characteristics of the system such as the efficiencies (anhydride yields), maximum anhydride concentrations, and overall lifetimes. Transient diphenic anhydrides tolerate steric hindrance ortho to the biaryl bond but are significantly affected by electronic effects, with electron-deficient substituents giving lower yields, peak conversions, and lifetimes. Furthermore, the results provide useful guidelines for the design of functional systems incorporating diphenic acid units.

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

Reversible assembly of silica nanoparticles at water–hydrocarbon interfaces controlled by SDS surfactant

Achieving reversible and tunable assembly of silica nanoparticles at liquid–liquid interfaces is vital for a wide range of scientific and technological applications including sustainable subsurface energy applications, catalysis, drug delivery and material synthesis. In this study, we report the mechanisms controlling the assembly of silica nanoparticles (dia. 50 nm and 100 nm) at water–heptane and water–toluene interfaces using sodium dodecyl sulfate (SDS) surfactant with concentrations ranging from 0.001–0.1 wt% using operando ultrasmall/small-angle X-ray scattering, cryogenic scanning electron microscopy imaging and classical molecular dynamics simulations. The results show that the assembly of silica nanoparticles at water–hydrocarbon interfaces can be tuned by controlling the concentrations of SDS. Silica nanoparticles are found to: (a) dominate the interfaces in the absence of interfacial SDS molecules, (b) coexist with SDS at the interfaces at low surfactant concentration of 0.001 wt% and (c) migrate toward the aqueous phase at a high SDS concentration of 0.1 wt%. Energetic analyses suggest that the van der Waals and electrostatic interactions between silica nanoparticles and SDS surfactants increase with SDS concentration. However, the favorable van der Waals and electrostatic interactions between the silica nanoparticles and toluene or heptane decrease with increasing SDS concentration. As a result, the silica nanoparticles migrate away from the water–hydrocarbon interface and towards bulk water at higher SDS concentrations. These calibrated investigations reveal the mechanistic basis for tuning silica nanoparticle assembly at complex interfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Optically addressable molecular spins for quantum information processing

Spin-bearing molecules are promising building blocks for quantum technologies as they can be chemically tuned, assembled into scalable arrays, and readily incorporated into diverse device architectures. In molecular systems, optically addressing ground-state spins would enable a wide range of applications in quantum information science, as has been demonstrated for solid-state defects. However, this important functionality has remained elusive for molecules. Here, we demonstrate such optical addressability in a series of synthesized organometallic, chromium(IV) molecules. These compounds display a ground-state spin that can be initialized and read out using light and coherently manipulated with microwaves. In addition, through atomistic modification of the molecular structure, we vary the spin and optical properties of these compounds, indicating promise for designer quantum systems synthesized from the bottom-up.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation

Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO 2 -concentrating mechanism by facilitating high CO 2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein–protein interactions that drive the assembly process. In this work, studies on the α-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate that this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate that CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Parallels between enzyme catalysis, electrocatalysis, and photoelectrosynthesis

Catalysts are central to accelerating chemistry in biology and technology. In biochemistry, the relationship between the velocity of an enzymatic reaction and the concentration of chemical substrates is described via the Michaelis-Menten model. Additionally, the modeling and benchmarking of synthetic molecular electrocatalysts are also well developed. However, such efforts have not been as rigorously extended to photoelectrosynthetic reactions, where, in addition to chemical substrates and charge carriers, light is a required reagent. In this perspective, we draw parallels between concepts involving enzyme catalytic efficiency, the benchmarking of molecular electrocatalysts, and the performance of photoelectrosynthetic assemblies, while highlighting key differences, assumptions, and limitations.

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

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

The typically rugged nature of molecular free energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for data-driven discovery of CVs parameterizing the important large scale motions of the system. A challenge to CV discovery is learning CVs invariant to symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multi-molecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate Permutation Invariant Vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation, and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand sampling of configurational phase space and obtain converged CVs and free energy landscapes. Here, we demonstrate the Permutationally Invariant Network for Enhanced Sampling (PINES) approach in applications to the self-assembly of a 13-atom Argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C 45 H 92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.

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

Moving beyond the Solvent-Tip Approximation to Determine Site-Specific Variations of Interfacial Water Structure through 3D Force Microscopy

Although interfacial solution structure impacts environmental, biological, and technological phenomena, including colloidal stability, protein assembly, heterogeneous nucleation, and water desalination, its molecular details remain poorly understood. Here, we visualize the three-dimensional (3D) hydration structure at the boehmite(010)-water interface using fast force mapping (FFM). Using a self-consistent scheme to decouple long-range tip-sample interactions from short-range solvation forces, we obtain the solution structure with lattice resolution. The results are benchmarked against molecular dynamics simulations that explicitly include the effects of the tip with different levels of approximation and systematically account for tip size, chemistry, and confinement effects. We find four laterally structured water layers within 1 nm of the surface, with the highest water densities at sites adjacent to hydroxyl groups. The key features beyond the first two layers can only be predicted using a full-scale simulation of the boehmite-water-silica system. Our findings further reveal a complex relationship between site-specific chemistry, water density, and long-range particle interactions; and present important advances toward quantitative data interpretation in 3D FFM.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystallization of binary nanocrystal superlattices and the relevance of short-range attraction

The synthesis of binary nanocrystal superlattices (BNSLs) enables the targeted integration of orthogonal physical properties, such as photoluminescence and magnetism, into a single superstructure, unlocking a vast design space for multifunctional materials. However, the formation mechanism of BNSLs remains poorly understood, restricting the prediction of the structure and properties of superlattices. Here we use a combination of in situ scattering and molecular simulation to elucidate the self-assembly of two common BNSLs (AlB 2 and NaZn 13 ) through emulsion templating. Our self-assembly experiments reveal that no intermediate structures precede the formation of the final binary phases, indicating that their formation proceeds through classical nucleation. Using simulations, we find that, despite the formation of AlB 2 and NaZn 13 typically being attributed to entropy, their self-assembly is most consistent with the nanocrystals possessing short-range interparticle attraction, which we find can accelerate nucleation kinetics in BNSLs. Here, we also find homogeneous, classical nucleation in simulations, corroborating our experiments. These results establish a robust correspondence between experiment and theory, paving the way towards prediction of BNSLs.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unraveling the mechanism of recognition of the 3’ splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60

Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML3’). We found that the PUF60–AdML3’ dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60’s two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML3’ revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF60 2 :AdML3’) stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3’ splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3’ splice sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Polarized Resonant X-ray Scattering to Measure Molecular Orientation and Conformation in Organic Nanostructures

The ordering of organic (carbon-based) molecules into nanostructures drives useful materials properties for applications such as organic light emitting diodes, flexible batteries, and polymer nanocarriers. However, there is a current lack of techniques to measure this ordering. X-ray scattering techniques involving molecular resonances have shown promise in identifying molecular types, locations, and orientation. However, resonant soft X-ray scattering (RSoXS) techniques have not been developed even lacking basic optical models. The objectives achieved by this research were the development of methods, models, and analysis techniques that harness these resonant phenomena in X-ray scattering measurements to quantitatively probe ordering of organic molecules within devices and nanostructures. This award resulted in 11 peer reviewed publications with two others soon to be submitted. New physical models for X-ray scattering that accurately describe these complex molecular resonances enable measurements of how molecules assemble, orient and conform at the nanometer scale. These new techniques were applied to both organic electronic devices and aqueous nanoparticles being developed for hydrocarbon sequestration. This new measurement capability will enable characterization of structure-property relationships that lead to disruptive technologies of printable, stretchable, and biocompatible devices based on organic materials.

14 SOLAR ENERGY↗
DOE OSTI2022

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dual Atomic Coherence in the Self-Assembly of Patchy Heterostructural Nanocrystals

Advances in the synthesis and self-assembly of nanocrystals have enabled researchers to create a plethora of different nanoparticle superlattices. But while many super lattices with complex types of translational order have been realized, rotational order of nanoparticle building blocks within the lattice is more difficult to achieve. Self-assembled superstructures with atomically coherent nanocrystal lattices, which are desirable due to their exceptional electronic and optical properties, have been fabricated only for a few selected systems. Here, we combine experiments with molecular dynamics (MD) simulations to study the self-assembly of heterostructural nanocrystals (HNCs), consisting of a near-spherical quantum dot (QD) host decorated with a small number of epitaxially grown gold nanocrystal (Au NC) "patches ". Self-assembly of these HNCs results in face-centered-cubic (fcc) superlattices with well-defined orientational relationships between the atomic lattices of both QD hosts and Au patches. MD simulations indicate that the observed dual atomic coherence is linked to the number, size, and relative positions of gold patches. Here this study provides a strategy for the design and fabrication of NC superlattices with large structural complexity and delicate orientational order.

77 NANOSCIENCE AND NANOTECHNOLOGY↗