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42 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Sequence-selective dynamic covalent assembly of information-bearing oligomers

Relatively robust dynamic covalent interactions have been employed extensively to mediate molecular self-assembly reactions; however, these assembly processes often do not converge to a thermodynamic equilibrium, instead yielding mixtures of kinetically-trapped species. Here, we report a dynamic covalent self-assembly process that mitigates kinetic trapping such that multiple unique oligomers bearing covalently coreactive pendant groups are able to undergo simultaneous, sequence-selective hybridization with their complementary strands to afford biomimetic, in-registry molecular ladders with covalent rungs. Analogous to the thermal cycling commonly employed for nucleic acid melting and annealing, this is achieved by raising and lowering the concentration of a multi-role reagent to effect quantitative dissociation and subsequently catalyze covalent bond rearrangement, affording selective assembly of the oligomeric sequences. The hybridization specificity afforded by this process further enabled information encoded in oligomers to be retrieved through selective hybridization with complementary, mass-labeled sequences.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications

Silica biomineralization is a naturally occurring process, wherein organisms use proteins and other biological structures to direct the formation of complex, hierarchical nanostructures. Discovery and characterization of such proteins and their underlying mechanisms spurred significant efforts to identify routes for biomimetic mineralization that reproduce the exquisite shapes and size selectivities found in nature. A common strategy has been the use of short peptide sequences with chemistry mimicking those found in natural systems, such as the use of the silaffin-derived R5 peptide. While progress has been made using this approach, there are many limitations that have prevented breakthroughs in biomimicry. To advance our ability to use charged macromolecules for silica formation, we propose to use sequence-defined synthetic polymers known as peptoids, or N-substituted polyglycines, which present significant capability for the precise tuning of sequence and structure beyond what can often be achieved with peptides alone. This study presents a computationally predicted design of these polymers that leads to the controlled formation of silica nanomaterials. We investigate surface adsorption and the mineralization process through analysis of binding mechanisms and energetics of the R5 system. Next, we synthesized two R5-inspired peptoids and validated our prediction in the design of mineralization polymers through characterization using surface plasmon resonance and electron microscopy. Here, this computationally guided study holds great promise for designing new sequences with unprecedented control of the placement of chemical functional groups, thus allowing for further unraveling of silicification mechanisms and the eventual design of sequence-defined synthetic polymers leading to the predictive synthesis of nanostructured functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2001

A Structural and Molecular Approach for the Study Biomarkers

Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.

Thomas-Keprta, Kathie↗
DOE OSTI2023

Accelerating Biomimetic Solar - Energy Harvesting: Mapping the Interaction Landscape of Plasmonic-Excitonic Hybrid Nanosystems (Final Report)

In general, excitonic and plasmonic nanoscale materials in close proximity show high potential for significant breakthroughs in energy related materials research. The interactions between these two kinds of materials result in coupled optical transitions (plexcitons), distinct from those of both the individual exciton and plasmon as well as from those of the sum of their constituents (synergistic effects). By linking together materials-research and physical-research approaches, this project contributes to a concerted approach on nanomaterials energy research. The project’s overall goal is to accelerate the development of well-defined plexcitonic model systems consisting of carefully engineered plasmonic and excitonic nanomaterial— essential for both gaining a fundamental understanding of plexcitonic nanomaterials and the development of novel design principles for biomimetic solar energy harvesting. During the 3-year project period and the terminal renewal with limited support for a 12-month period, we successfully synthesized and characterized (1) a robust excitonic nanomaterial and (2) a library of plasmonic nanoparticles as well as developed (3) a microfluidic platform for homogenous nanosynthesis as summarized below: (1) Robust Excitonic Nanomaterial. Supramolecular assemblies are Nature’s most successful material system for solar energy harvesting. However, photovoltaic devices based on artificial supramolecular assemblies continue to be stymied by disappointing efficiencies and poor stability. The conceptual failure may lie in current solar cell architectures, which rely on solidifying supramolecular assemblies as an ensemble into a solid matrix, neglecting the intrinsic fragility of the assemblies’ internal structure, thus disrupting or even destroying their delicate optoelectronic properties, that is, delicate Frenkel excitonic properties. Supramolecular assemblies may finally serve as usable light harvesting material systems for solar energy conversion technologies, only if they meet the following criteria: (a) Stability, that is, the fragile structure including its delicate Frenkel excitonic character needs to be stable, (b) Robustness, that is, resistant against elevated and fluctuating temperatures, and (c) Viability for device integration, that is, capable of being immobilized onto solid substrates. Here, by developing a nanocomposite via a tunable, cage-like scaffold design, we successfully provided stable supramolecular nanocomposites, that inhabit robust Frenkel excitons despite harming environmental conditions such as extreme heat stress. (2) Library of Plasmonic Nanoparticles. Naturally, current models describing plasmonic hybrid quantum states—plasmonic hybridizations—parallel those developed for molecular orbitals, equating individual plasmonic nanostructures with “atoms” and the plasmonic nanoassemblies with “molecules.” In analogy to organic synthesis, a suitably robust fabrication method would allow for “atom-like” manipulation of “molecule-like” plasmonic nanoassemblies; of high value for next-generation energy nanotechnologies. Despite this frequent comparison, current plasmonic nanoassembly fabrication methods favor top-down templating over wet-chemical synthesis, however, achieving precise control over nanostructure’s geometry and surface characteristics remain an art and a scientific challenge. The conceptual failure may lie in the current wet-chemical synthesis paradigm, as it relies on the accessibility of a multi-dimensional synthesis parameter space through limited, rather one-dimensional synthesis procedures by employing step-by-step approaches. Solution-based nanoarchitectonics for rational design of precisely built plasmonic nanoassemblies via solution-based fabrication may finally be possible only if multi-dimensional syntheses approaches are available that allow for comprehensive control over the plasmonic nanomaterials’ (a) Structural Properties and (b) Surface Properties. Here, by developing an innovative multidimensional 1,3-propanediol based polyol synthesis, we successfully provided control over the plasmonic building-block’s geometry (size and shape) together with its surface characteristics. Our results present a critical step toward the vision of a “periodic table-like” system for plasmonic materials based on straightforward wet-chemical syntheses for energy nanotechnologies. Developing deliberate modifications on this synthesis, we generated a library of plasmonic nanostructures covering the vast parameter space—opening the door for fundamental investigation of plexcitonic model systems. (3) Microfluidic Platform for Homogenous Nanosynthesis. Control over structural properties of plexcitonic nanocomposites remains a challenge due to current limitations in nanosynthesis techniques. Slight variations in nanostructure’s geometry impact their optoelectronic properties, demanding precise synthesis beyond the capabilities of solution-based (batch) synthesis processes. In contrast, the small, confined liquid volumes used in microfluidics—a reaction technique where the manipulation of fluids takes place in channels with dimensions of tens of micrometers—allows for homogenous synthesis conditions, providing excellent control of the reaction and, as a result, of the materials’ geopmetry and composition. However, thus far, the majority of plexcitonic systems has been developed via batch synthesis. Here, by successfully developing a two-channel microreactor, our microfluidic-supported synthesis approach combines the advantages of both microfluidics and batch platforms, allowing for precise spatio-temporal control over all synthesis parameters opening the possibility for homogenous nanosythnesis of well-defined plexcitonic model systems.

14 SOLAR ENERGY↗
DOE OSTI2022

Developing nanometer scale, atomically precise metallo-catalysts with Molecular Lego

We propose to create atomically precise, highly robust, nanometer scale macromolecules that organize biomimetic metal binding groups in designed three-dimensional pockets to accelerate specific polymerization reactions. These atomically precise catalysts will create atomically precise polymers with improved mechanical and environmental properties from renewable building blocks. We seek to create and study nanometer scale catalysts that mimic metallo-enzymes in their activity and selectivity because these larger catalysts will be able to make more extensive non-covalent contacts with the transition state of the growing polymer. These catalysts will have extended lifetimes because they will better protect the metals and higher activity because additional reactive groups can be brought in close contact with the active site to enhance reactivity. They will be far more tolerant to extremes of temperature and will not denature in non-aqueous solvents because they are held together by multiple, strong, covalent bonds. Our approach to catalysts could be used to develop catalysts to replace noble metal-based catalysts when targeting other reactions, because the geometry of the active site enforced by the Molecular Lego scaffolding will access new reactivity, mimicking how nature uses earth abundant metals for much of its catalysis. We will initially target Lewis acid-based catalysts that assemble aliphatic polyesters with improved stereoselectivity, tacticity and complex alternation of monomers. Aliphatic polyesters have received growing attention as attractive, environmentally benign, and sustainable alternatives to polymers developed from petroleum feedstocks. Aliphatic polyesters are environmentally friendly because they undergo facile hydrolytic degradation to benign products, and they have excellent properties and high biocompatibility. We will assemble these catalysts using unique “Spiroligomers” (aka Molecular Lego) chemistry developed in the Schafmeister group combined with the organometallic chemistry expertise of the Dobereiner group. Polymers are an attractive synthetic target of nanoscale atomically precise catalysts because their resulting structure, stereochemistry and tacticity has profound impact on their properties (crystalline vs amorphous) and provides a readout of the catalytic mechanism. Polymer synthesis also serves as an example of “atomically precise manufacturing” where atomically precise nanoscale catalysts construct polymers with atomic precision at increasing length scales.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Peptoid-Based Programmable 2D Nanomaterial Sensor for Selective and Sensitive Detection of H 2 S in Live Cells

During the past decades, a variety of two-dimensional (2D) nanosheets have been developed through supramolecular self-assembly. Among them, those assembled from sequence-defined molecules have received particularly attention because they enable a precise displaying of functional groups, including fluorescent dyes, within nanosheet surfaces. On the other hand, due to the fluorescence self-quenching, synthesis of organic 2D nanosheets exhibiting high fluorescence quantum yields is a significant challenge. Herein, we report the utilization of H 2 S-responsive probes as peptoid sidechains to design and synthesize crystalline 2D nanomembranes (2DNMs) as selective and sensitive H 2 S sensors. These 2DNM sensors exhibit a high quantum yield as a result of high crystallinity and tunable probe density. Compared with amorphous state of peptoid assembly and pre-assembled peptoid-probe conjugates, these crystalline 2DNM sensors exhibit a significantly strong fluorescence intensity and a high sensitivity (~ 0.36 nM). By sonication-cutting these 2DNM sensors into a colloidal form in aqueous solution, we further demonstrated the use of colloidal 2DNMs for detecting both exogenous and endogenous H 2 S inside cells or targeted cell organelles. As far as we know, this is the first example of using sequence-defined 2D nanomaterials for selective and sensitive detection of H 2 S. Because peptoids are biocompatible and peptoid-based 2DNMs are highly programmable, we expect that this new class of 2DNM sensors offer great potentials for detecting H 2 S and for biological applications.

2D nanomaterials↗