Dodecagonal quasicrystals of oil-swollen ionic surfactant micelles
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Jayaraman, Ashish↗
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Results for “molecular assembly”
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Hierarchical Chiral Self-Assembly of Nanocylinders Composed of Sequence-Defined Mesogenic Dimers
Chiral ensembles can arise through supramolecular curvature that resolves geometric frustrations in the packing of bent, achiral molecular or colloidal building blocks. Here, we leverage orthogonal protection−deprotection click chemistry to create sequence-defined mesogenic heterodimers exhibiting emergent chirality. We compare the hierarchical self-assembly of the synthesized asymmetric, achiral heterodimers, which differ only in the position of a methyl substituent. Both dimers form chiral spherulites composed of nanocylinders. However, the detailed arrangement of nanocylinders depends on the position of the methyl substituent and the crystallization conditions. Despite the chemical similarity, in one dimer, two crystalline forms are optically active. They form conglomerates of dextrorotatory and levorotatory spherulites. The other dimer forms more highly anisotropic spherulites that mask circular birefringence arising from the misorientation of nanocylinders, while mapping of nanocylinder directors reveals a sense at the spherulite surface. We propose that differences in nanocylinder arrangements may arise from changes in nanocylinder curvature and dimensions dictated by the methyl substituent position, inducing chirality. These results demonstrate multiscale hierarchical assembly relevant to dense systems of tubular structures and highlight the role of sequence and molecular design in directing the bottom-up hierarchical self-assembly and chirality of mesogenic systems.
Alkyls↗
Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ion Pairing Mediates Molecular Organization Across Liquid/Liquid Interfaces
Liquid/liquid interfaces play a central role in scientific fields ranging from nanomaterial synthesis and soft matter electronics to nuclear waste remediation and chemical separations. This diversity of functions arises from an interface’s ability to respond to changing conditions in its neighboring bulk phases. Understanding what drives this interfacial flexibility can provide novel avenues for designing new functional interfaces. However, limiting this progress is an inadequate understanding of the subtle intermolecular and interphase interactions taking place at the molecular level. Here, we use surface-specific vibrational sum frequency generation spectroscopy combined with atomistic molecular dynamics simulations to investigate the self-assembly and structure of model ionic oligomers consisting of an oligodimethylsiloxane (ODMS) tail covalently attached to a positively charged methyl imidazolium (MIM + ) head group at buried oil/aqueous interfaces. We show how the presence of seemingly innocuous salts can impart dramatic changes to the ODMS tail conformations in the oil phase via specific ion effects and ion-pairing interactions taking place in the aqueous phase. These specific ion interactions are shown to drive enhanced amphiphile adsorption, induce morphological changes, and disrupt emergent hydrogen-bonding structures at the interface. Tuning these interactions allows for independent control over the oligomer structure in the oil phase versus interfacial population changes and represents key mechanistic insight that is needed to control chemical reactions at liquid/liquid interfaces.
36 MATERIALS SCIENCE↗
Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold
The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. In this work, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GO x ), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme’s polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme’s proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Motion of Molecules in Supramolecular Scaffolds Enhances Bone Regeneration
The regeneration of human tissues is a great scientific challenge and a critical factor to achieve a long healthspan and prevent disabilities due to injury or disease. Materials chemistry can contribute to this goal with the development of bioactive supramolecular systems that can signal cells for regeneration. Recent work in our laboratory using in vivo models of spinal cord injury and cartilage regeneration has demonstrated that the motion of bioactive molecules in supramolecular scaffolds enhances receptor signaling. We report here on a novel molecular strategy to control supramolecular motion in filamentous assemblies using bone regeneration as a functional target. The supramolecular assemblies are composed of monomers that arrange, by design, with either parallel or antiparallel β-sheets, and some of them contain a terminal peptide sequence that binds BMP-2. We found that parallel β-sheet supramolecular assemblies promote greater osteogenic differentiation of progenitor cells in vitro relative to antiparallel assemblies, as well as superior quality of newly regenerated bone in a rat model of spinal fusion. Furthermore, these assemblies drastically reduce the dangerous supraphysiological dose of BMP-2 used clinically for spinal fusion. Here, we attribute the enhanced bioactivity to the weaker nature of hydrogen bonds in parallel relative to antiparallel β-sheet assemblies, which in turn allows greater supramolecular motion and cell signaling of the growth factor-binding molecules.
Anatomy↗
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.
59 BASIC BIOLOGICAL SCIENCES↗
EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks
Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.
Shen, Runze [Univ. of Texas, Houston, TX (United S↗
Parameters of fast and high-yield InAs/GaAs quantum dot semiconductor scintillator
InAs quantum dots (QDs) embedded into a waveguiding GaAs semiconductor matrix may produce scintillation detectors with exceptional speed and yield, making them valuable for nuclear security, medical imaging, and high energy physics applications. In this work, we developed thick (~25 μm) epitaxial heterostructres with high luminescence efficiency composed of self-assembled nano-engineered InAs QDs grown by molecular beam epitaxy. Here, the bulk GaAs acts as a stopping material for incident particles and as a waveguide when layer-transferred onto a low-index substrate. Waveguiding and self-absorption (< 1 cm –1 ) were studied using photoluminescence with scanning laser excitation and modeled with ray optics approximation and geometrical coupling of high-index waveguide to a collection fiber. Scintillating signals from α-particles were analyzed with an external photodiode (PD) and an integrated PD which provided an improved optical coupling. The mean charge collected by the integrated PD corresponded to 3 × 10 4 photoelectrons per 1 MeV of deposited energy, or ~13% of the theoretically achievable light yield. Combined with the previously measured QD scintillation time of 0.3-0.6 ns, this makes the InAs/GaAs QD heterostructures the fastest high yield scintillation material reported.
36 MATERIALS SCIENCE↗
Performance of Scintillation Detectors Based on Quantum Dots in a Semiconductor Matrix (Final Technical Report)
InAs Quantum Dots (QDs) embedded into GaAs semiconductor waveguide have unique scintillation properties, valuable for nuclear security, medical imaging, and high energy physics. In this work, we developed thick (~25um) epitaxial heterostructres with high luminescence efficiency composed of self-assembled nano-engineered InAs QDs grown by molecular beam epitaxy. In this type of detector, the GaAs matrix acts as a stopping material for charged particles or photons generating electrons captured by the QDs acting as luminescence centers. The QD medium is designed to provide fast capture of electrons into QDs (few ps), high QD luminescence efficiency at room temperature (>50%), and strong red-shift of photoluminescence (PL) from the GaAs absorption edge (>250nm). Typical devices consist of a 10-25um thick GaAs layer with embedded sheets of modulation p-type doped InAs QDs and an InGaAs photodetector tuned to the QD emission wavelength. The thick GaAs layer acts also as a waveguide when layer-transferred onto a low-index substrate. Waveguiding and self-absorption (~1cm -1 ) were studied using photoluminescence with scanning laser excitation and modeled with ray optics approximation and geometrical coupling of high-index waveguide to a collection fiber. Scintillating signals from α-particles were analyzed with both an external photodiode (PD) and an integrated PD which provided an improved optical coupling. In the former case, the external InGaAs PD was air-coupled to the scintillator and had the light collection efficiency of about 1% corresponding to limited light extraction through a planar interface with air due to total internal reflection. The mean charge collected by the integrated PD was in the range of (3÷5)×10 4 photoelectrons per 1 MeV of deposited energy, or ~13-20% of the theoretically achievable light yield. Timing of the integrated device was measured by wire-bonding it to the input of an 8 GHz IC. The scintillation response shows an extremely fast 0.3-0.6 ns decay constant and about 40-70 ps time resolution, limited by the system noise. The combined light yield and decay time makes the InAs/GaAs QD heterostructures the fastest high yield scintillation material reported making it valuable for high energy physics and medical imaging applications.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Calibration Results for the AXAF Flux Contamination Monitor
The AXAF Flux Contamination Monitor (FCM) serves the purposes of transferring the absolute flux calibration from the ground calibration at the X-Ray Calibration Facility (XRCF) to operation on orbit and of detecting any changes in molecular contamination of the High-Resolution Mirror Assembly (HRMA) between ground calibration and the post-launch activation. We describe the design, construction, and characterization of the FCM radioactive sources, and their placement on the Forward Contamination Cover (FCC). We present results from FCM measurements with the AXAF focal-plane instruments, particularly the AXAF CCD Imaging Spectrometer (ACIS), during the ground calibration phase at the XRCF in 1997. Finally, we describe the plans for FCM on-orbit measurements during observatory activation and for the subsequent analysis.
Elsner, R. F.↗
The Laboratory Production of Complex Organic Molecules in Simulated Interstellar Ices
Much of the volatiles in interstellar dense clouds exist in ices surrounding dust grains. Their low temperatures preclude most chemical reactions, but ionizing radiation can drive reactions that produce a suite of new species, many of which are complex organics. The Astrochemistry Lab at NASA-Ames studies the UV radiation processing of interstellar ice analogs to better identify the resulting products and establish links between interstellar chemistry, the organics in meteorites, and the origin of life on Earth. Once identified, the spectral properties of the products can be quantified to assist with the search for these species in space. Of particular interest are findings that UV irradiation of interstellar ice analogs produces molecules of importance in current living organisms, including quiriones, amphiphiles, and amino acids. Quinones play a variety of roles including electron transport and are used by all organisms. Studies show that quinones should be made wherever polycyclic aromatic hydrocarbons are irradiated in interstellar ices (Bernstein et al. 2001). Amphiphiles are also made when mixed molecular ices are irradiated. These amphiphiles self-assemble into membrane-walled vesicles when put in liquid water (Dworkin et al. 2001). Ice irradiation can also produce (Bernstein et al. 2002) and destroy amino acids (Ehrenfreund et al. 2001). Many of the same processes thought to make organics in space should yield products highly enriched in deuterium (D) (Sandford et al. 2001). The high D/H ratios in some interstellar species, and the knowledge that many of the organics in primitive meteorites are D-enriched, suggests that such linkages do exist. By using D as a tracer, we expect to learn more about the different chemical processes occurring in space and their relative importance in the production of different organic compounds and delivery to planetary surfaces.
Dworkin, Jason P.↗
Cleaning Genesis Sample Return Canister for Flight: Lessons for Planetary Sample Return
Sample return missions require chemical contamination to be minimized and potential sources of contamination to be documented and preserved for future use. Genesis focused on and successfully accomplished the following: - Early involvement provided input to mission design: a) cleanable materials and cleanable design; b) mission operation parameters to minimize contamination during flight. - Established contamination control authority at a high level and developed knowledge and respect for contamination control across all institutions at the working level. - Provided state-of-the-art spacecraft assembly cleanroom facilities for science canister assembly and function testing. Both particulate and airborne molecular contamination was minimized. - Using ultrapure water, cleaned spacecraft components to a very high level. Stainless steel components were cleaned to carbon monolayer levels (10 (sup 15) carbon atoms per square centimeter). - Established long-term curation facility Lessons learned and areas for improvement, include: - Bare aluminum is not a cleanable surface and should not be used for components requiring extreme levels of cleanliness. The problem is formation of oxides during rigorous cleaning. - Representative coupons of relevant spacecraft components (cut from the same block at the same time with identical surface finish and cleaning history) should be acquired, documented and preserved. Genesis experience suggests that creation of these coupons would be facilitated by specification on the engineering component drawings. - Component handling history is critical for interpretation of analytical results on returned samples. This set of relevant documents is not the same as typical documentation for one-way missions and does include data from several institutions, which need to be unified. Dedicated resources need to be provided for acquiring and archiving appropriate documents in one location with easy access for decades. - Dedicated, knowledgeable contamination control oversight should be provided at sites of fabrication and integration. Numerous excellent Genesis chemists and analytical facilities participated in the contamination oversight; however, additional oversight at fabrication sites would have been helpful.
Allton, J. H.↗
Predictive Modeling of the CDRA 4BMS
As part of NASA's Advanced Exploration Systems (AES) program and the Life Support Systems Project (LSSP), fully predictive models of the Four Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) on the International Space Station (ISS) are being developed. This virtual laboratory will be used to help reduce mass, power, and volume requirements for future missions. In this paper we describe current and planned modeling developments in the area of carbon dioxide removal to support future crewed Mars missions as well as the resolution of anomalies observed in the ISS CDRA.
Coker, Robert F.↗
Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes
Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. Here, in this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Obtaining cryogenic molecular transport data for analysis
The James Webb Space Telescope (JWST) has a primary mirror, made of 18 segments, and a secondary mirror (SM) that are used to direct the light of desired targets. While on orbit, the secondary mirror assembly (SMA) was stowed for approximately 10 days and was subject to molecular contamination outgassing from the cavity of the secondary mirror support structure (SMSS) in-board hinge (IBH) which contains cables, motors, resolvers, and coatings. The main concern during this period before SMA deployment is the accumulation of ice due to the lack of a heater on the SMA. The temperature differentials between the IBH surfaces and SMA could cause redistribution of contaminants. To address this concern, single layer insulation (SLI) was used to create adequate venting and path redirection of outgassing from the IBH. Two separate thermal vacuum tests were performed to quantify this contamination: one Z307 ASTM E 1559 materials test of the radiator paint used on the motor of the IBH and a separate test on a primary mirror backplane assembly (PMBA) qualification engineering test unit (ETU) of the IBH. These tests approximately followed the predicted SMA pre-deployment thermal environment. To quantify source rates in case of a leak, the motor and resolver sides were separated and quartz crystal microbalances (QCM) were used to measure the deposition of water. The SLI redesign and implementation and outgassing measurements to understand leak effects from the IBH were essential to mitigate the deposition of contamination on the SMA.
James Webb Space Telescope, contamination, cleanro↗
Obtaining Cryogenic Molecular Transport Data for Analysis
The James Webb Space Telescope (JWST) has a primary mirror, made of 18 segments, and a secondary mirror (SM) that are used to direct the light of desired targets. While on orbit, the secondary mirror assembly (SMA) was stowed for approximately 10 days and was subject to molecular contamination outgassing from the cavity of the secondary mirror support structure (SMSS) in-board hinge (IBH) which contains cables, motors, resolvers, and coatings. The main concern during this period before SMA deployment is the accumulation of ice due to the lack of a heater on the SMA. The temperature differentials between the IBH surfaces and SMA could cause redistribution of contaminants. To address this concern, single layer insulation (SLI) was used to create adequate venting and path redirection of outgassing from the IBH. Two separate thermal vacuum tests were performed to quantify this contamination: one Z307 ASTM E 1559 materials test of the radiator paint used on the motor of the IBH and a separate test on a primary mirror backplane assembly (PMBA) qualification engineering test unit (ETU) of the IBH. These tests approximately followed the predicted SMA pre-deployment thermal environment. To quantify source rates in case of a leak, the motor and resolver sides were separated and quartz crystal microbalances (QCM) were used to measure the deposition of water. The SLI redesign and implementation and outgassing measurements to understand leak effects from the IBH were essential to mitigate the deposition of contamination on the SMA. "
James Webb Space Telescope↗
Spatiotemporal Formation and Growth Kinetics of Polyelectrolyte Complex Micelles with Millisecond Resolution
We have directly observed the in situ self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. A synthesized neutral-charged diblock polycation and homopolyanion that we have previously investigated as a model charge-matched, core-shell micelle system were selected for this work. The initial micellization of the oppositely charged polyelectrolytes was completed within the dead time of mixing of 100 ms, followed by micelle growth and equilibration up to several seconds. By combining the structural evolution of the radius of gyration (R-g) with complementary molecular dynamics simulations, we show how the self-assemblies evolve incrementally in size over time through a two-step kinetic process: first, oppositely charged polyelectrolyte chains pair to form nascent aggregates that immediately assemble into spherical micelles, and second, these PEC micelles grow into larger micellar entities. Furthermore, this work has determined one possible kinetic pathway for the initial formation of PEC micelles, which provides useful physical insights for increasing fundamental understanding self-assembly dynamics, driven by polyelectrolyte complexation that occurs on ultrafast time scales.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗