Bio-inspired Macromolecules Containing Atomically Precise Catalytic Active Sites
Explore the source record for details and available documents.
09 BIOMASS FUELS↗
SEARCH · Engineering Papers
Results for “Macromolecules”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Chapter One - Spectrophotometric methods to probe the solution chemistry of lanthanide complexes with macromolecules
Explore the source record for details and available documents.
Chemistry - Inorganic, organic, physical and analy↗
Machine learning to build quantum-accurate models for biological macromolecules.
Abstract not provided.
Rackers, Joshua↗
New Directions in Biotechnology
The macromolecule crystallization program within NASA is undergoing considerable pressure, particularly budgetary pressure. While it has shown some successes, they have not lived up to the expectations of others, and technological advances may rapidly overtake the natural advantages offered by crystallization in microgravity. Concomitant with the microgravity effort has been a research program to study the macromolecule crystallization process. It was believed that a better understanding of the process would lead to growth of improved crystals for X-ray diffraction studies. The results of the various research efforts have been impressive in improving our understanding of macromolecule crystallization, but have not led to any improved structures. Macromolecule crystallization for structure determination is "one of", the job being unique for every protein and finished once a structure is obtained. However, the knowledge gained is not lost, but instead lays the foundation for developments in new areas of biotechnology and nanotechnology. In this it is highly analogous to studies into small molecule crystallization, the results of which have led to our present day microelectronics-based society. We are conducting preliminary experiments into areas such as designed macromolecule crystals, macromolecule-inorganic hybrid structures, and macromolecule-based nanotechnology. In addition, our protein crystallization studies are now being directed more towards industrial and new approaches to membrane protein crystallization.
Source record↗
LDRD Macromolcule Radiolysis Poster
Moving toward a circular carbon economy depends on enabling reuse of carbon-based macromolecules and increased recycling of waste products into higher value products. Macromolecules are challenging to valorize into products easily converted into liquid fuel or chemical feedstocks, due to their large and sometimes heterogeneous network of polymeric bonds. The novel aspect of this project is to show a proof of principle that radiolysis of macromolecules using “waste” radiation from energy production in the presence of radical capping donors presents an attractive opportunity to break down complex macromolecules into smaller molecules while controlling re-polymerization. This approach offers a new, cost-efficient way to utilize “waste” radiation and heat byproducts of nuclear energy production to convert a simple mixture of complex molecules into a complex mixture of small molecules, to be utilized as an energy source by the fuel industry, or to create value-added feedstocks for new polymers or commodity chemicals. Ionizing radiation can be harnessed to convert energy to molecules, adding value to low-value macromolecules as they are broken down into smaller, more easily separated feedstocks or fuels to be converted to a value-added product. This project will test 2 hypotheses. Hypothesis 1: Macromolecular materials that comprise biomass and coal or other macromolecules can be infused with radical capping donors (RCDs), and gamma irradiation of the resulting mixtures will produce ensembles of lower-molecular weight chemicals that can be more easily separated. If this expectation is realized, the conversion chemistry can be optimized by adjusting the feedstock composition, irradiation time, and choice of RCD.
02 - PETROLEUM↗
A Robust Biomarker
Polymers of bacterial origin, either through cell secretion or the degraded product of cell lysis, form isolated mucoidal strands as well as well-developed biofilms on interfaces. Biofilms are structurally and compositionally complex and are readily distinguishable from abiogenic films. These structures range in size from micrometers to decimeters, the latter occurring as the well-known, mineralised biofilms called stromatolites. Compositionally bacterial polymers are greater than 90 % water, with while the majority of the macromolecules forming the framework of the polymers consisting of polysaccharides (with and some nucteic acids and proteins). These macromolecules contain a vaste amount of functional groups, such as carboxyls, hydroxyls, and phosphoryls which are implicated in cation-binding. It is the elevated metal- binding capacity which provides the bacterial polymer with structural support and also helps to preserves it for up to 3.5 b.y. in the terrestrial rock record. The macromolecules, thus, can become rapidly mineralised and trapped in a mineral matrix. Through early and late diagenesis (bacterial degradation, burial, heat, pressure and time) they break down, losing the functional groups and, gradually, their hydrogen atoms. The degraded product is known as "kerogen". With further diagenesis and metamorphism, all the hydrogen atoms are lost and the carbonaceous matter becomes graphite. until the remnant carbonaceous material become graphitised. This last sentence reads a bit as if ALL these macromolecules break down and end up as graphite., but since we find 441 this is not true for all of the macromolecules. We have traced fossilised polymer and biofilms in rocks from throughout Earth's history, to rocks as old as the oldest being 3.5 b.y.-old. Furthermore, Time of Flight Secondary Ion Mass Spectrometry has been able to identify individual macromolecules of bacterial origin, the identities of which are still being investigated, in all the samples containing fossil biofilm, including the 3.5 b.y..-old carbonaceous cherts from South Africa and Australia. As a result of the unique compositional, structural and "mineralisable" properties of bacterial polymer and biofilms, we conclude that bacterial polymers and biofilms constitute a robust and reliable biomarker for life on Earth and could be a potential biomarker for extraterrestrial life.
Westall, F.↗
Collaborative Research: Polymer Macrocycles: A novel topology to control dynamics of rubbery materials
Understanding the dynamics of polymers of different topologies is an important field of study and one of the most important unanswered questions in this field is "how do circular polymers move," particularly in the melt state. New information suggests that molecular topology, specifically circular rings, impacts the response of materials in nanometer- scale confinement. The work performed here tackles these subjects through a collaboration in which specialists in polymer synthesis, polymer rheology and scattering methods, and in the physics of nanoconfinement work together to investigate the thermophysical behavior of circular macromolecules. The project goals are to use a novel synthesis method of "green" oxidative polymerization to produce high purity macrocycles and to investigate their linear viscoelastic behavior in order to fully characterize the dynamics of circular macromolecules to sizes that correspond to linear molecule entanglement densities higher than previously obtainable with synthetic polymers. Chemical chain end characterization and critical edge fractionation coupled with direct visualization of the prepared polymers through the use of polymer amplification methods are proposed in order to quantify the numbers of circular and linear molecules in each sample. The study of the linear viscoelastic response of blends of linear and circular molecules is also to be undertaken in the project. Nonlinear viscoelastic measurements, including extensional viscosity, are to be made. Strong differences in behavior between linear chains and circular ones also provides an important opportunity for new technology to break the "magic triangle" for tires: it is believed that improving one of the three key attributes - traction, wear, rolling resistance - necessarily sacrifices at least one of the others. Rubber made from cyclic polymers has the potential to break out of this triangle by reducing the so-called Payne effect in reinforced rubbers because circular macromolecules are less sensitive to nanoconfinement than their linear counterparts. The work has as one objective to characterize the impact of nanoconfinement on the behavior of large circular macromolecules. In addition, the dynamics of carbon black filled circular macromolecules are to be studied to test the hypothesis that the resulting rubbery materials will exhibit a reduced Payne effect.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Role of peracetic acid on the disruption of lignin packing structure and its consequence on lignin depolymerisation
Peracetic acid (PAA) is an effective oxidant capable of solubilising lignin and efficiently depolymerising it to selective phenolic compounds; however, the specific role by which PAA initiates the depolymerisation is still elusive. Herein, interaction between PAA and the lignin macromolecule and the consequent structural changes of the latter were studied by characterising the lignin packing structure and its associated changes during the oxidation process. While the lignin packing structure and its changes associated with the PAA-mediated oxidation were probed by X-ray diffraction, the impact of the PAA on different chemical functionalities present in the lignin structure was established by 13 C and 1 H– 13 C heteronuclear single-quantum coherence nuclear magnetic resonance (NMR) spectroscopy. Further, combining the NMR spectroscopy results, and the product distribution, we conclude that the predominant reaction pathway for the oxidative depolymerisation of lignin with PAA is the Baeyer–Villiger oxidation of the ketone formed by the oxidation of the benzylic hydroxyl group adjacent to the β-O-4 linkage. The experimental evidence provided herein corroborated that PAA instigates oxygen insertion to the lignin macromolecule resulting in disruption of its packing structures and facilitates depolymerisation. We also investigated various metal oxide and mixed metal oxide catalysts to identify effective catalysts that further enhance the efficiency of PAA-mediated depolymerisation of lignin and produce selective monomeric phenolic compounds. Techno-economic analysis was also conducted to identify the key parameters associated with this oxidative process that need to be considered for possible commercial application.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Density modification of cryo-EM maps
Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy of a map. Here, the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows the incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between the macromolecule and solvent are visible, and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here, model bias is reduced by using ensemble models that allow an estimation of model uncertainty. A test of model bias is presented that suggests that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map.
59 BASIC BIOLOGICAL SCIENCES↗
Fluid Physics and Macromolecular Crystal Growth in Microgravity
The molecular structure of biological macromolecules is important in understanding how these molecules work and has direct application to rational drug design for new medicines and for the improvement and development of industrial enzymes. In order to obtain the molecular structure, large, well formed, single macromolecule crystals are required. The growth of macromolecule crystals is a difficult task and is often hampered on the ground by fluid flows that result from the interaction of gravity with the crystal growth process. One such effect is the bulk movement of the crystal through the fluid due to sedimentation. A second is buoyancy driven convection close to the crystal surface. On the ground the crystallization process itself induces both of these flows. Buoyancy driven convection results from density differences between the bulk solution and fluid close to the crystal surface which has been depleted of macromolecules due to crystal growth. Schlieren photograph of a growing lysozyme crystal illustrating a 'growth plume' resulting from buoyancy driven convection. Both sedimentation and buoyancy driven convection have a negative effect on crystal growth and microgravity is seen as a way to both greatly reduce sedimentation and provide greater stability for 'depletion zones' around growing crystals. Some current crystal growth hardware however such as those based on a vapor diffusion techniques, may also be introducing unwanted Marangoni convection which becomes more pronounced in microgravity. Negative effects of g-jitter on crystal growth have also been observed. To study the magnitude of fluid flows around growing crystals we have attached a number of different fluorescent probes to lysozyme molecules. At low concentrations, less than 40% of the total protein, the probes do not appear to effect the crystal growth process. By using these probes we expect to determine not only the effect of induced flows due to crystal growth hardware design but also hope to optimize crystallization hardware so that destructive flows are minimized both on the ground and in microgravity.
Pusey, M.↗
A Model for Macromolecular Crystallization
Macromolecular crystallization is a complex process. involving a system which typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only several well defined contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can often be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric single chain macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.
Pusey, Marc L.↗
A Model for Tetragonal Lysozyme Crystal Nucleation and Growth
Macromolecular crystallization is a complex process, involving a system that typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only a few contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be difficult or impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric (single chain) macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. This model has been developed from experimental evidence based upon face growth rate, AFM, and fluorescence energy transfer data for the nucleation and growth of tetragonal lysozyme crystals.
Pusey, Marc L.↗
Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering
The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.
Models, Molecular↗
Chromatin activity precipitation method and system
Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.
59 BASIC BIOLOGICAL SCIENCES↗
A Curated Experimental Compilation Analyzed by Theory Is More than a Review
Macromolecules is an exceptional resource in the field of polymer science and now publishes more than 1000 original articles a year that set the standard for scientific rigor and creative insights. Over the years, these individual contributions have combined to build the foundation of polymer science, broadly and inclusively defined. In addition to the individual articles, many of which are being celebrated in this series of editorials, Macromolecules has published invaluable reviews and perspectives. These scholarly contributions integrate the insights and results from numerous sources into a unified whole and often recommend future directions for the field. Novices and experts alike benefit from these works that capture topics from emerging discoveries to long-pondered topics and everything in between. To explore the importance of Macromolecules’ reviews and perspectives, we considered their influence on the field and found the 1994 review by Fetters et al. entitled “Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties”1 to be a singularity. This review expertly curates and compiles a trove of data to build robust correlations between molecular characteristics and macroscopic viscoelastic properties of polymer melts, in the context of the tube model of entanglements.
36 MATERIALS SCIENCE↗
Native Chemical Ligation of Peptoid Oligomers
Bioorganic chemists are inspired by natural biopolymers to design peptidomimetic oligomers that can exhibit sequence-structure-function relationships. Biomimetic polymers can be synthesized to incorporate a specific sequence of nonbiological monomer units using a variety of iterative solution-phase or solid-phase reaction schemes. These protocols generally provide access to a vast diversity of oligomeric compounds but are limited with respect to their ability to attain protein-like chain lengths. This constraint can preclude access to sequence-defined synthetic macromolecules with sufficient sizes required to exhibit tertiary structure and other protein-mimetic attributes. In contrast, peptide chemists have overcome this limitation by developing convergent synthetic methods, such as native chemical ligation, to join individual, smaller peptide chains together to make larger peptides or full proteins. A similar convergent approach is needed to establish efficient synthetic routes to non-natural sequence-defined macromolecules. Herein, we adapt the peptide native chemical ligation method to peptoid oligomers, demonstrating how short chains can be conjoined to create sequence-defined peptoid macromolecules. Nanosheet-forming peptoid polymers with distinct surface loop display domains were generated by sequential ligation of several discrete fragments. This method provides a reliable convergent ligation route for sequence-defined polypeptoids that results in a native amide bond joining the fragments. We envision that this strategy will be useful in synthesizing peptoid-based proteomimetics that incorporate diverse chemical features.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The electrokinetic behavior of calcium oxalate monohydrate in macromolecular solutions
Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chrondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for chemical adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopopolysacchrides have greater affinity for the COM surface than the proteins. The amount of proteins that can chemically adsorb appears to be limited to approximately one monomolecular layer. When the surface charge is high, an insufficient number of proteins can chemically adsorb to neutralize or reverse the surface charge. The remaining surface charge is balanced by proteins held near the surface by longer range electrostatic forces only. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.
Curreri, P. A.↗
Microelectrophoretic study of calcium oxalate monohydrate in macromolecular solutions
Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopolysaccharides have greater affinity for the COM surface than the proteins. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.
Curreri, P. A.↗