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Results for “Noncovalent interactions”

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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66 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗
DOE OSTI2026

Computationally designed coiled coil ‘bundlemers’ as model colloidal nanoparticles for solution assembly and materials design (Final Report)

As a collaborative team at the University of Delaware and the University of Pennsylvania, Kloxin, Pochan and Saven designed new biomimetic nanomaterials de novo, leveraging a variety of complementary areas of expertise: computational design of biopolymers (Saven at the University of Pennsylvania), and synthesis and characterization (Kloxin and Pochan at the University of Delaware). Overall activities included: sequence-specific peptide synthesis; covalent crosslinking; noncovalent assembly; site-specific functionalization; and nanostructural characterization using electron microscopy and solution-phase (x-ray and neutron) scattering. Using natural and non-natural amino acids, the team created modular, functional peptide building blocks for elaboration of new nanostructured materials. Ultimately, the development of robust peptide-based, building blocks provides tools for researchers to readily produce complex nanomaterial structures in a wide range of applications. The project had three, interconnecting goals in an effort to provide the broader scientific community with a new peptide-based paradigm for materials design and characterization. First, we further developed the coiled-coil bundle-based toolbox (otherwise known as the ‘bundlemer’ toolbox) via computational design with experimental bundle assembly verification. Second, we developed new uses of covalent interactions, in addition to desired physical (noncovalent) interactions, to assemble bundlemers into 1-D polymer chains with targeted chain rigidity, length, and dispersity. Thirds, we used the above designs to experimentally realize (physical or covalent) polymers to target the creation of liquid crystals or to realize interparticle assembly into nanoporous lattices. The close integration of the three groups was instrumental in success of the biomolecular materials design, formation, and understanding for future designs.

36 MATERIALS SCIENCE↗
NASA NTRS1987

Electron tunneling through covalent and noncovalent pathways in proteins

A model is presented for electron tunneling in proteins which allows the donor-acceptor interaction to be mediated by the covalent bonds between amino acids and noncovalent contacts between amino acid chains. The important tunneling pathways are predicted to include mostly bonded groups with less favorable nonbonded interactions being important when the through bond pathway is prohibitively long. In some cases, vibrational motion of nonbonded groups along the tunneling pathway strongly influences the temperature dependence of the rate. Quantitative estimates for the sizes of these noncovalent interactions are made and their role in protein mediated electron transport is discussed.

Beratan, David N.↗
DOE OSTI2024

One-Pot Self-Assembly of Sequence-Controlled Mesoporous Heterostructures via Structure-Directing Agents

Multimaterial heterostructures have led to characteristics surpassing the individual components. Nature controls the architecture and placement of multiple materials through biomineralization of nanoparticles (NPs); however, synthetic heterostructure formation remains limited and generally departs from the elegance of self-assembly. Here, in this study, a class of block polymer structure-directing agents (SDAs) are developed containing repeat units capable of persistent (covalent) NP interactions that enable the direct fabrication of nanoscale porous heterostructures, where a single material is localized at the pore surface as a continuous layer. This SDA binding motif (design rule 1) enables sequence-controlled heterostructures, where the composition profile and interfaces correspond to the synthetic addition order. This approach is generalized with 5 material sequences using an SDA with only persistent SDA-NP interactions (“P-NP 1 –NP 2 ”; NP i = TiO 2 , Nb 2 O 5 , ZrO 2 ). Expanding these polymer SDA design guidelines, it is shown that the combination of both persistent and dynamic (noncovalent) SDA-NP interactions (“PD-NP 1 –NP 2 ”) improves the production of uniform interconnected porosity (design rule 2). The resulting competitive binding between two segments of the SDA (P- vs D-) requires additional time for the first NP type (NP 1 ) to reach and covalently attach to the SDA (design rule 3). The combination of these three design rules enables the direct self-assembly of heterostructures that localize a single material at the pore surface while preserving continuous porosity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Multi-scale computational screening and mechanistic insights of cyclic amines as solvents for improved lignocellulosic biomass processing

A computational screening workflow for the efficient deconstruction of cellulose, lignin and hemicellulose fractions of lignocellulosic biomass using cyclic amines as solvents. Lignocellulosic biomass is a promising feedstock for production of affordable fuels and chemicals from renewable resources. Effective solubilization and subsequent deconstruction of its cellulose, hemicellulose, and lignin fractions is essential for the viability of future biorefineries. This study used quantum chemistry-based equilibrium thermodynamics methods to evaluate the potential of 650 cyclic amines to solubilize cellulose, hemicellulose, and lignin. The activity coefficients of solvent - biopolymer interactions were predicted using the COSMO-RS (COnductor-like Screening MOdel for Real Solvents) method and used to identify cyclic amines that can efficiently dissolve and extract selective fractions of biopolymers during biomass pretreatment. Among the 650 cyclic amines, 1-piperazineethanmaine was predicted to be an effective solvent for extracting all three polymers and was experimentally shown to achieve the highest lignin removal (97.1%). Non-covalent interaction, reduced density gradient and quantum chemical calculations were performed to elucidate the dissolution mechanism of lignin, cellulose and hemicellulose and gain further molecular level insights into the interactions between the cyclic amines and biomass polymers that promote efficient solubilization and extraction. These analyses indicated that 1-piperazineethanmaine and 1-methylimidazole make noncovalent van der Waals, electrostatic interactions and hydrogen bonding with lignin, leading to enhanced lignin removal, while the strong intramolecular hydrogen bonding interactions in cellulose and hemicellulose result in weaker solvent-biopolymer interactions. Overall, the computational approach provided an efficient method for identifying cyclic amines tailored for optimal biomass pretreatment and resulted in the identification of a potential new class of solvents for effective biomass pretreatment.

Kumar, Nikhil↗
DOE OSTI2025

Electrochemically Mediated Au–C(sp 2 ) Anchors for Molecular Electronics

Terminal anchor groups play a key role in the stability and electronic properties of molecular junctions. Single molecule junctions typically consist of two preinstalled terminal anchors linking organic molecules to metal electrodes. Here, in this work, we show that p -terphenyl derivatives containing only a single terminal anchor show conductance features similar to junctions with two preinstalled terminal anchors. A set of p -terphenyl derivatives with one terminal anchor was prepared using automated chemical synthesis and characterized using single molecule electronics experiments, molecular dynamics (MD) simulations, bulk electrochemistry and spectroscopy, and nonequilibrium Green’s function-density functional theory (NEGF-DFT) calculations. Our results show that 4-amino- p -terphenyl (PPP) and related analogs exhibit a well-defined high conductance state that is diminished or absent in other p-terphenyl derivatives lacking a preinstalled amine terminal anchor or fluorine or methyl substitutions at the terminal para position. However, a low conductance state is observed in all amino- p -terphenyl derivatives with one preinstalled anchor due to molecular junctions formed by noncovalent dimeric π–π stacking interactions. The observed high conductance state diminishes upon the addition of reducing agents and is restored upon the addition of an oxidizing agent. Our results suggest that the high conductance state arises due to Au–C(sp 2 ) bond formation facilitated by a single electron oxidation event at the electrode surface. A series of control experiments with different anchor groups shows that primary amines play a key role in forming Au–C bonds for molecular junctions. Overall, these results suggest that Au–C bond formation gives rise to high conductance pathways in organic molecules containing only one preinstalled terminal anchor. Insights from this work can be leveraged in the design of molecular electronic devices, particularly in understanding the mechanisms of molecular binding and junction formation.

charge transport↗
NASA NTRS1995

Direct binding of F actin to the cytoplasmic domain of the alpha 2 integrin chain in vitro

The transmembrane integrins have been shown to interact with the cytoskeleton via noncovalent binding between cytoplasmic domains (CDs) of integrin beta chains and various actin binding proteins within the focal adhesion complex. Direct or indirect integrin alpha chain CD binding to the actin cytoskeleton has not been reported. We show here that actin, as an abundant constituent of focal adhesion complex proteins isolated from fibroblasts, binds strongly and specifically to alpha 2 CD, but not to alpha 1 CD peptide. Similar specific binding to alpha 2 CD peptide was seen for highly purified F actin, free of putative actin-binding proteins. The bound complex of actin and peptide was visualized directly by coprecipitation, and actin binding was abrogated by removal of a five amino acid sequence from the alpha 2 CD peptide. Our findings may explain the earlier observation that, while integrins alpha 2 beta 1 and alpha 1 beta 1 both bind to collagen, only alpha 2 beta 1 can mediate contraction of extracellular collagen matrices.

Non-NASA Center↗
DOE OSTI2025

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD + site. These inhibitors display varied affinities to different bacterial IMPDHs that are not easily rationalized by X-ray crystal structures of enzyme–inhibitor complexes. Inspection of X-ray crystal structures of 25 enzyme–inhibitor complexes, including 10 newly described, suggested that a mobile active site flap may be a structural determinant of inhibitor potency. Saturation transfer difference NMR experiments also suggested that the flap may contact the inhibitors to varying extents in different IMPDHs. Flap residue Leu413 contacted some inhibitors but was not structured in the crystal structures of other inhibitor complexes. The substitution of Leu413 with Phe or Ala in Bacillus anthracis IMPDH had inhibitor-selective effects, suggesting residue 413 could be a structural determinant of affinity. Curiously, the Ala substitution increased the potency of most inhibitors, even those that contacted Leu413 in the crystal structures. Presteady-state and steady-state kinetics experiments showed that the Leu413Ala substitution had comparable effects on inhibitor binding to the noncovalent E·IMP complex and the covalent intermediate E-XMP*, suggesting that the flap had similar interactions in both complexes. These results demonstrate that contacts do not necessarily indicate favorable interactions, and poorly structured mobile regions should not be discounted when assessing binding determinants.

Conformation↗
NASA NTRS2009

Functionalizing CNTs for Making Epoxy/CNT Composites

Functionalization of carbon nanotubes (CNTs) with linear molecular side chains of polyphenylene ether (PPE) has been shown to be effective in solubilizing the CNTs in the solvent components of solutions that are cast to make epoxy/CNT composite films. (In the absence of solubilization, the CNTs tend to clump together instead of becoming dispersed in solution as needed to impart, to the films, the desired CNT properties of electrical conductivity and mechanical strength.) Because the PPE functionalizes the CNTs in a noncovalent manner, the functionalization does not damage the CNTs. The functionalization can also be exploited to improve the interactions between CNTs and epoxy matrices to enhance the properties of the resulting composite films. In addition to the CNTs, solvent, epoxy resin, epoxy hardener, and PPE, a properly formulated solution also includes a small amount of polycarbonate, which serves to fill voids that, if allowed to remain, would degrade the performance of the film. To form the film, the solution is drop-cast or spin-cast, then the solvent is allowed to evaporate.

Chen, Jian↗
DOE OSTI2025

Electroplated Polymer‐Modified Carbon Fiber for Performance‐Enhancing Composite Interfaces

Carbon fiber composite performance relies on the fiber-matrix interface for effective load transfer. To enhance interfacial properties between the fiber and matrix, often carbon fiber surfaces are oxidatively and covalently modified to incorporate chemical functional groups. By contrast, here, noncovalent electrodeposition of functional polyelectrolyte is applied onto conducting carbon fibers from aqueous solutions. A natural polymer, chitosan (CS), is electro-deposited onto the fiber surface, which undergoes multi-scale physical interactions. The bound CS layer with abundant amine functionalities reacts with epoxy moieties within the matrix to improve the interfacial properties. The scalable and energy-efficient electrodeposition eliminates traditional functionalization and sizing requirements of carbon fiber while delivering significantly higher mechanical performance with enhanced consistency. For continuous fiber reinforced composites, compared to conventional fibers, apparent interlaminar shear strength increases by 27%, reaching ≈86 MPa. The short fiber composites with only 2–11 wt.% fibers exhibit ≈20% increase in tensile strength with a peak performance of 120 MPa. Unlike traditionally treated and sized carbon fiber, this approach delivers coated fibers with long shelf-life and allows recovery of both CS in electrolyte form and carbon fiber by continuous electrochemical processing of the modified fibers with inverse polarity; thus, it promotes overall fiber recyclability.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Protein Coatings Dictate the Dispersibility and Stability of Hydrophobic Zeolitic-Imidazolate Frameworks in Water

Metal–organic frameworks are promising materials for many biomedical technologies due to their ability to store and release large quantities of guest molecules in a predictable and tunable fashion. In biological fluids, proteins readily adsorb to the external surfaces of metal–organic framework particles through a combination of hydrophobic and electrostatic interactions. However, much remains to be understood about the nature of these protein coatings and how they influence the bulk properties of aqueous dispersions of metal–organic frameworks. Here, in this work, we show that a variety of proteins can be used to manipulate the properties of aqueous dispersions of zeolitic-imidazolate framework (ZIF) particles. Specifically, noncovalently associated protein coatings promote the formation of dispersions of hydrophobic ZIFs in water with high colloidal and hydrolytic stability, as long as the density of adsorbed proteins exceeds a critical, protein-dependent threshold. Further, these dispersions feature low viscosity and complete retention of gas carrying capacity. The wide range of properties accessible with protein coatings provides a highly modular approach to design hydrophobic metal–organic frameworks with properties tailored for specific biological applications.

adsorption↗
DOE OSTI2024

Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease

N-terminal autoprocessing from its polyprotein precursor enables creating the mature-like stable dimer interface of SARS-CoV-2 main protease (MPro), concomitant with the active site oxyanion loop equilibrium transitioning to the active conformation (E*) and onset of catalytic activity. Here, through mutagenesis of critical interface residues and evaluating noncovalent inhibitor (ensitrelvir, ESV) facilitated dimerization through its binding to MPro, we demonstrate that residues extending from Ser1 through Glu14 are critical for dimerization. Combined mutations G11A, E290A and R298A (MPro™) restrict dimerization even upon binding of ESV to monomeric MPro™ with an inhibitor dissociation constant of 7.4 ± 1.6 µM. Contrasting the covalent inhibitor NMV or GC373 binding to monomeric MPro, ESV binding enabled capturing the transition of the oxyanion loop conformations in the absence of a reactive warhead and independent of dimerization. Characterization of complexes by room-temperature X-ray crystallography reveals ESV bound to the E* state of monomeric MPro as well as an intermediate approaching the inactive state (E). It appears that the E* to E equilibrium shift occurs initially from G138-F140 residues, leading to the unwinding of the loop and formation of the 3 10 -helix. Finally, we describe a transient dimer structure of the MPro precursor held together through interactions of residues A5-G11 with distinct states of the active sites, E and E*, likely representing an intermediate in the autoprocessing pathway.

59 BASIC BIOLOGICAL SCIENCES↗