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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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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Simulations of Glass Transition and Mechanical Behavior of Off-Stoichiometric Crosslinked Polymers

Here, this work explores the influence of blend composition, network architecture, and hydrogen bonding on the material properties of crosslinked epoxy networks, focusing on the glass transition temperature (T g ) and Young’s modulus (Y). We used coarse-grained molecular dynamics simulations to simulate varying compositions of stiff and flexible components in epoxy monomer blends with varying excess of curative. We find that, without hydrogen bonding, networks of any composition show a monotonically increasing T g with decreasing excess curative, consistent with theory. In contrast, we find that when hydrogen bonding is introduced, the binary blend networks show significant enhancement in T g for lightly crosslinked systems. This result contributes to an explanation of the anomalous T g behavior observed experimentally in these systems. We further find that Y is generally enhanced by hydrogen bonds, especially below T g , demonstrating that hydrogen bonding has a significant influence on mechanical properties and can allow access to other desirable dynamic behavior, especially self-healing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

How Silica Surface Chemistry Modulates Interfacial Water: Insights from Machine Learning Molecular Dynamics

Controlling water structure and dynamics at silica interfaces are central to a wide range of technologies, including protective oxide layers for solar water splitting and nanoporous membranes. In this work, we develop a machine learning interatomic potential, trained via active learning, to achieve ab initio accuracy for water confined between hydroxylated silica surfaces over a range of silanol coverages and slit widths. We find that partially hydroxylated surfaces (50 and 75% OH) support stronger water−surface hydrogen bonding and more extended interfacial density profiles than fully hydroxylated (100% OH) surfaces, indicating that increasing OH coverage does not necessarily strengthen interfacial hydrogenbond networks. Translational diffusion decreases approximately linearly with slit width and OH coverage, whereas rotational dynamics respond nonlinearly. In particular, at the smallest slit width of 5 Å, 75% OH coverage produces an enhanced local tetrahedral ordered interfacial network that strongly suppresses reorientation, while 100% coverage yields a crowded, disordered interfacial layer that also hinders rotation. In contrast, the 50% OH coverage is sufficiently sparse that it does not markedly alter water structure or dynamics under confinement. These results show that coupled control of pore size and surface chemistry enables nonlinear tuning of interfacial water structure and transport, providing a design strategy for optimizing porous silica for either enhanced interfacial stability and controlled reactivity or rapid and selective transport.

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

Effect of the Segmental Structure of Thermoplastic Polyurethane (Hardness) on the Interfacial Adhesion of Textile-Grade Carbon Fiber Composites

In polymer composites, the fiber–matrix interface is primarily influenced by the surface treatment of the fibers and polymer morphology. Previous studies have investigated the effect of surface treatment of carbon fiber on the mechanical properties of the resulting composites. However, very few studies have explored the chemical structural modification of polymer effect on the fiber–matrix adhesion. In this work, the interfaces of soft thermoplastic polyurethane (S-TPU) and hard-segmented TPU (H-TPU) were investigated through surface, thermal, and mechanical characterization. A textile-grade carbon fiber (TCF) with 1% concentration of epoxy sizing (an emerging material for nonaerospace applications with 450 K filament tows) was used as a reinforcement to investigate the structure–property relationship at the interface. Atomic force microscopy results showed 39% higher surface roughness for S-TPU than for H-TPU. X-ray photoelectron spectroscopy results revealed a 550% increase in C=O content, which can provide multiple hydrogen bonding networks in H-TPU, and these C=O bonds can produce a strong chemical bond at the fiber–matrix interface. Additionally, dynamic mechanical analysis and differential scanning calorimetry results confirmed the presence of hydrogen bonding that enhances the cross-linked density by 232% in H-TPU compared to S-TPU. The improved mechanical properties of H-TPU composites, such as flexural, impact and tensile by 30, 50, and 130% compared to S-TPU composites, prove that the crystallinity and hydrogen bonding significantly increase the load bearing capacity due to the strong interface. The mechanical properties of TCF–TPU composites validate the formation of chemical bonds through a nucleophilic addition reaction at the interface and improve the bond strength of the composites. Thus, tailoring the polyurethane structure broadens the performance of segmented TPU in conjunction with TCF reinforcement, which has implications for cost-effective, high-strength composites.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism

Tryptophan indole lyase (TIL; [E.C. 4.1.99.1]) is a bacterial pyridoxal-5′-phosphate (PLP)-dependent enzyme that catalyzes reversible β-elimination of indole from L-tryptophan. The mechanism of elimination of indole from L-tryptophan starts with the formation of an external aldimine of the substrate and PLP, followed by deprotonation of the α-CH of the substrate, forming a resonance-stabilized quinonoid intermediate. Proton transfer to C3 of the indole ring and carbon–carbon bond cleavage of the quinonoid intermediate provide indole and aminoacrylate bound to PLP, which then releases indole, followed by iminopyruvate. We have now determined the X-ray crystal structures of TIL complexes with (3S)-dioxindolyl-l-alanine, an inhibitor, and with substrates L-tryptophan, 7-aza-L-tryptophan, and S-ethyl-l-cysteine (SEC) in the presence of benzimidazole (BZI), an isostere of the product indole. These structures show a mixture of gem-diamine, external aldimine, quinonoid, and aminoacrylate intermediates, in both open and closed active site conformations. In the closed conformations of L-tryptophan, (3S)-dioxindolyl-l-alanine, and 7-aza-L-tryptophan complexes, hydrogen bonds form between Asp-133 with N1 of the ligand heterocyclic ring and NE2 of His-458 in the small domain of TIL. This hydrogen bond also forms in the BZI complex with the aminoacrylate intermediates formed from both L-tryptophan and SEC. The closed quinonoid complex of 7-aza-L-tryptophan shows that the azaindole ring in the closed conformation is bent out of plane of the Cβ–C3 bond by about 40°, putting it in a geometry that leads toward the transition-state geometry. Thus, both conformational dynamics and substrate activation play critical roles in the reaction mechanism of the TIL.

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

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Crystal Growth, Single Crystal Structure, and Biological Activity of Thiazolo-Pyridine Dicarboxylic Acid Derivatives

Four novel TPDCA derivatives were prepared via a supersaturation method combining TPDCA with water, N-methyl-2-pyrrolidone (NMP), Na(PO 2 H 2 ), and ammonia solution: 2(C 9 H 7 NO 5 S)H 2 O (1), (C 9 H 7 NO 5 S)C 5 H 9 NO (2), (C 9 H 7 NO 5 S)Na(PO 2 H 2 ) (3), and (C 9 H 5 NO 5 S)(NH 4 )2(H 2 O) (4). Their crystal structures were determined by single-crystal X-ray diffraction. Compounds (1) and (2) crystallize in the monoclinic space groups P2 1 and P2 1 /c, respectively, whereas compounds (3) and (4) crystallize in the triclinic space group P1 - . Weak and moderate hydrogen bonds were detected in the four compounds. In the biological tests, (1) and (3) exhibited significant antibacterial activity against Escherichia coli and Staphylococcus aureus; in addition, (1) was cytotoxic against leukemia HL-60 cells with the IC 50 value of 158.5 ± 12.5 μM.

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

Vibrational Dynamics and Phase Transitions of Hydrazine to 50 GPa

The high pressure behavior of hydrazine, N 2 H 4 , has been investigated to 50 GPa at room temperature using infrared and Raman spectroscopy to explore pressure induced phase transitions and changes in hydrogen bonding. Three solid–solid phase transitions were detected at 11, 21, and 32 GPa on room temperature compression through dramatic changes in the lattice vibration and N–H stretching regions with increasing pressure in both measurement techniques. The transition to phase IV, which appears at 32 GPa, exhibits increased hydrogen bonding with significant hysteresis, persisting to 9 GPa on decompression. This work presents a detailed analysis of the pressure dependence of mode shifts and calculations of mode Grüneisen parameters as well as a determination of an approximate thermodynamic Grüneisen parameter. We compare these results to the behavior of other small molecular materials such as ammonia and water and explore the evolution of hydrogen bonding in hydrazine toward the symmetrically hydrogen bonded state, which has previously been suggested by theoretical computations.

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

Enhancing Biopolyester Backbone Rigidity with an Asymmetric Furanic Monomer

Biobased furanic polyesters can exhibit performance advantages over petroleum-derived polyesters, primarily due to their rigid furan-containing backbones. Herein, we develop two strategies to polymerize methyl 5-hydroxymethyl furanoate to poly(5-hydroxymethyl furanoate) (PHMF), a furan-based polyester with even greater backbone rigidity than poly(ethylene furanoate). Thermal, spectroscopic, and computational investigations of PHMF alongside analogous furan-based and phenyl-based polyesters suggest that the high furan content of PHMF leads to its high glass transition temperature, slow crystallization kinetics, and low amorphous mobility. Molecular dynamics simulations suggest that while the backbone of PHMF is exceptionally rigid, its amorphous phase is denser than its phenyl analog due to noncovalent interchain interactions. Together, these results highlight how asymmetric furan-based monomers can modulate key properties in biobased polyesters.

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

2D-Covalent Organic Frameworks with Interlayer Hydrogen Bonding Oriented through Designed Nonplanarity

We report the synthesis and characterization of a new class of 2D-covalent organic frameworks, called COFamides, whose layers are held together by amide hydrogen bonds. To accomplish this, we have designed monomers with a nonplanar structure that arises from steric crowding, forcing the amide side groups out of plane with the COF sheets orienting the hydrogen bonds between the layers. Here, the presence of these hydrogen bonds provides significant structural stabilization as demonstrated by comparison to control structures that lack hydrogen bonding capability, resulting in lower surface area and crystallinity. We have characterized both azine and imine-linked versions of these COFs, named COFamide-1 and -2, respectively, for their surface areas, pore sizes, and crystallinity. In addition to these more conventional characterization methods, we also used variable temperature infrared spectroscopy methods and van der Waals density functional calculations to directly observe the presence of hydrogen bonding.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Taming Molecular Folding: Anion-Templated Foldamers with Tunable Quaternary Structures

Higher-order foldamers represent a unique class of supramolecules at the forefront of molecular design. Herein we control quaternary folding using a novel approach that combines halogen bonding (XBing) and hydrogen bonding (HBing). We present the first anion-templated double helices induced by halogen bonds (XBs) and stabilized by “hydrogen bond enhanced halogen bonds” (HBeXBs). Our findings demonstrate that the number and orientation of hydrogen bond (HB) and XB donors significantly affect the quaternary structure and guest selectivity of two similar oligomers. Finally, this research offers new design elements to engineer foldamers and tailor their quaternary structure for specific guest binding.

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

Diaminopurine in Nonenzymatic RNA Template Copying

In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.

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

Synergistic Effects of the Electric Field Induced by Imidazolium Rotation and Hydrogen Bonding in Electrocatalysis of CO 2

The roles of the ionic liquid, 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIM][BF₄]), and water in controlling the mechanism, energetics, and electrocatalytic activity of CO₂ reduction to CO on silver in non-aqueous electrolytes were investigated. The first electron transfer occurs to CO₂ at reduced overpotentials when it is trapped between the planes of [EMIM]⁺ ring and electrode surface due to cation re-orientation as determined from voltammetry, in-situ surface-enhanced Raman spectroscopy, and density functional theory calculations. Within this interface, water up to 0.5 M does not induce significant faradaic activity, opposing the notion of it as a free proton source. Instead, water acts as a hydrogen bond donor and the proton is sourced from [EMIM]⁺. Furthermore, this study demonstrates that alcohols with varying acidity tune the hydrogen bonding network in the interfacial microenvironment to lower the energetics required for CO₂ reduction. Here, the hydrogen bonding suppresses the formation of inactive carboxylate species, thus preserving the catalytic activity of [EMIM]⁺. The ability to tune the hydrogen bonding network opens new avenues for advancing IL-mediated electrocatalytic reactions in non-aqueous electrolytes.

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

Molecular insights into the complex mechanics of plant epidermal cell walls

Computational analysis of cell walls Layers of intertwined fibers make up plant cell walls. The various types of fibers respond differently to deformation. Cellulose microfibrils, for example, can stretch or curve, changing their end-to-end length, and can also slide past each other, reorient relative directions, and bundle with neighboring microfibrils. Zhang et al. developed a computational model based on observations of onion skin epidermis that describes how these complex changes in space govern cell wall mechanics. The results inform ways to engineer multifunctional fibrous materials. Science , this issue p. 706

Science & Technology - Other Topics↗
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↗
DOE OSTI2021

Engineering Second Sphere Interactions in a Host–Guest Multicomponent Catalyst System for the Hydrogenation of Carbon Dioxide to Methanol

Many enzymes utilize interactions extending beyond the primary coordination sphere to enhance catalyst activity and/or selectivity. Such interactions could improve the efficacy of synthetic catalyst systems, but the supramolecular assemblies employed by biology to incorporate second sphere interactions are challenging to replicate in synthetic catalysts. Herein, a strategy is reported for efficiently manipulating outer sphere influence on catalyst reactivity by modulating host–guest interactions between a noncovalently encapsulated transitionmetal-based catalyst guest and a metal–organic framework (MOF) host. This composite consists of a ruthenium PNP pincer complex encapsulated in the MOF UiO-66 that is used in tandem with the zirconium oxide nodes of UiO-66 and a ruthenium PNN pincer complex to hydrogenate carbon dioxide to methanol. Due to the method used to incorporate the complexes in UiO-66, structure–activity relationships could be efficiently determined using a variety of functionalized UiO-66-X hosts. These investigations uncovered the beneficial effects of the ammonium functional group (i.e., UiO-66-NH 3 + ). Mechanistic experiments revealed that the ammonium functionality improved efficiency in the hydrogenation of carbon dioxide to formic acid, the first step in the cascade. Isotope effects and structure–activity relationships suggested that the primary role of the ammonium functionality is to serve as a general Brønsted acid. Importantly, the cooperative influence from the host was effective only with the functional group in close proximity to the encapsulated catalyst. Here, reactions carried out in the presence of molecular sieves to remove water highlighted the beneficial effects of the ammonium functional group in UiO-66-NH 3 + and resulted in a 4-fold increase in activity. As a result of the modular nature of the catalyst system, the highest reported turnover number (TON) (19 000) and turnover frequency (TOF) (9100 h –1 ) for the hydrogenation of carbon dioxide to methanol are obtained. Moreover, the reaction was readily recyclable, leading to a cumulative TON of 100 000 after 10 reaction cycles.

08 HYDROGEN↗