Search NASA⌕ Search

SEARCH · Search NASA

Results for “H-bonds”

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.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Synergetic Effects of Soil Organic Matter Components During Interactions with Minerals

Mineral-associated soil organic matter (SOM) is critical for stabilizing organic carbon and mitigating climate change. However, mineral-SOM interactions at the molecular scale, particularly synergetic adsorption through organic-organic interaction on the mineral surface known as organic multilayering, remain poorly understood. This study investigates the impact of organic multilayering on mineral-SOM interactions, by integrating macroscale experiments and molecular-scale simulations that assess the individual and sequential adsorption of major SOM compounds – lauric acid (lipid), pentaglycine (amino acid), trehalose (carbohydrate), and lignin onto soil minerals. Ferrihydrite, Al-hydroxide, and calcite are exposed to SOM compounds to determine adsorption affinities and binding energies. Results show that lauric acid has 20-40 times higher K d than pentaglycine, following the order K d (ferrihydrite) > K d (Al-hydroxide) >> K d (calcite). Molecular-scale simulations confirm that lauric acid has a higher binding energy (30.8 kcal/mol) on ferrihydrite than pentaglycine (6.0 kcal/mol), attributed to lipid hydrophobicity. The lower binding energy of pentaglycine results from its hydrophilic amide groups, facilitating partitioning into water. Sequential experiments examine how the first layer of lipid or amino acid affects the adsorption of carbohydrate/lignin, which show little or no individual adsorption affinities. Macroscale results reveal that lipid and amino acid adsorption induce ferrihydrite particle repulsion increasing reactive surface area and enhancing carbohydrate/lignin adsorption independently and synergistically through organic multilayering. Molecular-scale results reveal that amino acid adsorbed on ferrihydrite interacts more readily with lignin macroaggregates (preformed in solution) than with individual lignin units, indicating organic multilayering via H-bonding. Further, these findings reveal the molecular mechanisms of SOM-mineral interactions, crucial for enhancing soil carbon stabilization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2026

A Quantum Mechanical Study of Quartz (101) Interfacial Boundaries

Density functional theory (DFT) calculations were performed on periodic and molecular models to explore the energetics of bonding modes at quartz–quartz interfaces, common grain contacts in sandstones. Four interface types were modeled: H 2 O-mediated, silanol H-bond mediated, O–O peroxide bonds, and siloxane bonds. Each type of interface may exist in the subsurface of the Earth, depending upon water activity, temperature, and pressure, as interfacial structures are stable within DFT molecular dynamics simulations up to 473 K. The results predict interfacial energies SiOSi > SiOOSi > SiOH-6H 2 O > 2SiOH, as expected based on similar bond strengths in other systems. The proposed SiOOSi interface is not generally accounted for in chemomechanical models but could be important in sandstones at depth in the Earth. The implications for intergrain fracturing and H2 generation are discussed.

Hydrogen↗
DOE OSTI2026

Selective CO 2 Reduction by Bis(bipyridine)cobalt(II) Catalysts: The Role of Pendant Pyridine as a Proton Acceptor

Electrochemical CO 2 reduction reaction (CO 2 RR) catalyzed by molecular earth-abundant metal catalysts is a promising strategy to convert CO 2 into value-added products. One recent trend in this field has been focusing on the rational design of catalysts by incorporating redox-active ligands and modifying the secondary coordination sphere (SCS) to achieve efficient and selective CO 2 RR. Herein, we report a series of Co bis­(bipyridine) catalysts featuring various dangling groups, such as pyridine, tertiary amine, or butyl, in the secondary coordination sphere (Co-PyMe, Co-Py, Co-PrN, and Co-Bu). Efficient, selective electrocatalytic CO 2 RR was achieved by the complexes after the generation of triply reduced intermediate consisting of a Co I center and a dianionic ligand, producing CO as the major product and trace amount of H 2 . Strong correlations with the identity of dangling groups and turnover frequency (TOF) have been observed, in which Co-PyMe displayed the highest TOF (1086 s –1 in MeCN/H 2 O). Mechanistic studies indicated that the acceleration of CO 2 RR with pyridine-functionalized catalysts were derived from the protonation of pyridine dangling groups which participated as weak acids in the H-bonding network with exogenous proton sources, stabilizing CO 2 -bound intermediates and facilitating proton transfer. In addition, precatalytic CO 2 binding and activation at the third reduction (−2.1 V) was revealed by CV and SEC-IR studies. The resultant doubly reduced CO-bound species acted as a trapping state which inhibited CO 2 RR electrocatalysis. Regeneration of active species was accessed via reductive dissociation of CO at a more negative potential. In conclusion, this study highlights the combined effects of redox-active ligands and pyridine/pyridinium as SCS groups on CO 2 RR catalysis and provides design principles for future development of CO 2 RR catalysts utilizing pyridine/pyridiniums as SCS functional groups to fine-tune the catalytic activity.

CO2 reduction↗
DOE OSTI2024

Stable, Impermeable Hexacyanoferrate Anolyte for Nonaqueous Redox Flow Batteries

Redox-active molecules, or redoxmers, in nonaqueous redox flow batteries often suffer from membrane crossover and low electrochemical stability. Transforming inorganic polyionic redoxmers established for aqueous batteries into nonaqueous candidates is an attractive strategy to address these challenges. Here, in this study, we demonstrate such tailoring for hexacyanoferrate (HCF) by pairing the anions with tetra-n-butylammonium cation (TBA + ). TBA 3 HCF has good solubility in acetonitrile and >1 V lower redox potential vs the aqueous counterpart; thus, the familiar aqueous catholyte becomes a new nonaqueous anolyte. The lowering of redox potential correlates with replacement of water by acetonitrile in the solvation shell of HCF, which can be traced to H-bond formation between water and cyanide ligands. Symmetric flow cells indicate exceptional stability of HCF polyanions in nonaqueous electrolytes and Nafion membranes completely block HCF crossover in full cells. Ion pairing of metal complexes with organic counterions can be effective for developing promising redoxmers for nonaqueous flow batteries.

25 ENERGY STORAGE↗
DOE OSTI2026

Leveraging Hydration Forces for Size-Specific Nanoparticle Enrichment with a Redox-Responsive Silica-Binding Elastin-Like Polypeptide

Elastin-like polypeptides (ELPs) are low-complexity proteins that coacervate above a characteristic lower critical solution temperature (LCST). While the thermoresponsiveness of ELPs has been widely exploited in the biomedical and biomaterials fields, their ability to mediate nanoparticle assembly below their transition temperature remains largely unexplored. Here, we show that unmodified ELPs induce the reversible flocculation of silica nanoparticles (SiNPs) by forming backbone hydrogen bonds with surface silanols. Interparticle bridging is modulated by ELP length and concentration and by the presence of N- and C-terminal anchoring groups such as a cysteine residue and a Car9 silica-binding peptide. Using a redox-responsive fusion protein consisting of disulfide-bonded ELP domains terminated by Car9 segments, we stabilize 20 nm SiNPs under oxidizing conditions while triggering particle flocculation upon addition of reductant. We find that SiNP sedimentation under reducing conditions exhibits a sharp dependency on particle size that arises from the curvature-dependent structure of surface silanols. While the isolated silanols of SiNPs smaller than 30 nm are efficiently engaged by the ELP domains of Car9-anchored proteins, repulsion forces associated with the presence of a layer of molecular water together with increased electrostatic repulsion preclude efficient engagement of H-bonded silanols displayed on the surface of SiNPs larger than 60 nm. We harness these findings to selectively enrich SiNPs based on size and expand the concept to titania (TiO2) by demonstrating that rutile nanoparticles can be stabilized or sedimented with solid-binding ELPs by adjusting the solution pH to promote or discourage the formation of a hydration layer. These strategies should prove broadly useful for the separation of other oxides and their polymorphs and provide a tunable strategy for nanoparticle assembly and bioinspired colloidal design.

ELP↗
DOE OSTI2025

First-Principles Molecular Dynamics Simulations of Ammonia Adsorption onto MFI Zeolite Nanosheets

MFI zeolite nanosheet membranes are promising candidates for ammonia separation from nitrogen and hydrogen gases, yet questions remain on the origin of their high selectivity. Silanols, Si–OH, are present in high concentration at the surface of zeolite nanosheets, and force-field-based simulations indicate that surface adsorption at the silanols contributes to selectivity. Acidic silanol groups can chemically react with ammonia via transfer of a proton to form ammonium ions, which may further contribute to the ability of zeolite nanosheet membranes to separate ammonia from other gases. In this work, we used first-principles molecular dynamics techniques to simulate ammonia’s behavior within stacked MFI zeolite nanosheets. We found that at 523 K and a loading corresponding to 35 bar, conditions desired for the ammonia separation, about 30% of ammonia reacts with surface silanols. Our work explored H-bonding and proton transfer within this system.

ammonia↗
DOE OSTI2025

Symmetrization of Strong Hydrogen Bond under High Pressure in Bihydroxide-Ion-Containing NaCu 2 (SO 4 ) 2 ·H 3 O 2 Revealed by Experimental Charge Density, Single-Crystal Electron Diffraction, and Neutron Diffraction Studies

In minerals and inorganic compounds, strong hydrogen bonding can lead to the formation of complex ionic species such as the H 3 O 2 – bihydroxide anion and Zundel cation H 5 O 2 + . We studied [NaCu 2 (SO 4 ) 2 ·H 3 O 2 ] natrochalcite, which contains bihydroxide anions and undergoes hydrogen bond symmetrization at the lowest pressure reported so far among inorganic compounds. Hydrogen bond symmetrization leads to changes in the bulk modulus, seismic wave velocities, and proton mobility and plays a primary role in high-temperature superconductivity, but its characteristics are not well understood due to a lack of systematic studies and limitations of experimental methods sensitive to this subtle change. In this work, we applied experimental charge density analysis based on in situ single-crystal X-ray diffraction data, along with the single-crystal neutron and electron diffraction experiments, to probe the behavior of hydrogen atoms during the hydrogen bond symmetrization process under high-pressure conditions. On the way to the symmetrical H-bonding, natrochalcite undergoes a series of complex redistributions of electron density, which we trace with multipole refinement and detailed analysis of changes in the Laplacian of electron density values. Additionally, we deconvoluted the equation of state (volume of the unit cell vs pressure relation) into the atomic equation of states describing dependencies of atomic charges or volumes vs pressure.

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

Structural Evidence of Interanionic Hydrogen Bonding in Phosphoric Acid Solutions

Interanionic hydrogen bonding (IAHB) is a noncovalent interaction between like-charged ions that challenges conventional electrostatic understanding. This study provides direct structural evidence of IAHB in concentrated aqueous phosphoric acid (PA) solutions, which exhibit >60% dissociation under these conditions. Oxygen K-edge X-ray absorption fine structure spectroscopy, combined with electron affinity time-dependent density functional theory calculations, reveals the formation of stable, cyclic phosphate-phosphate IAHB dimers at PA concentrations ≥7 M. Extended X-ray absorption fine structure data show distinct long-range ordering consistent with these dimers, and near-edge X-ray absorption fine structure spectra confirm a concentration-dependent transition from monomeric to dimeric species. Energy decomposition analysis through density functional theory shows that the formation of solution-phase IAHB is energetically favored and is attributed to polarization of and the charge transfer between the two fragments driven by the surrounding solvent molecules, in addition to the permanent electrostatics. These findings offers crucial structural insights into the H-bonded networks in concentrated PA, highlighting the critical role of solvent in facilitating anion–anion association.

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

Concerted Electron-Ion Transport by Polyacrylonitrile Elucidated with Reactive Deep Learning Potentials

Charge transport in polymers, such as polyacrylonitrile (PAN), is crucial for electronics and energy storage. For instance, PAN can transport cations e.g., Li + , by facilitating dynamic cation-nitrile coordination in batteries. However, little is known regarding the underlying role of complex reactive polymer configurations. Herein, we develop a deep-learning potential, trained on ab initio energies and forces of nonequilibrium reactive PAN configurations, to unravel the kinetics of PAN cyclization initiated by a nucleophile (OH – dissociated from LiOH) attacking the terminal nitrile carbon. We find, based on the reaction free-energetics, rates, and charge analysis, that the nucleophile attack producing the first ring is the rate-limiting step, which subsequently triggers Li + -coupled electron transfer along the PAN backbone, causing ∼10 4 times faster sequential ring-formation of the remaining nitriles. PAN’s extended configurations, where dipolar and H-bonding interactions are minimal, enable such rapid kinetics. By validating our computational findings with IR and NMR experiments, we establish a pathway for designing reactive polymers with enhanced charge transport for energy applications.

Chahal-Crockett, Rajni [Oak Ridge National Laborat↗
DOE OSTI2025

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

Abstract MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.

Science & Technology - Other Topics↗
DOE OSTI2025

The impact of second coordination sphere functional group extension on product selectivity for manganese bipyridyl CO 2 reduction electrocatalysts

Utilizing the well established manganese bipyridyl class of homogeneous electrocatalyst, four new ligands are studied to probe the influence of distal, outer coordination sphere, H-bonding and steric effects on product selectivity for proton-coupled electrocatalytic CO 2 reduction. The presence of a simple acetate functional group in the second coordination sphere provides a high selectivy for CO 2 -to-CO conversion irrespective of proton source (H 2 O vs. PhOH) or applied potential. The o-(methoxybenzoate)phenyl second/outer coordination sphere at the bipyridyl 6,6′-positions imparts poor product selectivity. In contrast, upon conjugation of the acetate functional group with the N-Boc-alanine moiety, a CO : HCO 2 − product selectivity of ∼1 : 1 is observed at the high overpotential catalytic wave (for both H 2 O and PhOH acids). Computed enthalpy and free energy of activation parameters suggest that selective CO 2 insertion at the manganese hydride transition state is favored, over protonation, consistent with negligible hydrogen production during controlled potential electrolysis studies.

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

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

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

Hidden features in the OH-stretching spectra of amino acid decorated air–water interfaces

Chemical reactivity at the air–water interface is governed by the interfacial solvation of reactive species. For instance, during aqueous amino acid-based CO 2 absorption, water reorganizes around the reactive sites and couples dynamically with reaction pathways, facilitating the reaction. In this context, surface-sensitive vibrational sum-frequency generation (vSFG) spectroscopy can probe the OH stretch vibrations of interfacial water and determine the solvation structures around reactants and products, thereby furthering our understanding of the role of interfacial solvation. However, vSFG spectra of the air–water interface in the presence of charged species can be remarkably complex; key species-bound local water structures with distinct orientations may be hidden beneath prominent vSFG peaks arising from water–water hydrogen bonds and remain difficult to resolve. Here, we measure and compute vSFG spectra of the water OH stretch at air–water interfaces decorated with amino acids in their zwitterionic and anionic forms, as well as equimolar mixtures of these forms with bicarbonate. The latter represents post-CO 2 -absorption conditions. We find that computing depth- and frequency-dependent spectral densities—decomposed into contributions from water molecules hydrogen-bonded exclusively to other water molecules, exclusively to amines, exclusively to carboxylates, or shared between these polar/charged groups—is indispensable for accurate interpretation of the vSFG spectra. Key findings include orientational flip-flop in water sub-layers, strong carboxylate-water H-bonding, and water orientational ordering extending into the bulk aqueous phase induced by anionic amino acids. Here, this study provides a computational spectroscopic platform for improved understanding of interfacial solvation relevant to interfacial reactivity.

Air-water interface↗
DOE OSTI2025

Structure of the D1-Val185Asn mutated photosystem II complex with slow O–O bond formation reveals changes in the Cl1 water channel

During photosynthesis, the photosystem II (PSII) enzyme catalyzes the light-driven oxidation of water, fueling life on Earth by storing light energy and releasing O 2 as a byproduct. Determining the molecular mechanism for this water oxidation reaction has been of significant interest for the development of synthetic catalysts, but many details remain elusive. One of the open questions is how protons are strategically removed from the active site, a Mn 4 CaO 5 cluster called the oxygen-evolving complex (OEC), during the reaction cycle via conserved water channels, and how proton transfer contributes to O–O bond formation energetics. Site-directed mutagenesis studies have investigated the role of conserved amino acid side chains in facilitating proton transfer. One of the most influential mutations is the Val185Asn substitution on the D1 subunit, which substantially slows O 2 release kinetics without abolishing catalytic activity. Forming a molecular understanding of how this mutation affects the active site will provide insight into the water oxidation reaction mechanism. Here, we investigated the structural basis of the Val185Asn substitution by determining a 1.99 Å-resolution cryo-EM structure. We observed that Asn185 orients away from the OEC and donates a H-bond to Cl1, a conserved chloride ion. We furthermore observed an alternative D2-Glu312-facing conformation of the D2-Lys317 side chain in the Cl1 water channel, a conformation that is consistent with recent models for proton transfer. These changes also produce perturbations to the hydrogen-bonding network. Overall, these finding provide insight into proton transfer in the Cl1 channel and its effect on the water oxidation reaction mechanism.

cryo-EM↗
DOE OSTI2025

Flow-Driven Stretch Fluctuations Govern the Nonlinear Viscoelasticity of Elongating Associative Polymer Networks

We use nonequilibrium molecular dynamics simulations to verify recent tube-model predictions that associative polymer networks exhibit broad stretch fluctuations during elongational flow. Simulations further show that these fluctuating dynamics give rise to the rate-dependent extensional viscosity 𝜂 𝐸 measured in filament stretching experiments on H-bonding networks. Simulations model bivalent associative networks with a reactive bead-spring model for varying association strength and extensional strain rate. We observe that stretch fluctuations are driven by a new form of chain tumbling, where chains continually collapse and elongate as their associations break and reform within the advecting network. This produces a broad, nearly uniform distribution of chain stretch over a wide range of strain rates, manifesting as a rate-independent plateau in the extensional stress. Our results show that the nonlinear viscoelasticity of associative networks is dominated by large fluctuations in molecular response, which cannot be captured by current mean-field models.

biomimetic & bio-inspired materials↗
DOE OSTI2025

Autonomous Infrared and Small (Wide) Angle X-Ray Scattering (IR-S(W)AXS) Capability

Thin water films are 2-D, nanoconfined layers that form on solid surfaces exposed to humid atmospheres—environments ubiquitous across catalysis, corrosion science, soil science, and subsurface geochemistry. At relative humidity (RH) values below saturation, these films are Å–nm thick and exhibit properties that differ sharply from bulk water, including disrupted H-bonding and impeded mass transport. Owing to their high surface-to-volume ratio, dissolution of the solid can rapidly drive strong supersaturation with respect to secondary phases. Reactivity in thin water films is highly sensitive to film thickness, and critically, thickness evolves during reaction because the hygroscopicity of the interfacial system changes as ions accumulate or diminish in the film and as reaction products transform. To accurately probe and control these dynamics, a capability is needed that can measure and automatically maintain a constant water-film thickness while simultaneously monitoring solid dissolution, nucleation, and growth. This project developed an autonomous Infrared/Small Angle X-ray Scattering-Wide Angle X-ray Scattering (IR/(W)SAXS) for investigating reactivity in thin water films on solid surfaces exposed to humidified gases. The capability consists of an IR spectrometer, a (W)SAXS instrument, and a mass flow controller system for generating variably humidified gas flows to a custom reaction cell. Progress on each of the major components of the capability are detailed below.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

First Principles Molecular Dynamics Simulations of Ammonia Adsorption onto MFI Zeolite Nanosheets

MFI zeolite nanosheets membranes are promising candidates for ammonia separation from nitrogen and hydrogen, yet questions remain on the origin of their high selectivity. Silanols, Si-OH, are present in high concentration at the surface of zeolite nanosheets, and force-field-based simulations indicate that surface adsorption at the silanols contributes to selectivity. Silanols can chemically react with ammonia, which may further contribute to the ability of zeolite nanosheet membranes to separate it from other gases. In this work, we use first-principles molecular dynamics techniques to simulate ammonia’s behavior within stacked MFI zeolite nanosheets. We find that at 523 K and a loading corresponding to 35 bar, conditions desired for the ammonia separation, about 30% of ammonia reacts with surface silanols. Our work explores H-bonding and proton transfer within this system.

36 MATERIALS SCIENCE↗