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Results for “Hydrogen bond network”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Calcium silicate hydrate colloid at different humidities: Microstructure, deformation mechanism, and mechanical properties

Calcium silicate hydrate (C-S-H) is the main hydration product of Portland cement, while fundamental questions persist regarding its colloidal structure and water content. In this work, we developed a full atomistic C-S-H colloid model and investigated the physical and mechanical properties at different gel water concentrations. Water confined in nanometer gel pores degrades the mechanical properties of C-S-H because of its hydrolysis effect. A “ductile to brittle” transition was observed in the C-S-H colloid model with increasing gel water contents, evolving from transgranular failure to intergranular fracture. The gel water confined in nanometer-sized pores displays glassy characteristics, and it acts as a lubricant and facilitates structure distortions during the deformation. We elucidated the topology effect of the hydrogen bond network on the evolution of the viscoelasticity of C-S-H at different humidities. In conclusion, this work sheds light on the role of water in C-S-H colloids from nanostructure perspectives.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Traction-separation response of bilayer graphene interfaces: The role of an intercalated single atomic layer of water molecules and hydroxyl groups

Molecular dynamics simulations of the normal and shear traction-separation response of dry and wet bilayer graphene interfaces were performed. The influence of a single, atomic layer of water molecules sandwiched between graphene layers and hydroxyl functionalization on one or both layers were investigated. Hydroxyl groups provided a shielding effect during normal separation while favoring stick-slip friction under sliding conditions. The single, atomic layer of water molecules confined between hydrophilic and asymmetric hydrophobic/hydrophilic surfaces was found to ease sliding friction. The mechanisms arose from the balance between the attractive and repulsive graphene/water interactions through bridges of single water molecules between the two surfaces and the structure of the water monolayer under confinement for which an out-of-plane water/water hydrogen bond network could not be developed. The single, atomic layer of water molecules reduced the sliding friction the most when both surfaces were hydrophilic and lowered the sliding friction of the asymmetric hydrophobic/hydrophilic interfaces to that when both surfaces were hydrophobic. An optimal hydroxyl surface coverage of less than 10% may exist for efficient water lubrication, with diminishing effect with increasing number of hydroxyl groups. Finally, the findings offer a design strategy for assembling bilayer graphene interfaces with tailored friction and sliding contact properties.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Water transport through monolayer fullerene membrane

Water transport through nanoporous materials is important in water treatment, desalination, and nanofiltration. Two-dimensional (2D) membranes such as porous graphene have been explored for high-permeance water transport. However, water transport through a new class of 2D membranes based on two-dimensional covalently linked fullerene monolayers has not been fully explored. Here we use classical molecular dynamics simulations to investigate both vapor and liquid water transport through a monolayer fullerene membrane. We find that a quasi-tetragonal phase fullerene membrane possesses the right pore size and geometry that allows fast water vapor transport (∼ 50 g m −2 day −1 Pa −1 ) and water liquid transport (∼ 2.0 g m −2 day −1 Pa −1 ). Furthermore, simulation of sea water transport through the fullerene membrane shows 100 % salt rejection. The much faster vapor transport rate is attributed to the funnel-shaped pore and the optimal size that allows free rotation of water molecules permeating through, while the slower liquid transport is due to the need to desolvate a water molecule to break its hydrogen-bond network across the hydrophobic pore. This work shows the great potential of using monolayer fullerene membranes as 2D membranes for fast and selective water transport.

Desalination↗
DOE OSTI2021

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Iron corrosion in the “inert” supercritical CO 2 , ab initio dynamics insights: How impurities matter

Metal corrosion from exposure to supercritical fluids is a long-standing challenge lacking atomistic understanding for effective corrosion prevention in diverse important applications. Here, in this work, reactions relevant to corrosion in supercritical CO 2 (sCO 2 ), with H 2 O and NO 2 as impurities, are revealed using ab initio molecular dynamics and enhanced sampling methods. While little reactivity is observed in bulk sCO 2 , the iron surface is found to play a crucial almost-catalytic role in its own corrosion, activating the inert CO2 and hence facilitating $\ast$HCO 3 – and $\ast$CO 3 2– formation at the interface. Moreover, the hydrogen bond network of $\ast$H 2 O assists the H shuttling to the activated CO 2 and impurities, forming reactive species observed in experiments. Such atomistic insight elucidates the reaction mechanisms of metal corrosion in aqueous and supercritical fluids and can point to possible remedies.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Recovering high-purity uranyl nitrate from simulated used nuclear fuel dissolver solutions by crystallization: rejecting technetium

The separation of U from Tc and other problematic fission product elements like Mo and Ru, along with Sr, Zr, Cs, and Nd, has been achieved via the crystallization of uranyl nitrate hexahydrate (UNH). Rejection of technetium as pertechnetate anion ( 99 TcO 4 – ) is an especially important feature of this system, as it otherwise tends to follow U (VI) in extractive separations. It also raises the salient question regarding why this oxoanion cannot replace nitrate within the crystalline lattice of UNH. Results showed high-yield (>90 %), high-purity (>99 %) recovery of U as UNH from solutions containing 99 TcO 4 – by simple reduction of temperature from 60°C to 20°C. There was no observable interaction of 99 TcO 4 – with UO 2 2+ . The addition of other cations like, Sr 2+ , Zr 4+ , Cs + , and Nd 3+ , also did not form secondary, contaminant solid phases, leaving the > 99 % of the fission product elements in the mother liquor, while the U was recovered at > 90 %. Similarly, Mo and Ru, when added to the mixture, were shown to behave as the other fission-product elements, remaining in the mother liquor during crystallization. As a result, DFT calculations showed that, despite the higher binding strength of TcO 4 – , HMoO 4 – , and BiO 3 – with the UO 2 2+ cation compared to NO 3 – , the hydrogen-bonding network of the two coordinated ions and four waters of hydration in the UNH crystal structure is the driving force for the high specificity of this separation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Hyperfusogenic Mutations Destabilize the Postfusion Six-Helix Bundle of the Measles Virus Fusion Glycoprotein

Fusion of the host membrane and viral envelope by class I viral fusion proteins is driven by the assembly of a postfusion six-helix bundle formed through antiparallel interactions between N-terminal (HR1) and C-terminal (HR2) heptad-repeat regions. Although mutations in these regions of the measles virus (MeV) fusion (F) glycoprotein are known to promote neuropathogenic and hyperfusogenic phenotypes, their effects on postfusion core stability have not been systematically examined. Here, we combine peptide biophysics and X-ray crystallography to interrogate how mutations within the HR2 domain, present in native neuropathogenic MeV isolates (e.g., L454W and N462K) and laboratory-generated hyperfusogenic variants (e.g., L454M and T461A), influence postfusion 6HB assembly. Circular dichroism (CD) spectroscopy reveals that, with few exceptions, these mutations decrease postfusion core stability, despite their association with enhanced fusion activity. We also report the first crystal structure of the wild-type MeV postfusion core as well as structures of six hyperfusogenic variants, enabling high-resolution comparison of the molecular basis of destabilization. Structural analysis shows that these effects arise from localized perturbations to steric packing, hydrogen bonding networks, and helix-stabilizing interactions within HR2, while the overall 6HB architecture remains conserved. Together, these results indicate that hyperfusogenic mutations are not associated with stabilization of the postfusion state and are instead consistent with models in which hyperfusogenicity arises from a reduction in the energetic barrier to fusion, potentially through effects on prefusion stability or triggering efficiency. These findings establish key sequence-structure–stability relationships governing coiled-coil assembly and provide a framework for the design of HR1- and HR2-based fusion inhibitors.

Genetics↗
DOE OSTI2019

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA-repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light-harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH•) in the dark, despite a rapid FADH• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH• lifetime in the presence of 8-HDF. Millisecond time-resolved ultraviolet-visible spectroscopy showed the red-light-induced formation and decay of an absorbance band at 458 nm concomitant with flavin reduction. Time-resolved Fourier transform infrared (FTIR) spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control flavin protonation, indicating the involvement of N395 in the stabilization of FADH•. Fluorescence spectroscopy revealed a decrease in the energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to 8-HDF deprotonation. Finally, the discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of the antenna, introducing a new concept enabling CraCRY and possibly other bifunctional cryptochromes to fulfill their dual function.

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

Zwitterion Moieties in Polypeptides Synergistically Enhance the Release of Cellulose and Amorphous Polysaccharides from Plant Cell Walls

This study demonstrated that covalently localized zwitterionic moieties in zwitterionic polypeptides (ZIPs) effectively disrupt hydrogen bonds in cellulosic substrates, including filter paper and plant cell wall materials, without significant cytotoxicity. ZIPs with varying densities of zwitterionic side chains were synthesized via the postpolymerization modification of histidinecontaining oligopeptides. The newly developed ZIPs predominantly comprised repeating units with zwitterionically converted side chains. Such ZIPs can cleave multiple hydrogen bonds by anchoring the zwitterionic structure at specific sites, thereby partially dissociating the polysaccharide chains in the cell wall. They are especially effective in dissolving amorphous cellulose, even at low concentrations in aqueous solutions. Importantly, this effect was achieved with minimal cellular toxicity, harnessing the advantages of ionic liquid-like properties while mitigating their high-toxicity limitations. This biofriendly approach to cell wall denaturation highlights a novel method for controlling hydrogen bond networks in polysaccharides and cell walls. These findings indicate a new approach for reducing biomass recalcitrance and developing next-generation biobased materials and fuels derived from plant cell walls.

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

Polymorphism and Negative Linear Compressibility in Pyrazine-d4

Pyrazine (1,4-diazine) is a widely used linker in coordination polymers, molecular magnets, and metal–organic frameworks, yet its solid-state polymorphism is controlled by weak C–H···N interactions. Using variable-temperature and high-pressure neutron diffraction, a previously unrecognized low-temperature transition to phase IV is identified, showing that the form stabilized under pressure can also be accessed below ∼90 K at ambient pressure in the perdeuterated compound. The transition from phase III → IV involves a symmetry-breaking lattice distortion driven by the reorganization of C–H···N hydrogen bonds, accompanied by negative linear compressibility, which is primarily accommodated through the reduction in void-space within the structure. Structural analysis reveals that while the overall monoclinic framework of phase IV is preserved under both temperature and pressure routes, the evolution of hydrogen-bonded network is distinct depending on the pathway taken. These results establish pyrazine as a model molecular solid for studying pressure–temperature polymorphism and demonstrate how weak directional interactions can produce anomalous mechanical responses in organic crystals.

Ridley, Christopher J. [Oak Ridge National Laborat↗
DOE OSTI2025

Affinity for OH – Produces Four-Coordinated Zn 2+ Impurities in Hydrated Amorphous Calcium Carbonate

Using ab initio based molecular dynamics and electronic structure calculations, we show that Zn impurities in hydrated amorphous calcium carbonate (ACC) have a much lower coordination number than other divalent impurities due to covalent interactions between the 3d Zn shell and the oxygen atoms of the carbonate and water groups. Further, the local structure around Zn in ACC, including the predicted low coordination number, is confirmed by X-ray absorption spectroscopy of synthetic Zn-bearing ACC. The strong Zn–O chemical interaction leads to substantial water dissociation and slightly disrupts the hydrogen bonding network. Implications of Zn 2+ incorporation for ACC stability are discussed.

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

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. Here, we have utilized biotin–streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S 112 E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe II complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S 112 E. Two aqua ligands complete the primary coordination sphere of the Fe II center with both involved in hydrogen bond networks within Sav. The corresponding Fe III protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe III protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

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

VUV Photoionization Dynamics and Reactivity of Heterogeneous Water Clusters

This feature focuses on bridging isolated water and bulk water studies. It assembles experiments and theory on water clusters, mainly probed by vacuum ultraviolet (VUV) radiation, and summarizes what the effects are of intermolecular interactions on both the spectroscopy and the VUV-induced processes in water. In particular, it highlights studies of heterogeneous water clusters─those incorporating other molecular species such as naphthalene, methane, formic acid, and glycerol─which serve as model systems to investigate the fundamental roles of water in hydrogen bonding networks, proton transfer, and astrochemical processes. These mixed clusters provide a platform to revisit the stability of protonated water clusters and compile observations of ionization-induced structural rearrangements and fragmentation, especially in systems involving hydroxyl-rich cosolvents. This feature then explores energy transfer mechanisms in molecular clusters, following VUV photoexcitation. It concludes with potential future directions. First, we investigate excited-state dynamics in molecular clusters through direct probing, complementing the synchrotron studies discussed here. Second, exploring gas-phase molecule evaporation from confined spaces and interfaces using advanced spectroscopic techniques sheds light on these ubiquitous, yet currently debated, molecular processes.

Cluster chemistry↗
DOE OSTI2020

Microsolvation in V + (H 2 O) n Clusters Studied with Selected-Ion Infrared Spectroscopy

Gas phase ion-molecule clusters of the form V + (H 2 O) n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit red-shifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V + ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of AAD (acceptor-acceptor-donor) coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly-charged or doubly-charged cation-water clusters. Finally, this indicates that cation identity and charge-site location in the cluster can produce discernible spectral differences for clusters in this size range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Ion Pairing and Molecular Orientation at Liquid/Liquid Interfaces: Self-Assembly and Function

We report that molecular orientation plays a pivotal role in defining the functionality and chemistry of interfaces, yet accurate measurements probing this important feature are few, due, in part, to technical and analytical limitations in extracting information from molecular monolayers. For example, buried liquid/liquid interfaces, where a complex and poorly understood balance of inter- and intramolecular interactions impart structural constraints that facilitate the formation of supramolecular assemblies capable of new functions, are difficult to probe experimentally. Here, we use vibrational sum-frequency generation spectroscopy, numerical polarization analysis, and atomistic molecular dynamics simulations to probe molecular orientations at buried oil/aqueous interfaces decorated with amphiphilic oligomers. We show that the orientation of self-assembled oligomers changes upon the addition of salts in the aqueous phase. The evolution of these structures can be described by competitive ion effects in the aqueous phase altering the orientations of the tails extending into the oil phase. These specific anionic effects occur via interfacial ion pairing and associated changes in interfacial solvation and hydrogen-bonding networks. These findings provide more quantitative insight into orientational changes encountered during self-assembly and pave the way for the design of functional interfaces for chemical separations, neuromorphic computing applications, and related biomimetic systems.

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

Insights into Rotational and Translational Dynamics in Mixtures of Ethylene Glycol and Choline Chloride Using Nuclear Magnetic Resonance Techniques

This work examines molecular dynamics and interactions in ethylene glycol–choline chloride (EG–ChCl) mixtures across 0–33 mol % ChCl, spanning the true eutectic region near 17–20 mol % and the commonly used 1:2 formulation. We combine pulsed-field-gradient (PFG) diffusion, fast-field-cycling (FFC) relaxometry, temperature-dependent 13 C T 1 , and nuclear Overhauser effect spectroscopy (NOESY) to disentangle local from macroscopic dynamics. PFG and FFC show that both translational and average rotational motions largely track the strong increase in viscosity with ChCl content, with ethylene glycol consistently diffusing faster than the choline cation and no global dynamical anomaly at the eutectic composition. More subtle, site-specific composition effects nevertheless emerge. The ratio of the diffusion coefficient of the hydroxyl group of choline to the diffusion coefficient of the methyl group of choline displays a shallow minimum in the 17–25 mol % region, indicating a modest change in how the hydroxyl-bearing end of choline samples the underlying translational motion relative to the methyl groups. 13 C T 1 analysis shows that rotational correlation times at 25 °C generally increase with ChCl, reflecting viscosity-coupled slowing, while the CH 2 –N α site exhibits a small but reproducible deviation from this monotonic trend near the eutectic. NOESY spectra at similar compositions reveal enhanced cross-relaxation between EG and choline protons, consistent with increased headgroup–solvent contact density rather than a wholesale structural rearrangement. Overall, our multitechnique study demonstrates that EG–ChCl dynamics are predominantly viscosity-dominated, with the eutectic region acting as a subtle dynamical crossover where specific choline segments become maximally coupled to the hydrogen-bond network. These insights refine the structure–dynamics picture of choline-chloride DESs and provide practical guidance for tuning composition in electrochemical, separation, and catalytic applications.

diffusion↗
DOE OSTI2022

Chemical Potential Driven Reorganization of Anions between Stern and Diffuse Layers at the Air/Water Interface

We report ion adsorption and transfer at charged interfaces play key roles in various industrial and environmental processes. Molecular scale details of ion-ion, ion-water, and ion-surface interactions are still debated. Complex ions, such as SCN - and SeCN - , are particularly interesting due to their unexpected adsorption trends. Here, we combine vibrational sum frequency generation (VSFG) spectroscopy and surface-sensitive synchrotron X-ray studies to provide a detailed description of SeCN - adsorption at a floating charged monolayer. Polarimetry studies show that the average orientation of SeCN - anions with respect to the surface normal decreases from 45° to 22° with the increasing KSeCN concentration. Interfacial SeCN - coverage saturates at very low bulk concentrations, but their orientational organization, distribution between Stern and diffuse layers, and effects on the hydrogen-bonding network of the interfacial water continue to change with increasing bulk KSeCN concentration. These results show that the increasing chemical potential may lead to further reorganization of the adsorbed ions, even though the total interfacial ion population does not change. The reorganization of the interfacial ions and the water may be very important in chemical separations of heavy metals, where metal-anion complexes drive the selective ion transfer at aqueous interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗