Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “hydrogen 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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Probing Complex Chemical Processes at the Molecular Level with Vibrational Spectroscopy and X-ray Tools

Understanding the origins of structure and bonding at the molecular level in complex chemical systems spanning magnitudes in length and time is of paramount interest in physical chemistry. Here, we have coupled vibrational spectroscopy and X-ray based techniques with a series of microreactors and aerosol beams to tease out intricate and sometimes subtle interactions, such as hydrogen bonding, proton transfer, and noncovalent interactions. This allows for unraveling the self-assembly of arginine-oleic acid complexes in an aqueous solution and growth processes in a metal–organic framework. Terahertz and infrared spectroscopy provide an intimate view of the hydrogen-bond network and associated phase changes with temperature in neopentyl glycol. The hydrogen-bond network in aqueous glycerol aerosols and levels of protonation of nicotine in aqueous aerosols are visualized. Future directions in probing the hydrogen-bond networks in deep eutectic solvents and organic frameworks are described, and we suggest how X-ray scattering coupled to X-ray spectroscopy can offer insight into the reactivity of organic aerosols.

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

A High Energy X-ray Diffraction Study of Amorphous Indomethacin

Amorphous pharmaceuticals often possess a wide range of molecular conformations and bonding arrangements. The x-ray pair distribution function (PDF) method is a powerful technique for the characterization of variations in both intra-molecular and inter-molecular packing arrangements. Here, the x-ray PDF of amorphous Indomethacin is shown to be particularly sensitive to the preferred orientations of the chlorobenzyl ring found in isomers in the crystalline state. In some cases, the chlorobenzyl ring has no preferred torsional angle in the amorphous form, while in others evidence of distinct isomer orientations are observed. Amorphous samples with no preferred torsion angles of the chlorobenzyl ring are found to favor enhanced inter-molecular hydrogen bonding, and this is reflected in the intensity of the first sharp diffraction peak. These significant variations in structure rule out amorphous Indomethacin as a possible standard for x-ray PDF measurements. At high humidity, time resolved PDF's for >40 h reveal water molecules forming hydrogen bonds with Indomethacin molecules. Finally, a simple linear hydrogen bond model indicates that water molecules in the wet amorphous form have similar hydrogen bond strengths to those found between Indomethacin dimers or chains in the dry amorphous form.

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

Understanding Redox Organic Behavior in Deep Eutectic Solvents: Considerations for Molecular Design

Electrolytes based on deep eutectic solvents (DESs) coupled with redox active organic molecules have shown potential as a versatile and energy dense electrochemical energy storage system. However, progress in these systems has been held back by a lack of understanding of the irregular behavior displayed when redox active organic molecules are transitioned from other solvent systems. In this work, the hydrogen bonding characteristics of a series of redox organic molecules were investigated through infrared spectroscopy and molecular modeling. New understanding of these interactions was then used to explain their electrochemical behavior in a DES electrolyte. A model was used to predict the behavior of new derivatives towards the design of an optimized redox organic-DES system. Hydrogen bonding between the redox molecules and the solvent was found to significantly shift the potential of a redox reaction more positive when a hydrogen bond forms at the redox active site. It was predicted that functionalizing a molecule with electron withdrawing groups to lower the electron density of the redox active functional group lowers the strength of the hydrogen bond and thus alleviates the undesirable potential shift. This hypothesis was demonstrated by the addition of nitro groups to fluorenones.

25 ENERGY STORAGE↗
DOE OSTI2024

Crystal structure of ractopamine hydrochloride, C 18 H 24 NO 3 Cl

The crystal structure of ractopamine hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Ractopamine hydrochloride crystallizes in space groupPbca(#61) witha= 38.5871(49),b= 10.7691(3),c= 8.4003(2) Å,V= 3490.75(41) Å 3 , andZ= 8. The ractopamine cation contains two chiral centers, and the sample consists of a mixture of the S,S/R,R/S,R and R,S forms. Models for the two diastereomers S,S and S,R were refined, and yielded equivalent residuals, but the S,R form is significantly lower in energy. The crystal structure consists of layers of molecules parallel to thebc-plane. In each structure one of the H atoms on the protonated N atom acts as a donor in a strong discrete N–H⋯Cl hydrogen bond. Hydroxyl groups act as donors in O–H⋯Cl and O–H⋯O hydrogen bonds. Both the classical and C–H⋯Cl and C–H⋯O hydrogen bonds differ between the forms, helping to explain the large microstrain observed for the sample. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗
DOE OSTI2021

Visible light enables catalytic formation of weak chemical bonds with molecular hydrogen

The synthesis of weak chemical bonds at or near thermodynamic potential is a fundamental challenge in chemistry, with applications ranging from catalysis to biology to energy science. Proton-coupled electron transfer using molecular hydrogen is an attractive strategy for synthesizing weak element–hydrogen bonds, but the intrinsic thermodynamics presents a challenge for reactivity. Here we describe the direct photocatalytic synthesis of extremely weak element–hydrogen bonds of metal amido and metal imido complexes, as well as organic compounds with bond dissociation free energies as low as 31 kcal mol –1 . Key to this approach is the bifunctional behaviour of the chromophoric iridium hydride photocatalyst. Activation of molecular hydrogen occurs in the ground state and the resulting iridium hydride harvests visible light to enable spontaneous formation of weak chemical bonds near thermodynamic potential with no by-products. In conclusion, photophysical and mechanistic studies corroborate radical-based reaction pathways and highlight the uniqueness of this photodriven approach in promoting new catalytic chemistr

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

Descriptors of water aggregation

For this work, we rely on a total of 23 (cluster size, 8 structural, and 14 connectivity) descriptors to investigate structural patterns and connectivity motifs associated with water cluster aggregation. In addition to the cluster size n (number of molecules), the 8 structural descriptors can be further categorized into (i) one-body (intramolecular): covalent OH bond length (r OH ) and HOH bond angle (θ HOH ), (ii) two-body: OO distance (r OO ), OHO angle (θ OHO ), and HOOX dihedral angle ($\phi$ HOOX ), where X lies on the bisector of the HOH angle, (iii) three-body: OOO angle (θ OOO ), and (iv) many-body: modified tetrahedral order parameter (q) to account for two-, three-, four-, five-coordinated molecules (q m , m = 2, 3, 4, 5) and radius of gyration (R g ). The 14 connectivity descriptors are all many-body in nature and consist of the AD, AAD, ADD, AADD, AAAD, AAADD adjacencies [number of hydrogen bonds accepted (A) and donated (D) by each water molecule], Wiener index, Average Shortest Path Length, hydrogen bond saturation (% HB), and number of non-short-circuited three-membered cycles, four-membered cycles, five-membered cycles, six-membered cycles, and seven-membered cycles. We mined a previously reported database of 4 948 959 water cluster minima for (H 2 O) n , n = 3–25 to analyze the evolution and correlation of these descriptors for the clusters within 5 kcal/mol of the putative minima. It was found that r OH and % HB correlated strongly with cluster size n, which was identified as the strongest predictor of energetic stability. Marked changes in the adjacencies and cycle count were observed, lending insight into changes in the hydrogen bond network upon aggregation. A Principal Component Analysis (PCA) was employed to identify descriptor dependencies and group clusters into specific structural patterns across different cluster sizes. The results of this study inform our understanding of how water clusters evolve in size and what appropriate descriptors of their structural and connectivity patterns are with respect to system size, stability, and similarity. The approach described in this study is general and can be easily extended to other hydrogen-bonded systems.

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

Adsorption of furan, hexanoic acid, and alkanes in a hierarchical zeolite at reaction conditions: Insights from molecular simulations

Hierarchical zeolites containing both micropores and mesopores are valuable catalysts for facilitating reactions of large molecules. Furan acylation by fatty acids is a promising reaction for valorizing biomass, and the self-pillared pentasil (SPP) zeolite was found to perform particularly well for this reaction. To better understand the distribution of molecules in hierarchical zeolites at the elevated temperature (T = 523 K) and the elevated pressure (p >1 bar) associated with typical reaction conditions, unary and binary adsorption were predicted using Monte Carlo simulations in the isothermal–isobaric Gibbs ensemble. Adsorption of six species (furan, hexanoic acid, -hexane, -decane, -tetradecane, and 3,6-diethyloctane) was investigated from vapor, liquid, and supercritical phases, and loadings into the micropores, onto the mesopore surface, and in the mesopore interior of SPP were obtained. As pressure increases, -alkanes fill the micropores before loading the surface and then the interior of the mesopore, while furan and hexanoic acid adsorb strongly to the mesopore surface due to hydrogen bonding interactions with surface silanols. Hydrogen bonding interactions also draw hexanoic acid molecules in the micropore region toward the pore mouths, so their carboxylic acid group forms H-bonds with silanols, while the alkyl tails interact with the micropore walls. Mesopore condensation is observed for molecules below their critical point, and occurs when the Gibbs free energy of transfer into the mesopore interior and onto the mesopore surface converge. When hexanoic acid adsorption occurs in the presence of alkane solvents, then the selectivity and spatial distribution of hexanoic acid in the micropores and on the surface can be tuned by adjusting the fluid pressure and the alkane length and/or branching.

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

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O 2 •– . The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn 3+ and Mn 2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pK a s, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn 3+ and Mn 2+ redox states.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Quantitation of buried contamination by use of solvents. Part 1: Solvent degradation of amine cured epoxy resins

The solubility and/or swelling of cured epoxy resins was studied using the solubility parameter method. Determination of solubility parameters were found in order to select solvents for solvent-assisted degradation of cured epoxy polymers used in spacecraft. A method for improving recovery of seeded spores is suggested for assay of buried contaminants. Three commercial epoxy resins were cured using four different alkyl amines. For each resin-amine combination, three levels of amine were used, corresponding to 1/3, 2/3, and all of the amine required to react with the oxirane groups of the resin. The solubility parameters of the 36 resulting model compounds were determined in poorly and moderately hydrogen-bonded solvents. No strongly hydrogen-bonded solvents caused dissolution or swelling. The tolerance of cured resins is discussed in terms of polymer structure.

Rheineck, A. E.↗
NASA NTRS1986

Base pairing and base mis-pairing in nucleic acids

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Wang, A. H. J.↗
DOE OSTI2020

Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

Lucina pectinata live in high concentrations of hydrogen sulfide (H 2 S) and contains one hemoglobin, Hemoglobin I (HbI), transporting H 2 S and two hemoglobins, Hemoglobin II (HbII) and Hemoglobin (HbIII), transferring dioxygen to symbionts. HbII and HbIII contain B10 tyrosine (Tyr) and E7 glutamine (Gln) in the heme pocket generating an efficient hydrogen bonding network with the (HbII-HbIII)-O 2 species, leading to very low ligand dissociation rates. The results indicate that the oxy-hemeprotein is susceptible to pH from 4 to 9, at acidic conditions, and as a function of the potassium ferricyanide concentration, 100% of the met-aquo derivative is produced. Without a strong oxidant, pH 5 generates a small concentration of the met-aquo complex. The process is accelerated by the presence of salts, as indicated by the crystallization structures and UV–Vis spectra. The results suggest that acidic pH generates conformational changes associated with B10 and E7 heme pocket amino acids, weakening the (HbII-HbIII)-O 2 hydrogen bond network. The observation is supported by X-ray crystallography, since at pH 4 and 5, the heme-Fe tends to oxidize, while at pH 7, the oxy-heterodimer is present. Additionally, conformational changes are observed at higher pH by the presence of a 605 nm transition associated with the iron heme-Tyr interaction. Therefore, pH is one crucial factor regulating the (HbII-HbIII)-O 2 complex hydrogen-bonding network. Thus, it can be proposed that the hydrogen bonding adjustments between the heme bound O 2 and the Tyr and Gln amino acids contribute to oxygen dissociation from the (HbII-HbIII)-O 2 system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1985

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

NASA Discipline Exobiology↗
DOE OSTI2022

Superhydrophilicity of $α$-alumina surfaces results from tight binding of interfacial waters to specific aluminols

Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Here, contact angles at the alumina (0001) and ($11\bar{2}0$) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.

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

AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials

Intermolecular interactions are critical to many chemical phenomena, but their accurate computation using ab initio methods is often limited by computational cost. The recent emergence of machine learning (ML) potentials may be a promising alternative. Useful ML models should not only estimate accurate interaction energies but also predict smooth and asymptotically correct potential energy surfaces. However, existing ML models are not guaranteed to obey these constraints. Indeed, systemic deficiencies are apparent in the predictions of our previous hydrogen-bond model as well as the popular ANI-1X model, which we attribute to the use of an atomic energy partition. As a solution, we propose an alternative atomic-pairwise framework specifically for intermolecular ML potentials, and we introduce AP-Net—a neural network model for interaction energies. The AP-Net model is developed using this physically motivated atomic-pairwise paradigm and also exploits the interpretability of symmetry adapted perturbation theory (SAPT). We show that in contrast to other models, AP-Net produces smooth, physically meaningful intermolecular potentials exhibiting correct asymptotic behavior. Initially trained on only a limited number of mostly hydrogen-bonded dimers, AP-Net makes accurate predictions across the chemically diverse S66x8 dataset, demonstrating significant transferability. On a test set including experimental hydrogen-bonded dimers, AP-Net predicts total interaction energies with a mean absolute error of 0.37 kcal mol−1, reducing errors by a factor of 2–5 across SAPT components from previous neural network potentials. The pairwise interaction energies of the model are physically interpretable, and an investigation of predicted electrostatic energies suggests that the model “learns” the physics of hydrogen-bonded interactions.

Glick, Zachary L. (ORCID:0000000309002849)↗
DOE OSTI2023

Crystal structure of oxibendazole, C 12 H 15 N 3 O 3

The crystal structure of oxibendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxibendazole crystallizes in space group C2/c (#15) with a = 23.18673(22), b = 5.35136(5), c = 19.88932(13) Å, β = 97.0876(9)°, V = 2449.018(17) Å 3 , and Z = 8. The structure consists of hydrogen-bonded layers of planar molecules parallel to the bc-plane. Strong N–H∙∙∙N hydrogen bonds link the molecules into dimers, with a graph set R2,2(8). N–H∙∙∙O hydrogen bonds further link these dimers into layers parallel to the bc-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structure of elvitegravir Form II, C 23 H 23 ClFNO 5

The crystal structure of elvitegravir Form II has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Elvitegravir Form II crystallizes in space group P2 1 (#4) with a = 11.54842(7), b = 14.04367(5), c = 13.33333(8) Å, β = 90.0330(6)°, V = 2162.427(14) Å 3 , and Z = 4. The crystal structure consists of alternating layers of parallel molecules perpendicular to the b-axis. The mean planes of the oxoquinoline ring systems in molecules 1 and 2 are 1(22)-1 and -1(22)1. Between the stacks are layers of the halogenated phenyl rings. These exhibit herringbone stacking. In each molecule, the carboxylic acid group forms a strong intramolecular O–H∙∙∙O hydrogen bond to the nearby carbonyl group. The hydroxyl group of each molecule forms a strong hydrogen bond to the carbonyl group of the carboxylic acid of the other molecule. These O–H∙∙∙O hydrogen bonds link the molecules into dimers, with a graph set R2,2(18) > a > c. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Constructing Water‐Stable Porous Organic Salts via Suppressed Proton Integration Using Fluorinated Tetrazole Tectons

Porous organic salts (POSs) are an emerging class of materials with ordered ionic architectures, offering excellent proton transfer and water uptake properties. However, conventional POS synthesis via strong acid–base neutralization (e.g., ─SO₃H and ─NH₂) leads to extensive hydrogen bonding with water, compromising stability in aqueous and water-lean environments. Here, we address this challenge by designing POSs with hydrophobic porous channels and minimal hydrogen bonding formation. Our key innovation is the use of fluorinated tetrazole as a weak acid tecton and a tetra-substituted imidazole precursor devoid of active protons as the base. Single-crystal analysis and computational modeling reveal that the structural integrity of the synthesized POSs arises primarily from cation–anion interactions, with water confined as clusters in the pores, independent of hydrogen bonding with the scaffold. Robustness of the POS structure under aqueous and water-lean conditions is confirmed by X-ray and neutron scattering, as well as computational modeling, confirming preserved packing and crystal structures. The stability of POS is further demonstrated in aqueous iodine capture, with imidazolium cations and C–F functionalizations serving as strong adsorption sites. As a result, the approach developed herein further pushes the boundary of POS materials to withstand both aqueous and water-lean conditions.

Fluorinated tecton↗
DOE OSTI2025

Formation of Water Networks on Anionic Perylene

We present infrared photodissociation spectra of hydrated perylene anion clusters with up to four water molecules, as well as electronic structure calculations based on density functional theory. Water molecules form weak hydrogen bonds to the π system of the perylene anion. For clusters with more than one water molecule, water−water hydrogen bonds are formed, which generally appear to be stronger than water−π hydrogen bonds, especially for the trihydrate and tetrahydrate. The resulting water networks exist as water subclusters on the surface of the carbon frame of perylene. Here, we observe temperature-dependent dynamic effects, which highlight large amplitude motions of the water network and the shallowness of the potential energy surfaces governing the structures of these clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗