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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 OSTI2020

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Understanding the Chemical Complexity of Multicomponent Systems: Uranium Polyoxometalates as Nanosorbents

The overarching objective of this project was to develop a molecular-scale understanding of chemical interactions of the transuranic (TRU) elements with uranyl-based polyoxometalate nanoclusters (UPOMs). The specific goals that supported this overarching objective were to: (i) quantify TRU interactions with UPOMs as a function of TRU, carbonate, and UPOM concentration, pH, and temperature; (ii) examine the molecular-level bonding environment of TRU-UPOM complexes; and (iii) develop a rate expression capable of describing the sorption and reduction of TRU by UPOMs. The published literature suggests several potential interactions can occur in TRU-UPOM systems: (i) encapsulation of TRU and coordination with the internal ‘-yl’ oxygens of the UPOM, (ii) coordination of TRU with the external ‘-yl’ oxygens of the UPOM, and (iii) coordination of TRU with the bridging ligands (e.g., peroxo, hydroxo, oxalate) of the UPOM. The latter two may induce aggregation of the UPOMs. The concept of encapsulation is demonstrated by the X-ray diffraction structure of crystallized U 20 , which reveals a Na + cation under each pentagonal face (Sigmon et al., 2009). Computational modeling shows that, while the negative charge of U 20 is spread among all the oxygen atoms, the internal ‘-yl’ oxygens host the most negative charge (Miro and Bo, 2012). This negative charge is reduced through the complexation of the templating sodium ions in the interior of the UPOM. Furthermore, Nyman et al. (2011) shows that cesium can exit through the pentagonal window of U 28 in the aqueous phase, suggesting that the TRU elements, which are smaller than cesium, may be capable of entering a UPOM through these windows in an exchange reaction. Under this project, we focused on hafnium, neptunium, and plutonium interactions with UPOMs.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

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

Dynamic metal-linker bonds in metal–organic frameworks

Metal-linker bonds serve as the “glue” that binds metal ions to multitopic organic ligands in the porous materials known as metal–organic frameworks (MOFs). Despite ample evidence of bond lability in molecular and polymeric coordination compounds, the metal-linker bonds of MOFs were long assumed to be rigid and static. Given the importance of ligand fields in determining the behaviour of metal species, labile bonding in MOFs would help explain outstanding questions about MOF behaviour, while providing a design tool for controlling dynamic and stimuli-responsive optoelectronic, magnetic, catalytic, and mechanical phenomena. Here, in this work, we present emerging evidence that MOF metal-linker bonds exist in dynamic equilibria between weakly and tightly bond conformations, and that these equilibria respond to guest–host chemistry, drive phase change behavior, and exhibit size-dependence in MOF nanoparticles.

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

Bridging the Void: Halogen Bonding and Aromatic Interactions to Program Luminescence and Electronic Properties of π -Conjugated Materials in the Solid State

π-Conjugated materials are promising candidates for emerging organic optoelectronic devices empowered by molecular design. The unsolved challenges of predicting and controlling their packing as solids, central to their properties and performance, currently limits their practical application. As noncovalent interactions drive packing, control over such interactions are critical to bridging from chemical structure to functional properties. In molecular crystals, halogen bonding and interactions of aromatic rings have emerged as versatile tools for noncovalent control with tailored luminescence and electronic properties. Here, we describe how the interplay of these directional and tunable interactions can engineer properties, including stimuli-responsive behavior. Specifically, halogen bonding can provide robust designs for directing 2D molecular assembly, whereas the intentional interactions of aromatic rings can yield metastable, switchable packing modes, as well as programmed stacking between layers of chromophores. Examples, herein, demonstrate clear relationships between assembly by design and resulting solid-state properties, and strategies presented offer guidance for future designs of π-conjugated molecular materials using specific aromatic interactions and halogen bonding.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Hydrogen bonds and dispersion forces serving as molecular locks for tailored Group 11 bis(amidine) complexes

A flexible polydentate bis(amidine) ligand LH 2 , LH 2 = {CH 2 NH( t Bu)C=N-2-(6-MePy)} 2 , operates as a molecular lock for various coinage metal fragments and forms the dinuclear complexes [LH 2 (MCl) 2 ], M = Cu (1), Au (2), the coordination polymer [{(LH 2 ) 2 (py) 2 (AgCl) 3 }(py) 3 ] n (3), and the dimesityl-digold complex [LH 2 (AuMes) 2 ] (4) by formal insertion of MR fragments (M = Cu, Ag, Au; R = Cl, Mes) into the N–H∙∙∙N hydrogen bonds of LH 2 in yields of 43–95%. Complexes 1, 2, and 4 adopt C 2 -symmetrical structures in the solid state featuring two interconnected 11-membered rings that are locked by two intramolecular N–H∙∙∙R–M hydrogen bonds. QTAIM analyses of the computational geometry-optimized structures 1a, 2a, and 4a reveal 13, 11, and 22 additional bond critical points, respectively, all of which are related to weak intramolecular attractive interactions, predominantly representing dispersion forces, contributing to the conformational stabilization of the C2-symmetrical stereoisomers in the solid state. Variable-temperature 1 H NMR spectroscopy in combination with DFT calculations indicate a dynamic conformational interconversion between two C 2 -symmetrical ground state structures in solution (ΔG ‡ c = 11.1–13.8 kcal mol –1 ), which is accompanied by the formation of an intermediate possessing C i symmetry that retains the hydrogen bonds.

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

The Molecular Structures of Liquid and Glassy Nifedipine and Felodipine and Their Incorporation into PVP

Background: Amorphous drug formulations are commonly used to improve the solubility and bioavailability of poorly soluble molecular pharmaceuticals, yet less is known about their molecular conformations and local bonding interactions than their crystalline phases. Methods: High-energy X-ray diffraction structure factor measurements have been made on liquid and glassy nifedipine (NIF), felodipine (FEL), NIF 1:3 polyvinylpyrrolidone (PVP), and FEL 1:3 PVP wt.% mixtures. The corresponding X-ray pair distribution functions have been interpreted using empirical potential structure refinement using different models and density functional theory conformer calculations. Results: In both NIF and FEL, the NH···O inter-molecular hydrogen bonds between the pyridyl nitrogen and ester carbonyls are found to be considerably weaker than those observed in the crystalline polymorphs. For nifedipine, it is proposed that either inter-molecular NH…ON nitro bonds are present and/or a fraction (<20%) of conformational changes, with the aryl ring flipped, occur in the liquid state. For felodipine, the models indicate significant disorder associated with the methyl and ethyl side chains in the liquid state, with the main peak intensity at 3.0 Å arising from intra-molecular Cl-Cl atom pairs. When nifedipine molecules are incorporated into PVP, our models show they possess stronger NH···O bonds to the PVP polymer than felodipine molecules, which have stronger affinity for bonding to the polymer than to other felodipine molecules. Conclusions: The amorphous forms of both NIF and FEL show much weaker hydrogen bonding than found in their crystalline phases. Liquid NIF also exhibits configurations which are not observed in the crystal phases.

Amorphous Solid Dispersion↗
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 OSTI2020

Molecular growth upon ionization of van der Waals clusters containing HCCH and HCN is a pathway to prebiotic molecules

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain N∙∙∙H bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon–carbon and carbon–nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.

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

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structure-antioxidant activity relationships, QSAR, DFT calculation, and mechanisms of flavones and flavonols

DFT calculations were performed on nine flavones and flavonols to explain their high antioxidant activity and variations in their activity. Conformational analysis showed that only flavonols with 3-OH directed toward the B-ring are nonplanar; however, flavones and resulted radicals are planar. Hydroxyl group eligible for dissociation is the one with ortho OH directed toward it; otherwise, one of B-ring (in 2′ or 4′-position) hydroxyl group. There are two main factors responsible for stabilizing the resulted radicals and lowering the bond dissociation energy and hence there were found well correlated with the experimental activity. First, driving force resulted from the conversion of nonplanar flavonols to planar radicals accompanied by resonance toward the carbonyl group and H-bond formation with 3-OH and second, radical stabilization by H-bond with ortho hydroxyl group with resonance toward carbonyl or pyrone oxygen. All resonance and H-bonds were confirmed by spin density, bond length, and molecular orbital calculations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Molecular dynamics study on interface formation and bond strength of impact-welded Mg-steel joints

It was recently demonstrated that the vaporizing foil actuator welding (VFAW) method can directly join immiscible magnesium and steel alloys without coating or a third chemical element based intermetallic compound layer. The VFAW Mg/steel joint exhibits a mixed interface layer of up to 200μm thickness consisting of Mg matrix and Fe particles. Computer simulations have suggested the formation of the interlayer is from the high-velocity frictional shearing between the Mg/steel substrates during the oblique impact in the VFAW process. This paper investigates the formation of Mg-Fe interlayer under VFAW condition with different shearing velocities using molecular dynamics (MD) model, and studies the bonding strength under different scenarios. Finally, the results elucidate the critical role of shearing velocity and surface roughness in achieving Mg/Fe joint.

36 MATERIALS SCIENCE↗
DOE OSTI2023

New value of old knowledge: sulphur-based GaAs surface passivation and potential GaAs application in molecular electronics and spintronics

GaAs is well known for its extremely high electron mobility and direct band gap. Owing to the technological advances in silicon-based technology, GaAs has been limited to niche areas. This paper discusses the application of GaAs in molecular electronics and spintronics as a potential field for considering this amazing but challenging material. GaAs is challenging because its surface is characterized by a high density of surface states, which precludes the utilization of this semiconducting material in mainstream devices. Sulfur(S)-based passivation has been found to be significantly useful for reducing the effect of dangling bonds and was researched thoroughly. GaAs applications in molecular spintronics and electronics can benefit significantly from prior knowledge of GaAs and S interactions because S is a popular functional group for bonding molecular device elements with different semiconductors and metals. In this article, the problem associated with the GaAs surface is discussed in a tutorial form. A wide variety of surface passivation methods has been briefly introduced. We attempted to highlight the significant differences in the S-GaAs interactions for different S passivation methods. We also elaborate on the mechanisms and atomic-scale understanding of the variation in surface chemistry and reconstruction due to various S passivation methods. It is envisioned that GaAs and thiol-terminated molecule-based novel devices can exhibit innovative device characteristics and bring the added advantage of S-based passivation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

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

Enzymatic Nitrogen Insertion into Unactivated C–H Bonds

Selective functionalization of aliphatic C–H bonds, ubiquitous in molecular structures, could allow ready access to diverse chemical products. While enzymatic oxygenation of C–H bonds is well established, the analogous enzymatic nitrogen functionalization is still unknown; nature is reliant on pre-oxidized compounds for nitrogen incorporation. Likewise, synthetic methods for selective nitrogen derivatization of unbiased C–H bonds remain elusive. In this work, new-to-nature heme-containing nitrene transferases were used as starting points for the directed evolution of enzymes to selectively aminate and amidate unactivated C(sp3)–H sites. The desymmetrization of methyl- and ethylcyclohexane with divergent site selectivity is offered as demonstration. The evolved enzymes in these lineages are highly promiscuous and show activity towards a wide array of substrates, providing a foundation for further evolution of nitrene transferase function. Computational studies and kinetic isotope effects (KIEs) are consistent with a stepwise radical pathway involving an irreversible, enantiodetermining hydrogen atom transfer (HAT), followed by a lower-barrier diastereoselectivity determining radical rebound step. In-enzyme molecular dynamics (MD) simulations reveal a predominantly hydrophobic pocket with favorable dispersion interactions with the substrate. Here, by offering a direct path from saturated precursors, these enzymes present a new biochemical logic for accessing nitrogen-containing compounds.

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

Discovery of an Interlocked and Interwoven Molecular Topology in Nanocarbons via Dynamic C–C Bond Formation

Topologically complex carbon nanostructures are an exciting but largely unexplored class of materials due to their challenging synthesis. Previous methods are low yielding because they rely on irreversible C sp 2 −C sp 2 bond formation, which necessitates complex templating strategies to enforce entanglement. Here, reversible zirconocene coupling of alkynes is developed as a new method to access complex molecular topologies, where dynamic C−C bond formation facilitates entanglement under thermodynamic control, allowing the use of simple precursors without the need for preassembly. This strategy enables the scalable, high-yield synthesis of three topologically distinct nanocarbons, including the serendipitous discovery of a structure containing a new topological motif that was not previously identified or realized synthetically. This motif, consisting of an unusual combination of interlocking and interweaving, was recognized to be generalizable to a new topological class of molecules, introduced here as perplexanes.

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

Water-mediated ion transport in an anion exchange membrane

Water is a critical component in polyelectrolyte anion exchange membranes (AEMs). It plays a central role in ion transport in electrochemical systems. Gaining a better understanding of molecular transport and conductivity in AEMs has been challenged by the lack of a general methodology capable of capturing and connecting water dynamics, water structure, and ionic transport over time and length scales ranging from those associated with individual bond vibrations and molecular reorientations to those pertaining to macroscopic AEM performance. In this work, we use two-dimensional infrared spectroscopy and semiclassical simulations to examine how water molecules are arranged into successive solvation shells, and we explain how that structure influences the dynamics of bromide ion transport processes in polynorbornene-based materials. We find that the transition to the faster transport mechanism occurs when the reorientation of water molecules in the second solvation shell is fast, allowing a robust hydrogen bond network to form. Our findings provide molecular-level insights into AEMs with inherent transport of halide ions, and help pave the way towards a comprehensive understanding of hydroxide ion transport in AEMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗