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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Completely Multipolar Model for Many-Body Water–Ion and Ion–Ion Interactions

This work constructs an advanced force field, the Completely Multipolar Model (CMM), to quantitatively reproduce each term of an energy decomposition analysis (EDA) for aqueous solvated alkali metal cations and halide anions and their ion pairings. We find that all individual EDA terms remain well-approximated in the CMM for ion-water and ion-ion interactions, except for polarization, which shows errors due to the partial covalency of ion interactions near their equilibrium. We quantify the onset of the dative bonding regime by examining the change in molecular polarizability and Mayer bond indices as a function of distance, showing that partial covalency manifests by breaking the symmetry of atomic polarizabilities while strongly damping them at short-range. This motivates an environment-dependent atomic polarizability parameter that depends on the strength of the local electric field experienced by the ions to account for strong damping, with anisotropy introduced by atomic multipoles. The resulting CMM model for ions provides accurate dimer surfaces and three-body polarization and charge transfer compared to EDA, and shows excellent performance on various ion benchmarks including vibrational frequencies and cluster geometries.

Heindel, Joseph P↗
DOE OSTI2024

Revealing the Reaction Path of UVC Bond Rupture in Cyclic Disulfides with Ultrafast X-ray Scattering

Disulfide bonds are ubiquitous molecular motifs that influence the tertiary structure and biological functions of many proteins. Yet it is well known that the disulfide bond is photolabile when exposed to UVC radiation. The deep-UV induced S-S bond fragmentation kinetics on very fast time scales are especially pivotal to fully understand the photostability and photodamage repair mechanisms in proteins. In 1,2-dithiane, the smallest saturated cyclic molecule that mimics biologically active species with S-S bonds, we investigate the photochemistry upon 200 nm excitation by femtosecond time-resolved X-ray scattering in the gas phase using an X-ray free electron laser. In the femtosecond time domain, we discover a very fast reaction that generates molecular fragments with one and two sulfur atoms. On picosecond and nanosecond timescales, a complex network of reactions unfolds that, ultimately, completes the sulfur dissociation from the parent molecule.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Influences of Hydrogen Bonding-Based Stabilization of Bolaamphiphile Layers on Molecular Diffusion within Organic Nanotubes Having Inner Carboxyl Groups

This paper reports molecular diffusion behavior in two bolaamphiphile-based organic nanotubes having inner carboxyl groups with different inner dimeters (10 and 20 nm) and wall structures, COOH-ONT 10nm and COOH-ONT 20nm , using imaging fluorescence correlation spectroscopy (imaging FCS). Here, the results were compared to those previously obtained in a similar nanotube with inner amine groups (NH 2 -ONT 10nm ). COOH-ONT 10nm , as with NH 2 -ONT 10nm , were formed from a rolled bolaamphiphile layer incorporating triglycine moieties, whereas COOH-ONT 20nm consisted of four stacks of triglycine-free bolaamphiphile layers. Imaging FCS measurements were carried out for anionic sulforhodamine B (SRB), zwitterionic/cationic rhodamine B (RB) and cationic rhodamine-123 (R123) diffusing within ONTs (1–9 µm long) at different pH (3.4–8.4) and ionic strengths (1.6–500 mM). Diffusion coefficients (D) of these dyes in the ONTs were very small (0.01–0.1 µm 2 /s), reflecting the significant contributions of molecule-nanotube interactions to diffusion. The D of SRB was larger at higher pH and ionic strength, indicating the essential role of electrostatic repulsion that was enhanced by the deprotonation of the inner carboxyl groups. Importantly, the D of SRB was virtually independent of nanotube inner diameter and wall structure, indicating the diffusion of the hydrophilic molecule was controlled by short timescale adsorption/desorption processes onto the inner surface. In contrast, pH effects on D were less clear for relatively hydrophobic R123 and RB, suggesting the significant contributions of non-Coulombic interactions. Interestingly, the diffusion of these molecules in COOH-ONT 20nm was slower than in COOH-ONT 10nm . Slower diffusion in COOH-ONT20nm was attributable to relatively efficient partitioning of the hydrophobic dyes into the bolaamphiphile layers, which was reduced in COOH-ONT 10nm due to the stabilization of its layer by polyglycine-II-type hydrogen bonding networks. These results show that, by tuning the bolaamphiphile structures and their intermolecular interactions, unique environments can be created within the nanospaces for enhanced molecular separations and reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Quantum mechanics based non-bonded force field functions for use in molecular dynamics simulations of materials and systems: The nitrogen and oxygen columns

Accurate Force Fields (FFs) are essential for Molecular Dynamics (MD) simulations of the dynamics of realistic materials in terms of atomic-level interactions. The FF parameters of short-range valence interactions can be derived through Quantum Mechanical (QM) calculations on model systems practical for QM (<300 atoms). Similarly, the dynamic electrostatic interactions can be described with methods such as QEq or PQEq that allow charges and polarization to adjust dynamically. However, accurately extracting long-range van der Waals (vdW) interactions from QM calculations poses challenges due to the absence of a definitive method to distinguish between the different energetic components of electrostatics, polarization, vdW, hydrogen bonding, and valence interactions. To do this we use the Perdew–Burke–Ernzerhof flavor of Density Functional Theory, including empirical D3 vdW corrections, to predict the Equation of State for each element (keeping any covalent bonds fixed), from which we obtain the two-body vdW nonbond potential. Here, we extend these calculations to include non-bonded parameters for the N and O columns of the periodic table so that we now describe columns 15 (N), 16 (O), 17 (F), and 18 (Ne) of the periodic table. For these 20 elements, we find that the two-body vdW potentials can all be mapped to a single universal two-body curve, with just three scaling parameters: Re, De, and L. We refer to this as the Universal NonBond (UNB) potential. We expect this to be useful for new MD simulations and a helpful starting point to obtain UNB parameters for the remainder of the periodic table.

Chemistry↗
DOE OSTI2020

Molecular Interaction Regulates the Performance and Longevity of Defect Passivation for Metal Halide Perovskite Solar Cells

Defect passivation constitutes one of the most commonly used strategies to fabricate highly efficient perovskite solar cells (PSCs). However, the durability of the passivation effects under harsh operational conditions has not been extensively studied regardless of the weak and vulnerable secondary bonding between the molecular passivation agents and perovskite crystals. Here, we incorporated strategically designed passivating agents to investigate the effect of their interaction energies on the perovskite crystals and correlated these with the performance and longevity of the passivation effects. We unraveled that the passivation agents with a stronger interaction energy are advantageous not only for effective defect passivation but also to suppress defect migration. The prototypical PSCs treated with the optimal passivation agent exhibited superior performance and operational stability, retaining 81.9 and 85.3% of their initial performance under continuous illumination or nitrogen at 85 °C after 1008 h, respectively, while the reference device completely degraded during that time. Furthermore, this work provides important insights into designing operationally durable defect passivation agents for perovskite optoelectronic devices.

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

Dialing in Direct Air Capture of CO 2 by Crystal Engineering of Bis-iminoguanidines

Direct air capture (DAC) technologies that extract carbon dioxide from the atmosphere via chemical processes have the potential to restore the atmospheric CO 2 concentration to an optimal level. This study elucidates structure-property relationships in DAC by crystallization of bis-iminoguanidine (BIG) carbonate salts. Here, their crystal structures are analyzed by X-ray and neutron diffraction to accurately measure key structural parameters including molecular conformations, hydrogen bonding, and π-stacking. Experimental measurements of key properties, such as aqueous solubilities and regeneration energies and temperatures, are complemented by first-principles calculations of lattice and hydration free energies, as well as free energies of reactions with CO 2 , and BIG regenerations. Minor structural modifications in the molecular structure of the BIGs are found to result in major changes in the crystal structures and the aqueous solubilities within the series, leading to enhanced DAC.

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

Pathway toward Optical Cycling and Laser Cooling of Functionalized Arenes

Rapid and repeated photon cycling has enabled precision metrology and the development of quantum information systems using atoms and simple molecules. Extending optical cycling to structurally complex molecules would provide new capabilities in these areas, as well as in ultracold chemistry. Increased molecular complexity, however, makes realizing closed optical transitions more difficult. Building on already established strong optical cycling of diatomic, linear triatomic, and symmetric top molecules, recent work has pointed the way to cycling of larger molecules, including phenoxides. The paradigm for these systems is an optical cycling center bonded to a molecular ligand. Theory has suggested that cycling may be extended to even larger ligands, like naphthalene, pyrene, and coronene. For this paper, we study optical excitation and fluorescent vibrational branching of CaO-[illus. chemical structure], SrO-[illus. chemical structure], and CaO-[illus. chemical structure] and find only weak decay to excited vibrational states, indicating a promising path to full quantum control and laser cooling of large arene-based molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Determining the influence of temperature and pressure on the structural stability in a polyurea elastomer

The structural response of amorphous elastomers to applied pressure and temperature is of significant interest given their potential for blast and impact protection applications. While understanding disordered structures is often challenging, this study focuses on the ordered correlations that are present at the atomic level even in amorphous materials. This local order was characterized in polyurea elastomers with two molecular weights up to 6 GPa and ~280 °C using in situ energy dispersive X-ray diffraction at the Advanced Photon Source via total scattering techniques. The resulting structure factors and pair distribution functions indicate that the applied pressure reduced the free volume but had little effect on covalent bonds for both molecular weights. Temperature-induced order-disorder transitions that occur readily at ambient pressures within the temperature range studied here were not observed, their onset likely delayed by the limited chain mobility associated with the free volume reduction. In conclusion, this study demonstrates that total scattering offers insights into the high-pressure structure of disordered polymers that are otherwise inaccessible using more conventional X-ray scattering techniques.

42 ENGINEERING↗
DOE OSTI2025

Structural and Dynamic Heterogeneity of Deep Eutectic Solvents Composed of Choline Chloride and Ortho-Phenol Derivatives

Structural, thermal, and dynamic properties of four deep eutectic solvents comprising choline chloride paired with ortho-phenolic derivative hydrogen-bond donors were probed using experiments and molecular simulations. The hydrogen-bond donors include phenol, catechol, o-chlorophenol, and o-cresol, in a 3:1 mixture with the hydrogen-bond acceptor choline chloride. Density, viscosity, and pulsed-field gradient NMR diffusivity measurements were conducted over a range of temperatures. Classical and ab initio molecular dynamics simulation results match experimental data reasonably well. Furthermore, the simulation results were then used to perform a more detailed analysis of the local structure and dynamics of these systems.

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

First-Principles Simulations of CuCl in High-Temperature Water Vapor

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(H 2 O) n , where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Geochim. Cosmochim. Acta2014, 129, 33–53]. However, the precise nature of these clusters is difficult to probe experimentally. Moreover, there are some discrepancies between experimental estimates of average cluster size and prior simulation work [Mei, Y. Geofluids2018, 2018, 4279124]. Here, we have performed first-principles Monte Carlo (MC) and molecular dynamics (MD) simulations to explore these clusters in finer detail. We find that molecular dynamics is not the most appropriate technique for studying aggregation in vapor phases, even at relatively high temperatures. Specifically, our MD simulations exhibit substantial problems in adequately sampling the equilibrium cluster size distribution. In contrast, MC simulations with specialized cluster moves are able to accurately sample the phase space of hydrogen-bonding vapors. At all densities, we find a stable, slightly distorted linear H 2 O–Cu–Cl structure, which is in agreement with the earlier simulations, surrounded by a variable number of water molecules. The surrounding water molecules do not form a well-defined second solvation shell but rather a loose network of hydrogen-bonded water with molecular CuCl on the outside edge of the water cluster. We also find a broad distribution of hydration numbers, especially at higher densities. In contrast to previous simulation work but in agreement with experimental data, we find that the average hydration number substantially increases with increasing density. Moreover, the value of the hydration number depends on the choice of cluster definition.

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

Replacing Pyridine with Pyrazine in Molecular Cobalt Catalysts: Effects on Electrochemical Properties and Aqueous H2 Generation

Four new molecular Co(II)tetrapyridyl complexes were synthesized and evaluated for their activity as catalysts for proton reduction in aqueous environments. The pyridine groups around the macrocycle were substituted for either one or two pyrazine groups. Single crystal X-ray analysis shows that the pyrazine groups have minimal impact on the Co(II)–N bond lengths and molecular geometry in general. X-band EPR spectroscopy confirms the Co(II) oxidation state and the electronic environment of the Co(II) center are only very slightly perturbed by the substitution of pyrazine groups around the macrocycle. The substitution of pyrazine groups has a substantial impact on the observed metal- and ligand-centered reduction potentials as well as the overall H2 catalytic activity in a multimolecular system using the [Ru(2,2′-bipyridine)3]Cl2 photosensitizer and ascorbic acid as a sacrificial electron donor. The results reveal interesting trends between the H2 catalytic activity for each catalyst and the driving force for electron transfer between either the reduced photosensitizer to catalyst step or the catalyst to proton reduction step. The work presented here showcases how even the difference of a single atom in a molecular catalyst can have an important impact on activity and suggests a pathway to optimize the photocatalytic activity and stability of molecular systems.

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

Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.

Williams, Lewis J. [University of Essex, Colcheste↗
DOE OSTI2022

I ntera C hem : Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics

InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree–Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.

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

Molecular Dynamics Simulation and Theoretical Analysis of Structural Relaxation, Bond Exchange Dynamics, and Glass Transition in Vitrimers

Vitrimers are a class of polymer networks featuring dynamic covalent cross-links that can undergo associative bond exchange. There has been recent interest in these materials due to their promise as recyclable thermosets or self-healing polymers because of the ability of vitrimer networks to rearrange at the molecular level and undergo macroscopic flow. However, the practical use of these materials often occurs in the supercooled regime or glassy state, where the implications of dynamic bonds are complicated by the interplay between slow activated segmental dynamics, cross-link (i.e., bond-exchange) kinetics, and ultimately material properties. Here, in this paper, we combine coarse-grained molecular dynamics simulation and microscopic statistical mechanical theory to understand how cross-linking kinetics affect material dynamics and how this couples to segmental relaxation of the polymeric network strands across a spectrum of length and time scales, especially in the supercooled regime. We characterize the Kuhn segmental alpha relaxation time and bond exchange time for vitrimer systems across various cross-link densities, temperatures, and bond exchange rates. Simulation and theory both exhibit a bending-up behavior for bond exchange time upon cooling, suggesting a coupling between bond exchange dynamics and segmental relaxation that intensifies with faster bond exchange kinetics. We also found bond exchange dynamics have an impact on Kuhn segment alpha relaxation time, which is most significant at higher cross-link densities. Both these effects are most prominent when the bond exchange time is similar to the Kuhn segment alpha relaxation time, and the resulting coupling of these two relaxation processes is tied to both the probability of a free end to find a bonded pair and the time scale of the constraints imposed by the dynamic cross-links. This relationship is reflected by a cross-link dependence of a theoretical parameter which represents the quantitative degree of coupling between bond exchange and segmental dynamics. Overall, the combination of simulation and theory clarifies the intricate interaction between bond kinetics and segmental relaxation and demonstrates the ability to provide molecular-level insights into vitrimer dynamics over a wide temperature range.

dynamic relaxation↗
DOE OSTI2020

Hydrogen Bonding Optimizes Singlet Fission in Carboxylic Acid Functionalized Anthradithiophene Films

The rate of singlet fission, the process of generating two triplet excitons with photoexcitation of one singlet exciton, depends on a combination of singlet/triplet energy balance and intermolecular coupling. In this work, we perform carboxylic acid functionalization of anthradithiophene (ADT) derivatives that result in hydrogen bonds that drive molecular orientation and strong electronic coupling of polycrystalline ADT thin films, leading to ultrafast singlet fission without significant enthalpic driving force. ADT with a single carboxylic acid group exhibits weak intermolecular coupling and slow and inefficient singlet fission, much like the parent ADT, and substitution of different alkylsilyl solubilizing groups has little effect. However, the addition of two carboxylic acid groups on either end of the long axis favors significant coupling and crystallinity in as-deposited thin films that increase the effective singlet fission rate by roughly three orders of magnitude. The properties of the triplet pair, particularly its propensity to form long-lived independent triplets, are also influenced by the degree of long-range intermolecular coupling. The enhancement of intermolecular coupling specific to singlet fission using the ubiquitous cyclic hydrogen bonding motif could impact triplet pair utilization schemes in a variety of contexts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗