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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Revealing the relationship between molecular weight of lignin and its color, UV-protecting property

Lignin has great potential as a natural, green, and sustainable broad-spectrum sunscreen active ingredient. However, the coexistence of dark color and sunscreen properties hinders its application in cosmetics. In this study, we focus on the effects of the molecular weight of lignin on tis UV-protecting property and color in order to prepare lignin-based sunscreen with high performance. We report a prepared sunscreen containing low molecular weight lignin (F5, <1000 g/mol) exhibits good UV-protecting property (sun protection factor (SPF) = 7.14) and light color advantages (ΔE = 46.2). Moreover, a strong synergistic effect on UV-protecting property exists between low molecular weight lignin and ethylhexyl methoxycinnamate (EHMC), resulting in high SPF of F5@EHMC-based sunscreen (55.56). Additionally, added TiO 2 can efficiently mitigate the dark color of lignin-based sunscreens due to prominent covering power of TiO 2 . Moreover, lignin-based sunscreens have good biocompatibility with HaCaT cells. This work is useful for understanding the mechanism of the UV-protecting property and dark color of lignin, and for designing an efficient and safe lignin-based sunscreen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multidimensional molecular high-harmonic spectroscopy: A road map for charge migration studies

This work discusses recent experimental and theoretical analyses of high-harmonic spectroscopy in small molecules, with the aim of characterizing charge migration. We discuss the formulation of molecular high-harmonic spectra followed by methods to extract molecular-target-specific information, both in experiments and ab initio simulations. We present measured and simulated high-harmonic spectra from carbon dioxide and carbonyl sulfide to illustrate the necessity for multidimensional analyses for high-harmonic spectroscopies that include both the spectral amplitude and phase. Leveraging these results, we examine how such multidimensional analyses pave the way for the study of charge migration with high-harmonic spectroscopy and illustrate the beneficial role a static molecular feature can play when probing dynamics. Finally, we briefly expand our scope with an outlook on the critical role of integrating theoretical and experimental approaches, beyond just high-harmonic spectroscopy, for the development of versatile harmonic spectroscopic probes of charge migration.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Molecular mechanisms of thickness-dependent water desalination in polyamide reverse-osmosis membranes

Here, using non-equilibrium molecular simulations, we systematically elaborate the relationships among synthesis (membrane's thickness and morphology), atomic-scale transport mechanism, and separation performance (permeability and selectivity) for 3D-printed polyamide (PA) membranes. Results indicated that water diffusion, swelling ratio, water flux, and water permeance proportionally decrease with increasing membrane thickness (4.0–32.5 nm). PA membranes with different thicknesses can achieve almost 100% salt rejection over the simulation time. Importantly, water permeability exponentially decreases with increasing thickness, and 15 nm is identified as the critical membrane thickness for efficient water transport. The discontinuous water-available space spreads all over PA membranes with thicknesses greater than 5 nm, allowing water molecules to jump by way of the temporary open-and-close pores. However, the connected water-useable space exists in PA membranes with thicknesses below 5 nm, offering the continuous channels to dominate water transport. More significantly, pore distribution is more homogeneous as the thickness increases. The applied high pressures can lead to membrane compaction during reverse osmosis and the thicker membranes show a lower compression ratio. In short, these investigations provide molecular insights for effectively designing and manufacturing PA membranes for water desalination and treatment at the molecular level.

42 ENGINEERING↗
DOE OSTI2021

High-salinity brine desalination with amine-based temperature swing solvent extraction: A molecular dynamics study

Solvent extraction desalination (SED) is a promising technique for efficiently treating high salinity brines. However, only a few studies in the literature have investigated the influence of the molecular characteristics of the organic solvents on the emergent performance of the separation process. Thus, in this work we investigate the influence of the molecular structure of four different secondary amines on the desalination process of a concentrated aqueous solution of NaCl. Molecular dynamics simulations and free energy calculations are used to obtain the thermodynamic and structural properties of the pure solvent bulk phase, as well as a homogeneous solvent-water bulk mixture. Furthermore, solvent-water and solvent-brine interfacial systems are used to explicitly analyze the water partitioning behavior in the relevant temperature range for SED. The water solubilization in these secondary amines is found to be an exothermic process. Additionally, although the hydrogen-bonding interaction between the water and solvent molecules are beneficial, this interaction is not necessarily the dominant factor for ranking the water solubility performance of the different solvents. Finally, the excess volume of mixing of the bulk solvent-water mixture, as well as the electrostatic surface features of the solvents are also found to provide important clues for screening solvent behavior.

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

Energy Transfer Mechanisms in Large Low-Bandgap Polymers from Time-Resolved Experiments and Nonadiabatic Molecular Dynamics Calculations

Conjugated polymers offer unprecedented chemical tunability for modulating energy transfer in a multitude of infrared light applications. In this work, we use a combination of time-resolved spectroscopic experiments and nonadiabatic molecular dynamics calculations to probe the photochemistry and nonradiative transitions in a recently synthesized narrow bandgap donor–acceptor conjugated polymer based on alternating cyclopentadithiophene and electronegative benzothiadiazole heterocycles. Using large-scale semi-empirical nonadiabatic molecular dynamics, which can treat a large 260-atom hexamer, we calculate an S 5 → S 1 lifetime of 34.75 fs, which is consistent with our time-resolved spectroscopic data. Our simulations suggest that vibronic motions of the central carbons in the cyclopentadithiophene functional groups are predominantly involved in the nonradiative transitions, and the excitation becomes more localized on a monomer fragment over time. The combined use of time-resolved experiments and nonadiabatic molecular dynamics calculations in this work provides mechanistic insight into chemical functionalities that can be tuned to enhance energy transfer in other prospective low-bandgap polymer materials.

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

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

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

Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy

To resolve the fleeting structures of lanthanide Ln 3+ aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln 3+ aqua ions in explicit water solvent using pseudopotentials and basis sets recently optimized for lanthanides and (ii) measured the symmetry of the hydrating waters about Ln 3+ ions (Nd 3+ , Dy 3+ , Er 3+ , Lu 3+ ) for the first time with extended X-ray absorption fine structure (EXAFS). EXAFS spectra were measured experimentally and generated from AIMD trajectories to directly compare simulation, which concurrently considers the electronic structure and the atomic dynamics in solution, with experiment. In this study, we performed a comprehensive evaluation of EXAFS multiple-scattering analysis (up to 6.5 Å) to measure Ln–O distances and angular correlations (i.e., symmetry) and elucidate the molecular geometry of the first hydration shell. This evaluation, in combination with symmetry-dependent L 3 - and L 1 -edge spectral analysis, shows that the AIMD simulations remarkably reproduces the experimental EXAFS data. The error in the predicted Ln–O distances is less than 0.07 Å for the later lanthanides, while we observed excellent agreement with predicted distances within experimental uncertainty for the early lanthanides. Our analysis revealed a dynamic, symmetrically disordered first coordination shell, which does not conform to a single molecular geometry for most lanthanides. This work sheds critical light on the highly elusive coordination geometry of the Ln 3+ aqua ions.

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

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

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

Quantum-Based Molecular Dynamics Simulations Using Tensor Cores

Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix–matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born–Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born–Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.

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

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

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

Nonadiabatic Molecular Dynamics by Multiconfiguration Pair-Density Functional Theory

Herein, we present the first implementation of multiconfiguration pair-density functional theory (MC-PDFT) ab initio molecular dynamics. MC-PDFT is a multireference electronic structure method that in many cases has a similar accuracy (or even better accuracy) the complete active space second-order perturbation theory (CASPT2) at a significantly lower computational cost. In this study, we introduced MC-PDFT analytical gradients into the SHARC molecular dynamics program for ab initio, nonadiabatic molecular dynamics simulations. We verify our implementation by examining the intersystem crossing dynamics of thioformaldehyde, and we observe excellent agreement with recent CASPT2 and experimental findings. Moreover, with MC-PDFT, we could perform dynamics simulations with the 12 electron in 10 orbitals active space that was computationally too expensive for direct dynamics with CASPT2.

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

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

The binding free energy between a ligand and its target protein is an essential quantity to know at all stages of the drug discovery pipeline. Assessing this value computationally can offer insight into where efforts should be focused in the pursuit of effective therapeutics to treat a myriad of diseases. In this work, we examine the computation of alchemical relative binding free energies with an eye for assessing reproducibility across popular molecular dynamics packages and free energy estimators. The focus of this work is on 54 ligand transformations from a diverse set of protein targets: MCL1, PTP1B, TYK2, CDK2, and thrombin. These targets are studied with three popular molecular dynamics packages: OpenMM, NAMD2, and NAMD3 alpha. Trajectories collected with these packages are used to compare relative binding free energies calculated with thermodynamic integration and free energy perturbation methods. The resulting binding free energies show good agreement between molecular dynamics packages with an average mean unsigned error between them of 0.50 kcal/mol. The correlation between packages is very good, with the lowest Spearman’s, Pearson’s and Kendall’s tau correlation coefficients being 0.92, 0.91, and 0.76, respectively. Agreement between thermodynamic integration and free energy perturbation is shown to be very good when using ensemble averaging.

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

Molecular Glue Discovery: Current and Future Approaches

The intracellular interactions of biomolecules can be maneuvered to redirect signaling, reprogram the cell cycle, or decrease infectivity using only a few dozen atoms. Such "molecular glues," which can drive both novel and known interactions between protein partners, represent an enticing therapeutic strategy. Here, we review the methods and approaches that have led to the identification of small-molecule molecular glues. We first classify current FDA-approved molecular glues to facilitate the selection of discovery methods. We then survey two broad discovery method strategies, where we highlight the importance of factors such as experimental conditions, software packages, and genetic tools for success. In conclusion, we hope that this curation of methodologies for directed discovery will inspire diverse research efforts targeting a multitude of human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Atomic-Level Features for Kinetic Monte Carlo Models of Complex Chemistry from Molecular Dynamics Simulations

The high computational cost of evaluating atomic interactions recently motivated the development of computationally inexpensive kinetic models, which can be parametrized from MD simulations of complex chemistry of thousands of species or other processes and accelerate the prediction of the chemical evolution by up to four order of magnitude. Such models go beyond the commonly employed potential energy surface fitting methods in that they are aimed purely at describing kinetic effects. So far, such kinetic models utilize molecular descriptions of reactions and have been constrained to only reproduce molecules previously observed in MD simulations. Therefore, these descriptions fail to predict the reactivity of unobserved molecules, for example in the case of large molecules or solids. In this work, we propose a new approach for the extraction of reaction mechanisms and reaction rates from MD simulations, namely the use of atomic-level features. Using the complex chemical network of hydrocarbon pyrolysis as example, it is demonstrated that kinetic models built using atomic features are able to explore chemical reaction pathways never observed in the MD simulations used to parametrize them, a critical feature to describe rare events. Atomic-level features are shown to construct reaction mechanisms and estimate reaction rates of unknown molecular species from elementary atomic events. Through comparisons of the model ability to extrapolate to longer simulation timescales and different chemical compositions than the ones used for parameterization, it is demonstrated that kinetic models employing atomic features retain the same level of accuracy and transferability as the use of features based on molecular species, while being more compact and parametrized with less data. We also find that atomic features can better describe the formation of large molecules enabling the simultaneous description of small molecules and condensed phases.

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

Interaction–Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG + G + TG + G + g – )-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as “preparation energy” or “reorganization energy”. We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme’s efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction–deletion in 2-nitrobenzene-1,3-diol.

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

Insights into Sorption and Molecular Transport of Aqueous Glucose into Zeolite Nanopores

Liquid-phase heterogeneous catalysis using zeolites is important for biomass conversion to fuels and chemicals. There is a substantial body of work on gas-phase sorption in zeolites with different topologies; however, studies investigating the diffusion of complex molecules in liquid medium into zeolitic nanopores are scarce. Here, we present a molecular dynamics study to understand the sorption and diffusion of aqueous β-d-glucose into β-zeolite silicate at T = 395 K and P = 1 bar. Through 2-μs-long molecular dynamics trajectories, we reveal the role of the solvent, the kinetics of the pore filling, and the effect of the water model on these properties. We find that the glucose and water loading is a function of the initial glucose concentration. Although the glucose concentration increases monotonically with the initial glucose concentration, the water loading exhibits a nonmonotonic behavior. At the highest initial concentration (~20 wt %), we find that the equilibrium loading of glucose is approximately five molecules per unit cell and displays a weak dependence on the water model. Glucose molecules follow a single-file diffusion in the nanopores due to confinement. Here, the dynamics of glucose and water molecules slows significantly at the interface. The average residence time for glucose molecules is an order of magnitude larger than that in the bulk solution, while it is about twice as large for the water molecules. Our simulations reveal critical molecular details of the glucose molecule’s local environment inside the zeolite pore relevant to catalytic conversion of biomass to valuable chemicals.

09 BIOMASS FUELS↗
DOE OSTI2022

Infrared Spectroscopy of Li + Solvation in EmimBF 4 and in Propylene Carbonate: Ab Initio Molecular Dynamics and Experiment

Infrared (IR) spectra of solutions of the lithium salt LiBF 4 in the ionic liquid 1-ethyl-3-methylimidazolium tetrafluoroborate (EmimBF 4 ) and in the organic solvent propylene carbonate (PC) are studied via infrared spectroscopy and ab initio molecular dynamics (AIMD) simulations. The measurements show that the major effects of LiBF 4 in both solutions, compared to their neat counterparts, are the appearance of a new broad band in the 300-450 cm -1 frequency region and a broadening of the IR structure in the 900-1200 cm -1 region with the development of a new peak at 980 cm -1 . Computational analysis indicates that hindered translational motions of Li + in its solvation cage are mainly responsible for the former, while the latter is due to Li + -induced structural changes and accompanying vibrational frequency shifts of constituent ions and molecules of the solutions. In addition, molecular motions in these and lower frequency regions are generally correlated, disclosing the collective nature of the vibrational dynamics, which involve multiple ions/molecules. Herein, detailed analysis of these features via AIMD simulations of the spectrum and its components arising from auto- and cross-correlations of motions of constituent molecular species, combined with generalized normal modes of the solutions and normal modes of small Li + -containing clusters, is presented. Furthermore, other minor spectral changes caused by the lithium salt as well as the interaction-induced effect on IR spectra are also discussed.

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

How Rigid Are Anthranilamide Molecular Electrets?

As important as molecular electrets are for electronic materials and devices, conformational fluctuations strongly impact their macrodipoles and intrinsic properties. Herein, we employ molecular dynamics (MD) simulations with the polarizable charge equilibrium (PQEq) method to investigate the persistence length (L P ) of molecular electrets composed of anthranilamide (Aa) residues. The PQEq-MD dissipates the accepted static notions about Aa macromolecules, and L P represents the shortest Aa rigid segments. The classical model with a single L P value does not describe these oligomers. Introducing multiple L P values for the same macromolecule follows the observed trends and discerns the enhanced rigidity in their middle sections from the reduced stiffness at their terminal regions. Furthermore, L P distinctly depends on solvent polarity. The Aa oligomers maintain extended conformations in nonpolar solvents with L P exceeding 4 nm, while in polar media, increased conformational fluctuations reduce L P to about 2 nm. These characteristics set key guidelines about the utility of Aa conjugates for charge-transfer systems within organic electronics and energy engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗