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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Science & Technology - Other Topics↗
DOE OSTI2023

Gaussian approximation potentials for accurate thermal properties of two-dimensional materials

Two-dimensional materials (2DMs) continue to attract a lot of attention, particularly for their extreme flexibility and superior thermal properties. Molecular dynamics simulations are among the most powerful methods for computing these properties, but their reliability depends on the accuracy of interatomic interactions. While first principles approaches provide the most accurate description of interatomic forces, they are computationally expensive. In contrast, classical force fields are computationally efficient, but have limited accuracy in interatomic force description. Machine learning interatomic potentials, such as Gaussian Approximation Potentials, trained on density functional theory (DFT) calculations offer a compromise by providing both accurate estimation and computational efficiency. Here, in this work, we present a systematic procedure to develop Gaussian approximation potentials for selected 2DMs, graphene, buckled silicene, and h-XN (X = B, Al, and Ga, as binary compounds) structures. We validate our approach through calculations that require various levels of accuracy in interatomic interactions. The calculated phonon dispersion curves and lattice thermal conductivity, obtained through harmonic and anharmonic force constants (including fourth order) are in excellent agreement with DFT results. HIPHIVE calculations, in which the generated GAP potentials were used to compute higher-order force constants instead of DFT, demonstrated the first-principles level accuracy of the potentials for interatomic force description. Molecular dynamics simulations based on phonon density of states calculations, which agree closely with DFT-based calculations, also show the success of the generated potentials in high-temperature simulations.

2D Materials↗
DOE OSTI2022

Polar liquids at charged interfaces: A dipolar shell theory

The structure of polar liquids and electrolytic solutions, such as water and aqueous electrolytes, at interfaces underlies numerous phenomena in physics, chemistry, biology, and engineering. In this work, we develop a continuum theory that captures the essential features of dielectric screening by polar liquids at charged interfaces, including decaying spatial oscillations in charge and mass, starting from the molecular properties of the solvent. The theory predicts an anisotropic dielectric tensor of interfacial polar liquids previously studied in molecular dynamics simulations. We explore the effect of the interfacial polar liquid properties on the capacitance of the electrode/electrolyte interface and on hydration forces between two plane-parallel polarized surfaces. In the linear response approximation, we obtain simple formulas for the characteristic decay lengths of molecular and ionic profiles at the interface.

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

Prediction of Research/Motor Octane Number and Octane Sensitivity Using Artificial Neural Networks

Octane sensitivity (OS), dfined as the research octane number (RON) minus the motor octane number (MON) of a given fuel, has gained interest among researchers due to its apparent ffect on knocking conditions in internal combustion engines. Compounds with a high OS enable higher efficiencies, especially with respect to advanced compression ignition engines. RON/MON must be experimentally tested to determine OS; however, the experimental methods utilized require a substantial amount of time, a significant monetary investment, and specialized equipment. To this end, predictive computational models trained with existing experimental data and molecular properties would allow for the preemptive screening of compounds prior to performing these experiments. The present work proposes two methods for predicting the OS of a given compound: using artficial neural networks (ANNs) trained with quantitative structure-property relationship (QSPR) descriptors to predict RON and MON individually to compute OS from RON/MON predictions (derived octane sensitivity, dOS), and using an ANN trained with QSPR descriptors to directly predict OS. ANNs trained to predict RON and MON achieved test set root-mean-square errors (RMSEs) of 10.499 and 7.551 respectively. dOS calculations were found to have a test set RMSE of 6.432 while predicting OS directly resulted in a test set RMSE of 7.019, showing it is more bene cial to obtain OS from RON/MON predictions than predicting it directly. Furthermore, relationships between individual QSPR descriptors and RON/MON/OS are discussed, highlighting correlations between specfic molecular features and these properties.

09 BIOMASS FUELS↗
DOE OSTI2025

Probing specific ion effects at air-aqueous dibutyl phosphate interfaces using vibrational sum frequency generation spectroscopy

Molecular properties at air–liquid and liquid–liquid interface hold the key to many processes involving molecular transport across phase boundaries from aerosol formation to carbon cycling and material separation using solvent extraction techniques. Using dibutyl phosphate (DBP) as a representative for partially aqueous soluble surfactants, the specific ion effect (SIE) of the Hofmeister series cations Cs + , Na + , Li + , and Mg 2+ on the partition and interaction between surfactant molecules and water molecules in the air–aqueous interface are investigated using vibrational sum frequency generation spectroscopy and surface tension measurements. In the presence of 1 mM and 1M bulk aqueous phase ionic strength salt concentrations, fundamental qualitative relationships are observed for the salting out of DBP relative to bulk aqueous phase nitrate salt concentrations and the specific cations species. At 1 mM ionic strength, the interfacial charge and hence the interfacial potential modulates the electrostatic interactions; in particular, the counter cations partially screen the negatively charged interface induced by the DBP in a direct Hofmeister order. At 1M ionic strength, the electric field at the interface or interfacial potential is effectively neutralized, and the counter cations promote the partitioning of DBP to the interface depending on their specific interaction with the DBP head group and metal ion hydration properties. The present results lay a foundation to study SIEs of heavier metals on hydrophobic-aqueous DBP interfaces.

Louie, Christina [Washington State University, Pul↗
DOE OSTI2023

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units–accelerated quantum chemistry in the cloud, artificial intelligence–driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.

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

Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds’ intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.

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

Competing Singlet Fission and Excimer Formation in Solid Fluorinated 1,3-Diphenylisobenzofurans

Singlet fission (kSF) and excimer formation (kEXC) rate constants along with other photophysical properties of thin solid layers of 1,3-diphenylisobenzofuran and 11 of its fluorinated derivatives have been determined. The molecular properties of these compounds are similar, but their crystal packing varies widely. Most of them undergo singlet fission whereas excitation in others is trapped in excimers. The trend in rate constants kSF agrees qualitatively with results of calculations by a simplified version of the frontier orbital model for a molecular pair. The main shortcoming of the model is discussed.

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

Advancing molecular machine learning representations with stereoelectronics-infused molecular graphs

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have used strings, fingerprints, global features and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a new approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects, enhancing expressivity and interpretability. Learning to predict the stereoelectronics-infused representation with a tailored double graph neural network workflow enables its application to any downstream molecular machine learning task without expensive quantum-chemical calculations. We show that the explicit addition of stereoelectronic information substantially improves the performance of message-passing two-dimensional machine learning models for molecular property prediction. We show that the learned representations trained on small molecules can accurately extrapolate to much larger molecular structures, yielding chemical insight into orbital interactions for previously intractable systems, such as entire proteins, opening new avenues of molecular design. Finally, we have developed a web application (simg.cheme.cmu.edu) where users can rapidly explore stereoelectronic information for their own molecular systems.

Boiko, Daniil A↗
DOE OSTI2020

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

Abstract Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.

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

Active learning enables generation of molecules that advance the known Pareto front

Although generative models hold promise for discovering molecules with optimized desired properties, they often fail to suggest synthesizable molecules that improve upon the properties of the structures represented in the training distribution. We find that this limitation arises not only from the molecule generation process itself, but also from the poor generalization capabilities of molecular property predictors. We address this challenge by creating a closed-loop molecule generation pipeline with iterative retraining on new quantum chemical simulation data. Compared against static, single-pass generative modeling approaches, only our closed-loop iterative workflow generates molecules with properties extending beyond the training distribution (up to 0.44 standard deviations beyond the original range) and achieves a 79% improvement in out-of-distribution molecule classification accuracy. Furthermore, by conditioning molecular generation on thermodynamic stability data obtained during the iterative loop, the proportion of stable and hence potentially synthesizable molecules generated is 3.5x higher than the next-best model.

Chemistry↗
DOE OSTI2022

Diffusion Monte Carlo approaches for studying nuclear quantum effects in fluxional molecules

Abstract Diffusion quantum Monte Carlo (DMC) provides a powerful approach for obtaining the ground state energy and wave function of molecules, ions, and molecular clusters. The approach is uniquely well suited for studies of fluxional molecules, which undergo large amplitude vibrational motions even in their ground state. In contrast to the electronic structure problem, where the wave function must be antisymmetric with respect to exchange of any pair of electrons, the wave function for the ground vibrational state is nodeless. This greatly simplifies the application of DMC for vibrational problems. Because there is not a single potential function that can be used to describe the intramolecular and intermolecular interactions in all molecular systems, most methods that are used to describe nuclear quantum effects rely on a carefully chosen zero‐order description of the molecular vibrations. In contrast, DMC calculations can be performed in Cartesian coordinates, making the DMC algorithm easily transferable between different chemical systems. In this contribution, the theory that underlies DMC will be discussed along with important considerations for performing DMC calculations. Extensions for evaluating vibrationally excited states and molecular properties are also discussed. Insights that can be obtained from DMC calculations are illustrated in the context of the protonated water clusters. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Spectroscopy

Chemistry↗
DOE OSTI2026

Expanding the Domain of Applicability of Machine Learning Models with Limited Data for Drug Property Prediction

Accurate machine learning models for predicting small molecule interactions with biological targets are essential for therapeutic discovery, biothreat response, and computational drug design, but their performance is often limited for understudied targets with sparse experimental data. To address this challenge, we developed and evaluated methods to improve molecular property prediction under low-data conditions, using the NimA-related kinase (NEK) family as a proof-of-concept. This work focused on two complementary goals within the ATOM Modeling PipeLine (AMPL) and the Generative Molecular Design (GMD) loop: expanding model applicability through transfer learning, representation learning, feature scaling, sampling strategies, and active-learning-inspired compound selection; and enabling efficient virtual screening to prioritize compounds that balance predicted activity, design objectives, and synthetic accessibility.

organic↗
DOE OSTI2022

SOMAS: a platform for data-driven material discovery in redox flow battery development

Abstract Aqueous organic redox flow batteries offer an environmentally benign, tunable, and safe route to large-scale energy storage. The energy density is one of the key performance parameters of organic redox flow batteries, which critically depends on the solubility of the redox-active molecule in water. Prediction of aqueous solubility remains a challenge in chemistry. Recently, machine learning models have been developed for molecular properties prediction in chemistry and material science. The fidelity of a machine learning model critically depends on the diversity, accuracy, and abundancy of the training datasets. We build a comprehensive open access organic molecular database “Solubility of Organic Molecules in Aqueous Solution” (SOMAS) containing about 12,000 molecules that covers wider chemical and solubility regimes suitable for aqueous organic redox flow battery development efforts. In addition to experimental solubility, we also provide eight distinctive quantum descriptors including optimized geometry derived from high-throughput density functional theory calculations along with six molecular descriptors for each molecule. SOMAS builds a critical foundation for future efforts in artificial intelligence-based solubility prediction models.

25 ENERGY STORAGE↗
DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Extracting the excitonic Hamiltonian of a chlorophyll dimer from broadband two-dimensional electronic spectroscopy

We apply Frenkel exciton theory to model the entire Q-band of a tightly bound chlorophyll dimer inspired by the photosynthetic reaction center of photosystem II. The potential of broadband two-dimensional electronic spectroscopy experiment spanning the Qx and Qy regions to extract the parameters of the model dimer Hamiltonian is examined through theoretical simulations of the experiment. We find that the local nature of Qx excitation enables identification of molecular properties of the delocalized Qy excitons. Specifically, we demonstrate that the cross-peak region, where excitation energy is resonant with Qy while detection is at Qx, contains specific spectral signatures that can reveal the full real-space molecular Hamiltonian, a task that is impossible by considering the Qy transitions alone. System–bath coupling and site energy disorder in realistic systems may limit the resolution of these spectral signatures due to spectral congestion.

Chemistry↗
DOE OSTI2024

Chemical reaction enhanced graph learning for molecule representation

Abstract Motivation Molecular representation learning (MRL) models molecules with low-dimensional vectors to support biological and chemical applications. Current methods primarily rely on intrinsic molecular information to learn molecular representations, but they often overlook effectively integrating domain knowledge into MRL. Results In this article, we develop a reaction-enhanced graph learning (RXGL) framework for MRL, utilizing chemical reactions as domain knowledge. RXGL introduces dual graph learning modules to model molecule representation. One module employs graph convolutions on molecular graphs to capture molecule structures. The other module constructs a reaction-aware graph from chemical reactions and designs a novel graph attention network on this graph to integrate reaction-level relations into molecular modeling. To refine molecule representations, we design a reaction-based relation learning task, which considers the relations between the reactant and product sides in reactions. In addition, we introduce a cross-view contrastive task to strengthen the cooperative associations between molecular and reaction-aware graph learning. Experiment results show that our RXGL achieves strong performance in various downstream tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation The code is publicly available at https://github.com/coder-ACAC/RLM.

Biochemistry & Molecular Biology↗