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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Towards C P -violation studies on superheavy molecules: Theoretical and experimental perspectives

Molecules containing superheavy atoms can be artificially created to serve as sensitive probes to study symmetry-violating phenomena. Here, we provide detailed theoretical studies of quantities relevant to the electron electric dipole moment (eEDM) and nucleus-electron scalar-pseudoscalar interactions in diatomic molecules containing superheavy lawrencium nuclei. The sensitivity to parity and time (or, equivalently, CP) reversal violating properties is studied for different neutral and ionic molecules. The effective electric fields in these systems are found to be about 3–4 times larger than other known molecules on which eEDM experiments are being performed. Similarly, these superheavy molecules exhibit an enhancement of more than 3 times for CP-violating scalar-pseudoscalar nucleus-electron interactions. Our preliminary analysis using the Woods-Saxon nuclear model also demonstrates that these results are sensitive to the diffuse surface interactions inside the Lr nucleus. We also briefly comment on some experimental aspects by discussing the production of these systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2007

The Chemistry of Multiply Deuterated Molecules in Protoplanetary Disks: I. The Outer Disk

We present new models of the deuterium chemistry in protoplanetary disks, including, for the first time, multiply deuterated species. We use these models to explore whether observations in combination with models can give us clues as to which desorption processes occur in disks.We find, in common with other authors, that photodesorption can allow strongly bound molecules such as HDO to exist in the gas phase in a layer above the midplane. Models including this process give the best agreement with the observations. In the midplane, cosmic-ray heating can desorb weakly bound molecules such as CO and N2. We find the observations suggest that N2 is gaseous in this region, but that CO must be retained on the grains to account for the observed DCO+/HCO+. This could be achieved by CO having a higher binding energy than N2 (as may be the case when these molecules are accreted onto water ice) or by a smaller cosmic-ray desorption rate for CO than assumed here, as suggested by recent theoretical work. For gaseous molecules the calculated deuteration can be greatly changed by chemical processing in the disk from the input molecular cloud values. On the grains singly deuterated species tend to retain the D/H ratio set in the molecular cloud, whereas multiply deuterated species are more affected by the disk chemistry. Consequently, the D/H ratios observed in comets may be partly set in the parent cloud and partly in the disk, depending on the molecule.

circumstellar matter↗
DOE OSTI2020

Semiconducting Small Molecules as Active Materials for p-Type Accumulation Mode Organic Electrochemical Transistors

A series of semiconducting small molecules with bithiophene or bis-3,4-ethylenedioxythiophene cores are designed and synthesized. The molecules display stable reversible oxidation in solution and can be reversibly oxidized in the solid state with aqueous electrolyte when functionalized with polar triethylene glycol side chains. Evidence of promising ion injection properties observed with cyclic voltammetry is complemented by strong electrochromism probed by spectroelectrochemistry. Blending these molecules with high molecular weight polyethylene oxide (PEO) is found to improve both ion injection and thin film stability. The molecules and their corresponding PEO blends are investigated as active layers in organic electrochemical transistors (OECTs). For the most promising molecule:polymer blend (P4E4:PEO), p-type accumulation mode OECTs with µA drain currents, μS peak transconductances, and a µC* figure-of-merit value of 0.81 F V -1 cm -1 s -1 are obtained.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The hydrogen bond between tryptophan and the host molecule induced fluorescence enhancement

Abstract Tryptophan is one of important amino acids in the human body, therefore its detection is particularly important. The 3,5‐bis(4‐pyridyl)‐4‐amino‐1,2,4‐triazole (BPAT) organic molecule was designed to be used as fluorescence detectors to detect tryptophan molecules for the interaction between the host and the guest. BPAT shows good sensitivity and selectivity towards tryptophan compared with other amino acid molecules. The limit of detection obtained from formula 3δ/K SV is considered to be 5.43 × 10 −7 mol/L. We speculated that this change is mainly caused by the hydrogen bond between tryptophan and the host molecule BPAT. This conjecture was verified by the controlled experiments with other host molecules.

Yang, Xi↗
DOE OSTI2025

Layers Can Be Deceiving: A Hopping Model for Small Molecule Diffusion in TATB Crystal

Sorption of small molecule gases in materials can play a significant role in their long‐term stability and compatibility within multi‐material assemblies. While many material properties of the insensitive high explosive TATB (1,3,5‐triamino‐2,4,6‐trinitrobenzene) are well understood, very little is known regarding its permeability to gases. TATB crystal exhibits a graphitic‐like layered packing structure that evokes a mental schema in which the layers form nanoscopic channels, but it is unclear whether this structure promotes gas transport. Here, we use molecular dynamics (MD) simulations to predict transport of small molecules through TATB single crystal. An approach to fit classical force fields is developed to model TATB interactions with H 2 O, He, Ne, and Ar, which is then combined with steered MD to probe gas transport along selected directions in the crystal. We find that small molecule transport occurs via a hopping mechanism that exhibits distinct jumps between interstitial sites and is substantially faster normal to the layers as compared to through them. This result stems from the finding that intralayer junctions between adjacent TATB molecules are the most stable interstitial sites and that energetic barriers are lower for hopping between adjacent layers. An empirical model for diffusion rate based on the MD data shows that the rate decays exponentially with increasing molecular radius and is negligibly small for all molecules larger than He, including common atmospheric gases. These findings have implications for the interpretation of experiments that measure surface area, material response to extreme conditions, and are expected to help constrain models for material aging.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Effect of Methyl Groups on Formation of Ordered or Layered Graphitic Materials from Aromatic Molecules

Abstract Developing functionally complex carbon materials from small aromatic molecules requires an understanding of how the chemistry and structure of its constituent molecules evolve and crosslink, to achieve a tailorable set of functional properties. Here, molecular dynamics (MD) simulations are used to isolate the effect of methyl groups on condensation reactions during the oxidative process and evaluate the impact on elastic modulus by considering three monodisperse pyrene‐based systems with increasing methyl group fraction. A parameter to quantify the reaction progression is designed by computing the number of new covalent bonds formed. Utilizing the previously developed MD framework, it is found that increasing methylation leads to an almost doubling of bond formation, a larger fraction of the new bonds oriented in the direction of tensile stress, and a higher basal plane alignment of the precursor molecules along the direction of tensile stress, resulting in enhanced tensile modulus. Additionally, via experiments, it is demonstrated that precursors with a higher fraction of methyl groups result in a higher alignment of molecules. Moreover, increased methylation results in the lower spread of single molecule alignment which may lead to smaller variations in tensile modulus and more consistent properties in carbon materials derived from methyl‐rich precursors.

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

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules

Abstract An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the Automated Topology Builder (ATB, atb.uq.edu.au) database. OFraMP identifies and compares alternative molecular fragments from the ATB database, which contains over 890,000 pre-parameterized molecules, using a novel hierarchical matching procedure. Atoms are considered within the context of an extended local environment (buffer region) with the degree of similarity between an atom in the target molecule and that in the proposed match controlled by varying the size of the buffer region. Adjacent matching atoms are combined into progressively larger matched sub-structures. The user then selects the most appropriate match. OFraMP also allows users to manually alter interaction parameters and automates the submission of missing substructures to the ATB in order to generate parameters for atoms in environments not represented in the existing database. The utility of OFraMP is illustrated using the anti-cancer agent paclitaxel and a dendrimer used in organic semiconductor devices. Graphical abstract OFraMP applied to paclitaxel (ATB ID 35922).

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

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein–protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

X-ray multiphoton-induced Coulomb explosion images complex single molecules

Following structural dynamics in real time is a fundamental goal towards a better understanding of chemical reactions. Recording snapshots of individual molecules with ultrashort exposure times is a key ingredient towards this goal, as atoms move on femtosecond (10 -15 s) timescales. For condensed-phase samples, ultrafast, atomically resolved structure determination has been demonstrated using X-ray and electron diffraction. Pioneering experiments have also started addressing gaseous samples. However, they face the problem of low target densities, low scattering cross sections and random spatial orientation of the molecules. Therefore, obtaining images of entire, isolated molecules capturing all constituents, including hydrogen atoms, remains challenging. Here we demonstrate that intense femtosecond pulses from an X-ray free-electron laser trigger rapid and complete Coulomb explosions of 2-iodopyridine and 2-iodopyrazine molecules. We obtain intriguingly clear momentum images depicting ten or eleven atoms, including all the hydrogens, and thus overcome a so-far impregnable barrier for complete Coulomb explosion imaging—its limitation on molecules consisting of three to five atoms. In combination with state-of-the-art multi-coincidence techniques and elaborate theoretical modelling, this allows tracing ultrafast hydrogen emission and obtaining information on the result of intramolecular electron rearrangement. Our work represents an important step towards imaging femtosecond chemistry via Coulomb explosion.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).

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

Magnetic molecules lose identity when connected to different combinations of magnetic metal electrodes in MTJ-based molecular spintronics devices (MTJMSD)

Abstract Understanding the magnetic molecules’ interaction with different combinations of metal electrodes is vital to advancing the molecular spintronics field. This paper describes experimental and theoretical understanding showing how paramagnetic single-molecule magnet (SMM) catalyzes long-range effects on metal electrodes and, in that process, loses its basic magnetic properties. For the first time, our Monte Carlo simulations, verified for consistency with regards to experimental studies, discuss the properties of the whole device and a generic paramagnetic molecule analog (GPMA) connected to the combinations of ferromagnet-ferromagnet, ferromagnet-paramagnet, and ferromagnet-antiferromagnet metal electrodes. We studied the magnetic moment vs. magnetic field of GPMA exchange coupled between two metal electrodes along the exposed side edge of cross junction-shaped magnetic tunnel junction (MTJ). We also studied GPMA-metal electrode interfaces’ magnetic moment vs. magnetic field response. We have also found that the MTJ dimension impacted the molecule response. This study suggests that SMM spin at the MTJ exposed sides offers a unique and high-yield method of connecting molecules to virtually endless magnetic and nonmagnetic electrodes and observing unprecedented phenomena in the molecular spintronics field.

42 ENGINEERING↗
DOE OSTI2020

Probing radical–molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. The examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.

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 OSTI2022

Diffusion characteristics of water molecules in a lamellar structure formed by triblock copolymers

The distribution and diffusion of water molecules are playing important roles in determining self-assembly and transport properties of polymeric systems. Small-angle neutron scattering (SANS) experiments and molecular dynamics (MD) simulation have been applied to understand the distribution of water molecules and their dynamics in the lamellar membrane formed by Pluronic L62 block copolymers. Penetration of water molecules into the polyethylene oxide (PEO) layers of the membranes has been estimated using scattering length density (SLD) profiles obtained from SANS measurements, which agree well with the molecular distribution observed from MD simulations. The water diffusion coefficient at different regions of the lamellar membrane was further investigated using MD simulation. The diffusion characteristic shows a transition from normal to anomalous diffusion as the position of the water molecule changes from the bulk to PEO and to the polypropylene oxide (PPO) layer. Here we find that water molecules within the PEO or PPO layers follow subdiffusive dynamics, which can be interpreted by the model of fractional Brownian motion.

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

Beyond electrical conductance: progress and prospects in single-molecule junctions

The idea of using individual molecules as conducting wires, regulators, and interconnects for charges in electronic circuitry has catalyzed the vibrant development of the field of single-molecule electronics. The ability to reliably and repeatedly construct single-molecule junctions (SMJs) has enabled the study of charge transport through a broad spectrum of individual molecules. Over the past decade, the capability of the SMJ platform has been greatly expanded thanks to the development of new experimental techniques and the integration of knowledge and methodologies from other disciplines. New opportunities beyond electrical conductance have emerged at the atomic and molecular scale. It has been demonstrated in many recent studies that the SMJ can now serve as a powerful and versatile tool to address critical physical and chemical questions that are otherwise inaccessible. Furthermore, this perspective focuses on the new capabilities and functionalities of the SMJ beyond conductance measurements and how they have enabled the investigation of crucial single-molecule processes and advanced our understanding beyond molecular electronics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Precision ultranarrow-linewidth resonance excitation (PURE) preparation of a molecular beam of nitric oxide molecules for inelastic scattering with argon

We recently reported a novel technique that utilizes narrow-linewidth lasers to selectively excite molecules into a pure quantum state with a well-resolved, tunable distribution of velocities [O. A. Krohn and D. W. Chandler, J. Phys. Chem. Lett. 15(50), 12455–12463 (2024)]. We refer to the preparation of molecules by this technique as precision ultranarrow-linewidth resonant excitation (PURE) preparation. Here, in this study, we pair this PURE preparation methodology with active frequency stabilization of the quantum cascade laser that drives the excitation. In doing so, highly velocity-resolved packets of molecules are possible, with the limitations of this velocity resolution set by the stability of the laser locking and the spectral linewidth of the transition. We show that side-of-fringe locking to a Doppler-broadened absorption spectrum of our target molecule is sufficiently stable for PURE preparation of molecules for long timescales (several hours) with highly resolved velocity spreads (σ < 3 m/s). To demonstrate the scientific utility of this new capability, we present differential cross sections from scattering between a neat molecular beam of argon and a velocity-selected beam of nitric oxide (NO) in a pure quantum state. We observe well-resolved quantum diffraction oscillations in the forward-scattered collisions as well as general trends consistent with prior characterized collisions of NO + Ar.

Krohn, Olivia A. [Sandia National Laboratories (SN↗
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↗