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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2023

Modeling single-molecule stretching experiments using statistical thermodynamics

Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these experiments are valuable, and these relations can be obtained through the statistical thermodynamics of idealized model systems representing the experiments. Since the specific thermodynamic ensembles manifested by the experiments affect the outcome, primarily for small molecules, the stretching device must be included in the idealized model system. Though the model for the stretched molecule might be exactly solvable, including the device in the model often prevents analytic solutions. In the limit of large or small device stiffness, the isometric or isotensional ensembles can provide effective approximations, but the device effects are missing. Here a dual set of asymptotically correct statistical thermodynamic theories are applied to develop accurate approximations for the full model system that includes both the molecule and the device. In conclusion, the asymptotic theories are first demonstrated to be accurate using the freely jointed chain model and then using molecular dynamics calculations of a single polyethylene chain.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Alignment Thresholds of Molecules

Molecules have long been known to align in moderately intense, far off-resonance laser fields with a large variety of applications in physics and optics. Here, we illustrate and describe the physical origin of a previously unexplored phenomenon in the adiabatic alignment dynamics of molecules, which is fundamentally interesting and also has an important practical implication. Specifically, the intensity dependence of the degree of adiabatic alignment exhibits a threshold behavior, below which molecules are isotropically distributed rotationally and above which the alignment rapidly reaches a plateau. Furthermore, we show that both the intensity and the temperature dependencies of the alignment of all linear molecules exhibit universal curves and derive analytical forms to describe these dependencies. Finally, we illustrate that the alignment threshold occurs very generally at a lower intensity than the off-resonance ionization threshold, a numerical observation that is readily illustrated analytically. The threshold behavior is attributed to a tunneling mechanism that rapidly switches off at the threshold intensity, where tunneling between the potential wells corresponding to the two orientations of the aligned molecules becomes impossible. The universal threshold behavior of molecular alignment is a simple phenomenon, but one that was not realized before and can be readily tested experimentally.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Raman Sideband Cooling of Molecules in an Optical Tweezer Array to the 3D Motional Ground State

Ultracold polar molecules are promising for quantum information processing and searches for physics beyond the standard model. Laser cooling to ultracold temperatures is an established technique for trapped diatomic and triatomic molecules. Further cooling of the molecules to near the motional ground state is crucial for reducing various dephasings in quantum and precision applications. In this work, we demonstrate Raman sideband cooling (RSC) of CaF molecules in optical tweezers to near their motional ground state, with average motional occupation quantum numbers of n ¯ x = 0.16 ( 12 ) , n ¯ y = 0.17 ( 17 ) (radial directions), and n ¯ z = 0.22 ( 16 ) (axial direction), and a 3-D motional-ground-state probability of 54 ± 18 % of the molecules that survive the RSC. This process paves the way to increase molecular coherence times in optical tweezers for robust quantum computation and simulation applications. Published by the American Physical Society 2024

Physics↗
DOE OSTI2026

Quantum-State-Controlled Collisions of Ultracold Polyatomic Molecules

Collisions between ultracold calcium monohydroxide (CaOH) molecules are realized and studied. Inelastic collision rate constants are measured for CaOH prepared in ground and excited vibrational states, and the electric field dependence of these rates is measured for molecules in single quantum states of the parity-doubled bending mode. Theoretical calculations of collision rate coefficients are performed and found to agree with measured values. The lowest collisional loss rates are for states with repulsive long-range potentials that shield ultracold molecules from loss channels at short distance. These results unveil the collisional behavior of parity-doublet molecules in the ultracold regime and lay the foundation for future experiments to evaporatively cool polyatomic molecules to quantum degeneracy.

Vilas, Nathaniel B. [Harvard University, Cambridge↗
DOE OSTI2023

Dipolar spin-exchange and entanglement between molecules in an optical tweezer array

Ultracold polar molecules are promising candidate qubits for quantum computing and quantum simulations. Their long-lived molecular rotational states form robust qubits, and the long-range dipolar interaction between molecules provides quantum entanglement. In this work, we demonstrate dipolar spin-exchange interactions between single calcium monofluoride (CaF) molecules trapped in an optical tweezer array. We realized the spin- 1 2 quantum XY model by encoding an effective spin- 1 2 system into the rotational states of the molecules and used it to generate a Bell state through an iSWAP operation. Conditioned on the verified existence of molecules in both tweezers at the end of the measurement, we obtained a Bell state fidelity of 0.89(6). Using interleaved tweezer arrays, we demonstrate single-site molecular addressability.

Science & Technology - Other Topics↗
DOE OSTI2025

Observation of the distribution of nuclear magnetization in a molecule

Precise experimental control and interrogation of molecules and calculations of their structure are enriching the investigation of nuclear and particle physics phenomena. Molecules containing heavy, octupole-deformed nuclei, such as radium, are of particular interest. Here, we report precision laser spectroscopy measurements and theoretical calculations of the structure of the radioactive radium monofluoride molecule 225 Ra 19 F. Our results reveal fine details of the short-range electron-nucleus interaction, indicating the high sensitivity of this molecule to the distribution of magnetization, within the radium nucleus. Here, these results provide a stringent test of the description of the electronic wave function inside the nuclear volume, highlighting the suitability of these molecules for investigating subatomic phenomena.

Nuclear structure↗
DOE OSTI2023

Bloom filters for molecules

Abstract Ultra-large chemical libraries are reaching 10s to 100s of billions of molecules. A challenge for these libraries is to efficiently check if a proposed molecule is present. Here we propose and study Bloom filters for testing if a molecule is present in a set using either string or fingerprint representations. Bloom filters are small enough to hold billions of molecules in just a few GB of memory and check membership in sub milliseconds. We found string representations can have a false positive rate below 1% and require significantly less storage than using fingerprints. Canonical SMILES with Bloom filters with the simple FNV (Fowler-Noll-Voll) hashing function provide fast and accurate membership tests with small memory requirements. We provide a general implementation and specific filters for detecting if a molecule is purchasable, patented, or a natural product according to existing databases at https://github.com/whitead/molbloom .

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

Molecule Origins of Dipolar Character in Excited Electronic States

The molecular level origins for symmetry breaking in the excited state of symmetrical quadrupolar molecules, particularly in polar solvents, was investigated using time-dependent density functional theory approaches. Molecules of the form ADA (A/D electron accepting/donating respectively), have been shown to break their symmetry upon excitation, producing an intramolecular charge transfer event and permanent dipole. Current research indicates that polar solvents stabilize the charge transfer event thereby producing asymmetrical solvent dynamics on opposite ends of the molecules. In this work key structural features of the molecule were identified including (1) incorporation of cyano groups, (2) rotation of grafted phenyl rings, and (3) the length of the conjugated R group chain. More specifically, incorporation of cyano groups appears to decrease the magnitude of the dipole in the excited state, thereby indicating that solvent interactions at these groups do not stabilize the charge transfer. While the rotation of the phenyl groups appears to be necessary to break the symmetry of the excited state in the molecule.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Capturing Ultrafast Electron Driven Chemical Reactions in Molecules

The goals of this project are to develop experimental tools to investigate the dynamics of dissociative electron attachment (DEA) reactions in real time. In a DEA reaction, the attachment of a low energy electron to a molecule results in bond breaking and the fragmentation of the molecule. A new instrument has been designed and is under construction to perform time-resolved photoelectron and photo-fragment spectroscopy following electron transfer from an iodide anion to a molecule within a mass-selected molecular dimer. Iodide binds only weakly through the dipole interaction with many polar molecules, and such molecules forming a dimer with iodide undergo only small changes from the equilibrium geometry in isolation. When the electron is transferred from the iodide, the iodine atom is no longer bound, so the electron transfer step can be considered analogous to electron attachment and brings the key advantage of ultrafast timing precision. The experiments proposed here will establish the experimental tools to interrogate the dynamics of dissociative electron attachment on the fundamental timescales of the nuclear motion, by simultaneously probing the valence electronic structure and the fragmentation pathways.

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

Ab Initio Quantum Information Processor Design with Single-Molecule Magnets: A Multiscale Modeling Approach (Final Report)

This final report summarizes the team's efforts to develop a multiscale modeling approach that ranges from different levels of ab-initio quantum chemistry simulations to effective models and time-dependent external control, and to use this approach to systematically design quantum information processors with TbPc 2 single-molecule magnets. The impact of the work is two-fold: (i) New quantum chemistry simulation techniques capable of treating complex, multiscale problems such as the TbPc 2 molecule were developed, and (ii) the prospects for building quantum processors based on single-molecule magnets coupled by superconducting transmission line resonators were analyzed. The outcomes of this project revealed that current technology is at the cusp of being able to realize the main components of such a processor, and they highlighted the need to achieve stronger molecule-resonator interactions to enhance the viability of this approach. The multiscale modeling techniques developed during this project are general and transferable to other molecules and will thus have a broad impact on the field of quantum chemistry. Methods for controlling and simulating many coupled qubits developed here will also impact other quantum information technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ~40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ~3.7 billion candidate molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Targeting a Conserved Lysine in the Hydrophobic Pocket of HIV-1 gp41 Improves Small Molecule Antiviral Activity

Human Immunodeficiency virus (HIV-1) fusion is mediated by glycoprotein-41, a protein that has not been widely exploited as a drug target. Small molecules directed at the gp41 ectodomain have proved to be poorly drug-like, having moderate efficacy, high hydrophobicity and/or high molecular weight. We recently investigated conversion of a fairly potent hydrophobic inhibitor into a covalent binder, by modifying it to react with a lysine residue on the protein. We demonstrated a 10-fold improvement in antiviral efficacy. Here, we continue this study, utilizing instead molecules with better inherent drug-like properties. Molecules possessing low to no antiviral activity as equilibrium binders were converted into µM inhibitors upon addition of an electrophilic warhead in the form of a sulfotetrafluorophenyl (STP) activated ester. We confirmed specificity for gp41 and for entry. The small size of the inhibitors described here offers an opportunity to expand their reach into neighboring pockets while retaining drug-likeness. STP esterification of equilibrium binders is a promising avenue to explore for inhibiting HIV-1 entry. Many gp41 targeting molecules studied over the years possess carboxylic acid groups which can be easily converted into the corresponding STP ester. It may be worth the effort to evaluate a library of such inhibitors as a way forward to small molecule inhibition of fusion of HIV and possibly other enveloped viruses.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1973

Molecule formation by inverse predissociation

The general theory of inverse predissociation is described, and is applied to specific molecules. The list of molecules which can be formed by radiative association will be lengthened considerably by considering this phenomenon. Typical rate constants for diatoms will lie in the range 10 to the minus 16th power to 10 to the minus 20th power cu cm/sec/molecule, with the heavy atom molecules such as CN, CO, or NO generally having larger rates than the hydrides. An attempt is made to point out what molecular characteristics determine the radiative association rate and also to make estimates of what rates may be expected for various interstellar molecules. The formal theory is developed, and the molecular properties are discussed which determine the inverse predissociation rate. The details of the theory as applied to specific interstellar molecules are studied.

Julienne, P. S.↗