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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE 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↗
DOE OSTI2022

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated nitrogen atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. Furthermore, these results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

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

Molecular packing modulation enabling optimized blend morphology and efficient all small molecule organic solar cells

The molecular planarity of a small molecule donor is one of the key factors affecting its molecular packing behavior, the morphology of the related active blend and thus the photovoltaic properties of all small molecule organic solar cells (ASM-OSCs). Here, a series of new benzodithiophene (BDT)-based A-π-D-π-A type small molecules were developed, namely SD1, SD2 and SD3, by combining the chemical modification of side chain (sulfuration), π-bridge (alkoxy groups introducing) and end group (different type or different alkyl chain). The sulfuration of the BDT side chains and introducing alkoxy group to the π-bridge could induce intermolecular S … S and intramolecular S … O non-covalent interactions for higher planarity of these small molecules. The rhodanine and cyanoacetate end groups showed less effect on the optical and electronic properties but significantly affected the molecular packing behavior and blend morphology. From SD1:Y6-T to SD2:Y6-T and SD3:Y6-T, the face-to-face packing was gradually reduced, while the face-to-edge packing was increased, which resulted in lowered exciton dissociation efficiency, further decreased the device performance. SD1:Y6-T blend exhibited more favorable face-to-face packing and ideal morphology for efficient charge dissociation and transport, contributing to a champion PCE of 10.12%. This work provided a deep insight of the donor and acceptor packing behavior effect on the photovoltaic property by molecular design.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction

We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction.

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

Single molecule characterization of anomalous transport in a thin, anisotropic film

Here, the diffusion of small, charged molecules incorporated in an anisotropic polyelectrolyte multilayers (PEMs) was tracked in three dimensions by combining single-molecule fluorescence localization (to characterize lateral diffusion) with Förster resonance energy transfer (FRET) between diffusing molecules and the supporting surface (to measure diffusion in the surface-normal direction). Analysis of the surface-normal diffusion required model-based statistical analysis to account for the inherently noisy FRET signal. Combining these distinct single-molecule methods, which are inherently sensitive to different length scales, permitted simultaneous characterization of severely anisotropic diffusion, which was more than three orders of magnitude slower in the surface-normal direction. We hypothesize that the anomalously slow surface-normal diffusion was related to the periodic distribution of charge in the PEM, which created electrostatic barriers. The motion was strongly subdiffusive, with anomalous temporal scaling exponents in lateral and normal directions, suggesting a connection to the transient, random fractal conformation of polymer chains in the film’s matrix.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Competing Intermolecular and Molecule–Surface Interactions: Dipole–Dipole-Driven Patterns in Mixed Carborane Self-Assembled Monolayers

Carboranedithiol isomers adsorbing with opposite orientations of their dipoles on surfaces are self-assembled together to form mixed monolayers where both lateral dipole–dipole and lateral thiol–thiolate (S–H···S) interactions provide enhanced stability over single-component monolayers. Here, we demonstrate the first instance of the ability to map individual isomers in a mixed monolayer using the model system carboranedithiols on Au{111}. The addition of methyl groups to one isomer provides both an enhanced dipole moment and extra apparent height for differentiation via scanning tunneling microscopy (STM). Associated computational investigations rationalize favorable interactions of mixed pairs and the associated stability changes that arise from these interactions. Both STM images and Monte Carlo simulations yield similarly structured mixed monolayers, where approximately 10% of the molecules have reversed dipole moment orientations but no direct chemical attachment to the surface, leading to homogeneous monolayers with no apparent phase separation. Deprotonating the thiols by depositing the molecules under basic conditions eliminates the lateral S–H···S interactions while accentuating the dipole–dipole forces. The molecular system investigated is composed of isomeric molecules with opposite orientations of dipoles and identical surface packing, which enables the mapping of individual molecules within the mixed monolayers and enables analyses of the contributions of the relatively weak lateral interactions to the overall stability of the assemblies.

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

Accurate Prediction of Adiabatic Ionization Potentials of Organic Molecules using Quantum Chemistry Assisted Machine Learning

In previous work (Dandu et al., J. Phys. Chem. A, 2022, 126, 4528–4536), we were successful in predicting accurate atomization energies of organic molecules using machine learning (ML) models, obtaining an accuracy as low as 0.1 kcal/mol compared to the G4MP2 method. In this work, we extend the use of these ML models to adiabatic ionization potentials on data sets of energies generated using quantum chemical calculations. Atomic specific corrections that were found to improve atomization energies from quantum chemical calculations have also been used in this study to improve ionization potentials. Here, the quantum chemical calculations were performed on 3405 molecules containing eight or fewer non-hydrogen atoms derived from the QM9 data set, using the B3LYP functional with the 6–31G(2df,p) basis set for optimization. Low-fidelity IPs for these structures were obtained using two density functional methods: B3LYP/6–31+G(2df,p) and ωB97XD/6–311+G(3df,2p). Highly accurate G4MP2 calculations were performed on these optimized structures to obtain high-fidelity IPs to use in ML models based on the low-fidelity IPs. Our best performing ML methods gave IPs of organic molecules within a mean absolute deviation of 0.035 eV from the G4MP2 IPs for the whole data set. This work demonstrates that ML predictions assisted by quantum chemical calculations can be used to successfully predict IPs of organic molecules for use in high throughput screening.

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

Single-Molecule Fluorescence Investigations of Solute Transport Dynamics in Nanostructured Membrane Separation Materials

Many materials used for membrane separations comprise of nanoscale structures such as pores and domains. Such nanostructures often control the solute permeability and selectivity of separation membranes. Thus, for future development of highly efficient separation membranes, it is important to understand the structural and chemical properties of these nanostructures, and also their influences on solute transport dynamics. For the last two decades, single-molecule fluorescence techniques have been used to measure the detailed dynamics of solute molecules diffusing in various nanostructured materials, giving valuable insights into molecular transport mechanisms influenced by nanoscale material heterogeneity. This Perspective will discuss recent single-molecule fluorescence studies on solute diffusion in materials relevant to membrane separations, including dense polymer films and nanoporous materials. These studies have revealed the formation and properties of nanostructures, and unique transport dynamics of solute molecules manipulated by their confinement and partitioning to the nanostructures, which play key roles in membrane separations. Furthermore, this Perspective will also point out scientific challenges toward thorough understanding of molecular-level mechanisms in membrane separations.

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

Photoluminescence Switching in Quantum Dots Connected with Carboxylic Acid and Thiocarboxylic Acid End-Group Diarylethene Molecules

We contrast the switching of photoluminescence (PL) of PbS quantum dots (QDs) cross-linked with photochromic diarylethene molecules with different end groups, 4,4′-(1-cyclopentene-1,2-diyl)bis[5-methyl-2-thiophenecarboxylic acid] ( 1C ) and 4,4′-(1-cyclopentene-1,2-diyl)bis[5-methyl-2-thiophenethiocarboxylic acid] ( 2T ). Our results show that the QDs cross-linked with the carboxylic acid end group molecules ( 1C ) exhibit a greater amount of switching in photoluminescence intensity compared to QDs cross-linked with the thiocarboxylic acid end group ( 2T ). We also demonstrate that regardless of the molecule used, greater switching amounts are observed for smaller quantum dots. Varying these parameters allows for the fabrication of photoswitches with tunable PL change. We relate these observations to the differences in the HOMO energy levels between the QDs and the photochromic molecules. Our findings demonstrate how the size of the QDs and the energy levels of the linker ligands influences the charge tunneling rate and thus the PL switching performance in tunneling-based photoswitches.

36 MATERIALS SCIENCE↗