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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

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

Simulating molecular polaritons in the collective regime using few-molecule models

The study of molecular polaritons beyond simple quantum emitter ensemble models (e.g., Tavis–Cummings) is challenging due to the large dimensionality of these systems and the complex interplay of molecular electronic and nuclear degrees of freedom. This complexity constrains existing models to either coarse-grain the rich physics and chemistry of the molecular degrees of freedom or artificially limit the description to a small number of molecules. In this work, we exploit permutational symmetries to drastically reduce the computational cost of ab initio quantum dynamics simulations for large N . Furthermore, we discover an emergent hierarchy of timescales present in these systems, that justifies the use of an effective single molecule to approximately capture the dynamics of the entire ensemble, an approximation that becomes exact as N → ∞. We also systematically derive finite N corrections to the dynamics and show that addition of k extra effective molecules is enough to account for phenomena whose rates scale as 𝒪( N − k ). Based on this result, we discuss how to seamlessly modify existing single-molecule strong coupling models to describe the dynamics of the corresponding ensemble. We call this approach collective dynamics using truncated equations (CUT-E), benchmark it against well-known results of polariton relaxation rates, and apply it to describe a universal cavity-assisted energy funneling mechanism between different molecular species. Beyond being a computationally efficient tool, this formalism provides an intuitive picture for understanding the role of bright and dark states in chemical reactivity, necessary to generate robust strategies for polariton chemistry.

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

Can increasing the size and flexibility of a molecule reduce decoherence and prolong charge migration?

Coherent superposition of electronic states, created by ionizing a molecule, can initiate ultrafast dynamics of the electron density. Correlation between nuclear and electron motions, however, typically dissipates the electronic coherence in only a few femtoseconds, especially in larger and more flexible molecules. We, therefore, use ab initio semiclassical dynamics to study decoherence in a sequence of analogous organic molecules of increasing size and find, surprisingly, that extending the carbon skeleton in propynal analogs slows down decoherence and prolongs charge migration. To elucidate this observation, we decompose the overall decoherence into contributions from individual vibrational modes and show that: 1) The initial decay of electronic coherence is caused by high- and intermediate-frequency vibrations via momentum separation of nuclear wavepackets evolving on different electronic surfaces. 2) At later times, the coherence disappears completely due to the increasing position separation in the low-frequency modes. 3) In agreement with another study, we observe that only normal modes that preserve the symmetry of the molecule induce decoherence. All together, we justify the enhanced charge migration by a combination of increased hole-mixing and the disappearance of decoherence contributions from specific vibrational modes—CO stretching in butynal and various H rockings in pentynal.

Science & Technology - Other Topics↗
DOE OSTI2025

Conveyor-belt magneto-optical trapping of molecules

Abstract Laser cooling is used to produce ultracold atoms and molecules for quantum science and precision measurement applications. Molecules are more challenging to cool than atoms due to their vibrational and rotational internal degrees of freedom. Molecular rotations lead to the use of type-II transitions ( F ⩾ F ′ ) for magneto-optical trapping (MOT). When typical red detuned light frequencies are applied to these transitions, sub-Doppler heating is induced, resulting in higher temperatures and larger molecular cloud sizes than realized with the type-I MOTs most often used with atoms. To improve type-II MOTs, Jarvis et al (2018 Phys. Rev. Lett. 120 083201) proposed a blue-detuned MOT to be applied after initial cooling and capture with a red-detuned MOT. This was successfully implemented (Burau et al 2023 Phys. Rev. Lett. 130 193401; Jorapur et al 2024 Phys. Rev. Lett. 132 163403; Li et al 2024 Phys. Rev. Lett. 132 233402), realizing colder and denser molecular samples. Very recently, Hallas et al (2024 arXiv:2404.03636) demonstrated a blue-detuned MOT with a ‘1+2’ configuration that resulted in even stronger compression of the molecular cloud. Here, we describe and characterize theoretically the conveyor-belt mechanism that underlies this observed enhanced compression. We perform numerical simulations of the conveyor-belt mechanism using both stochastic Schrödinger equation and optical Bloch equation approaches. We investigate the conveyor-belt MOT characteristics in relation to laser parameters, g -factors and the structure of the molecule, and find that conveyor-belt trapping should be applicable to a wide range of laser-coolable molecules.

Li, Grace K. (ORCID:0000000277223355)↗
DOE OSTI2018

Inelastic and deep inelastic neutron spectroscopy of water molecules under ultra-confinement

Water confined within sub-nanometer channels of silicate minerals presents an extreme case of confinement, where the restricted molecules are situated in channels whose diameter is not much larger than the water molecule itself. Recently, we discovered a new quantum tunneling state of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. Several peaks were observed in the inelastic neutron scattering (INS) spectra which were uniquely assigned to water quantum tunnelling. In addition, the water proton momentum distribution measured with deep inelastic neutron scattering (DINS) at 4.3 K directly showed coherent delocalization of the water protons in the ground state. The obtained average kinetic energy (EK ) of the water protons was found to be ~30% less than it is in bulk liquid water and ice phases. In the current work we present INS and DINS study of water in single crystal beryl in wider temperature range, T=5–260 K, where we observed significant increase of EK of the confined water protons with temperature increase. The obtained INS data also indicate that with increasing temperature water molecules are progressively involved in hydrogen bonding (HB) with the beryl cage, while HB is almost absent at low temperatures.

Kolesnikov, Alexander I.↗
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↗
DOE OSTI2020

Shaping attosecond pulses by controlling the minima in high-order harmonic generation through alignment of CO 2 molecules

In this paper, we report a simple method for generating shaped attosecond pulses by using a CO 2 molecule. Unlike most other molecules, owing to its unique energy and angle dependence and the presence of deep minima in the photoionization transition dipole moment, the shape of harmonic spectra, especially the position and depth of minima, can be readily controlled by tuning the degree of alignment. The sensitive alignment dependence of the minima is due to the coherent interference of a laser-induced dipole from each molecule when CO 2 molecules are moderately aligned, but not when they are well aligned or when they are isotropically distributed. Such a sensitivity offers a simple way of controlling the spectral amplitude and phase of the generated harmonics and thus shaping the generated attosecond pulses, for example, producing structured attosecond pulses by splitting a single burst into two. We illustrate how such pulses are generated and how to characterize them. This method offers a simple way to shape attosecond pulses at the generation step. It can be easily implemented experimentally to generate attosecond pulses with strong phase variations for unique applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Resonance-enhanced x-ray multiple ionization of a polyatomic molecule

Extremely high charge states of atoms and molecules can be created when they are irradiated by intense x-ray pulses. At certain x-ray photon energies, electron ejection from atoms can be drastically enhanced by transient resonances created during the sequential ionization process. In this study we report on the observation of such resonance effects in a molecule, CH 3 I, and show the photon-energy-dependent shift of resonance-induced structures in ion charge state distributions. By comparing the ion charge state distribution of CH 3 I with that from ionization of atomic xenon, molecule-specific features are observed, which can be attributed to ultrafast intramolecular charge rearrangement. In addition, we experimentally demonstrate that the charge-rearrangement-enhanced x-ray ionization of molecules, previously found with hard x rays, also plays a role in the soft x-ray regime.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Mapping and controlling ultrafast dynamics of highly excited H 2 molecules by VUV-IR pump-probe schemes

Here, we used ultrashort femtosecond vacuum ultraviolet (VUV) and infrared (IR) pulses in a pump-probe scheme to map the dynamics and nonequilibrium dissociation channels of excited neutral H 2 molecules. A nuclear wave packet is created in the B 1 Σ$+\atop{u}$ state of the neutral H 2 molecule by absorption of the ninth harmonic of the driving infrared laser field. Due to the large stretching amplitude of the molecule excited in the B 1 Σ$+\atop{u}$ electronic state, the effective H 2 + ionization potential changes significantly as the nuclear wave packet vibrates in the bound, highly electronically and vibrationally excited B potential-energy curve. We probed such dynamics by ionizing the excited neutral molecule using time-delayed VUV-or-IR radiation. We identified the nonequilibrium dissociation channels by utilizing three-dimensional momentum imaging of the ion fragments. We also found that different dissociation channels can be controlled, to some extent, by changing the IR laser intensity and by choosing the wavelength of the probe laser light. Furthermore, we concluded that even in a benchmark molecular system such as H 2 *, the interpretation of the nonequilibrium multiphoton and multicolor ionization processes is still a challenging task, requiring intricate theoretical analysis.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Crystal structure of a 2:1 piroxicam–gentisic acid co-crystal featuring neutral and zwitterionic piroxicam molecules

A new 2:1 co-crystal of piroxicam and gentisic acid [systematic name: 4-hydroxy-1,1-dioxo- N -(pyridin-2-yl)-2 H -1λ 6 ,2-benzothiazine-3-carboxamide–2-(4-oxido-1,1-dioxo-2 H -1λ 6 ,2-benzothiazine-3-amido)pyridin-1-ium–2,5-dihydroxybenzoic acid, 2C 15 H 13 N 3 O 4 S·C 7 H 6 O 4 ] has been synthesized using a microfluidic platform and initially identified using Raman spectroscopy. In the co-crystal, one piroxicam molecule is in its neutral form and an intramolecular O—H...O hydrogen bond is observed. The other piroxicam molecule is zwitterionic (proton transfer from the OH group to the pyridine N atom) and two intramolecular N—H...O hydrogen bonds occur. The gentisic acid molecule shows whole-molecule disorder over two sets of sites in a 0.809(2):0.191(2) ratio. In the crystal, extensive hydrogen bonding between the components forms layers propagating in the ab plane.

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

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Control of long-distance motion of single molecules on a surface

Spatial control over molecular movement is typically limited because motion at the atomic scale follows stochastic processes. Here, we used scanning tunneling microscopy to bring single molecules into a stable orientation of high translational mobility where they moved along precisely defined tracks. Single dibromoterfluorene molecules moved over large distances of 150 nanometers with extremely high spatial precision of 0.1 angstrom across a silver (111) surface. The electrostatic nature of the effect enabled the selective application of repulsive and attractive forces to send or receive single molecules. The high control allows us to precisely move an individual and specific molecular entity between two separate probes, opening avenues for velocity measurements and thus energy dissipation studies of single molecules in real time during diffusion and collision.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Observation of microwave shielding of ultracold molecules

Harnessing the potential wide-ranging quantum science applications of molecules will require control of their interactions. Here, we used microwave radiation to directly engineer and tune the interaction potentials between ultracold calcium monofluoride (CaF) molecules. By merging two optical tweezers, each containing a single molecule, we probed collisions in three dimensions. The correct combination of microwave frequency and power created an effective repulsive shield, which suppressed the inelastic loss rate by a factor of six, in agreement with theoretical calculations. The demonstrated microwave shielding shows a general route to the creation of long-lived, dense samples of ultracold polar molecules and evaporative cooling.

Anderegg, Loïc↗
DOE OSTI2023

Direct observation of chirality-induced spin selectivity in electron donor–acceptor molecules

The role of chirality in determining the spin dynamics of photoinduced electron transfer in donor-acceptor molecules remains an open question. Although chirality-induced spin selectivity (CISS) has been demonstrated in molecules bound to substrates, experimental information about whether this process influences spin dynamics in the molecules themselves is lacking. Here we used time-resolved electron paramagnetic resonance spectroscopy to show that CISS strongly influences the spin dynamics of isolated covalent donor–chiral bridge–acceptor (D-Bχ-A) molecules in which selective photoexcitation of D is followed by two rapid, sequential electron-transfer events to yield D •+ -Bχ-A •– . Exploiting this phenomenon affords the possibility of using chiral molecular building blocks to control electron spin states in quantum information applications.

Science & Technology - Other Topics↗
DOE OSTI2021

Ultrafast Imaging of Molecules with Electron Diffraction

Photoexcited molecules convert light into chemical and mechanical energy through changes in electronic and nuclear structure that take place on femtosecond timescales. Gas phase ultrafast electron diffraction (GUED) is an ideal tool to probe the nuclear geometry evolution of the molecules and complements spectroscopic methods that are mostly sensitive to the electronic state. GUED is a passive probing tool that does not alter the molecular properties during the probing process and is sensitive to the spatial distribution of charge in the molecule, including both electrons and nuclei. Improvements in temporal resolution have enabled GUED to capture coherent nuclear motions in molecules in the excited and ground electronic states with femtosecond and subangstrom resolution. Here we present the basic theory of GUED and explain what information is encoded in the diffraction signal, review how GUED has been used to observe coherent structural dynamics in recent experiments, and discuss the advantages and limitations of the method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

An automated framework for NMR chemical shift calculations of small organic molecules

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties - specifically NMR chemical shifts in this manuscript - via the open source, high-performance omputational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model (COSMO). The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Machine learning prediction of accurate atomization energies of organic molecules from low-fidelity quantum chemical calculations

Recent studies illustrate how machine learning (ML) can be used to bypass a core challenge of molecular modeling: the trade-off between accuracy and computational cost. Here, we assess multiple ML approaches for predicting the atomization energy of organic molecules. Our resulting models learn the difference between low-fidelity, B3LYP, and high-accuracy, G4MP2, atomization energies and predict the G4MP2 atomization energy to 0.005 eV (mean absolute error) for molecules with less than nine heavy atoms (training set of 117,232 entries, test set 13,026) and 0.012 eV for a small set of 66 molecules with between 10 and 14 heavy atoms. As a result, our two best models, which have different accuracy/speed trade-offs, enable the efficient prediction of G4MP2-level energies for large molecules and are available through a simple web interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Cooling Molecules with Laser Light (Final Report)

Certain diatomic molecules are disposed to laser cooling in the way successfully applied to certain atoms and that ushered in a revolution in ultracold atomic physics, an identification first made at Los Alamos and which took root during this program. Despite their manipulation into numerous achievements, atoms are nonetheless mundane denizens of the quantum world. Molecules, on the other hand, with their internal degrees of freedom and rich dynamical interplay, provide considerably more complexity. Two main goals of this program were to demonstrate the feasibility of laser-cooling molecules to the same temperatures as laser-cooled atoms and introduce a means for collecting laser-cooled molecules into dense ensembles, a foundational start of studies and applications of ultracold matter without equivalence in atomic systems.

74 ATOMIC AND MOLECULAR PHYSICS↗