Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MOLECULES”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule?

Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique “fingerprint” of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. Here we demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

ZnO quantum dot–molecule conjugates: Chemical interactions, charge dynamics, and spin polarization

Conjugates between molecules and quantum dots (QDs) have been explored for a range of potential applications from photocatalysis and photovoltaics to quantum information science technologies. A particularly ubiquitous material in many of these applications are ZnO QDs since they can accept and transport electrons and can also act as hosts for unique spin states. Conjugates between molecular light absorbers and ZnO QDs have been explored for decades as components in dye-sensitized solar cells. Recently, these materials have also attracted interest for their ability to produce spin-polarized states upon photoexcitation. The current paper employs a series of light absorbing perylene molecules with different ZnO QD sizes to explore key features of these QD–molecule conjugates: (1) chemical interactions, (2) charge dynamics, and (3) spin polarization. The chemical interactions between the molecules and QDs are determined with binding equilibria and reveal dramatic impact of ligand size. The charge transfer dynamics from photoexcited perylenes to ZnO QDs were found to depend exponentially on the linker length. Finally, time-resolved electron paramagnetic resonance experiments reveal that these conjugates generate spin-polarized states in the form of radical pairs and triplets. These spin states hold promise as potential qubits and also offer an avenue to efficiently sensitize molecular triplets.

Hernandez, Frida S. [Amherst College, MA (United S↗
DOE OSTI2020

Strong mutual increase in the efficiency of isotope-selective laser IR dissociation of molecules under nonequilibrium thermodynamic conditions of the compression shock under irradiation in a bimolecular mixture

We have revealed a strong (by a factor of 2 to 5) mutual increase in the yield of IR molecular dissociation (by the example of CF{sub 2}HCl and CF{sub 3}Br) and a significant (by a factor of 1.5 to 3) lowering of dissociation thresholds in the nonequilibrium thermodynamic conditions of compression shock in the irradiation of the molecules by resonance IR laser radiation in the bimolecular mixture in comparison with their individual irradiation. This opens up the possibility to perform efficient isotope-selective IR dissociation of molecules at lower excitation energy densities (Φ ⩽ 1.5 – 2.0 J cm{sup −2}) and thereby to improve the dissociation selectivity. This was demonstrated by the example of chlorine- and bromine-isotope selective dissociation of the specified molecules, which are characterised by quite small (less than 0.25 cm{sup −1}) isotope shifts in the IR vibrational absorption spectra excited by laser radiation. The enrichment coefficients K {sub enr}({sup 35}Cl / {sup 37}Cl) = 0.90 ± 0.05 in the residual CF{sub 2}HCl gas and K {sub enr}({sup 79}Br / {sup 81}Br) in the resultant Br{sub 2} product are obtained when the CF{sub 2}HCl : CF{sub 3}Br = 1 : 1 molecular mixture and CF{sub 3}Br molecules, respectively, are irradiated by the 9R(30) CO{sub 2} laser line (frequency, 1084.635 cm{sup −1}) at an energy density Φ ≈ 1.3 J cm{sup −2}. (laser isotope separation)

36 MATERIALS SCIENCE↗
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 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 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 OSTI2023

In planta single-molecule imaging and holographic force spectroscopy to study real-time, multimodal turnover dynamics of polysaccharides and associated carbohydrate metabolites

Cellular production of polysaccharides from simple sugar molecules serves critical roles in a variety of metabolic processes essential to the survival of every living organism. In the context of photosynthetically fixed carbon, cell wall polysaccharides synthesis is particularly of interest for increased biomass accumulation for human food, animal feed, and bioenergy related applications. Despite a long history of research in plant cell biology, our understanding of in planta cell wall biosynthesis and its regulation is far from complete due to lack of a comprehensive microscopy toolkit that encompass the multiple spatial and temporal scales in which cell wall polysaccharides fibrils are synthesized and assembled into intricate cell wall networks. In this project, a multidisciplinary team of scientists from Rutgers University, Vanderbilt University, and Oak Ridge National Laboratory carried out innovative multimodal, multiscale microscopy studies of cell wall synthesis using single-molecule force-spectroscopy, super-resolution fluorescence microscopy, and in vivo live cell imaging. Our novel multimodal and holistic imaging approach revealed plant cell wall polysaccharides synthesis processes in unprecedented detail across multiple spatiotemporal scales, from a single-molecule to a single-cell. Besides, the team has made technical and scientific innovations across multiple research fields—microscopy, bioengineering, single-molecule biophysics, and plant biology, etc.—to accomplish the goals. The results from this project will greatly advance the mechanistic and holistic understanding of in planta cell wall synthesis, which will accelerate the development of better transgenic crops for bioenergy applications. Moreover, the new toolbox, combining powerful advanced microscopy assays with cell/protein engineering, will have broader impacts on molecular and cellular biology fields by paving the way for studying cellular processes occurring across multiple physical scales with multimodal microscopy methodologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules (Final Report)

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Photoinitiated Reactions of Molecules and Radicals in Molecular Beams

The UV photochemistry of organic molecules is a fundamental process that governs reactions in the atmosphere, synthetic chemistry, processing of organic aerosols, and biological damage in living tissues. In many organic molecules, the ensuing evolution involves pathways that are in competition, giving rise to different products, isomerization, coupling to other electronic states, and secondary reactive collisions. Because photodissociation is usually fast (picoseconds to microseconds), these processes are far from equilibrium and are controlled by kinetic competition and dynamical forces. The work accomplished was focused primarily on the photochemistry of alpha-keto carboxylic acids, a group of acids produced from natural sources, which are implicated in aerosol formation and biological processes. In the atmosphere, they are destroyed mainly by solar radiation. Studying their photochemistry has been surprisingly difficult because of the complexity of their excited electronic states, and the effect of collisions and secondary reactions. The second project investigated the lifetime of excited electronic states of pyrazine and picoline and had both experimental and theoretical aspects. The work focused on a model molecule, pyruvic acid (PA), because it was hypothesized that it should be a good source of the unstable carbene, methylhydroxycarbene (MHC). PA has an internal hydrogen bond that controls the evolution of its decomposition. The decomposition was studied following excitation to two of its lowest excited states reached by laser irradiation at 351 and 193 nm. The photodissociation dynamics in the absence and presence of collisions was monitored and compared. Understanding the UV photochemistry requires the use of complementary experimental approaches. Two methods were enlisted, which together generated a comprehensive and detailed set of results: (i) The time-sliced velocity map imaging (SVMI) instrument at USC was exploited to determine kinetic energy release of fragments, fast dissociation timescales, and internal state distributions of fragments for which Resonance Enhanced Multiphoton Ionization (REMPI) schemes exist; and (ii) The multiplexed photoionization mass spectrometer (MPIMS) setup developed at the Sandia Combustion Research Facility was used for product discovery, achieved by exploiting tunable narrowband VUV radiation at the Advanced Light Source (ALS), and to follow in real time their subsequent unimolecular and bimolecular reactions. The experimental conditions ranged from collisionless molecular beams to study nascent products to flow reactors of variable pressures to study subsequent bimolecular reactions of the products. The goals stated above were successfully accomplished. By exciting PA to its lowest excited state, MHC was identified as the only primary product and its isomerization to vinylalcohol and acetaldehyde was directly observed in real time. Moreover, we reported the first bimolecular reaction of MHC, which was with acetaldehyde, and identified its reaction product. This paves the way for the study of other reactions of this important carbene intermediate. When excitation was carried out at 193 nm, which imparted much higher energy to PA, many more products were directly observed in real time, some deriving from three-body dissociation. Quantitative branching ratios and secondary reactions of radical products were also determined and analyzed. The studies of pyrazine and picoline focused on the second excited state of these molecules and showed (via ionization studies) that their excited states were very short lived (<100 fs) because of efficient couplings to lower electronic states via vibronic coupling. Theoretical work on modeling the absorption spectrum and decay mechanisms of the excited states are in progress in collaboration with theoreticians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗