Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “single molecule”

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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

ThAu 2 – , ThAu 2 O – , and ThAuOH – anions: Photoelectron spectroscopic and theoretical characterization

The thorium–gold negative ions ThAu 2 – , ThAu 2 O – , and ThAuOH – have been observed and experimentally characterized by anion photoelectron spectroscopy. These experiments are accompanied by extensive ab initio electronic structure calculations using a relativistic composite methodology based primarily on coupled cluster singles and doubles with perturbative triples calculations. The theoretical electron affinities (EAs) at 0 K agree with the experimental adiabatic EAs to within 0.02 eV for all species. Two separate isomers were located in the calculations for ThAuOH – , and detachment from both of these appears to be present in the photoelectron spectrum. Excited electronic states of the neutral molecules are reported at the equation of motion-coupled cluster singles and doubles level of theory. Atomization energies and heats of formation are also calculated for each neutral species and have expected uncertainties of 3 and 4 kcal/mol, respectively. The σ bonds between Th and Au are determined by natural bond orbital analysis to consist of predominately sd hybrids on Th bonding with the Au 6s orbital. In order to investigate the correspondence between the bonding in Th–Au and Th–F molecules, a limited number of calculations were also carried out on most of the F-analogs of this study. These results demonstrate that Au does behave like F in these cases, although the Th–F σ bonds are much more ionic compared to Th–Au. This results in an EA for ThF 2 that is 10 kcal/mol smaller than that of ThAu 2 . The EA values for the Th(IV) species, i.e., ThX 2 O and ThXOH, only differed, however, by 3–4 kcal/mol.

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

Understanding and Tailoring Diffusion and Co-Adsorption Inside the Confined Pores of Metal-Organic Frameworks (Final Scientific/Technical Report for Award DE-SC0019902)

The aim of this program was to gain a fundamental understanding of the behavior of various guest molecules in nano-confined environments, such as metal organic frameworks (MOFs), using a combination of novel synthesis, ab initio modeling, and in situ characterization. Through this project, we developed a concise understanding of the mechanisms that control adsorption/desorption of gaseous molecules and their mixtures, leading to design/synthesis guidelines for MOFs with desired functionality. We further developed methods to disentangle kinetic from thermodynamic effects during adsorption, as well as to characterize the interactions at play. In the first funding cycle, the focus was on the unambiguously characterization of co-adsorption and diffusion of gasses/vapors and their mixtures. In the second funding cycle, the focus was on characterizing the effects of the nano-confinement on the kinetics and thermodynamics of adsorption processes inside MOFs, again with an emphasis on mixtures of gasses and vapors. The nano-confinement can tip the thermodynamic vs. kinetic balance, and current understanding and theory based on single-component analysis can lead to incorrect predictions for mixtures. This is of particular interest in real-world applications, where gasses/vapors are typically mixed, contain impurities, or are often exposed to humid conditions. Our main findings were: (i) within confined environments the adsorption behavior of mixed gasses/vapors can be drastically different from the “sum” of the corresponding single phases; (ii) co-adsorption is often competitive and detrimental to performance, but it can also be cooperative and beneficial; (iii) in some co-adsorbed gasses/vapors, molecules that are strongly bound in the single-component phase can be replaced by molecules that are nominally weaker bound (molecular exchange) due to guest-guest interactions that lower the kinetic barriers and favor the final adsorption state; (iv) kinetic and thermodynamic effects can be precisely controlled through pore-size engineering and synthesis; and, (v) kinetic effects can be identified and disentangled from thermodynamic effects during adsorption through a series of sequential and simultaneous gas loading measurements. The short-term goal of this program was the controlling and understanding of common MOF systems in real-world situations where gasses/vapors are mixed, which will have an important impact on industrial processes and applications from gas storage and sequestration to catalysis and sensors. The long-term goals include the development of theoretical and experimental methods for gaining a fundamental understanding of adsorption/reaction processes within MOFs, as well as new guidelines for synthesizing MOFs with tailored physical and chemical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Hybrid Absorption–Crystallization Strategies for the Direct Air Capture of CO2 Using Phase-Changing Guanidium Bases: Insights from in Operando X-ray Scattering and Infrared Spectroscopy Measurements

Efforts to limit rising concentrations of CO 2 have motivated the development of negative emission technologies. Direct air capture (DAC) of CO 2 is one of the negative emissions technologies that has been proposed for the direct removal of CO 2 from the atmosphere. Phase-changing bis(iminonoguanidine) (BIG) sorbents have been developed for the direct air capture of CO 2 . These phase changing sorbents, specifically glyoxal-bis(iminoguanidine) (GBIG), involve (1) CO 2 absorption with aqueous amino acid salts, such as K- or Na-glycinate to yield bicarbonate-rich solutions, (2) crystallization of the bicarbonate anions with a BIG solid, which regenerates the amino acid, and (3) solid-state CO 2 release from the carbonate crystals and BIG regeneration. Despite the promising potential of these materials, their structural evolution during the thermal regeneration of the BIG solids, chemical regeneration of the sodium or potassium glycinate solvents, and the crystallization behavior of CO 2 -loaded BIG bicarbonate remain to be evaluated and understood in detail. The aim of this study is to probe these knowledge gaps. In situ wide-angle X-ray Scattering (WAXS) results show that CO 2 and water molecules in GBIG bicarbonate are simultaneously released in a single step during the thermal regeneration of the sorbent at 97 – 134 °C. In situ ATR-FTIR measurements showed that sodium glycinate and GBIG bicarbonate are simultaneously generated when GBIG, glycine, and sodium bicarbonate are reacted. The crystallization of GBIG bicarbonate from GBIG and CO 2 -loaded monoethanolamine (MEA) occurs rapidly in the first 10 min of the reaction, as determined using in situ GI-SAXS measurements. Overall, the insights from these studies are essential for the scalable implementation of CO 2 capture technologies using these phase-changing sorbents.

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

The CNK–HYP scaffolding complex promotes RAF activation by enhancing KSR–MEK interaction

The RAS–MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1–BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR–MEK interaction, which in turn enhances RAF–KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR–MEK–CNK–HYP complex reveals a ring-like arrangement of the CNK–HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR–MEK interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

graphenv: a Python library for reinforcement learning on graph search spaces

Many important and challenging problems in combinatorial optimization (CO) can be expressed as graph search problems, in which graph vertices represent full or partial solutions and edges represent decisions that connect them. Graph structure not only introduces strong relational inductive biases for learning (Battaglia et al., 2018) - in this context, by providing a way to explicitly model the value of transitioning (along edges) between one search state (vertex) and the next - but lends itself to problems both with and without clearly defined algebraic structure. For example, classic CO problems on graphs such as the Traveling Salesman Problem (TSP) can be expressed as either pure graph search or integer programs. Other problems, however, such as molecular optimization, do no have concise algebraic formulations and yet are readily implemented as a graph search (V. et al., 2022; Zhou et al., 2019). Such "model-free" problems constitute a large fraction of modern reinforcement learning (RL) research owing to the fact that it is often much easier to write a forward simulation that expresses all of the state transitions and rewards, than to write down the precise mathematical expression of the full optimization problem. In the case of molecular optimization, for example, one can use domain knowledge alongside existing software libraries to model the effect of adding a single bond or atom to an existing but incomplete molecule, and let the RL algorithm build a model of how good a given decision is by "experiencing" the simulated environment many times through. In contrast, a model-based mathematical formulation that fully expresses all the chemical and physical constraints is intractable. In recent years, RL has emerged as an effective paradigm for optimizing searches over graphs and led to state-of-the-art heuristics for games like Go and chess, as well as for classical CO problems such as the TSP. This combination of graph search and RL, while powerful, requires non-trivial software to execute, especially when combining advanced state representations such as Graph Neural Networks (GNN) with scalable RL algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Selective filling of n-hexane in a tight nanopore

Abstract Molecular sieving may occur when two molecules compete for a nanopore. In nearly all known examples, the nanopore is larger than the molecule that selectively enters the pore. Here, we experimentally demonstrate the ability of single-wall carbon nanotubes with a van der Waals pore size of 0.42 nm to separate n-hexane from cyclohexane—despite the fact that both molecules have kinetic diameters larger than the rigid nanopore. This unexpected finding challenges our current understanding of nanopore selectivity and how molecules may enter a tight channel. Ab initio molecular dynamics simulations reveal that n-hexane molecules stretch by nearly 11.2% inside the nanotube pore. Although at a relatively low probability (28.5% overall), the stretched state of n-hexane does exist in the bulk solution, allowing the molecule to enter the tight pore even at room temperature. These insights open up opportunities to engineer nanopore selectivity based on the molecular degrees of freedom.

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

Impact of Classical and Quantum Light on Donor–Acceptor–Donor Molecules

Investigations of entangled and classical two-photon absorption have been carried out for six donor (D)–acceptor (A)–donor (D) compounds containing the dithieno pyrrole (DTP) unit as donor and acceptors with systematically varied electronic properties. Comparing ETPA (quantum) and TPA (classical) results reveals that the ETPA cross section decreases with increasing TPA cross section for molecules with highly off-resonant excited states for single-photon excitation. Theory (TDDFT) results are in semiquantitative agreement with this anticorrelated behavior due to the dependence of the ETPA cross section but not TPA on the two-photon excited state lifetime. Furthermore, the largest cross section is found for a DTP derivative that has a single photon excitation energy closest to resonance with half the two-photon excitation energy. These results are important for the possible use of quantum light for low-intensity energy-conversion applications.

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

Threshold Ionization Spectroscopy and Theoretical Calculations of LnO (Ln = La and Ce)

Mass-analyzed threshold ionization (MATI) spectroscopy was used to measure the vibronic spectra of LnO (Ln = La and Ce). Single-reference coupled cluster and relativistic multireference configuration calculations were carried out to compare with the measured vibronic energies. The spectrum of LaO displays a single vibronic band system, while that of CeO shows multiple ones. The ionization energies of LaO and CeO are measured as 5.2446 (6) and 5.3332(6) eV, respectively, which are a hundredfold improvement over the literature values. The vibrational energies of the neutral molecule and corresponding ion reveal the charge effect on the metal-oxygen bond of both species. The single band system in the spectrum of LaO arises from the transition of the ground state of the neutral molecule with the La(6s 1 )O(2p 6 ) valence configuration to the ground state of the singly charged ion with the La(6s o )O(2p 6 ) configuration. Here, the multiple band systems in the spectrum of CeO are attributed to the spin-orbit coupling for the Ce(4f 1 6s 1 )O(2p 6 ) configuration of the neutral molecule and an excited state for the Ce(4f 1 )O(2p 6 ) configuration of the ion.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Electron-ion coincidence measurements of molecular dynamics with intense X-ray pulses

Molecules can sequentially absorb multiple photons when irradiated by an intense X-ray pulse from a free-electron laser. If the time delay between two photoabsorption events can be determined, this enables pump-probe experiments with a single X-ray pulse, where the absorption of the first photon induces electronic and nuclear dynamics that are probed by the absorption of the second photon. Here we show a realization of such a single-pulse X-ray pump-probe scheme on N 2 molecules, using the X-ray induced dissociation process as an internal clock that is read out via coincident detection of photoelectrons and fragment ions. By coincidence analysis of the kinetic energies of the ionic fragments and photoelectrons, the transition from a bound molecular dication to two isolated atomic ions is observed through the energy shift of the inner-shell electrons. Via ab-initio simulations, we are able to map characteristic features in the kinetic energy release and photoelectron spectrum to specific delay times between photoabsorptions. In contrast to previous studies where nuclear motions were typically revealed by measuring ion kinetics, our work shows that inner-shell photoelectron energies can also be sensitive probes of nuclear dynamics, which adds one more dimension to the study of light-matter interactions with X-ray pulses.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Rydberg-atom-based single-photon detection for haloscope axion searches

We propose a Rydberg-atom-based single-photon detector for signal readout in dark matter haloscope experiments between 40 μ eV and 200 μ eV (10 GHz and 50 GHz). At these frequencies, standard haloscope readout using linear amplifiers is limited by quantum measurement noise, which can be avoided by using a single-photon detector. Our single-photon detection scheme can offer scan rate enhancements up to a factor of 10 4 over traditional linear amplifier readout, and is compatible with many different haloscope cavities. We identify multiple haloscope designs that could use our Rydberg-atom-based single-photon detector to search for QCD axions with masses above 40 μ eV (10 GHz), currently a minimally explored parameter space. Published by the American Physical Society 2024

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes

In this work, we develop a quartic-scaling implementation of coupled-cluster singles and doubles (CCSD) based on low-rank tensor hypercontraction (THC) factorizations of both the electron repulsion integrals (ERIs) and the doubles amplitudes. This extends our rank-reduced (RR) coupled-cluster method to incorporate higher-order tensor factorizations. The THC factorization of the doubles amplitudes accounts for most of the gain in computational efficiency as it is sufficient, in conjunction with a Cholesky decomposition of the ERIs, to reduce the computational complexity of most contributions to the CCSD amplitude equations. Further THC factorization of the ERIs reduces the complexity of certain terms arising from nested commutators between the doubles excitation operator and the two-electron operator. We implement this new algorithm using graphical processing units and demonstrate that it enables CCSD calculations for molecules with 250 atoms and 2500 basis functions using a single computer node. Furthermore, we show that the new method computes correlation energies with comparable accuracy to the underlying RR-CCSD method.

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

Explicitly correlated coupled cluster method for accurate treatment of open-shell molecules with hundreds of atoms

We present a near-linear scaling formulation of the explicitly correlated coupled-cluster singles and doubles with the perturbative triples method [CCSD(T)F12¯] for high-spin states of open-shell species. The approach is based on the conventional open-shell CCSD formalism [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] utilizing the domain local pair-natural orbitals (DLPNO) framework. The use of spin-independent set of pair-natural orbitals ensures exact agreement with the closed-shell formalism reported previously, with only marginally impact on the cost (e.g., the open-shell formalism is only 1.5 times slower than the closed-shell counterpart for the C160H322 n-alkane, with the measured size complexity of ≈1.2). Evaluation of coupled-cluster energies near the complete-basis-set (CBS) limit for open-shell systems with more than 550 atoms and 5000 basis functions is feasible on a single multi-core computer in less than 3 days. The aug-cc-pVTZ DLPNO-CCSD(T)F12¯ contribution to the heat of formation for the 50 largest molecules among the 348 core combustion species benchmark set [J. Klippenstein et al., J. Phys. Chem. A 121, 6580–6602 (2017)] had root-mean-square deviation (RMSD) from the extrapolated CBS CCSD(T) reference values of 0.3 kcal/mol. For a more challenging set of 50 reactions involving small closed- and open-shell molecules [G. Knizia et al., J. Chem. Phys. 130, 054104 (2009)], the aug-cc-pVQ(+d)Z DLPNO-CCSD(T)F12¯ yielded a RMSD of ∼0.4 kcal/mol with respect to the CBS CCSD(T) estimate.

Kumar, Ashutosh (ORCID:0000000175896030)↗
DOE OSTI2024

Controlled molecule injector for cold, dense, and pure molecular beams at the European x-ray free-electron laser

A permanently available molecular-beam injection setup for controlled molecules (COMO) was installed and commissioned at the small quantum systems (SQS) instrument at the European x-ray free-electron laser (EuXFEL). A b-type electrostatic deflector allows for pure state-, size-, and isomer-selected samples of polar molecules and clusters. The source provides a rotationally cold (T ≈ 1 K) and dense (ρ ≈ 10 8 cm −3 ) molecular beam with pulse durations up to 100 µs generated by a new version of the Even-Lavie valve. Here, a performance overview of the COMO setup is presented along with characterization experiments performed both with an optical laser at the Center for Free-Electron-Laser Science and with x rays at EuXFEL under burst-mode operation. COMO was designed to be attached to different instruments at the EuXFEL, in particular, the SQS and single particles, clusters, and biomolecules (SPB) instruments. This advanced controlled-molecules injection setup enables x-ray free-electron laser studies using highly defined samples with soft and hard x-ray FEL radiation for applications ranging from atomic, molecular, and cluster physics to elementary processes in chemistry and biology.

He, Lanhai↗
DOE OSTI2022

Role of Bimetallic Interactions in the Enhancement of Catalytic CO 2 Reduction by a Macrocyclic Cobalt Catalyst

The use of two metal centers in a CO 2 reduction catalyst that work together synergistically, with similar or complementary functions, can potentially lead to a significant reduction in overpotential, enhance catalytic activity and/or selectivity, and/or enable access to cascade strategies where each metal center catalyzes a different step in the conversion of CO 2 to a fuel. Here, the bimetallic reactivity of two metal centers has been identified as the primary route for the reduction of CO 2 to CO promoted by the macrocycle, [Co(HMD)] 2+ (HMD = 5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene), based on the experimental characterization of all major steps of the proposed catalytic cycle using pulse radiolysis time-resolved IR (PR-TRIR) spectroscopy, corroborated by density functional theory (DFT) calculations and IR spectroelectrochemistry (IR-SEC). A bimetallic intermediate is formed in situ from two singly reduced [Co(HMD)] + species bridged by a CO 2 molecule, and the presence of a coordinating species, e.g., formate anion, appears to assist in the formation of such an intermediate. In this work, it has been demonstrated that this reactivity enables access to elementary steps with lower energy requirements, resulting in overall catalysis being kinetically more facile compared to the mononuclear pathway. A two-step approach that combines chemical reduction followed by PR-TRIR has been successfully used for probing the structure and reactivity of reactive intermediates involved in the advanced stages of a catalytic cycle, which are rarely interrogated using experimental techniques.

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

Aging power spectrum of membrane protein transport and other subordinated random walks

Single-particle tracking offers detailed information about the motion of molecules in complex environments such as those encountered in live cells, but the interpretation of experimental data is challenging. One of the most powerful tools in the characterization of random processes is the power spectral density. However, because anomalous diffusion processes in complex systems are usually not stationary, the traditional Wiener-Khinchin theorem for the analysis of power spectral densities is invalid. Here, we employ a recently developed tool named aging Wiener-Khinchin theorem to derive the power spectral density of fractional Brownian motion coexisting with a scale-free continuous time random walk, the two most typical anomalous diffusion processes. Using this analysis, we characterize the motion of voltage-gated sodium channels on the surface of hippocampal neurons. Our results show aging where the power spectral density can either increase or decrease with observation time depending on the specific parameters of both underlying processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Resonant Auger decay of iodobenzene below the I 4d edge

New data are presented on the resonant Auger decay of iodobenzene (C 6 H 5 I) in the region of the I 4d –1 ionization threshold. The excited molecules decay by participator and spectator processes to populate single-hole valence states and two-hole, one-particle excited states of the cation, providing new information on the structure of C 6 H 5 I + . Excitation of dissociative C 6 H 5 I (I 4d 5/2,3/2 –1 )σ* resonances can, in principle, result in ultrafast dissociation to C 6 H 5 + I** and the subsequent autoionization of I**, but no evidence for this process is observed. Finally, the results are compared with our recent study of the resonant Auger decay of methyl iodide (CH 3 I).

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

Direct tests of cytochrome c and c 1 functions in the electron transport chain of malaria parasites

The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.

60 APPLIED LIFE SCIENCES↗