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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences

Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5'-AAAGTTT-3'. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Hypermetallic polar molecules for precision measurements

Laser cooling is a powerful method to control molecules for applications in precision measurement, as well as quantum information, many-body physics, and fundamental chemistry. However, many optically-active metal centers in valence states which are promising for these applications, especially precision measurement, are difficult to laser cool. In order to extend the control afforded by laser cooling to a wider array of promising atoms, we consider the use of small, hypermetallic molecules that contain multiple metal centers. We provide a detailed analysis of YbCCCa and YbCCAl as prototypical examples with different spin multiplicities, and consider their feasibility for precision measurements making use of the heavy Yb atom. We find that these molecules are linear and feature metal-centered valence electrons, and study the complex hybridization and spin structures that are relevant to photon cycling and laser cooling. Our findings suggest that this hypermetallic approach may be a versatile tool for experimental control of metal species that do not otherwise efficiently cycle photons, and could present a new polyatomic platform for state-of-the-art precision measurements.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Retrieval of full angular- and energy-dependent complex transition dipoles in the molecular frame from laser-induced high-order harmonic signals with aligned molecules

High-order harmonic signals generated in molecules are the consequence of coherent summation of complex laser-induced transition dipoles $\textit{d}(θ, ω)$ with each fixed-in-space molecule; here $\theta$ is the angle of the molecular axis with respect to the laser polarization axis and $\omega$ is the harmonic energy. In the so-called rotational coherent spectroscopy, it is proposed to extract the fixed-in-space $\textit{d}(θ, ω)$ in the molecular frame by measuring harmonics generated by a probing laser from the rotational molecular wave packets that have been prepared by a prior pump laser. By varying the time delay between the two lasers, methods have been utilized to extract the $\theta$ dependence of both the amplitude and phase of each individual harmonic, but the relative phase between harmonics cannot be retrieved. Here we report that this limitation can be removed. It requires the additional measurement of harmonic spectra versus the pump-probe angles at one fixed time delay. The two-dimensional input harmonic data (time-delay and pump-probe angle) are then used to retrieve the full complex transition dipole $\textit{d}(θ, ω)$ using a retrieval method based on machine learning algorithms. Finally, we demonstrate this method on N 2 and CO 2 molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Robust control of the minima of high-order harmonics by fine-tuning the alignment of CO 2 molecules for shaping attosecond pulses and probing molecular alignment

In a recent paper, we reported that the position and depth of the minima in the harmonic spectra of CO 2 molecules can be dramatically manipulated by a slight change of the degree of alignment, thus providing a convenient method of shaping attosecond pulses which could lead to the splitting of a typical single attosecond burst into two. Here, we demonstrate that harmonic minima can also be dramatically controlled by changing the pump-probe angles to shape attosecond pulses. In the meanwhile, since the pump-probe angle-dependent harmonic spectra are very sensitive to the degree of alignment, harmonic spectra can also be used to calibrate the alignment distribution of molecules. In this work we identify such robust control of harmonic generation is due to the optical property of CO 2 and the coherent harmonic emission from the oriented molecules. The photoionization transition dipoles (PITDs) of CO 2 exhibit deep minima that change rapidly with molecular orientations accompanied by large phase changes of π in PITDs, thus leading to strong interference when the dipoles are added up coherently.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Two-photon photoassociation spectroscopy of an ultracold heteronuclear molecule

In this work, we report on two-photon photoassociation (PA) spectroscopy of ultracold heteronuclear LiRb molecules. This is used to determine the binding energies of the loosely bound levels of the electronic ground singlet and the lowest triplet states of LiRb. We observe strong two-photon PA lines with power broadened linewidths greater than 20 GHz at relatively low laser intensity of 30W/cm2. The implication of this observation on direct atom to molecule conversion using stimulated Raman adiabatic passage is discussed and the prospect for electronic ground-state molecule production is theoretically analyzed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Extraction of geometrical structure of ethylene molecules by laser-induced electron diffraction combined with ab initio scattering calculations

In this paper, we measured angle-resolved high-energy electron spectra emitted from ${\mathrm{C}}_{2}{\mathrm{H}}_{4}$ in an intense laser field, extracted field-free electron-ion elastic scattering differential cross sections (DCSs) according to quantitative rescattering theory, and obtained molecular contrast factors (MCFs) subtracting the incoherent sum of DCSs of all the atoms in the molecule. Comparing the results with ab initio scattering calculations and employing least-squares fitting, we have extracted the C-C and C-H bond lengths of the molecule with ${\sim}5$ % uncertainty. Finally, this approach opens the way to retrieve the structure of hydrocarbon molecules, potentially at high temporal resolution, employing low collision energies where electron scattering is sensitive to the hydrogen atoms; and where the independent atom model calculations may fail to reproduce the experimentally extracted MCF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Generation of circularly polarized XUV and soft-x-ray high-order harmonics by homonuclear and heteronuclear diatomic molecules subject to bichromatic counter-rotating circularly polarized intense laser fields

Recently, studies of bright circularly polarized high-harmonic beams from atoms in the soft-x-ray region as a source for x-ray magnetic circular dichroism measurement in a tabletop-scale setup have received considerable attention. In this paper, we address the problem with molecular targets and perform a detailed quantum study of H 2 +, CO, and N 2 molecules in bichromatic counter-rotating circularly polarized laser fields where we adopt wavelengths (1300 and 790 nm) and intensities (2 × 10 14 W/cm 2 ) reported in a recent experiment [Proc. Natl. Acad. Sci. USA 112, 14206 (2015)]. Our treatment of multiphoton processes in homonuclear and heteronuclear diatomic molecules is nonperturbative and based on the time-dependent density-functional theory for multielectron systems. The calculated radiation spectrum contains doublets of left and right circularly polarized harmonics with high-energy photons in the XUV and soft-x-ray ranges. Overall, our results reveal intriguing and substantially different nonlinear optical responses for homonuclear and heteronuclear diatomic molecules subject to circularly polarized intense laser fields. We study in detail the below- and above-threshold harmonic regions and analyze the ellipticity and phase of the generated harmonic peaks.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Slow spin relaxation in single endohedral fullerene molecules

Well-protected magnetization, tunable quantum states, and long spin-relaxation time are desired for the use of magnetic molecules in spintronics and quantum information technologies. In this work, endohedral fullerene molecules M@C 28 with different transition-metal cores were explored through systematic first-principles calculations and spin dynamics analyses. Many of them have bias-tunable structure, stable magnetization, and sizable magnetic anisotropy energy. Furthermore, some of them may have spin-relaxation time up to several milliseconds for their quantum spin states at high temperature (~10 K) after full consideration of spin-vibration couplings. In conclusion, our results suggest that these M@C 28 provide a rich pool of single-molecule magnets for diverse applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH 2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidal C ≡ C feature in PHTB can be ascribed to its twisted nature. The ability to simulate such subatomic images in nc-AFM reflects the accuracy and efficiency of calculating quantum forces in real space.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗
DOE OSTI2024

Invariant Features for Accurate Predictions of Quantum Chemical UV-vis Spectra of Organic Molecules

Including invariance of global properties of a phys-ical system as an intrinsic feature in graph neural networks (GNNs) enhances the model's robustness and generalizability and reduces the amount of training data required to obtain a desired accuracy for predictions of these properties. Existing open source GNN libraries construct invariant features only for specific GNN architectures. This precludes the generalization of invariant features to arbitrary message passing neural network (MPNN) layers which, in turn, precludes the use of these libraries for new, user-specified predictive tasks. To address this limitation, we implement invariant MPNNs into the flexible and scalable HydraGNN architecture. HydraGNN enables a seamless switch between various MPNNs in a unified layer sequence and allows for a fair comparison between the predictive performance of different MPNNs. We trained this enhanced HydraGNN archi-tecture on the ultraviolet-visible (UV-vis) spectrum of GDB-9 molecules, a feature that describes the molecule's electronic exci-tation modes, computed with time-dependent density functional tight binding (TD-DFTB) and available open source through the GDB-9-Ex dataset. We assess the robustness (i.e., accuracy and generalizability) of the predictions obtained using different invariant MPNNs with respect to different values of the full width at half maximum (FWHM) for the Gaussian smearing of the theoretical peaks. Our numerical results show that incorporating invariance in the HydraGNN architecture significantly enhances both accuracy and generalizability in predicting UV-vis spectra of organic molecules.

Baker, Justin↗
DOE OSTI2019

Molecular docking predictions of fragrance binding to human leukocyte antigen molecules

Abstract Background Over 4000 small chemicals have been identified as allergens capable of inducing skin sensitization. Many sensitizers are hypothesized to act as haptens producing novel antigens, which can be presented to T cells by human leukocyte antigens (HLAs). Recent studies suggest that some chemical allergens use hapten‐independent mechanisms. Objective To determine whether molecular docking can identify HLA molecules that bind skin‐sensitizing chemical allergens. Methods Structural models of HLA molecules were used as the basis for molecular docking of 22 chemical allergens. Allergens predicted to bind HLA‐B*57:01 were tested for their ability to stimulate T cells by the use of proliferation and interferon‐gamma enzyme‐linked immunospot assays. Results Chemical allergens that did not satisfy the criteria for hapten activity in vitro were predicted to bind more strongly to common HLA isoforms than those with known hapten activity. HLA‐B*57:01, which is an HLA allele required for drug hypersensitivity reactions, was predicted to bind several allergens, including benzyl benzoate, benzyl cinnamate, and benzyl salicylate. In in vitro T cell stimulation assays, benzyl salicylate and benzyl cinnamate were found to stimulate T cell responses from HLA‐B*57:01 carriers. Conclusions These data suggest that small‐molecule skin sensitizers have the potential to interact with HLA, and show that T cell‐based in vitro assays may be used to evaluate the immunogenicity of skin‐sensitizing chemicals.

Schutte, Ryan J.↗
DOE OSTI2016

Metal-assisted polyatomic SIMS and laser desorption/ionization for enhanced small molecule imaging of bacterial biofilms

Mass spectrometry imaging (MSI) has become an important analytical tool for many sectors of science and medicine. As the application of MSI expands into new areas of inquiry, existing methodologies must be adapted and improved to meet emerging challenges. In particular salient is the need for small molecule imaging methods that are compatible with complex multicomponent systems, a challenge that is amplified by the effects of analyte migration and matrix interference. Furthermore, with a focus on microbial biofilms from the opportunistic pathogen Pseudomonas aeruginosa, the relative advantages of two established microprobe-based MSI techniques—polyatomic secondary ion mass spectrometry (SIMS) and laser desorption/ionization—are compared, with emphasis on exploring the effect of surface metallization on small molecule imaging. A combination of qualitative image comparison and multivariate statistical analysis demonstrates that sputtering microbial biofilms with a 2.5 nm layer of gold selectively enhances C 60 -SIMS ionization for several molecular classes including rhamnolipids and 2-alkyl-quinolones. Metallization also leads to the reduction of in-source fragmentation and subsequent ionization of media-specific background polymers, which improves spectral purity and image quality. Our findings show that the influence of metallization upon ionization is strongly dependent on both the surface architecture and the analyte class, and further demonstrate that metal-assisted C 60 -SIMS is a viable method for small molecule imaging of intact molecular ions in complex biological systems. VC 2016 American Vacuum Society.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Waveform-dependent air fluorescence from neutral and ionic nitrogen molecules

Laser-induced air fluorescence in the ultraviolet regime is primarily attributed to transitions between the C and B states in excited neutral N 2 molecules and between the B and X states in N$^+_2$ ions. However, the mechanism underlying the former remains contentious, as direct population to the C state by light fields is forbidden by electron spin constraints. In this work, we investigate the mechanism of air fluorescence from excited neutral N 2 molecules by carrier-envelope phase–stabilized sub–4 femtosecond pulses. Our results show that fluorescence from N$^+_2$ ions reaches a maximum with cosine-like pulses, while fluorescence from excited neutral N 2 molecules peaks with sine-like pulses. In addition, by scanning the chirp of the driving pulse, we find that ionic fluorescence is maximized with chirp-free pulses, whereas neutral fluorescence favors negatively chirped pulses. These observations, supported by classical trajectory Monte Carlo simulations, support the mechanism of intersystem crossing from excited spin-singlet states, which are populated via recollision-induced strong-field excitation.

Science & Technology - Other Topics↗
DOE OSTI2023

Rational design of Lewis base molecules for stable and efficient inverted perovskite solar cells

Lewis base molecules that bind undercoordinated lead atoms at interfaces and grain boundaries (GBs) are known to enhance the durability of metal halide perovskite solar cells (PSCs). Using density functional theory calculations, we found that phosphine-containing molecules have the strongest binding energy among members of a library of Lewis base molecules studied herein. Experimentally, we found that the best inverted PSC treated with 1,3-bis(diphenylphosphino)propane (DPPP), a diphosphine Lewis base that passivates, binds, and bridges interfaces and GBs, retained a power conversion efficiency (PCE) slightly higher than its initial PCE of ~23% after continuous operation under simulated AM1.5 illumination at the maximum power point and at ~40°C for >3500 hours. DPPP-treated devices showed a similar increase in PCE after being kept under open-circuit conditions at 85°C for >1500 hours.

14 SOLAR ENERGY↗
DOE OSTI2022

Optical O 2 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria

From a metabolic perspective, molecular oxygen (O 2 ) is arguably the most significant constituent of Earth’s atmosphere. Nearly every facet of microbial physiology is sensitive to the presence and concentration of O 2 , which is the most favorable terminal electron acceptor used by organisms and also a dangerously reactive oxidant. As O 2 has such sweeping implications for physiology, researchers have developed diverse approaches to measure O 2 concentrations in natural and laboratory settings. Recent improvements to phosphorescent O 2 sensors piqued our interest due to the promise of optical measurement of spatiotemporal O 2 dynamics. However, we found that our preferred bacterial model, Pseudomonas aeruginosa PA14, secretes more than one molecule that quenches such sen sors, complicating O 2 measurements in PA14 cultures and biofilms. Assaying supernatants from cultures of 9 bacterial species demonstrated that this phenotype is common: all super natants quenched a soluble O 2 probe substantially. Phosphorescent O 2 probes are often embedded in solid support for protection, but an embedded probe called O 2 NS was quenched by most supernatants as well. Measurements using pure compounds indicated that quenching is due to interactions with redox-active small molecules, including phena zines and flavins. Uncharged and weakly polar molecules like pyocyanin were especially potent quenchers of O 2 NS. These findings underscore that optical O 2 measurements made in the presence of bacteria should be carefully controlled to ensure that O 2 , and not bacterial secretions, is measured, and motivate the design of custom O 2 probes for specific organisms to circumvent sensitivity to redox-active metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Beams of fast neutral atoms and molecules in low-pressure gas-discharge plasma

Fast neutral atom and molecule beams have been studied, the beams being produced in a vacuum chamber at nitrogen, argon, or helium pressure of 0.1-10 Pa due to charge-exchange collisions of ions accelerated in the sheath between the glow discharge plasma and a negative grid immersed therein. From a flat grid, two broad beams of molecules with continuous distribution of their energy from zero up to e(U + U{sub c}) (where U is voltage between the grid and the vacuum chamber and U{sub c} is cathode fall of the discharge) are propagating in opposite directions. The beam propagating from the concave surface of a 0.2-m-diameter grid is focused within a 10-mm-diameter spot on the target surface. When a 0.2-m-diameter 0.2-m-high cylindrical grid covered by end disks and composed of parallel 1.5-mm-diameter knitting needles spaced by 4.5 mm is immersed in the plasma, the accelerated ions pass through the gaps between the needles, turn inside the grid into fast atoms or molecules, and escape from the grid through the gaps on its opposite side. The Doppler shift of spectral lines allows for measuring the fast atom energy, which corresponds to the potential difference between the plasma inside the chamber and the plasma produced as a result of charge-exchange collisions inside the cylindrical grid.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2011

Quantum-chemical study of adsorption of 2-propanol molecule on a GaAs (100) surface

Quantum-chemical cluster calculations employing density functional theory are used to study the adsorption mechanism of 2-propanol molecules on a Ga-rich GaAs (100) surface. It is shown that 2-propanol molecules can be adsorbed either molecularly or dissociatively. Dissociation of 2-propanol molecules at the GaAs(100) surface can proceed with the rupture of an O-H or C-OH bond. The state with the rupture of the C-OH bond has the lowest energy among all possible adsorption states. However, for transition into this state, a very high barrier should be overcome, which is possible only at the semiconductor/liquid interface. The calculated adsorption path agrees well with the available experimental data on the interaction of 2-propanol with the GaAs (100) surface.

36 MATERIALS SCIENCE↗