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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Atomic-Scale Dynamic Mechanisms of Embedded MoS 2 Wires

Nanowires composed of a 1:1 stoichiometry of transition metals and chalcogen ions can be fabricated from two-dimensional transition metal dichalcogenides (TMDs) by using electron beam irradiation. Wires fabricated through in situ experiments can be geometrically connected to TMD sheets in various ways, and their physical properties can vary accordingly. Understanding the structural transformation caused by electron beams is critical for designing wire-sheet structures for nanoelectronics. In this study, we report the behavior of nanowires formed inside a monolayer MoS 2 sheet by combining phase-contrast images and large-scale atomistic modeling. Here we investigate the effect of vacancies on the dynamic evolution of wires, such as rotations with different edge structures and breaking, by considering the interactions between MoS wires and MoS 2 nanosheets. The obtained insights can be applied to other monolayer TMDs to guide the behavior of TMD wires and fabricate favorable geometries for various applications.

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

LEU Fission Plate: Experimental Prototype Design Document

The Ultracold Neutron (UCN) source at LANSCE is currently the source of the highest density of UCN in the world. We intend to use innovative new solutions to boost our UCN density in order to maintain our leadership in this competitive field. Prior studies suggest that a fission plate neutron multiplier made from low enriched uranium (LEU) installed between our spallation target and UCN source moderator can boost the density by up to a factor of ten. Here we present a prototype of this idea that uses an existing one liter volume of LEU that can boost the UCN density by roughly a factor of 2. Additional simulation studies presented here also suggest that we may find more gains by replacing some of the moderator or reflector geometries with beryllium.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1992

Hard X-ray tests of the unified model for an ultraviolet-detected sample of Seyfert 2 galaxies

An ultraviolet-detected sample of Seyfert 2 galaxies shows heavy photoelectric absorption in the hard X-ray band. The presence of UV emission combined with hard X-ray absorption argues strongly for a special geometry which must have the general properties of the Antonucci and Miller unified model. The observations of this sample are consistent with the picture in which the hard X-ray photons are viewed directly through the obscuring matter (molecular torus?) and the optical, UV, and soft X-ray continuum are seen in scattered light. The large range in X-ray column densities implies that there must be a large variation in intrinsic thicknesses of molecular tori, an assumption not found in the simplest of unified models. Furthermore, constraints based on the cosmic X-ray background suggest that some of the underlying assumptions of the unified model are wrong.

Mulchaey, John S.↗
NASA NTRS1993

Abundance inhomogeneities and atmospheric structure in CN-bimodal globular cluster giants

It has been suggested by several authors that the sodium and aluminum abundance variations correlating with CN-band strength, frequently observed in CN-bimodal globular cluster giants, could be spurious manifestations of different temperature structures in the 'CN-strong' and 'CN-weak' stars, caused by different molecular line blanketing related to the C, N, and O trio. For stellar parameters generally appropriate to giants in the intermediate metallicity CN-bimodal cluster M4, we demonstrate through new model atmosphere calculations, employing opacity sampling and spherical geometry, that the observed abundance anomalies cannot be the result of atmospheric temperature structure. Our results using spherical geometry are compared to identical calculations performed with plane-parallel geometry: the effects of atmospheric extension on derived abundances for all lines considered amount to less than 0.1 dex.

Drake, Jeremy J.↗
DOE OSTI2021

Vibrational Sum-Frequency Generation Hyperspectral Microscopy for Molecular Self-Assembled Systems

In this review, we discuss the recent developments and applications of vibrational sum-frequency generation (VSFG) microscopy. This hyperspectral imaging technique can resolve systems without inversion symmetry, such as surfaces, interfaces and noncentrosymmetric self-assembled materials, in the spatial, temporal, and spectral domains. We discuss two common VSFG microscopy geometries: wide-field and confocal point-scanning. We then introduce the principle of VSFG and the relationships between hyperspectral imaging with traditional spectroscopy, microscopy, and time-resolved measurements. We further highlight crucial applications of VSFG microscopy in self-assembled monolayers, cellulose in plants, collagen fibers, and lattice self-assembled biomimetic materials. In these systems, VSFG microscopy reveals relationships between physical properties that would otherwise be hidden without being spectrally, spatially, and temporally resolved. Lastly, we discuss the recent development of ultrafast transient VSFG microscopy, which can spatially measure the ultrafast vibrational dynamics of self-assembled materials. The review ends with an outlook on the technical challenges of and scientific potential for VSFG microscopy.

Chemistry↗
NASA NTRS2018

Exploring Li-Air Batteries for High Specific Energy and High Power Applications: A Simulation Study

Commercialization of lithium-air batteries face many challenges, such as electrolyte decomposition, short cycle life, low energy efficiency, low power density, etc. However, commercialization of Li-air batteries for mass sensitive applications such as electric vehicles, portable power source, and drones is more challenging due to additional constraints of safety, electrolyte evaporation, high specific energy requirements, and reliable discharge times. In this presentation, we will present our finite element simulation results comparing Li-O2 and Li-air batteries using power density, energy density, specific power, and discharge times as metrics to evaluate different electrolytes and electrode geometry to reduce total mass and maximize discharge current. We use a finite element model and a discharge product model developed in which is based on porous electrode and concentrated electrolyte theories and the discharge product is modeled using quantum tunneling; for reaction kinetics and oxygen diffusion, an improved model was used. The electrolyte properties such as ion conductivity and ion diffusion were obtained from Molecular Dynamics (MD) simulations while the other parameters for the finite element model were calibrated to match experiments at high discharge current densities (>1.5 mA/cm2). The mass densities of different electrolytes were computed using MD simulations as well. For this presentation, we examine the practical electrochemical mass of a system at different current ratings, the sensitivity of mass to the use of ambient air as compared to pure oxygen as well as the electrolyte, which affects maximum current density and the total mass associated with the electrolyte (which includes the mass of additional components), and, the optimization of battery geometry for total discharge time, average discharge voltage, maximum discharge current, and minimum electrochemical mass.

Mehta, M.↗
DOE OSTI2024

TaZr_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys tantalum-zirconium (Ta-Zr). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach \cite{PAW}. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Ta and Zr. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on NERSC-Perlmutter and OLCF-Summit using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Cases 1-10 have been run without generating the file 'vaspout.h5'. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for binary alloys is AXBY, where A and B refer to the constituents, whereas X and Y are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: FILES contained in each subdirectory with name "case-N" where N ranges between 11 and 80, extremes included: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. KPOINTS: input file that specifies the Bloch vectors (k points) used to sample the Brillouin zone 3. 0.POSCAR: input file that defines the atomic structure of a system 4. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 6. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 7. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 8. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. OUTCAR: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 10. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 11. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 12. vasprun.xml: contains similar information to OUTCAR, but in an xml format. 13. CHGCAR: contains the charge density data of a system. This data is crucial for analyzing electronic structures, calculating electrostatic potential, and studying the distribution of charge in a crystal or molecular system FILES contained in each subdirectory with name "case-N" where N ranges between 1 and 10 and between 81 and 100, extremes included: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. KPOINTS: input file that specifies the Bloch vectors (k points) used to sample the Brillouin zone 3. {ID}.POSCAR: input file that defines the atomic structure of a system at the beginning of ID execution of geometry optimization with PREC=LOW 4. {ID}.CONTCAR: output file that provides the atomic positions and cell parameters at the end of ID execution of geometry optimization with PREC=LOW in the INCAR file 5. {ID}.OUTCAR: output file that contains detailed information about the progress of a calculation after the ID execution of geometry optimization that has been run with the precision variable set to PREC=Low in the INCAR file 6. rlx1.{ID}.out: file with diagnostic information about the execution of the ID execution of the geometry optimization with precision variable set to PREC=Low in the INCAR file 7. N{ID}.POSCAR: input file that defines the atomic structure of a system after the geometry optimization run at low precision. This represents the input for the ID execution of the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 8. N{ID}.CONTCAR: output file that provides the atomic positions and cell parameters after the ID execution of the geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 9. N{ID}.OUTCAR: output file that contains detailed information about the progress of a calculation after the ID execution of the geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 10. rlx2.{ID}.out: file with diagnostic information about the ID execution of geometry optimization with precision variable set to PREC=Normal in the INCAR file 11. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 12. vasprun.xml: contains similar information to OUTCAR, but in an xml format. 13. CHGCAR: contains the charge density data of a system. This data is crucial for analyzing electronic structures, calculating electrostatic potential, and studying the distribution of charge in a crystal or molecular system This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216. REFERENCES (1) Kresse, G. & Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. review B 47, 558 (1993). (2) Kresse, G. & Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium. Phys. Rev. B 49, 14251 (1994) (3) Kresse, G. & Furthmüller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. materials science 6, 15–50 (1996) (4) Kresse, G. & Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. review B 54, 11169 (1996) (5) Kresse, G. & Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. review b 59, 1758 (1999)

36 MATERIALS SCIENCE↗
DOE OSTI2021

The FMO-DFTB Method

Although the fragment molecular orbital (FMO) method enables electronic structure calculations with near-linear scaling behavior with respect to system size, the computational cost of ab initio methods typically employed in conjunction with FMO is still prohibitive for routine calculations of very large systems or long timescale molecular dynamics simulations. We, therefore, combined the FMO and density-functional tight-binding (DFTB) method, which is one of the emerging semi-empirical quantum chemical methods, and have demonstrated that FMO-DFTB is capable of performing geometry optimizations for systems containing up to one million atoms using limited computational resources. In this chapter, we will review the basics of the DFTB method first before introducing FMO-DFTB, focusing on the relationship with density functional theory and other FMO methodologies. We also demonstrate the latest scalings of FMO-DFTB2 and DFTB3 using three-dimensional water clusters, showing that the most favorable scaling is O(N1.16). Applications of FMO-DFTB to various systems are briefly summarized, and an outlook to future applications is provided.

Nishimoto, Yoshio↗
DOE OSTI2024

Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution

Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. Here, to accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO 3 ) 3 dissolved in acetonitrile with a terpyridine ligand (terpyNO 2 ), and Nd(NO 3 ) 3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO 3 ) 3 (terpyNO 2 ) and Nd(NO 3 )(acetonitrile) 3 , with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.

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

Materials Data on H5ClO6 by Materials Project

H5O2(H2O)4(HClO4)2H5O6ClClO4 crystallizes in the triclinic P1 space group. The structure is zero-dimensional and consists of one molecular hydrogen;dihydrate molecule, four water molecules, one ClO4 cluster, one H5O6Cl cluster, and two HClO4 clusters. In the ClO4 cluster, there are four inequivalent O sites. In the first O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.47 Å. In the second O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.47 Å. In the third O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.47 Å. In the fourth O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.46 Å. Cl is bonded in a tetrahedral geometry to four O atoms. In the H5O6Cl cluster, there are five inequivalent H sites. In the first H site, H is bonded in a single-bond geometry to two O atoms. There is one shorter (1.00 Å) and one longer (1.71 Å) H–O bond length. In the second H site, H is bonded in a linear geometry to two O atoms. There is one shorter (1.20 Å) and one longer (1.24 Å) H–O bond length. In the third H site, H is bonded in a single-bond geometry to one O atom. The H–O bond length is 0.99 Å. In the fourth H site, H is bonded in a single-bond geometry to one O atom. The H–O bond length is 0.99 Å. In the fifth H site, H is bonded in a single-bond geometry to one O atom. The H–O bond length is 0.98 Å. There are six inequivalent O sites. In the first O site, O is bonded in a distorted single-bond geometry to one Cl atom. The O–Cl bond length is 1.46 Å. In the second O site, O is bonded in a distorted bent 120 degrees geometry to one H and one Cl atom. The O–Cl bond length is 1.47 Å. In the third O site, O is bonded in a trigonal non-coplanar geometry to three H atoms. In the fourth O site, O is bonded in a trigonal non-coplanar geometry to three H atoms. In the fifth O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.49 Å. In the sixth O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.45 Å. Cl is bonded in a tetrahedral geometry to four O atoms. In one of the HClO4 clusters, H is bonded in a single-bond geometry to one O atom. The H–O bond length is 1.00 Å. There are four inequivalent O sites. In the first O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.43 Å. In the second O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.44 Å. In the third O site, O is bonded in a distorted water-like geometry to one H and one Cl atom. The O–Cl bond length is 1.63 Å. In the fourth O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.43 Å. Cl is bonded in a tetrahedral geometry to four O atoms. In one of the HClO4 clusters, H is bonded in a single-bond geometry to one O atom. The H–O bond length is 1.00 Å. There are four inequivalent O sites. In the first O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.43 Å. In the second O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.43 Å. In the third O site, O is bonded in a single-bond geometry to one Cl atom. The O–Cl bond length is 1.43 Å. In the fourth O site, O is bonded in a distorted water-like geometry to one H and one Cl atom. The O–Cl bond length is 1.64 Å. Cl is bonded in a tetrahedral geometry to four O atoms.

36 MATERIALS SCIENCE↗
NASA NTRS1982

Polyimides: Tribological properties and their use as lubricants

Friction, wear, and wear mechanisms of several different polyimide films, solid bodies, composites, and bonded solid lubricant films are compared and discussed. In addition, the effect of such parameters as temperatures, type of atmosphere, contact stress, and specimen configuration are investigated. A friction and wear transition occurs in some polyimides at elevated temperatures and this transition is related to molecular relaxations that occur in polyimides. Friction and wear data from an accelerated test (pin-on-disk) are compared to similar data from an end use test device (plain spherical bearing), and to other polymers investigated in a similar geometry.

Fusaro, R. L.↗
NASA NTRS1984

Polyimides - Tribological properties and their use as lubricants

Friction, wear, and wear mechanisms of several different polyimide films, solid bodies, composites, and bonded solid lubricant films are compared and discussed. In addition, the effect of such parameters as temperatures, type of atmosphere, contact stress, and specimen configuration are investigated. A friction and wear transition occurs in some polyimides at elevated temperatures and this transition is related to molecular relaxations that occur in polyimides. Friction and wear data from an accelerated test (pin-on-disk) are compared to similar data from an end use test device (plain spherical bearing), and to other polymers investigated in a similar geometry.

Fusaro, R. L.↗
NASA NTRS2021

An Aerodynamics Database for Aerocapture of a Conceptual Morphable Entry System at Mars

An aerodynamics database for aerocapture of a conceptual morphable entry system at Mars was developed. The vehicle is envisioned to employ deflections of its geometry to modulate angle of attack and sideslip angle for trajectory control. Modified Newtonian methods were used to compute hypersonic continuum aerodynamics. Direct simulation Monte Carlo calculations were carried out to compute data in the rarefied transitional regime. Free-molecular theory was used to compute values in the free-molecular regime. A bridging function method was then used to bridge data from all three flow regimes together and produce a database that can be used for future trajectory simulations to assess the vehicle’s performance. The vehicle was found to have the control authority in hypersonic continuum to effect an 18 deg change in the trim angle of attack using a 10 deg deflection of the pitching control surfaces. Similarly, a 6 deg change in the trim sideslip angle could be achieved with a 5 deg deflection of the yawing control surfaces. Different configurations of the vehicle were found to be statically stable in pitch and yaw in the continuum regime, but unstable in the rarefied and free-molecular regimes.

aerocapture↗
DOE OSTI2022

CRISPR–Cas9 bends and twists DNA to read its sequence

In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9–RNA–DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 ‘reads’ snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

All-optical sampling of few-cycle infrared pulses using tunneling in a solid

Recent developments in ultrafast laser technology have resulted in novel few-cycle sources in the mid-infrared. Accurately characterizing the time-dependent intensities and electric field waveforms of such laser pulses is essential to their applications in strong-field physics and attosecond pulse generation, but this remains a challenge. Recently, it was shown that tunnel ionization can provide an ultrafast temporal “gate” for characterizing high-energy few-cycle laser waveforms capable of ionizing air. Here, we show that tunneling and multiphoton excitation in a dielectric solid can provide a means to measure lower-energy and longer-wavelength pulses, and we apply the technique to characterize microjoule-level near- and mid-infrared pulses. The method lends itself to both all-optical and on-chip detection of laser waveforms, as well as single-shot detection geometries.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.

Nielson, Felicity F.↗
NASA NTRS1984

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Magnesium/chemistry↗
DOE OSTI2022

Predictive coarse-grained (CG) modeling of morphologies in polymer nanocomposites with specific and directional intermolecular interactions (Final Report)

The overarching goal of the proposed work was to develop predictive models for investigating structure and dynamics in soft materials with chemistries that have specific and directional molecular interactions. The motivation behind studying materials with specific and directional interactions lies in the many desirable features these interactions provide when designing novel soft materials. Soft materials with specific and direction interactions (such as hydrogen bonds or H-bonds) can have a) thermally reversible phase behavior with different functions with varying temperature, b) precisely tuned nanostructure with desirable geometries that afford unique physical properties (e.g., color response, mechanical properties) and c) well-mixed/blended morphologies that are useful for variety of applications in energy field (e.g., materials for batteries require use of blended polymers where one domain gives superior mechanical properties and one domain promotes electrical conduction). Notably, biology makes extensive use of specific and directional interactions, in many cases based on H-bonds, to construct materials with precisely defined architectures and properties. Engineered soft materials with precisely tuned nanostructures and improved processiblity through thermoresponsive phase behavior are useful in numerous applications that are relevant to the Department of Energy (DOE) including high efficiency electronic devices, light-weight high-strength composite materials for batteries and fuel cells, and polymer membranes for separations, etc. While past computational studies have been tremendously useful in understanding molecular phenomena and guiding synthesis of new macromolecular soft materials for a wide variety of applications, the inability to capture small scale specific and directional interactions alongside macromolecular length and time scales represented a key limitation of most studies to date. Our work in this project addressed this grand challenge in computational materials chemistry, i.e., ability to model the anisotropic, directional, and specific interactions that govern the behavior of many macromolecular soft matter systems of interest, thus, has greatly expanded the predictive potential of simulations. Specifically the key outcomes were: successful development of new coarse-grained (CG) polymer models to study generic and specific polymer chemistries in which hydrogen-bonding interactions are dominant. These CG models were then used in molecular simulations to study structure and thermodynamics in polymer nanocomposites and blends; some studies were conducted in collaboration with experimentalists. We also published a perspective and a viewpoint which included some of the work we completed in this DOE project; we believe these perspective and viewpoint articles guide other researchers in the soft materials community on how to extend the computational approaches and models we have developed for the purposes of their studies.

36 MATERIALS SCIENCE↗