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At least 1,189 records · Page 66

Theoretical study of the structures and electron affinities of the dimers and trimers of the group IB metals (Cu, Ag, and Au)

The molecular structure of both the neutral and negatively charged diatomic and triatomic systems containing the Cu, Ag, and Au metals are determined from ab initio calculations. For the neutral triatomic systems, the lowest energy structure is found to be triangular. The relative stability of the 2A1 and 2B2 structures can be predicted simply by knowing the constituent diatomic bond distances and atomic electron affinities (EAs). The lowest energy structure is linear for all of the negative ions. For anionic clusters containing Au, the Au atom(s) preferentially occupy the terminal position(s). The EAs of the heteronuclear systems can be predicted relatively accurately from a weighted average of the corresponding homonuclear systems. Although the theoretical EAs are systematically too small, accurate predictions for the EAs of the triatomics are obtained by uniformly scaling the ab initio results using the accurate experimental EA values available for the atoms and homonuclear diatomics.

Bauschlicher, Charles W., Jr.↗

Internal vibrations of a molecule consisting of rigid segments. I - Non-interacting internal vibrations

For molecular crystals, a procedure is proposed for interpreting experimentally determined atomic mean square anisotropic displacement parameters (ADPs) in terms of the overall molecular vibration together with internal vibrations with the assumption that the molecule consists of a set of linked rigid segments. The internal librations (molecular torsional or bending modes) are described using the variable internal coordinates of the segmented body. With this procedure, the experimental ADPs obtained from crystal structure determinations involving six small molecules (sym-trinitrobenzene, adenosine, tetra-cyanoquinodimethane, benzamide, alpha-cyanoacetic acid hydrazide and N-acetyl-L-tryptophan methylamide) have been analyzed. As a consequence, vibrational corrections to the bond lengths and angles of the molecule are calculated as well as the frequencies and force constants for each internal torsional or bending vibration.

He, X. M.↗

Boson Fermion Nucleus Polynuclear Structure: Monograph #11

The boson fermion nucleus (BFN) structure indicates the possibility of stable, nonradioactive polynuclear structures bound by the strong nuclear force. In the process of making polynuclear structures, BFN self-ordering on the nuclear level as a stable structure resembles the self-ordering of carbon atoms at the atomic level into buckminsterfullerene, graphene sheet, or graphene nanotubes. This natural assembly derives from the modulation of electron orbital collapse, which decreases coulomb repulsion between atoms and allows a natural reordering among nuclear structures by modulating the permeability of free space. Polynuclear material would be unearthly in tensile strength, thermal and electrical conductivity, and heat of disassociation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Autonomous self-repair in piezoelectric molecular crystals

Living tissue uses stress-accumulated electrical charge to close wounds. Self-repairing synthetic materials, which are typically soft and amorphous, usually require external stimuli, prolonged physical contact, and long healing times. We overcome many of these limitations in piezoelectric bipyrazole organic crystals, which recombine following mechanical fracture without any external direction, autonomously self-healing in milliseconds with crystallographic precision. Kelvin probe force microscopy, birefringence experiments, and atomic-resolution structural studies reveal that these noncentrosymmetric crystals, with a combination of hydrogen bonds and dispersive interactions, develop large stress-induced opposite electrical charges on fracture surfaces, prompting an electrostatically driven precise recombination of the pieces via diffusionless self-healing.

Bhunia, Surojit↗

Polaron absorption in aligned conjugated polymer films: breakdown of adiabatic treatments and going beyond the conventional mid-gap state model

This study provides the first experimental polarized intermolecular and intramolecular optical absorption components of field-induced polarons in regioregular poly(3-hexylthiophene-2,5-diyl), rr-P3HT, a polymer semiconductor. Highly aligned rr-P3HT thin films were prepared by a high temperature shear-alignment process that orients polymer backbones along the shearing direction. rr-P3HT in-plane molecular orientation was measured by electron diffraction, and out-of-plane orientation was measured through series of synchrotron X-ray scattering techniques. Then, with molecular orientation quantified, polarized charge modulation spectroscopy was used to probe mid-IR polaron absorption in the ℏω = 0.075 — 0.75 eV range and unambiguously assign intermolecular and intramolecular optical absorption components of hole polarons in rr-P3HT. This data represents the first experimental quantification of these polarized components and allowed long-standing theoretical predictions to be compared to experimental results. The experimental data is discrepant with predictions of polaron absorption based on an adiabatic framework that works under the Born–Oppenheimer approximation, but the data is entirely consistent with a more recent nonadiabatic treatment of absorption based on a modified Holstein Hamiltonian. This nonadiabatic treatment was used to show that both intermolecular and intramolecular polaron coherence break down at length scales significantly smaller than estimated structural coherence in either direction. Importantly, this strongly suggests that polaron delocalization is fundamentally limited by energetic disorder in rr-P3HT.

36 MATERIALS SCIENCE↗

Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike’s stability. Taken together, the network approach serves as a valuable tool to evaluate communication “hot-spots” in proteins to guide design of stable immunogens.

60 APPLIED LIFE SCIENCES↗

Alloying effects on low-energy recoil events in concentrated solid-solution alloys

Alloying elements at low-concentrations into pure metals is usually adopted to improve their mechanical properties and irradiation performance. Recently developed single-phase concentrated solid-solution alloys (CSAs) comprised of two or more elements, all at high concentrations, have demonstrated good radiation resistance. CSAs are characterized by their extreme disordered states that arise from the random arrangement of different elements and accompanied random local lattice distortions. In this work, we investigate low-energy recoil events in Ni 0.5 X 0.5 (X = Fe and Co) CSAs and Ni 0.8 X 0.2 (X = Fe, Co, Cr, and Pd) CSAs using ab initio molecular dynamics simulations to understand the effects of different disorder on defect production in CSAs. The threshold displacement energies are determined along three high-symmetric directions by randomly choosing independent primary knock-on atoms in each direction. As expected, the threshold energies in Ni and its CSAs are anisotropic, with the highest values found in the [111] direction. The calculated threshold energies of Fe in NiFe are smaller than those in NiCo and Ni, especially along the [111] direction. An inspection of the atomic trajectories inside the collision cascade reveals that the effect of chemical disorder outweighs the site-to-site lattice distortions in determining the threshold energies. Especially, different interaction properties between elements due to their different electronic structures are responsible for the observed different threshold energies. Finally, the local environment dependence of threshold energies suggests that local elemental arrangement can be used to understand and predict threshold energies in disordered alloys.

36 MATERIALS SCIENCE↗

High-resolution CARMA Observation of Molecular Gas in the North America and Pelican Nebulae

In this paper, we present the first results from a CARMA high-resolution {sup 12}CO(1-0), {sup 13}CO(1-0), and C{sup 18}O(1-0) molecular line survey of the North America and Pelican (NAP) Nebulae. CARMA observations have been combined with single-dish data from the Purple Mountain 13.7 m telescope, to add short spacings and to produce high-dynamic-range images. We find that the molecular gas is predominantly shaped by the W80 H ii bubble, driven by an O star. Several bright rims noted in the observation are probably remnant molecular clouds, heated and stripped by the massive star. Matching these rims in molecular lines and optical images, we construct a model of the three-dimensional structure of the NAP complex. Two groups of molecular clumps/filaments are on the near side of the bubble: one is being pushed toward us, whereas the other is moving toward the bubble. Another group is on the far side of the bubble, and moving away. The young stellar objects in the Gulf region reside in three different clusters, each hosted by a cloud from one of the three molecular clump groups. Although all gas content in the NAP is impacted by feedback from the central O star, some regions show no signs of star formation, while other areas clearly exhibit star formation activity. Additional molecular gas being carved by feedback includes cometary structures in the Pelican Head region, and the boomerang features at the boundary of the Gulf region. The results show that the NAP complex is an ideal place for the study of feedback effects on star formation.

74 ATOMIC AND MOLECULAR PHYSICS↗

Excited-State and Nonadiabatic Molecular Dynamics Methods with Broad Applicability

Electronically excited states play a pivotal role in the capture, transformation, storage, and emission of radiative energy. Despite much recent progress for small model systems, excited state properties and dynamics in many larger molecular devices and materials have remained elusive for experiment and theory. Nonadiabatic transitions between electronic states turn radiative energy into heat and are particularly difficult to control. This project aims to develop new electronic structure and nonadiabatic molecular dynamics (NAMD) methods to simulate, predict, and ultimately control the flow and transformation of excitation energy in a wide-range of light-driven molecular devices such as dyes, photocatalysts, and fluorescence emitters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design & Assembly of Atomically-Precise Quantum Materials & Devices (Final Report)

Atomic-layer honeycomb materials (Xene, where “X” may stand for a number of different elements) are a promising platform for new quantum states. When X is a heavier element such as tin (Sn) or bismuth (Bi), the edges of the honeycomb may conduct electron charge or spin without resistance - an effect that could persist up to room temperature in some cases. The type of edge states, and their robustness at room temperature, depend sensitively on (a) the substrate material that the Xene is sitting on; (b) out-of-plane buckling of the honeycomb structure; (c) the pattern of atoms or molecules sitting atop the honeycomb. This sensitivity suggests that Xene edge states could be tuned and rearranged to construct nanoscale electronic or spintronic devices. We report on theoretical progress in modeling the assembly and structure of Xenes, and their underlying substrates and overlaying atoms. Specifically, we model the stability of Sn atoms forming a single atomic layer (“stanene”), the stability and phase transitions

36 MATERIALS SCIENCE↗

Computational study of the electrostatic potential and charges of multivalent ionic liquid molecules

The electrostatic interactions in ionic liquids (ILs) can be difficult to quantify, but this information is very valuable for improving intermolecular potentials for performing molecular-level simulations. Although polarizable forcefields can provide improved accuracy, the computational efficiency of fixed charge molecular models is often preferred for larger systems. Here, we propose a multi-scale screening approach for analyzing the charge scaling behavior and other electrostatic properties of ILs, which is more attainable than previous analysis methods that rely on the IL crystalline structures. Based on isolated molecules and small clusters, we study the electrostatic potential properties and charges of multivalent IL molecules using density-functional theory calculations and ab initio molecular dynamics simulations. The charges of the IL molecules are calculated and compared using several different charge estimation techniques. Although there are some differences among the estimated partial charges on the atoms, the total anion and cation charges are very similar. In conclusion, the charge scaling factors are substantial, and they are only slightly affected by the IL cluster size model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectroscopic Investigation into P(NDI2OD-T2) Charge Localization

P(NDI2OD-T2), commonly referred to as N2200, stands out as a promising electron-transporting (n-type) polymer for low-cost, flexible (photo)electrochemical applications due to its reversible two-electron reduction and high electron mobility. UV–vis spectroelectrochemistry in the tetrabutyl ammonium hexafluorophosphate/acetonitrile electrolyte shows two sets of chemically reversible redox signals in the cyclic voltammetry corresponding to the reduction of the neutral polymer film to polaronic and bipolaronic species. These electrochemical signatures suggest a distinct electronic reorganization upon reduction (polaron/bipolaron formation), highlighting the need for molecular-level insights into how charges are accommodated within the polymer backbone. While it has been previously hypothesized that charge predominantly localizes on the naphthalene diimide (NDI) unit during reductive charging, specific changes in atomic environments that confirm this localization have not been characterized in n-type polymers. Herein, we use near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to probe electronic transitions in an electrochemically charged polymer to deduce charge localization. The O K-edge (1s) spectra exhibit two distinct π* peaks; the intensity of the lower-energy π* a peak that corresponds to an excitation to a largely localized carbonyl state decreases with reductive potentials relative to the higher-energy π* b peak. We corroborate this with Raman spectroscopy at different potentials, which shows a decrease in intensity on the C–C/C═C and C═O stretching bands of NDI as well as a red shift of the carbonyl band due to the formation of a polaron on the NDI. Additionally, new Raman active NDI signals associated with elongated C═O and C═C bonds are observed at lower energy during the formation of charged states. Together with theoretical calculations, these findings show that the injected charge spatially localizes on the NDI units and is dominantly distributed on the carbonyl groups. In conclusion, the combination of NEXAFS, optical and vibrational spectroscopies, and theoretical calculations is generalizable to other pi-conjugated polymers and can identify charge localization for the further development of organic semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The role of manganese in CoMnO x catalysts for selective long-chain hydrocarbon production via Fischer-Tropsch synthesis

Cobalt is an efficient catalyst for Fischer–Tropsch synthesis (FTS) of hydrocarbons from syngas (CO + H 2 ) with enhanced selectivity for long-chain hydrocarbons when promoted by Manganese. However, the molecular scale origin of the enhancement remains unclear. Here we present an experimental and theoretical study using model catalysts consisting of crystalline CoMnO x nanoparticles and thin films, where Co and Mn are mixed at the sub-nm scale. Employing TEM and in-situ X-ray spectroscopies (XRD, APXPS, and XAS), we determine the catalyst’s atomic structure, chemical state, reactive species, and their evolution under FTS conditions. We show the concentration of CH x , the key intermediates, increases rapidly on CoMnO x , while no increase occurs without Mn. DFT simulations reveal that basic O sites in CoMnO x bind hydrogen atoms resulting from H 2 dissociation on Co 0 sites, making them less available to react with CH x intermediates, thus hindering chain termination reactions, which promotes the formation of long-chain hydrocarbons.

36 MATERIALS SCIENCE↗

Aladyn - Adaptive Neural Network Molecular Dynamics Simulation Code: Computational Materials Mini-Application

This report provides an overview and commands description of the Computational Materials mini-application, Aladyn. Aladyn is a simple molecular dynamics code written in FORTRAN 2008, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of quantum mechanics-based energy calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. The Aladyn code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing many core architectures based on graphic processing units (GPUs). The effort is related to the High Performance Computing Incubator (HPCI) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗

High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9

The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Opportunities for fundamental physics research with radioactive molecules

Molecules containing short-lived, radioactive nuclei are uniquely positioned to enable a wide range of scientific discoveries in the areas of fundamental symmetries, astrophysics, nuclear structure, and chemistry. Recent advances in the ability to create, cool, and control complex molecules down to the quantum level, along with recent and upcoming advances in radioactive species production at several facilities around the world, create a compelling opportunity to coordinate and combine these efforts to bring precision measurement and control to molecules containing extreme nuclei. In this paper, we review the scientific case for studying radioactive molecules, discuss recent atomic, molecular, nuclear, astrophysical, and chemical advances which provide the foundation for their study, describe the facilities where these species are and will be produced, and provide an outlook for the future of this nascent field.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Accelerating Biomimetic Solar - Energy Harvesting: Mapping the Interaction Landscape of Plasmonic-Excitonic Hybrid Nanosystems (Final Report)

In general, excitonic and plasmonic nanoscale materials in close proximity show high potential for significant breakthroughs in energy related materials research. The interactions between these two kinds of materials result in coupled optical transitions (plexcitons), distinct from those of both the individual exciton and plasmon as well as from those of the sum of their constituents (synergistic effects). By linking together materials-research and physical-research approaches, this project contributes to a concerted approach on nanomaterials energy research. The project’s overall goal is to accelerate the development of well-defined plexcitonic model systems consisting of carefully engineered plasmonic and excitonic nanomaterial— essential for both gaining a fundamental understanding of plexcitonic nanomaterials and the development of novel design principles for biomimetic solar energy harvesting. During the 3-year project period and the terminal renewal with limited support for a 12-month period, we successfully synthesized and characterized (1) a robust excitonic nanomaterial and (2) a library of plasmonic nanoparticles as well as developed (3) a microfluidic platform for homogenous nanosynthesis as summarized below: (1) Robust Excitonic Nanomaterial. Supramolecular assemblies are Nature’s most successful material system for solar energy harvesting. However, photovoltaic devices based on artificial supramolecular assemblies continue to be stymied by disappointing efficiencies and poor stability. The conceptual failure may lie in current solar cell architectures, which rely on solidifying supramolecular assemblies as an ensemble into a solid matrix, neglecting the intrinsic fragility of the assemblies’ internal structure, thus disrupting or even destroying their delicate optoelectronic properties, that is, delicate Frenkel excitonic properties. Supramolecular assemblies may finally serve as usable light harvesting material systems for solar energy conversion technologies, only if they meet the following criteria: (a) Stability, that is, the fragile structure including its delicate Frenkel excitonic character needs to be stable, (b) Robustness, that is, resistant against elevated and fluctuating temperatures, and (c) Viability for device integration, that is, capable of being immobilized onto solid substrates. Here, by developing a nanocomposite via a tunable, cage-like scaffold design, we successfully provided stable supramolecular nanocomposites, that inhabit robust Frenkel excitons despite harming environmental conditions such as extreme heat stress. (2) Library of Plasmonic Nanoparticles. Naturally, current models describing plasmonic hybrid quantum states—plasmonic hybridizations—parallel those developed for molecular orbitals, equating individual plasmonic nanostructures with “atoms” and the plasmonic nanoassemblies with “molecules.” In analogy to organic synthesis, a suitably robust fabrication method would allow for “atom-like” manipulation of “molecule-like” plasmonic nanoassemblies; of high value for next-generation energy nanotechnologies. Despite this frequent comparison, current plasmonic nanoassembly fabrication methods favor top-down templating over wet-chemical synthesis, however, achieving precise control over nanostructure’s geometry and surface characteristics remain an art and a scientific challenge. The conceptual failure may lie in the current wet-chemical synthesis paradigm, as it relies on the accessibility of a multi-dimensional synthesis parameter space through limited, rather one-dimensional synthesis procedures by employing step-by-step approaches. Solution-based nanoarchitectonics for rational design of precisely built plasmonic nanoassemblies via solution-based fabrication may finally be possible only if multi-dimensional syntheses approaches are available that allow for comprehensive control over the plasmonic nanomaterials’ (a) Structural Properties and (b) Surface Properties. Here, by developing an innovative multidimensional 1,3-propanediol based polyol synthesis, we successfully provided control over the plasmonic building-block’s geometry (size and shape) together with its surface characteristics. Our results present a critical step toward the vision of a “periodic table-like” system for plasmonic materials based on straightforward wet-chemical syntheses for energy nanotechnologies. Developing deliberate modifications on this synthesis, we generated a library of plasmonic nanostructures covering the vast parameter space—opening the door for fundamental investigation of plexcitonic model systems. (3) Microfluidic Platform for Homogenous Nanosynthesis. Control over structural properties of plexcitonic nanocomposites remains a challenge due to current limitations in nanosynthesis techniques. Slight variations in nanostructure’s geometry impact their optoelectronic properties, demanding precise synthesis beyond the capabilities of solution-based (batch) synthesis processes. In contrast, the small, confined liquid volumes used in microfluidics—a reaction technique where the manipulation of fluids takes place in channels with dimensions of tens of micrometers—allows for homogenous synthesis conditions, providing excellent control of the reaction and, as a result, of the materials’ geopmetry and composition. However, thus far, the majority of plexcitonic systems has been developed via batch synthesis. Here, by successfully developing a two-channel microreactor, our microfluidic-supported synthesis approach combines the advantages of both microfluidics and batch platforms, allowing for precise spatio-temporal control over all synthesis parameters opening the possibility for homogenous nanosythnesis of well-defined plexcitonic model systems.

14 SOLAR ENERGY↗

Substrate-Dependent Study of Chain Orientation and Order in Alkylphosphonic Acid Self-Assembled Monolayers for ALD Blocking

For years, many efforts in area selective atomic layer deposition (AS-ALD) have focused on trying to achieve high-quality self-assembled monolayers (SAMs), which have been shown by a number of studies to be effective for blocking deposition. In this work, we show that in some cases where a densely packed SAM is not formed, significant ALD inhibition may still be realized. The formation of octadecylphosphonic acid (ODPA) SAMs was evaluated on four metal substrates: Cu, Co, W, and Ru. The molecular orientation, chain packing, and relative surface coverage were evaluated using near-edge X-ray absorption fine structure (NEXAFS), Fourier transform infrared (FTIR) spectroscopy, and electrochemical impedance spectroscopy (EIS). ODPA SAMs formed on Co, Cu, and W showed strong angular dependence of the NEXAFS signal whereas ODPA on Ru did not, suggesting a disordered layer was formed on Ru. Additionally, EIS and FTIR spectroscopy confirmed that Co and Cu form densely packed, “crystal-like” SAMs whereas Ru and W form less dense monolayers, a surprising result since W-ODPA was previously shown to inhibit the ALD of ZnO and Al 2 O 3 best among all the substrates. This work suggests that multiple factors play a role in SAM-based AS-ALD, not just the SAM quality. Therefore, metrological averaging techniques (e.g., WCA and FTIR spectroscopy) commonly used for evaluating SAMs to predict their suitability for ALD inhibition should be supplemented by more atomically sensitive methods. Finally, it highlights important considerations for describing the mechanism of SAM-based selective ALD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗