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Results for “Directed Molecular Evolution”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Bent HgI 2 Molecules in the Melt and Sulfide Glasses: Implications for Nonlinear Optics

Nonlinear optical (NLO) crystals are widely used in advanced photonic technologies for second harmonic and difference frequency generation (SHG and DFG, respectively), producing coherent light at frequencies where existing lasers are unavailable. Isotropic glasses do not exhibit SHG or DFG, except temporarily induced anisotropy under external stimuli. Nevertheless, recent reports on glasses with chiral structural motifs show promising permanent NLO properties. We introduce an alternative solution: hybrid molecular/network glasses with noncentrosymmetric HgI 2 monomers. Mercury (II) iodide consists of linear HgI 2 triatomic molecules in the vapor phase and in the yellow orthorhombic polymorph stable above 400 K. At lower temperatures, the tetragonal red form is composed of corner-sharing HgI 4/2 tetrahedra forming a layered extended framework. There is a gap in the molecular evolution; direct structural measurements of the liquid HgI 2 phase are missing. Using high-energy X-ray scattering, pulsed neutron diffraction, and Raman spectroscopy supported by structural and vibrational modeling, we show that the mercury(II) iodide melt and HgI 2 -containing sulfide glasses are built up by bent HgI 2 monomers (the bond angle <I-Hg-I = 156 ± 2° in the melt). Here, the noncentrosymmetric entities imply intrinsic optical nonlinearity of the second order, confirmed by a strong SHG response.

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

Spatially Offset Femtosecond Stimulated Raman Spectroscopy: Observing Exciton Transport through a Vibrational Lens

To design better molecular electronic devices, we need a strong understanding of how charges or excitons propagate, as many efficiency losses arise during transport. Exciton transport has been difficult to study because excitons tend to be short-lived, have short diffusion lengths, and can easily recombine. Here, we debut spatially offset femtosecond stimulated Raman spectroscopy (SO-FSRS), a three-pulse ultrafast microscopy technique. By offsetting the photoexcitation beam, we can monitor Raman spectral changes as a function of both time and position. We used SO-FSRS on 6,13-bis(triisopropylsilylethynyl) pentacene, a well-studied organic semiconductor used in photovoltaics and field-effect transistors. Furthermore, we demonstrated that the fast exciton and free charge carrier transport axes are identical and observed that exciton transport is less anisotropic by a factor of ~3. SO-FSRS is the first technique that directly tracks molecular structural evolution during exciton transport, which can provide roadmaps for tailor-making molecules for specific electronic devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2022

Seeing structural evolution of organic molecular nano-crystallites using 4D scanning confocal electron diffraction (4D-SCED)

Abstract Direct observation of organic molecular nanocrystals and their evolution using electron microscopy is extremely challenging, due to their radiation sensitivity and complex structure. Here, we introduce 4D-scanning confocal electron diffraction (4D-SCED), which enables direct in situ observation of bulk heterojunction (BHJ) thin films. 4D-SCED combines confocal electron optic setup with a pixelated detector to record focused spot-like diffraction patterns with high angular resolution, using an order of magnitude lower dose than previous methods. We apply it to study an active layer in organic solar cells, namely DRCN5T:PC 71 BM BHJ thin films. Structural details of DRCN5T nano-crystallites oriented both in- and out-of-plane are imaged at ~5 nm resolution and dose budget of ~5 e − /Å 2 . We use in situ annealing to observe the growth of the donor crystals, evolution of the crystal orientation, and progressive enrichment of PC 71 BM at interfaces. This highly dose-efficient method opens more possibilities for studying beam sensitive soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Best of both worlds: Enforcing detailed balance in machine learning models of transition rates

The slow microstructural evolution of materials often plays a key role in determining material properties. When the unit steps of the evolution process are slow, direct simulation approaches such as molecular dynamics become prohibitive and Kinetic Monte-Carlo (kMC) algorithms, where the state-to-state evolution of the system is represented in terms of a continuous-time Markov chain, are instead frequently relied upon to efficiently predict long-time evolution. The accuracy of kMC simulations however relies on the complete and accurate knowledge of reaction pathways and corresponding kinetics. This requirement becomes extremely stringent in complex systems such as concentrated alloys where the astronomical number of local atomic configurations makes the a priori tabulation of all possible transitions impractical. Machine learning models of transition kinetics have been used to mitigate this problem by enabling the efficient on-the-fly prediction of kinetic parameters. While conventional KMC methods based on transition state theory naturally yield reversible dynamics that exactly obey the detailed balance criterion, providing strong guarantees on the properties of the stationary distribution, many recently-proposed ML-based approaches to barrier predictions provide no such guarantees. In this study, we derive conditions under which physics-informed ML architectures exactly enforce the detailed balance condition by construction, even when relying on non-extensive descriptions of states in terms of local environments around mobile defects. In conclusion, using the diffusion of a vacancy in a concentrated alloy as an example, we show that such ML architectures also exhibit superior performance in terms of prediction accuracy, demonstrating that the imposition of physical constraints can facilitate the accurate learning of barriers at no increase in computational cost.

36 MATERIALS SCIENCE↗
DOE OSTI2016

The formation and dynamical evolution of young star clusters

Recent observations have revealed a variety of young star clusters, including embedded systems, young massive clusters, and associations. We study the formation and dynamical evolution of these clusters using a combination of simulations and theoretical models. Our simulations start with a turbulent molecular cloud that collapses under its own gravity. The stars are assumed to form in the densest regions in the collapsing cloud after an initial free-fall time of the molecular cloud. The dynamical evolution of these stellar distributions is continued by means of direct N-body simulations. The molecular clouds typical of the Milky Way Galaxy tend to form embedded clusters that evolve to resemble open clusters. The associations were initially considerably more clumpy, but they lost their irregularity in about a dynamical timescale, due to the relaxation process. The densest molecular clouds, which are absent in the Milky Way but are typical in starburst galaxies, form massive, young star clusters. They indeed are rare in the Milky Way. Our models indicate a distinct evolutionary path from molecular clouds to open clusters and associations or to massive star clusters. The mass–radius relation for both types of evolutionary tracks excellently matches the observations. According to our calculations, the time evolution of the half-mass–radius relation for open clusters and associations follows r{sub h}/pc=2.7(t{sub age}/pc){sup 2/3}, whereas for massive star clusters r{sub h}/pc=0.34(t{sub age}/Myr){sup 2/3}. Both trends are consistent with the observed age–mass–radius relation for clusters in the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Ion correlations drive charge overscreening and heterogeneous nucleation at solid–aqueous electrolyte interfaces

Significance Ion distributions at charged solid–water interfaces, referred to as the electrical double layer (EDL), are poorly understood at high ion concentrations, in part due to the lack of molecular-scale descriptions of the interactions between adsorbed hydrated ions. Here, direct visualization of the salinity-dependent evolution of EDL structure reveals molecular origins of nonclassical transformation of the EDL, in which charge overscreening and heterogeneous nucleation are driven by ion–ion correlations at the interfaces. This manifestation of the atomistic basis of nonclassical behaviors provides a much-needed understanding of the impact of ion cooperativity at charged interfaces for the development of predictive models for element transport in natural environments and advanced technologies for material growth and synthesis in saline environments.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Time Dependent Structural Evolution of Porous Organic Cage CC3

Porous organic cage compounds are emerged with remarkable structural diversity and functionality that have applications in gas separation, catalysis and energy storage. Fundamental understanding of nucleation and growth of such materials have significant implications for understanding molecularly directed self-assembly phenomena. Herein we followed the structural evolution of a prototypical type of porous organic cage, CC3 as a function of synthesis time. Three distinctive crystal formation stages were identified: at short synthesis times, a rapid crystal growth stage in which amorphous agglomerates transformed into larger irregular particles was observed. At intermediate synthesis times, a decrease in crystal size over time was observed presumably due to crystal fragmentation, redissolution and/or homogeneous nucleation led. Finally, at longer synthesis times, a regrowth process was observed in which particles coalesced through Ostwald ripening leading to a continuous increase in crystal size. Molecular simulation studies, based on the construction of in silico CC3 models and simulation of XRD patterns and nitrogen isotherms, confirm the samples at different synthesis times to be a mixture of CC3α and CC3 amorphous phases. The CC3α phase is found to contract at different synthesis times, and the amorphous phase is found to essentially disappear at the longest synthesis time. Nitrogen and carbon dioxide adsorption properties of these CC3 phases were evaluated, and were highly dependent on synthesis time.

Growth↗
DOE OSTI2019

Direct dioxygen evolution in collisions of carbon dioxide with surfaces

The intramolecular conversion of CO 2 to molecular oxygen is an exotic reaction, rarely observed even with extreme optical or electronic excitation means. Here we show that this reaction occurs readily when CO 2 ions scatter from solid surfaces in a two-step sequential collision process at hyperthermal incidence energies. The produced O 2 is preferentially ionized by charge transfer from the surface over the predominant atomic oxygen product, leading to direct detection of both O 2 + and O 2 - . First-principles simulations of the collisional dynamics reveal that O 2 production proceeds via strongly-bent CO 2 configurations, without visiting other intermediates. Bent CO 2 provides dynamic access to the symmetric dissociation of CO2 to C+O2 with a calculated yield of 1 to 2% depending on molecular orientation. This unexpected collision-induced transformation of individual CO 2 molecules provides an accessible pathway for generating O 2 in astrophysical environments and may inspire plasmadriven electro- and photo-catalytic strategies for terrestrial CO 2 reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crossing the Oxo‐Peroxo Wall for Selective Electrochemical Epoxidation

Electrochemical oxidation in water requires the formation of reactive oxygen species to be able to oxidize unsaturated hydrocarbons to epoxides, aldehydes, and ketones. These reactions, broadly classified as alternative oxidation reactions (AOR), directly compete with the prevalent oxygen evolution reaction (OER). In molecular catalysis, the Oxo-Wall dictates a transition from a stable oxo intermediate (OER active) to a meta-stable metal-oxo (OER inactive) generally occurs. In this work on heterogeneous catalysis, the same Oxo-Wall applies, however, a meta-stable oxo preferentially coordinates with lattice oxygen to form a more stable surface peroxo intermediate. A universal free energy onset of this process is identified at 3.39 eV under electrochemical activation in water and show that it is completely decoupled from the OER oxo species. Such decoupling gives rise to a new region of oxygen reactivity relevant for AOR where a selective oxidation of the unsaturated C-C bonds is predicted to occur instead of OER. A distinct AOR overpotential volcano is constructed and identify recently reported electrocatalysts, including palladium-platinum for propylene epoxidation and silver-nickel for ethylene epoxidation, along with others such as TiO 2 and CuO. Broader implications and limitations of electrochemical AOR are discussed, highlighting their potential to enable electrochemically enhanced thermal catalysis.

Electrocatalysis↗
DOE OSTI2022

Electronic coherences in nonadiabatic molecular photophysics revealed by time-resolved photoelectron spectroscopy

Significance Time-resolved photoelectron spectroscopy (TRPES) is a promising technique for the study of ultrafast molecular processes, such as the nonadiabatic dynamics taking place at conical intersections. Directly accessing the evolution of the coherences generated at the conical intersection should provide most valuable dynamical information. However, the signals are dominated by background contributions due to state populations, and most theoretical treatments completely neglect the role of the coherences. Here we show that distinguishable signatures of molecular coherences appear in TRPES. These can be recorded using currently available ultrashort pulses and unambiguously extracted at the postprocessing stage. The technique thus provides direct access to nonadiabatic coherence dynamics.

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

Switchable wetting of oxygen-evolving oxide catalysts

The surface wettability of catalysts is typically controlled via surface treatments that promote catalytic performance. Here we report on potential-regulated hydrophobicity/hydrophilicity at cobalt-based oxide interfaces with an alkaline solution. The switchable wetting of single particles, directly related to their activity and stability towards the oxygen evolution reaction, was revealed by electrochemical liquid-phase transmission electron microscopy. Analysis of the movement of the liquid in real time revealed distinctive wettability behaviour associated with specific potential ranges. At low potentials, an overall reduction of the hydrophobicity of the oxides was probed. Upon reversible reconstruction towards the surface oxyhydroxide phase, electrowetting was found to cause a change in the interfacial capacitance. At high potentials, the evolution of molecular oxygen, confirmed by operando electron energy-loss spectroscopy, was accompanied by a globally thinner liquid layer. This work directly links the physical wetting with the chemical oxygen evolution reaction of single particles, providing fundamental insights into solid–liquid interfacial interactions of oxygen-evolving oxides.

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

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Formation and Evolution of Metallocene Single-Molecule Circuits with Direct Gold-π Links

Single molecule circuits with group 8 metallocenes are formed without additional linker groups in Scanning Tunnelling Microscope-based break junction (STMBJ) measurements at cryogenic and room temperature conditions with gold (Au) electrodes. We investigate the nature of this direct gold-π binding motif and its affect on molecular conductance and persistence characteristics during junction evolution. The measurement technique under cryogenic conditions tracks molecular plateaus through the full cycle of extension and compression. Analysis reveals that junction persistence when the metal electrodes are pushed together correlates with whether electrodes are locally sharp or blunt, suggesting distinct scenarios for metallocene junction formation and evolution. The top and bottom surfaces of the "barrel" shaped metallocenes present the electron-rich π system of cyclopentadienyl rings which interacts with the gold electrodes in two distinct ways. An undercoordinated gold atom on a sharp tip forms a donor-acceptor bond to a specific carbon atom in the ring. However, a small, flat patch on a dull tip can bind more strongly to the ring as a whole through Van der Waals interactions. Density functional theory (DFT) based calculations of model electrode structures provide an atomic-scale picture of these scenarios, demonstrating the role of these bonding motifs during junction evolution and showing that the conductance is relatively independent of tip atomic-scale structure. Furthermore, the non-specific interaction of the cyclopentadienyl rings with the electrodes enables extended conductance plateaus, a mechanism distinct from that identified for the more commonly studied, rod-shaped organic molecular wires.

25 ENERGY STORAGE↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2023

Unfaulting mechanisms of interstitial Frank loops in fluorite-structured ThO 2

Unfaulting of Frank loops in irradiated fluorite-structured oxides is of significance for understanding microstructural evolution. However, the mechanisms have not yet been directly observed. To this end, we utilize molecular dynamics to reveal the atomistic details related to the unfaulting process of interstitial Frank loops in ThO 2 , which involve a single pair or multiple pairs of co-propagating Shockley partials to annihilate the stacking faults. Here, we find that the unfaulting is achieved via a synchronous shear of the partial pairs to remove the extrinsic stacking fault in the cation sublattice and the intrinsic stacking fault in the anion sublattice. The high mobility of oxygen at the dislocation core may reduce the activation barriers of dislocation nucleation and migration. These findings provide a fundamental understanding of the transformation of faulted loops in irradiated ThO 2 , and could be transferable to other fluorite-structured oxides.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

In vitro continuous protein evolution empowered by machine learning and automation

Directed evolution has become one of the most successful and powerful tools for protein engineering. However, the efforts required for designing, constructing, and screening a large library of variants can be laborious, time-consuming, and costly. With the recent advent of machine learning (ML) in the directed evolution of proteins, researchers can now evaluate variants in silico and guide a more efficient directed evolution campaign. Furthermore, recent advancements in laboratory automation have enabled the rapid execution of long, complex experiments for high-throughput data acquisition in both industrial and academic settings, thus providing the means to collect a large quantity of data required to develop ML models for protein engineering. In this perspective, here we propose a closed-loop in vitro continuous protein evolution framework that leverages the best of both worlds, ML and automation, and provide a brief overview of the recent developments in the field.

59 BASIC BIOLOGICAL SCIENCES↗