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All sources NASA NTRS DOE OSTI

DOE OSTI2020

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Data-Driven Discovery of Linear Molecular Probes with Optimal Selective Affinity for PFAS in Water

Approaches to tackle the wide and growing variety of highly persistent per- and polyfluoroalkyl substances (PFAS) are of pressing global need because of their detrimental human health effects, such as cancer, birth defects, and hormone imbalance. Sensitive, selective, and easy-to-use real-time sensors to monitor and detect PFAS and sorbents to extract them are critical to meeting government-mandated environmental concentrations. In this work, we combine all-atom molecular dynamics simulations, enhanced sampling, deep representational learning, and Bayesian optimization to perform high-throughput virtual screening for highly sensitive and selective molecular probes. Our molecular design space consists of 3850 linear hydrocarbon chains with varying degrees of halogenation with and without amine- and phosphine-based headgroups. By employing a data-driven search process, we efficiently explore the molecular design space to optimize the sensitivity to perfluorooctanesulfonic acid (PFOS) as a prototypical PFAS analyte and selectivity relative to a sodium dodecyl sulfate (SDS) interferent. We calculate 504 Gibbs free energies of probe-analyte and probe-interferent interactions and identify probes with PFOS association free energies of up to (-ΔG PFOS ) = 9.8 ± 0.2 kJ/mol and selectivities relative to SDS of (-ΔΔG PFOS–SDS ) = 3.1 ± 1.5 kJ/mol. A C 11 Br 23 P(CH 3 ) 2 probe containing 11 backbone brominated carbons and a tertiary phosphine headgroup possesses the most sensitive binding constant to PFOS within the defined search space of K b PFOS = 177.4 ± 12.7, and a semibrominated probe C 5 H 11 C 7 Br 14 N(CH 3 ) 2 containing 12 backbone carbons and a tertiary amine headgroup possesses the highest selectivity relative to SDS of K b PFOS /K b SDS = 4.6 ± 1.7. A retrospective analysis of our data to extract interpretable design rules reveals that the sensitivity of linear hydrogenated probes increases by approximately 1 kJ/mol per C–C bond. The addition or removal of halogen atoms and amine or phosphine headgroups produces nonmonotonic changes in both sensitivity and selectivity with changes to the sensitivity of up to 2.5 kJ/mol. Finally, this work places empirical limitations on the performance of a wide range of linear probes for PFOS detection and offers a generic strategy for high-throughput computational screening to promote selective and sensitive binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1994

Method development for compensating temperature effects in pressure sensitive paint measurements

Pressure sensitive luminescent paints (PSP) have recently emerged as a viable technique for aerodynamic pressure measurements. The technique uses a surface coating which contains probe molecules that luminesce when excited by light of an appropriate wavelength. The photoluminescence of these materials is known to be quenched by the presence of molecular oxygen. Since oxygen is a fixed mole fraction of the air, the coating's luminescence intensity varies inversely with air pressure. Digital imaging of the luminescence varying across a coated surface produces a pressure distribution map over that surface. One difficulty encountered with this technique is the temperature effect on the luminescence intensity. Present PSP formulations have significant sensitivity to temperature. At the moment, the most practical way of correcting for temperature effects is to calibrate the paint in place at the operating temperatures by using a few well-placed pressure taps. This study is looking at development of temperature indicating coatings that can be applied and measured concurrently with PSP, and use the temperature measurement to compute the correct pressure. Two methods for this dual paint formulation are proposed. One method will use a coating that consists of temperature sensitive phosphors in a polymer matrix. This is similar in construction to PSP, except that the probe molecules used are selected primarily for their temperature sensitivity. Both organic phosphors (e.g., europium thenoyltrifluoroacetonate, bioprobes) and inorganic phosphors (e.g., Mg4(F)GeO6:Mn, La2O2S:Eu, Radelin Type phosphors, Sylvania Type phosphors) will be evaluated for their temperature sensing potential. The next method will involve a novel coating composing of five membered heterocyclic conducting polymers which are known to show temperature dependent luminescence (e.g., poly(3-alkylthiopene), poly(3-alkylselenophene), poly(3-alkylfuran)). Both methods will involve applying a bottom layer of temperature sensitive coating followed by a top coating of PSP. An oxygen-impermeable polymer can be used as the temperature sensitive coating matrix, or it can be layered in between the coatings to prevent oxygen quenching of the bottom coating's luminescence. The probe molecules of the coatings will be excited by a broad band of light, with the different emissions detected and measured at their distinct wavelengths. Developmental research of these coatings is still in progress; however, preliminary results look very promising.

Demandante, Carlo Greg N.↗

DOE OSTI2025

An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules

Activity-based protein profiling (ABPP) is a chemoproteomic technique that uses small molecule probes to label active enzymes selectively and covalently in complex proteomes. Competitive ABPP, which involves treatment of the active proteome with an analyte of interest, is especially powerful for profiling how small molecules impact specific protein activities. Advances in higher throughput workflows have made it possible to generate extensive competitive ABPP data across diverse biological samples, making this approach highly appealing for characterizing shared and unique proteins affected by perturbations such as drug or chemical exposures. To use the competitive ABPP approach effectively to understand potential adverse effects of chemicals of concern (CoC), a wide range of concentrations may be needed, particularly for chemicals that lack potency or toxicity data. In this work, we present an integral competitive ABPP method that enables target sensitivity determination for different organophosphate (OP) pesticides as model toxicants. Using previously developed OP-ABPs, we optimized conditions for tandem mass tag (TMT) multiplexing of ABPP samples and compared conventional competitive ABPP involving samples at discrete paraoxon concentrations to pooled samples across that same concentration range. We then expanded our approach to compare protein target sensitivities toward two additional OP pesticides, chlorpyrifos oxon and malaoxon. The results showed that differences in integral intensities for the pooled competition sample can be used to evaluate the relative sensitivity of specific proteins without increasing the overall number of samples. For 8 CoC concentrations of interest, this strategy reduced the number of TMT plexes and the corresponding number of LC–MS/MS analyses 3-fold. In conclusion, we envision the integral ABPP (IABPP) method will provide a means to screen diverse chemicals more rapidly to identify both high and low sensitivity protein targets.

activity-based probes↗

DOE OSTI2024

Controlling Bond Scission Pathways of Isopropanol on Fe- and Pt-Modified Mo 2 N Model Surfaces and Powder Catalysts

Biomass valorization can be used to produce value-added chemicals and fuels from renewable biomass resources by upgrading them via selective bond scission while retaining certain functional groups. Specifically, upgrading biomass through the dehydrogenation of alcohols to carbonyl compounds has gained interest as a method of utilizing biomass-derived alcohols while additionally producing H 2 . In this work, isopropanol was used as a probe molecule to control bond scission selectivity over Fe- and Pt-modified molybdenum nitride (Mo 2 N) model surfaces and powder catalysts. Trends in the selectivity toward dehydration and dehydrogenation were dependent on both the type and coverage of the metal overlayer on model surfaces. These results were then extended to the corresponding powder catalysts to demonstrate how model surface studies can inform the design of supported catalysts. Density functional theory calculations provided insights into controlling the dehydration and dehydrogenation pathways. In conclusion, this work shows that a fundamental understanding of the reactivity and intermediates on Mo 2 N-based model surfaces can be applied to understand the catalytic performance of metal-modified Mo 2 N powder catalysts, and also demonstrates that Mo 2 N-based catalysts are potentially promising materials for upgrading biomass-derived oxygenates.

09 BIOMASS FUELS↗

NASA NTRS2011

Biochemical Sensors Using Carbon Nanotube Arrays

Method and system for detecting presence of biomolecules in a selected subset, or in each of several selected subsets, in a fluid. Each of an array of two or more carbon nanotubes ("CNTs") is connected at a first CNT end to one or more electronics devices, each of which senses a selected electrochemical signal that is generated when a target biomolecule in the selected subset becomes attached to a functionalized second end of the CNT, which is covalently bonded with a probe molecule. This approach indicates when target biomolecules in the selected subset are present and indicates presence or absence of target biomolecules in two or more selected subsets. Alternatively, presence of absence of an analyte can be detected.

Li, Jun↗

NASA NTRS1991

Infrared variability of Jupiter and Saturn

Infrared spectroscopy provides unique insights into the chemistry and dynamics of the atmospheres of Jupiter and Saturn, and of the enigmatic satellite of Saturn, Titan. The 5 micron spectral region of these objects is transparent to deep levels, and is therefore particularly useful for the identification of molecules that are present at very low (parts per billion) concentrations. In Titan, 5 micron observations probe atmospheric layers at or near the surface. Ground-based spectroscopy complements Voyager, Galileo, and Cassini measurements. The spectroscopy is sensitive to lower mixing ratios for selected molecules, while the on-board mass and infrared spectrometers probe molecules and levels that are inaccessible form the ground. The observations also provide time-based data for preparation of the upcoming missions.

Knacke, Roger↗

NASA NTRS1988

Infrared spectroscopy of Jupiter and Saturn

High resolution infrared spectoscopy provides unique insights into the chemistry and dynamics of the atmospheres of Jupiter and Saturn. The 5 micrometer spectral region, which is transparent to deep levels, is particularly useful for the identification of molecules that are present at very low (parts per billion) concentrations. These are tracers of convective and strongly non-equilibrium processes in the atmosphere. High resolution ground-based spectroscopy complements Voyager and Galileo measurements. Spectroscopy is sensitive to lower mixing levels for selected molecules, while the on-board mass spectrometers probe molecules that are spectroscopically inaccessible. Analysis and modeling of the 4.7 micrometer carbon monoxide in Jupiter was completed. CO is present at a mole fraction of 1.6 plus or minus 0.3 x 10 to the 9th power and concentrated in the troposphere. At this abundance, it must be convected upward from much deeper levels in Jupiter where the temperature is near 1100 K. Thus CO is a tracer of the deep atmosphere which is otherwise unobservable. The oxygen abundance in Jupiter (as measured by the CO abundance) is near solar. Chemical or physical process must deplete the major oxygen carrier, water. Germane, GeH4, was discovered on Saturn at amole fraction of 4 plus or minus 2 x 10 to the 10th power.

Knacke, Roger↗

DOE OSTI2023

Case Study: Calorimetry

This chapter presents the use of adsorption microcalorimetry to study acid-base catalysis over mixed metal oxides. Understanding the acid-base properties of catalysts is of paramount importance for steering product selectivity in a wide variety of catalytic industrial processes. In particular, catalytic conversion of biomass into biofuels and chemicals demands comprehensive understanding of the acid-base properties of the catalyst to selectively convert functional groups. Herein, the use of probe molecules to measure the strength and density of acid and basic sites on mixed metal oxide surfaces is introduced. Further, the challenges when characterizing mixed metal oxides, presenting surface reconstruction, are explained. An example displays how combining adsorption calorimetry with ab initio calculations explains the activation of a reactant on the surface of a mixed metal oxide. Acid-base catalysis over nanoshapes is studied to unveil that different nanoshapes lead to different extents of surface reconstruction, which ultimately affect acid-base catalysis. The use of steady-state isotopic transient kinetic analysis (SSITKA), in combination with adsorption microcalorimetry, unveils that surface reconstruction of a set of perovskites impacts the density of active sites to a greater extent than the intrinsic reactivity of the active site. At the end of this chapter, fundamental insights into catalyst transient behavior during isomerization of n-butane, and the reaction mechanism for conversion of 4-methylpentan-2-ol, are presented.

Polo Garzon, Felipe↗

DOE OSTI2025

Layers Can Be Deceiving: A Hopping Model for Small Molecule Diffusion in TATB Crystal

Sorption of small molecule gases in materials can play a significant role in their long‐term stability and compatibility within multi‐material assemblies. While many material properties of the insensitive high explosive TATB (1,3,5‐triamino‐2,4,6‐trinitrobenzene) are well understood, very little is known regarding its permeability to gases. TATB crystal exhibits a graphitic‐like layered packing structure that evokes a mental schema in which the layers form nanoscopic channels, but it is unclear whether this structure promotes gas transport. Here, we use molecular dynamics (MD) simulations to predict transport of small molecules through TATB single crystal. An approach to fit classical force fields is developed to model TATB interactions with H 2 O, He, Ne, and Ar, which is then combined with steered MD to probe gas transport along selected directions in the crystal. We find that small molecule transport occurs via a hopping mechanism that exhibits distinct jumps between interstitial sites and is substantially faster normal to the layers as compared to through them. This result stems from the finding that intralayer junctions between adjacent TATB molecules are the most stable interstitial sites and that energetic barriers are lower for hopping between adjacent layers. An empirical model for diffusion rate based on the MD data shows that the rate decays exponentially with increasing molecular radius and is negligibly small for all molecules larger than He, including common atmospheric gases. These findings have implications for the interpretation of experiments that measure surface area, material response to extreme conditions, and are expected to help constrain models for material aging.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Long-term super-resolution inner mitochondrial membrane imaging with a lipid probe

The inner mitochondrial membrane (IMM) generates power to drive cell function, and its dynamics control mitochondrial health and cellular homeostasis. Here, we describe the cell-permeant, lipid-like small molecule MAO-N 3 and use it to assemble high-density environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells and multiple cell states. MAO-N 3 pairs with strain-promoted azide–alkyne click chemistry-reactive fluorophores to support HIDE imaging using confocal, structured illumination, single-molecule localization and stimulated emission depletion microscopy, all with significantly improved resistance to photobleaching. These probes generate images with excellent spatial and temporal resolution, require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes (even under conditions that amplify the effects of mitochondrial toxins) and can visualize mitochondrial dynamics for 12.5 h. This probe will enable comprehensive studies of IMM dynamics with high temporal and spatial resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Resonant Stimulated X-ray Raman Spectroscopy of Mixed-Valence Manganese Complexes

Resonant stimulated X-ray Raman spectroscopy of the bimetallic [Mn III Mn IV (μ-O) 2 (μ-OAC)(tacn) 2 ] 2+ manganese complex is investigated in a simulation study. A pump–probe sequence of resonant X-ray Raman excitations is employed to generate and monitor valence-electron wave packets at selected regions in the molecule, by exploiting element specific core-excited states. A two-color protocol is presented, with pump and probe pulses tuned to the Mn and N K-edges. A natural orbital decomposition allows the visualization of the electron dynamics underlying the signal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Engineering Active Sites of Metal/Metal Oxide Catalysts by Oxide Ligand Overlayers

Abstract Engineering sites of supported metal catalysts is essential to enhancing activity and selectivity. Such enhancement is typically achieved by particle size modification, surface alloying, or attaching molecular ligands. Yet, control strategies for complex, multifunctional molecules and catalysts, where selectivity is crucial, are lacking. Here, we demonstrate that submonolayer WO x with tunable coverage preferentially decorates well‐coordinated Pt terrace sites as a stable ligand. By combining experimental kinetics with probe molecules, in situ spectroscopies, and first‐principles modeling, we show that the WO x coverage on Pt modifies the metal‐to‐acid site balance while retaining the acid strength intact and results in optimal reactivity for metal‐acid catalyzed reactions at a specific metal, size, and support‐dependent WO x coverage. The oxide can also alter the reactant adsorption mode, reversing selectivity and pathways from terrace‐ to step‐dominated, as evidenced in furfural decarbonylation and hydrogenation. The insights open avenues for improving metal/metal oxide catalysts beyond the specific system.

Zhou, Jiahua↗

DOE OSTI2024

Probing and Understanding the Spatial and Energy Distributions of Plasmonic Hot Carriers via Single-Molecule Quantum Transport

The generation of hot carriers in plasmonic nanostructures offers new transformative opportunities for a range of applications, including solar energy harvesting, photochemistry, and photodetection. To better understand such phenomena, this project aims to develop an experimental approach to study and understand hot carrier distributions in photoexcited plasmonic nanostructures. The developed experimental approach, combining scanning probe-based single-molecule quantum transport measurements with plasmonic excitation methods, leverages nanoscopic single molecules as quantum energy filters to selectively access hot carriers in a variety of plasmonic nanostructures. This report summarizes the key outcomes, impacts, and lessons learned in the first two years of the project. Over the past two years, important progress was made in achieving the project's goals, including the development of the scanning probe-based experimental platform, fabrication of plasmonic nanostructures, and design and synthesis of the desired molecular candidates. Insights from this research will pave the path toward the development of technologies that will improve the way we harvest solar energy and drive chemical reactions and ultimately help transition the U.S. to a clean and sustainable society.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Support modification by phosphonic acid ligands controls ethylene hydroformylation on single-atom rhodium sites

To investigate the ability of surface-bound ligands to control activity toward ethylene hydroformylation, we modified site-isolated Rh 1 /TiO 2 with a series of substituted benzyl phosphonic acids. We found that modification of the support by phosphonic acids reduced break-in times for hydroformylation by 4× and increased absolute hydroformylation activity by up to 18× compared to unmodified catalyst at 150 °C. All functionalized catalysts improved hydroformylation activity by at least 9× and improved selectivity by between 7× and 60× relative to the unmodified catalyst. Carbon monoxide probe–molecule spectroscopy indicated that the enhancements in activity among modified samples were due to changes in the local environment of the active Rh site. Specifically, the bite angle of adsorbed carbon monoxide, as determined from infrared spectra, correlated with hydroformylation activity. These findings demonstrate that Rh 1 active sites are highly sensitive to modification of the support with organic ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Chromatin activity precipitation method and system

Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2004

Miniaturized multiplex label-free electronic chip for rapid nucleic acid analysis based on carbon nanotube nanoelectrode arrays

BACKGROUND: Reducing cost and time is the major concern in clinical diagnostics, particularly in molecular diagnostics. Miniaturization technologies have been recognized as promising solutions to provide low-cost microchips for diagnostics. With the recent advancement in nanotechnologies, it is possible to further improve detection sensitivity and simplify sample preparation by incorporating nanoscale elements in diagnostics devices. A fusion of micro- and nanotechnologies with biology has great potential for the development of low-cost disposable chips for rapid molecular analysis that can be carried out with simple handheld devices. APPROACH: Vertically aligned multiwalled carbon nanotubes (MWNTs) are fabricated on predeposited microelectrode pads and encapsulated in SiO2 dielectrics with only the very end exposed at the surface to form an inlaid nanoelectrode array (NEA). The NEA is used to collect the electrochemical signal associated with the target molecules binding to the probe molecules, which are covalently attached to the end of the MWNTs. CONTENT: A 3 x 3 microelectrode array is presented to demonstrate the miniaturization and multiplexing capability. A randomly distributed MWNT NEA is fabricated on each microelectrode pad. Selective functionalization of the MWNT end with a specific oligonucleotide probe and passivation of the SiO2 surface with ethylene glycol moieties are discussed. Ru(bpy)2+ -mediator-amplified guanine oxidation is used to directly measure the electrochemical signal associated with target molecules. SUMMARY: The discussed MWNT NEAs have ultrahigh sensitivity in direct electrochemical detection of guanine bases in the nucleic acid target. Fewer than approximately 1000 target nucleic acid molecules can be measured with a single microelectrode pad of approximately 20 x 20 microm2, which approaches the detection limit of laser scanners in fluorescence-based DNA microarray techniques. MWNT NEAs can be easily integrated with microelectronic circuitry and microfluidics for development of a fully automated system for rapid molecular analysis with minimum cost.

Carbon↗

DOE OSTI2022

Effects of pore connectivity and tortuosity on the dynamics of fluids confined in sub-nanometer pores

Dynamical behavior of fluids under nano-pore confinement is studied extensively as it has important implications for several industrial as well as geological processes. Pore network in many porous materials exhibits a varied degree of inter connections. The extent of this pore connectivity may affect the structural and dynamical behavior of the confined fluid. However, studies of fluid confinement addressing these effects systematically are lacking. In this paper we report molecular dynamics simulation studies addressing the effects of pore connectivity on the dynamics of two representative fluids – CO 2 and ethane in silicalite by systematically varying the degree of pore connectivity through selectively blocking some pore space with immobile methane molecules. By selectively turning off the pore spaces in the shape of straight, or tortuous zigzag channels, we also probe the effects of pore tortuosity. In general, pore connectivity is found to facilitate both the translational as well as rotational dynamics of both fluids, while the intermolecular modes of vibration in both fluids remain largely unaffected. The effects of providing connections between a set of straight or zigzag channel-like pores are however more nuanced. Pore tortuosity facilitates the rotational motion, but suppresses the translational motion of CO 2 , while its effects on the rotational and translational motion of ethane are less pronounced. The intermolecular vibrational modes of both fluids shift to higher energies with an increase in the number of tortuous pores. The results reported here provide a detailed molecular level understanding of the effects of pore connectivity on the dynamics of fluids and thus have implications for applications like fluid separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗