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At least 343 records · Page 19

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DOE OSTI2019

Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples

The current gold standard for unambiguous molecular identification in metabolomics analysis is comparing two or more orthogonal properties from the analysis of authentic reference materials (standards) to experimental data acquired in the same laboratory with the same analytical methods. This represents a significant limitation for comprehensive chemical identification of small molecules in complex samples. The process is time-consuming and costly, and the majority of molecules are not yet represented by standards. Thus, there is a need to assemble evidence for the presence of small molecules in complex samples through the use of libraries containing calculated chemical properties. To address this need, we developed a Multi-Attribute Matching Engine (MAME) and a library derived in-part from our in silico Chemical Library Engine (ISiCLE). Here, we describe an initial evaluation of these methods in a blinded analysis of synthetic chemical mixtures as part of the U.S. Environmental Protection Agency’s (EPA) Non-Targeted Analysis Collaborative Trial (ENTACT, Phase 1). For molecules in all mixtures, the initial blinded false negative rate (FNR), false discovery rate (FDR), and accuracy were 57%, 77%, and 91%, respectively. For high evidence scores, the FDR was 35%. After unblinding of the sample compositions, we optimized the scoring parameters to better exploit the available evidence, and increased the accuracy for molecules suspected as present. The final FNR, FDR, and accuracy were 67%, 53%, and 96%, respectively. For high evidence scores, the FDR was 10%. This study demonstrates that multi-attribute matching methods in conjunction with in silico libraries may one day enable reduced reliance on experimentally-derived libraries for building evidence for the presence of molecules in complex samples.

Nunez, Jamie↗

DOE OSTI2017

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2020

Self-Assembled Solute Networks in Crowded Electrolyte Solutions and Nanoconfinement of Charged Redoxmer Molecules

Redoxmers are electrochemically active organic molecules storing charge and energy in electrolyte fluids circulating through redox flow batteries (RFBs). Such molecules typically have solvent-repelling cores and solvent-attracting pendant groups introduced to increase solubility in liquid electrolytes. These two features can facilitate nanoscale aggregation of the redoxmer molecules in crowded solutions. In some cases, this aggregation leads to the emergence of continuous networks of solute molecules in contact, and the solution becomes microscopically heterogeneous. In this study, we used small-angle X-ray scattering (SAXS) and molecular dynamics modeling to demonstrate formation of such networks and examine structural factors controlling this self-assembly. We also show that salt ions become excluded from these solute aggregates into small pockets of electrolytes, where these ions strongly associate. This confinement by exclusion is also likely to occur to charged redoxmer molecules in a “sea” of neutral precursors coexisting in the same solution. Here, we demonstrate that the decay lifetime of the confined charged molecules in such solutions can increase several fold compared to dilute solutions. We attribute this behavior to a “microreactor effect” on reverse reactions of the confined species during their decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Barrierless On-Surface Metal Incorporation in Phthalocyanine-Based Molecules

On-surface metalation of metal-free phthalocyanine derivatives is a simple and solvent-free way to fabricate MPc compounds. Using phthalocyanine (H 2 Pc) molecules on Ag(111) as an example, we investigated the atomic-scale mechanisms of on-surface metalation processes using first-principles calculations based on density functional theory. When the molecules are deposited on a substrate first, we find that transition-metal atoms, except for Zn, drop directly from the vacuum into the molecule’s cavity without an energy barrier and bond with the inner four nitrogen atoms, with the two pyrrolic H atoms still in place. Subsequently, the two H atoms transfer to the substrate by overcoming small energy barriers and diffuse away. The substrate participates in the reaction by hybridization. In the alternative process, when metal atoms are adsorbed first on the surface and the H 2 Pc molecules are then added, the metal atoms diffuse into the cavity of the molecule via the molecule–surface interface by overcoming finite energy barriers. Finally, the above results provide insights into the on-surface metalation that can guide the control of the reaction pathway and products at the atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Role of H 2 O in Catalytic Conversion of C 1 Molecules

Due to their role in controlling global climate change, the selective conversion of C 1 molecules such as CH 4 , CO, and CO 2 has attracted widespread attention. Typically, H 2 O competes with the reactant molecules to adsorb on the active sites and therefore inhibits the reaction or causes catalyst deactivation. However, H 2 O can also participate in the catalytic conversion of C 1 molecules as a reactant or a promoter. Herein, we provide a perspective on recent progress in the mechanistic studies of H 2 O-mediated conversion of C 1 molecules. We aim to provide an in-depth and systematic understanding of H 2 O as a promoter, a proton-transfer agent, an oxidant, a direct source of hydrogen or oxygen, and its influence on the catalytic activity, selectivity, and stability. We also summarize strategies for modifying catalysts or catalytic microenvironments by chemical or physical means to optimize the positive effects and minimize the negative effects of H 2 O on the reactions of C 1 molecules. Finally, we discuss challenges and opportunities in catalyst design, characterization techniques, and theoretical modeling of the H 2 O-mediated catalytic conversion of C 1 molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Precise synthesis and photovoltaic properties of giant molecule acceptors

Series of giant molecule acceptors DY, TY and QY with two, three and four small molecule acceptor subunits are synthesized by a stepwise synthetic method and used for systematically investigating the influence of subunit numbers on the structure-property relationship from small molecule acceptor YDT to giant molecule acceptors and to polymerized small molecule acceptor PY-IT. Among these acceptors-based devices, the TY-based film shows proper donor/acceptor phase separation, higher charge transfer state yield and longer charge transfer state lifetime. Combining with the highest electron mobility, more efficient exciton dissociation and lower charge carrier recombination properties, the TY-based device exhibits the highest power conversion efficiency of 16.32%. These results indicate that the subunit number in these acceptors has significant influence on their photovoltaic properties. This stepwise synthetic method of giant molecule acceptors will be beneficial to diversify their structures and promote their applications in high-efficiency and stable organic solar cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Parity-doublet coherence times in optically trapped polyatomic molecules

Polyatomic molecules provide complex internal structures that are ideal for applications in quantum information science, quantum simulation and precision searches for physics beyond the standard model. A key feature of polyatomic molecules is the presence of parity-doublet states. These structures, which generically arise from the rotational and vibrational degrees of freedom afforded by polyatomic molecules, are a powerful feature to pursue diverse quantum science applications. Linear triatomic molecules contain ℓ-type parity-doublet states in the vibrational bending mode, which are predicted to exhibit robust coherence properties. Here we report optically trapped CaOH molecules prepared in ℓ-type parity-doublet states and realize a bare qubit coherence time of $T$$^{*}_{2}$, which is longer than the 0.36 s lifetime of the bending mode. We suppress differential Stark shifts by cancelling ambient electric fields using molecular spectroscopy and characterize parity-dependent trap shifts, which are found to limit the coherence time. Furthermore, the parity-doublet coherence times achieved in this work are a defining milestone for the use of polyatomic molecules in quantum science.

Quantum information↗

DOE OSTI2017

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followed by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2 +H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2022

Highly efficient organic solar cells with superior deformability enabled by diluting the small molecule acceptor content

Developing efficient organic solar cells (OSCs) with strong mechanical deformability is important to be addressed to ensure their operational reliability in wearable electronics. However, it is challenging to achieve mechanically robust polymer/small molecule OSCs with an efficiency over 17% due to the abundant brittle donor/acceptor (D/A) interface. Decreasing the small molecule content can reduce the brittle D/A interface area to enhance deformability, but it may also cause discontinuous electron-conducting regions and thus deteriorate photovoltaic performance. Here, we incorporate a polymer donor (D18) into a binary PTQ10cm-BTP-PhC6 system at a constant PTQ10:m-BTP-PhC6 ratio of 1 : 1.2 to minimize the D/A interfacial area and modulate phase separation, and subsequently fabricate mechanically reliable OSCs with high efficiency. The large incorporation of D18 molecules increases the crystallinity of m-BTP-PhC6 molecules because of the poor interaction between D18 and the two host materials, affording sufficient pathways for efficient charge percolation at a large D/A ratio. More importantly, highly aggregated m-BTP-PhC6 molecules help to minimize the D/A interfacial area, enabling ternary films with better deformability than their binary counterparts. As a result, ternary OSCs with a large D/A ratio of 1.5 : 1.2 exhibit a high efficiency of 17.3% with a crack-onset strain (COS) of 8.8%, which significantly outperforms their binary counterparts with an efficiency of 13.8% and a COS of 4.4%. Finally, diluting the content of small molecules and controlling intermolecular interaction through the introduction of the second polymer donor represents a promising strategy to fabricate efficient OSCs with superior deformability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Conjugation effect of amine molecules in non-aqueous Mg redox flow batteries

Nonaqueous magnesium redox flow batteries (Mg RFBs) are attractive for low-cost, high-energy-density and long-cycle-life stationary energy storage applications. However, state-of-the-art cathode redox-active molecules suffer from low solubility and low redox potential. Herein, we screened a range of cathode redox-active molecules and identified amine molecules as optimal to couple with the Mg anode. The properties of amine derivatives and their performances were collected to establish the correlation between molecular structures and electrochemical performances. The redox potential and solubility of these amine molecules were influenced by the π-conjugated and non-conjugated structures of amine derivatives. Density functional theory (DFT) simulations and the inverse aromatic fluctuation index (FLU −1 ) verified that conjugation had an important role in stabilizing the molecule and increasing its redox potential. Notably, tris[4-(diethylamino)phenyl]amine (TDPA) achieved the highest theoretical energy density (∼120 Wh L −1 ) due to its high solubility (∼0.9 M) and voltage (∼2.5 V vs. Mg/Mg 2+ ). We also demonstrated that ether solvents were crucial for stable, high-solubility catholytes, while bulk anions did not affect the redox potential of these p-type molecules. In a Mg-amine RFB configuration, the battery delivered 2.50 V, a specific discharge capacity of 106.5 mAh g −1 , an initial coulombic efficiency of 90.74%, and a capacity retention of 93.88% after 150 cycles.

Qin, Yunan [University of Utah, Salt Lake City, UT↗

DOE OSTI2016

Electric-field-driven electron-transfer in mixed-valence molecules

Molecular quantum-dot cellular automata is a computing paradigm in which digital information is encoded by the charge configuration of a mixed-valence molecule. General-purpose computing can be achieved by arranging these compounds on a substrate and exploiting intermolecular Coulombic coupling. The operation of such a device relies on nonequilibrium electron transfer (ET), whereby the time-varying electric field of one molecule induces an ET event in a neighboring molecule. The magnitude of the electric fields can be quite large because of close spatial proximity, and the induced ET rate is a measure of the nonequilibrium response of the molecule. We calculate the electric-field-driven ET rate for a model mixed-valence compound. The mixed-valence molecule is regarded as a two-state electronic system coupled to a molecular vibrational mode, which is, in turn, coupled to a thermal environment. Both the electronic and vibrational degrees-of-freedom are treated quantum mechanically, and the dissipative vibrational-bath interaction is modeled with the Lindblad equation. This approach captures both tunneling and nonadiabatic dynamics. Relationships between microscopic molecular properties and the driven ET rate are explored for two time-dependent applied fields: an abruptly switched field and a linearly ramped field. In both cases, the driven ET rate is only weakly temperature dependent. When the model is applied using parameters appropriate to a specific mixed-valence molecule, diferrocenylacetylene, terahertz-range ET transfer rates are predicted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Phevamine A, a small molecule that suppresses plant immune responses

Bacterial plant pathogens cause significant crop damage worldwide. They invade plant cells by producing a variety of virulence factors, including small-molecule toxins and phytohormone mimics. Virulence of the model pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) is regulated in part by the sigma factor HrpL. Our study of the HrpL regulon identified an uncharacterized, three-gene operon in Pto that is controlled by HrpL and related to the Erwinia hrp-associated systemic virulence (hsv) operon. Here, we demonstrate that the hsv operon contributes to the virulence of Pto on Arabidopsis thaliana and suppresses bacteria-induced immune responses. We show that the hsv-encoded enzymes in Pto synthesize a small molecule, phevamine A. This molecule consists of L-phenylalanine, L-valine, and a modified spermidine, and is different from known small molecules produced by phytopathogens. We show that phevamine A suppresses a potentiation effect of spermidine and L-arginine on the reactive oxygen species burst generated upon recognition of bacterial flagellin. The hsv operon is found in the genomes of divergent bacterial genera, including ~37% of P. syringae genomes, suggesting that phevamine A is a widely distributed virulence factor in phytopathogens. Our work identifies a small-molecule virulence factor and reveals a mechanism by which bacterial pathogens overcome plant defense. This work highlights the power of omics approaches in identifying important small molecules in bacteria–host interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Theory of strong-field sequential double ionization of polyatomic molecules

Understanding of strong-field sequential double ionization (SDI) of molecules by a highly intense infrared laser pulse could be the key to observing electron motion in molecules in the attosecond to femtosecond timescale. Based on a novel density matrix approach for SDI (DM-SDI), a recent theoretical study has shown that SDI can be used as a probe to monitor the changes in vibronic coherence in homonuclear diatomic molecules. In this article, we extend the DM-SDI model to general molecules that could possess permanent dipole moments and arbitrary symmetry. We apply the model to SDI of a water molecule and identify the formation pathway of individual dication states. We further deduce that kinetic energy release spectra from two- and three-body fragments could carry the signature of vibronic coherence between the lowest two states of the water cation. Furthermore, our results suggest that observables from the SDI probe can be interpreted intuitively with only the knowledge of electronic structures of populated ionic states, making the SDI probe to be a highly desirable probing scheme for vibronic coherence in generic molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Switching the conductance of a single molecule: Lessons from molecular junctions

The concept of using single molecules as functional building blocks in electronic circuitry represents the ultimate device miniaturization and has garnered tremendous attention from physics, chemistry, and engineering. Recent advances in single-molecule junction techniques have enabled direct investigation of charge transport in a quasi-one-dimensional conduction channel composed of an individual molecule. Furthermore, one of the main research focuses over the past decade has been to understand the conductance switching effect of single molecules as it is essential for developing molecular-scale optoelectronics, computing, and sensing applications. In this perspective, we highlight the established physical and chemical mechanisms for single-molecule conductance switching behavior and examine the associated stimuli in single-molecule junction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Generation, Detection and characterization of Gas-Phase Transition Metal containing Molecules

The objective of this project was to generate, detect, and characterize small, gas-phase, metal containing molecules. In addition to being relevant to high temperature chemical environments (e.g. plasmas and combustion), gas-phase experiments on metal containing molecules serve as the most direct link to a molecular-level theoretical model for catalysis. Catalysis (i.e. the addition of a small about of recoverable material to control the rate and direction of a chemical reaction) is critical to the petroleum and pharmaceutical industries as well as environmental remediation. Currently, the majority of catalytic materials are based on very expensive metals such as platinum (Pt), palladium (Pd), iridium (Ir,) rhenium (Re), and rhodium (Rh). For example, the catalyst used for converting linear hydrocarbon molecules (e.g. hexane) to cyclic molecules (e.g. cyclohexane) is a mixture of Pt and Re suspended on alumina. It enables straight chain alkanes to be converted into branched-chain alkanes, cyclohexanes and aromatic hydrocarbons which are used, amongst other things, to enhance the octane number of petrol. A second example is the heterogeneous catalysis used in automobile exhaust systems to: a) decrease nitrogen oxide; b) reduce carbon monoxide; and c) oxidize unburned hydrocarbons. The exhaust is vented through a high-surface area chamber lined with Pt, Pd, and Rh. For example, the carbon monoxide is catalytically converted to carbon dioxide by reaction with oxygen. The research results from this work have been published in readily accessible journals1-28. The ground and excited electronic state properties of small metal containing molecules that we determine were: a) electronic state distributions and lifetimes, b) vibrational frequencies, c) bond lengths and angles, d) hyperfine interactions, e) permanent electric dipole moments, mel, and f) magnetic dipoles, μ m . In general terms, μ el , gives insight into the charge distribution and mm into the number and nature of the unpaired electrons. Analysis of the hyperfine interactions (i.e. Fermi-contact, nuclear electric quadrupole, etc.) is particularly insightful because it results from the interaction of nuclei with non-zero spin and the chemically important valence electrons. The bulk of the spectroscopic techniques used in these studies exploit the sensitivity of laser induced fluorescence (LIF) detection. The spectroscopic schemes employed include: a) cw and pulsed laser field-free(FF) excitation and dispersed LIF (DLIF); b) optical Stark; c) optical Zeeman; d) pump/probe microwave double resonance (PPMODR); e) fluorescence lifetimes, and f) resonant and non-resonant two-photon ionization TOF mass spectrometry. Vibrational spacing, force constants and electronic states distributions are derived from the analysis of pulsed dye laser excitation and DLIF spectra. Geometric structure (bond lengths and angles) and hyperfine parameters are derived from the analysis of cw-laser LIF and PPMODR spectra. Permanent electric dipole moments, mel,, and magnetic dipole moments, mm, are derived from the analysis of optical Stark and Zeeman spectra, respectively. Transition moments are derived from the analysis of radiative lifetimes. A supersonic molecular beam sample of these ephemeral molecules is generated by skimming the products of either a laser ablation/reaction source or a d.c. discharge source.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Electrochemical Detection of Single Molecules in Nanogap Electrode Fluidic Devices

The purpose of this project was to gain a fundamental understanding of molecular diffusion in nanogap electrodes and the diffusive behavior of single molecules undergoing electron transfer. Electrochemical methods for single molecule detection have remained elusive due to the vanishingly small currents involved in single molecule electron transfer. Electrochemical detection of single molecules undergoing redox cycling would enable detection of single enzymes, proteins, and DNA strands resulting in new and improved ultrasensitive sensing devices impacting Detection At The Limits research challenge (DATL), supporting needs in DHS and DoD. We attempted to integrate orthogonal validation techniques, Total Internal Reflection Fluorescence Microscopy (TIRF), and molecular simulation to clarify (1) the mechanism leading to current build up due to redox cycling and (2) diffusion and adsorption of single molecules undergoing redox reactions. While creation of nanogap electrodes with transparent windows was ultimately successful in this project (along with TIRF demonstration of single molecule imaging), time and methods constraints did not allow final electrochemical measurements to be coupled for simultaneous interrogation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Models and Processes to Extract Drug-like Molecules From Natural Language Text

Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of viral research. However, this literature is too large for human review and features unusual vocabularies for which existing named entity recognition (NER) models are ineffective. We report here on a project that leverages both human and artificial intelligence to detect references to such molecules in free text. We present 1) a iterative model-in-the-loop method that makes judicious use of scarce human expertise in generating training data for a NER model, and 2) the application and evaluation of this method to the problem of identifying drug-like molecules in the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198,875 papers. We show that by repeatedly presenting human labelers only with samples for which an evolving NER model is uncertain, our human-machine hybrid pipeline requires only modest amounts of non-expert human labeling time (tens of hours to label 1778 samples) to generate an NER model with an F-1 score of 80.5%—on par with that of non-expert humans—and when applied to CORD’19, identifies 10,912 putative drug-like molecules. This enriched the computational screening team’s targets by 3,591 molecules, of which 18 ranked in the top 0.1% of all 6.6 million molecules screened for docking against the 3CLPro protein.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (Φ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, Φ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

77 NANOSCIENCE AND NANOTECHNOLOGY↗