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DOE OSTI2021

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Geometry-complete diffusion for 3D molecule generation and optimization

Abstract Generative deep learning methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a denoising diffusion framework. However, such methods are unable to learn important geometric properties of 3D molecules, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which notably hinders their ability to generate valid large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset and the larger GEOM-Drugs dataset, respectively. Importantly, we demonstrate that GCDM’s generative denoising process enables the model to generate a significant proportion of valid and energetically-stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but can be repurposed to consistently optimize the geometry and chemical composition of existing 3D molecules for molecular stability and property specificity, demonstrating new versatility of molecular diffusion models. Code and data are freely available on GitHub .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Identification of bioprivileged molecules: expansion of a computational approach to broader molecular space

As interest in biobased chemicals grows, and their application space expands, computational tools to navigate molecule space as a complement to experimental approaches are imperative. This work expands upon previous work that identified candidate bioprivileged molecules from the C 6 H x O y (C6) subspace. It refines the framework that was developed previously to better refine the molecules according to their biological origin and applies it to three new subspaces of chemical structure: C 4 H x O y (C4), C 5 H x O y (C5), and C 7 H x O y (C7). For C5 and C7, roughly the top 100 bioprivileged candidates were identified, and the enhanced framework was applied to recast slightly the previous list of the top 100 C6 molecules. In addition, all top candidates were analyzed for their key functional moieties using a random forest model, and this algorithm was applied to compare the functional group space occupied by bioprivileged molecules of various databases of molecules with a focus on evaluating how closely the molecules were aligned with those known to biology. Furthermore, with the present work's focus on automation and data science principles, the framework can be easily expanded to include other chemical formulae to screen for bioprivileged candidates. As a result, this in turn facilitates the retrosynthesis process inherent in the framework to identify those bioprivileged intermediates in other subspaces that lead to target molecules.

42 ENGINEERING↗

DOE OSTI2014

Research Update: Molecular electronics: The single-molecule switch and transistor

In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

42 ENGINEERING↗

DOE OSTI2022

Coupling, lifetimes, and “strong coupling” maps for single molecules at plasmonic interfaces

The interaction between excited states of a molecule and excited states of a metal nanostructure (e.g., plasmons) leads to hybrid states with modified optical properties. When plasmon resonance is swept through molecular transition frequency, an avoided crossing may be observed, which is often regarded as a signature of strong coupling between plasmons and molecules. Such strong coupling is expected to be realized when 2|$\langle$U$\rangle$|/ℏΓ > 1, where $\langle$U$\rangle$ and Γ are the molecule–plasmon coupling and the spectral width of the optical transition, respectively. Because both $\langle$U$\rangle$ and Γ strongly increase with decreasing distance between a molecule and a plasmonic structure, it is not obvious that this condition can be satisfied for any molecule–metal surface distance. Here, in this work, we investigate the behavior of $\langle$U$\rangle$ and Γ for several geometries. Surprisingly, we find that if the only contributions to Γ are lifetime broadenings associated with the radiative and nonradiative relaxation of a single molecular vibronic transition, including effects on molecular radiative and nonradiative lifetimes induced by the metal, the criterion 2|$\langle$U$\rangle$|/ℏΓ > 1 is easily satisfied by many configurations irrespective of the metal–molecule distance. This implies that the Rabi splitting can be observed in such structures if other sources of broadening are suppressed. Additionally, when the molecule–metal surface distance is varied keeping all other molecular and metal parameters constant, this behavior is mitigated due to the spectral shift associated with the same molecule–plasmon interaction, making the observation of Rabi splitting more challenging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS2005

Ice photochemistry as a source of amino acids and other organic molecules in meteorites, and implications for the origin of life and the search for life in the Solar System

The tons of extraterrestrial organic material that come to the Earth every day probably helped to made the Earth habitable, and possibly played a role in the origin of life. At the astrochemistry lab (http://www.astrochem.orq) we investigate the formation and distribution of organic molecules in space and consider the impact such molecules may have on the habitability of planets and the search for life in the Solar System. The organic compounds in meteorites include amino acids, aromatics of various sorts including purine and pyrimidine bases, and fatty acids that form bi-layer vesicles. The origin of many of these species remains mysterious, but in recent years we and others have performed experiments that suggest low temperature radiation chemistry could account for the presence and deuterium enrichment of many of these molecules. . I will present our laboratory experiments that show the viability of low temperature radiation chemistry as a source of organic molecules such as;amino acids (Nature, 2002, 416, 401-403), amphiphiles (Astrobiology, 2003, 2, 371, Proc. Nat. Acad. Sci. 2001, 98, 815), quinones (Science, 1999, 283, 1135) and other functionalized aromatic compounds (Meteoritics, 2001, 36, 351 ; Astrophysical Journal., 2003, 582, L25), some of which were invoked as potential biomarkers in the Alan Hills 84001 Martian meteorite. Understanding how components of proteins and DNA could form in sterile space environments is also of relevance to our search for life elsewhere in the Solar System, the great task now ahead of NASA. If we find evidence of Life elsewhere in the Solar System it will probably be in form of chemical biomarkers, quintessentially biological molecules that indicate the presence of micro-organisms. While most people think of molecules such as amino acids, and nucleo-bases as good candidate biomarkers, these molecules are produced non-biotically in space and are expected to be present on the surface of other planets even in the absence of Life. Understanding the range of non-biological organic molecules which could act as false biomarkers in space is a prerequisite for any reasonable search for Life on other worlds.

Bernstein, Max↗

NASA NTRS2017

Electrochemical Detection of the Molecules of Life

All forms of life on Earth contain cellular machinery that can transform and regulate chemical energy through metabolic pathways. These processes are oxidation-reduction reactions that are performed by four key classes of molecules: flavins, nicotinamaides, porphyrins, and quinones. By detecting the electrochemical interaction of these redox-active molecules with an electrode, a method of differentiating them by their class could be established and incorporated into future life-detecting missions. This body of work investigates the electrochemistry of ubiquitous molecules found in life and how they may be detected. Molecules can oxidise or reduce the surface of an electrode - giving or receiving electrons - and these interactions are represented by changes in current with respect to an applied voltage. This relationship varies with: electrolyte type and concentration, working electrode material, the redox-active molecule itself, and scan rate. Flavin adenine dinucleotide (FAD), riboflavin, nicotinamide adenine dinucleotide (NADH), and anthraquinone are all molecules found intracellularly in almost all living organisms. An organism-synthesised extracellular redox-active molecule, Plumbagin, was also selected as part of this study. The goal of this work is to detect these molecules in seawater and assess its application in searching for life on Ocean Worlds.

astrobiolog↗

DOE OSTI2014

Nanodevices for generating power from molecules and batteryless sensing

A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2015

Nanodevices for generating power from molecules and batteryless sensing

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

Nanodevices for generating power from molecules and batteryless sensing

36 MATERIALS SCIENCE↗

DOE OSTI2018

Modulating the Electronic Properties and Magnetism of Bilayer Phosphorene with Small Gas Molecules Adsorbing

First-principles calculations based on the density functional theory have been performed to investigate the physisorption of small gas molecules, including CO, H{sub 2}, H{sub 2}O, NH{sub 3}, NO, NO{sub 2}, and O{sub 2}, on the surface of bilayer phosphorene. The calculated results show that (1) CO, NH{sub 3}, NO, and O{sub 2} molecules act as charge donors, whereas H{sub 2}O, H{sub 2}, and NO{sub 2} molecules serve as charge acceptors. (2) The interaction between O{sub 2} molecule and bilayer phosphorene is strongest among all the researched gas molecules.(3) The physisorption of gas molecules on bilayer phosphorene produces prominent charge transfer, which not only makes phosphorene a promising candidate as a gas sensor, but also provides a valid approach to changing the polarity of phosphorene. (4) The band structure of phosphorene is also modulated by decorating with gas molecules, the NO, O{sub 2}, and NO{sub 2} adsorbed bilayer phosphorene system exhibits magnetism, and NO (O{sub 2})-adsorbed phosphorene is a typical n(p)-type semiconductor. (5) In addition, the band gap of CO/H{sub 2}O adsorbed bilayer phosphorene decreases by exerting increasing external electric fields, which suggests that applying an external electric field would be an effective way to tune the electronic properties of phosphorene and broaden the way to the application of phosphorene in nanoelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Molecular flexure and atom trapping with sexiphenyl molecules by scanning tunneling microscope manipulation

Molecular flexure, and molecule-metal contact of para-sexiphenyl molecules on a Ag(111) surface are investigated by using low temperature scanning tunneling microscopy, and molecular manipulations. Atom trapping with sexiphenyl molecules is realized by laterally manipulating the molecules onto individual silver atoms and up to three silver atoms have been trapped. We also demonstrate breaking of a silver dimer into individual silver atoms by atom trapping. STM manipulation experiments show that the molecule-metal complexes formed by the atom trapping are mechanically stable. Moreover, Lateral manipulation of a single sexiphenyl across a Ag(111) atomic step highlights how the molecule moves across step-edges; the molecule can easily conform across the step and it recovers original configuration after the manipulation.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Fluorescence Imaging of Single-Molecule Retention Trajectories in Reversed-Phase Chromatographic Particles

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. Furthermore, the simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement

Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules attain the configuration of a “brush”: these PE brushes, due to their ability to form hydrogen bonds (HBs) with water via the PE functional groups, act as a source of soft and active nanoconfinement for the brush-trapped water molecules. In this paper, we study the effects of PE brush-induced confinement on the structure, dynamics and energetics of the water-water and water-PE HBs. Our results indicate a significant weakening of the HBs from bulk to sparsely grafted to densely grafted brushes. i.e., by increasing the degree of brush-induced nanoconfinement. We explain that this weakening of water-water HBs is caused by the disruption of the extended network of water molecules within the brush-induced nanoconfinement. This is confirmed by performing a ring structure analysis of the water molecules, which yields a reduction in the average ring size at higher degrees of brush-induced nanoconfinement (i.e., at higher brush grafting densities). Furthermore, we investigate the role of HB on the orientational dynamics of the water molecules. Here, we observe that the rotational motion of the water molecules becomes sluggish inside the PE brushes. Recent findings have indicated that the water and counterions trapped in brush-induced nanoconfinement demonstrate structures (in combination with the PE functional group) analogous to that in “water-in-salt” electrolytes that have seen extensive recent uses for Li-ion battery applications. However, the rotational dynamics of water molecules inside the brush-induced nanoconfinement is found to be distinctly different from that of conventional “water-in-salt” electrolytes in absence of any confinement; therefore, the present study will provide the necessary platform towards conceptualizing polymer-based nanoconfinement for battery applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry

Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. In this paper, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule–ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Two-dimensional-lattice-confined single-molecule-like aggregates

Intermolecular distance largely determines the optoelectronic properties of organic matter. Conventional organic luminescent molecules are commonly used either as aggregates or as single molecules that are diluted in a foreigner matrix. They have garnered great research interest in recent decades for a variety of applications, including light-emitting diodes, lasers and quantum technologies, among others. However, there is still a knowledge gap on how these molecules behave between the aggregation and dilution states. Here we report an unprecedented phase of molecular aggregate that forms in a two-dimensional hybrid perovskite superlattice with a near-equilibrium distance, which we refer to as a single-molecule-like aggregate (SMA). By implementing two-dimensional superlattices, the organic emitters are held in proximity, but, surprisingly, remain electronically isolated, thereby resulting in a near-unity photoluminescence quantum yield, akin to that of single molecules. Moreover, the emitters within the perovskite superlattices demonstrate strong alignment and dense packing resembling aggregates, allowing for the observation of robust directional emission, substantially enhanced radiative recombination and efficient lasing. Molecular dynamics simulations together with single-crystal structure analysis emphasize the critical role of the internal rotational and vibrational degrees of freedom of the molecules in the two-dimensional lattice for creating the exclusive SMA phase. Furthermore, this two-dimensional superlattice unifies the paradoxical properties of single molecules and aggregates, thus offering exciting possibilities for advanced spectroscopic and photonic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Determining the exact number of dye molecules attached to colloidal CdSe/ZnS quantum dots in Förster resonant energy transfer assemblies

Semiconductor quantum dots functionalized with organic dye molecules are important tools for biological sensor applications. Energy transfer between the quantum dot and the attached dyes can be utilized for sensing. Though important, the determination of the real number of dye molecules attached per quantum dot is rather difficult. In this work, a method will be presented to determine the number of ATTO-590 dye molecules attached to CdSe/ZnS quantum dots based on time resolved spectral analysis. The energy transfer from the excited quantum dot to the attached ATTO-590 dye leads to a reduced lifetime of the quantum dot's excitons. The higher the concentration of dye molecules, the shorter the excitonic lifetime becomes. However, the number of dye molecules attached per quantum dot will vary. Therefore, for correctly explaining the decay of the luminescence upon photoexcitation of the quantum dot, it is necessary to take into account the distribution of the number of dyes attached per quantum dot. A Poisson distribution of the ATTO-590 dye molecules not only leads to excellent agreement between experimental and theoretical decay curves but also additionally yields the average number of dye molecules attached per quantum dot. In this way, the number of dyes per quantum dot can be conveniently determined.

77 NANOSCIENCE AND NANOTECHNOLOGY↗