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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS1976

Interstellar molecules

Progress in the discovery and study of interstellar molecules is summarized. The 36 molecular species thus far identified in interstellar space are listed in several groups which include simple hydrides, oxides, and sulfides, various derivatives of ammonia, molecules involving linear carbon chains, cyanides, and molecules related in structure to formaldehyde, alcohols, or ethers. Several free radicals are described, the discovery of molecules in external galaxies is discussed, and possible mechanisms for molecular formation are noted. Methods for examining relative isotopic abundances by measuring molecules in interstellar clouds are outlined, mechanisms for the excitation of interstellar molecules are reviewed, and values are presented for the C-12/C-13 abundance ratio in a number of interstellar clouds. The detection of interstellar masers is discussed along with pumping mechanisms and masing transitions in H2CO, CH, OH, and SiO. The nature of dense interstellar clouds is examined in terms of several simple and complex cloud models, with emphasis on multiple condensation models.

Townes, C. H.↗
NASA NTRS1981

Radio observations of molecules in the interstellar gas

Since 1968, radio astronomy has made it possible to identify nearly 50 molecules in the dense concentrations of the interstellar gas now generally termed molecular clouds. Most interstellar molecules are familiar stable compounds. However, one-fifth of the discovered species are ions, radicals, and acetylenic carbon chains so reactive in the laboratory that before being detected in space they had rarely been observed or were entirely unknown. The heavy atom backbone of the known interstellar molecules is a linear chain of C, N, O, or S. Si is found in two diatomic molecules. Rings and branched chains are missing. The most readily observed spectral lines of most interstellar molecules correspond to rotational transitions at millimeter wavelengths. These are generally excited by H2 collisions. A number of rare isotopic species are observed in interstellar molecules. Isotopic ratios differing from those on Earth exist, and can in almost all cases be attributed to stellar nucleosynthesis since the formation of the solar system.

Thaddeus, P.↗
NASA NTRS1997

Exotic Molecules in Space: A Coordinated Astronomical, Laboratory, and Theoretical Study

The past year has been a period of spectacular progress in our investigation of exotic molecules of astrophysical interest. During this period an entirely new spectrometer for the investigation of reactive molecules was finished: a Fourier-transform microwave spectrometer with a supersonic molecular beam. The instrument is operating almost flawlessly, and during the above period of less than two years has discovered the 23 new carbon chain and ring-chain molecules. Seventeen research papers, nearly all in leading refereed journals such as the Astrophysical Journal and the Journal of Chemical Physics have been published. At least five more papers are being prepared for publication. Already four of our new molecules have been detected in space with large radio telescopes. In many ways the most interesting of these is HC(11)N, which now ranks as the largest molecule definitely identified beyond the solar system. Nearly all the other new molecules are candidates for astronomical detection, and we will be disappointed if a number of them are not found as more sensitive receivers and larger telescopes are constructed. During the next year we expect this wave of discovery to continue, and to insure rapid progress we have designed an even more sensitive spectrometer which will operate at the temperature of liquid helium. The goal of this system is to enhance the sensitivity of Fourier-transform spectroscopy by a further factor of 20 to 50, achieving this by reducing the amplifier and thermal noise to levels routinely achieved in radio astronomy. This new instrument offers a number of technical challenges in cryogenic and microwave engineering, but none of these appears to be insurmountable, and our current schedule is to have the helium cooled system operating within the next six months. A number of investigations continued with our conventional free space spectrometer, which remains a powerful complement to our new FTM instrument.

Thaddeus, Patrick↗
NASA NTRS2004

Formation and Destruction Processes of Interstellar Dust: From Organic Molecules to carbonaceous Grains

The study of the formation and destruction processes of cosmic dust is essential to understand and to quantify the budget of extraterrestrial organic molecules. interstellar dust presents a continuous size distribution from large molecules, radicals and ions to nanometer-sized particles to micron-sized grains. The lower end of the dust size distribution is thought to be responsible for the ubiquitous spectral features that are seen in emission in the IR (UIBs) and in absorption in the visible (DIBs). The higher end of the dust-size distribution is thought to be responsible for the continuum emission plateau that is seen in the IR and for the strong absorption seen in the interstellar UV extinction curve. All these spectral signatures are characteristic of cosmic organic materials that are ubiquitous and present in various forms from gas-phase molecules to solid-state grains. Although dust with all its components plays an important role in the evolution of interstellar chemistry and in the formation of organic molecules, little is known on the formation and destruction processes of dust. Recent space observations in the UV (HST) and in the IR (ISO) help place size constraints on the molecular component of carbonaceous IS dust and indicate that small (ie., subnanometer) PAHs cannot contribute significantly to the IS features in the UV and in the IR. Studies of large molecular and nano-sized IS dust analogs formed from PAH precursors have been performed in our laboratory under conditions that simulate diffuse ISM environments (the particles are cold -100 K vibrational energy, isolated in the gas phase and exposed to a high-energy discharge environment in a cold plasma). The species (molecules, molecular fragments, ions, nanoparticles, etc) formed in the pulsed discharge nozzle (PDN) plasma source are detected with a high-sensitivity cavity ring-down spectrometer (CRDS). We will present new experimental results that indicate that nanoparticles are generated in the plasma. From these unique measurements, we derive information on the nature, the size and the structure of interstellar dust particles, the growth and the destruction processes of IS dust and the resulting budget of extraterrestrial organic molecules.

Salama, F.↗
NASA NTRS2005

Electronic Transport through Self Assembled Thiol Molecules: Effect of Monolayer Order, Dynamics and Temperature

We present the charge transport and tunneling conductance of self assembled organic thiol molecules and discuss the influence of order and dynamics in the monolayer on the transport behavior and the effect of temperature. Conjugated thiol molecular wires and organometals such as terpyridine metal complexes provide a new platform for molecular electronic devices and we study their self assembly on Au(111) substrates by the scanning tunneling microscope. Determining the organization of the molecule and the ability to control the nature of its interface with the substrate is important for reliable performance of the molecular electronic devices. By concurrent scanning tunneling microscopy and spectroscopy studies on SAMs formed from oligo (phenelyne ethynelyne) monolayers with and without molecular order, we show that packing and order determine the response of a self assembled monolayer (SAM) to competing interactions. Molecular resolution STM imaging in vacuum shows that the OPES adopt an imcommensurate SAM structure on Au(111) with a rectangular unit cell. Tunneling spectroscopic measurements were performed on the SAM as a function of junction resistance. STS results show that the I-Vs are non linear and asymmetric due to the inherent asymmetry in the molecular structure, with larger currents at negative sample biases. The asymmetry increases with increasing junction resistance due to the asymmetry in the coupling to the leads. This is brought out clearly in the differential conductance, which also shows a gap at the Fermi level. We also studied the effect of order and dynamics in the monolayer on the charge transport and found that competing forces between the electric field, intermolecular interactions, tip-molecule physisorption and substrate-molecule chemisorption impact the transport measurements and its reliability and that the presence of molecular order is very important for reproducible transport measurements. Thus while developing new electronic platforms based on molecules, it is important to have a good control of the molecule-substrate interface, for the devices to perform reliably. While such a control would minimize fluctuations and dynamics in the ensemble, the real challenge is to develop device architectures that are tolerant to fluctuations, since they cannot be totally eliminated in these low dimensional soft systems. Results of temperature dependent STS measurements will also be discussed.

Dholakia, Geetha↗
NASA NTRS2007

Electron-Molecule Col1isions: Quantitative Approaches, and the Legacy of Aaron Temkin

This article, on electron-molecule collisions, is dedicated to the legacy of my good friend and sometime collaborator, Aaron Temkin on his retirement from the NASA-Goddard Space Flight Center after many years of work at the highest intellectual level in the theoretical treatment of electron-atom and electron-molecule scattering. Aaron's contributions to the manner in which we think about electron-molecule collisions is clear to all of us who have worked in this field. I doubt that the great progress that has occurred in the computational treatment of such complex collision problems could have happened without these contributions. For a brief historical account, see the discussion of Temkin's contribution to electron-molecule scattering in the first article of this volume by Dr. A. K. Bhatia. In this article, I will concentrate on the application of the so called, non-adiabatic R-matrix theory, to vibrational excitation and dissociative attachment, although I will also present some results applying the Linear Algebraic and Kohn-Variational methods to vibrational excitation. As a starting point for almost all computationally effective approaches to electron-molecule collisions, is the fixed nuclei approximation. That is, one recognizes, just as one does with molecular bound states, that there is a separation of electronic(fast) and nuclear(s1ow) degrees of freedom. This separation makes it possible to "freeze" the nuclei in space, calculate the collision parameters for the frozen molecule and then, somehow to add back the vibrations and rotations. The manner in which this is done, depends on the details of the collision problem. It is the work of Aaron and a number of other researchers that has provided the guidance necessary to resolve these issues.

Schneider, B.I.↗
NASA NTRS2009

Combustion of Organic Molecules by the Thermal Decomposition of Perchlorate Salts: Implications for Organics at the Mars Phoenix Scout Landing Site

The Mars 2007 Phoenix Scout Mission successfully landed on May 25, 2008 and operated on the northern plains of Mars for 150 sols. The primary mission objective was to study the history of water and evaluate the potential for past and present habitability in Martian arctic ice-rich soil [1]. Phoenix landed near 68 N latitude on polygonal terrain created by ice layers that are a few centimeters under loose soil materials. The Phoenix Mission is assessing the potential for habitability by searching for organic molecules in the ice or icy soils at the landing site. Organic molecules are necessary building blocks for life, although their presence in the ice or soil does not indicate life itself. Phoenix searched for organic molecules by heating soil/ice samples in the Thermal and Evolved-Gas Analyzer (TEGA, [2]). TEGA consists of 8 differential scanning calorimeter (DSC) ovens integrated with a magnetic-sector mass spectrometer with a mass range of 2-140 daltons [2]. Endothermic and exothermic reactions are recorded by the TEGA DSC as samples are heated from ambient to ~1000 C. Evolved gases, including any organic molecules and their fragments, are simultaneously measured by the mass spectrometer during heating. Phoenix TEGA data are still under analysis; however, no organic fragments have been identified to date in the evolved gas analysis (EGA). The MECA Wet Chemistry Lab (WCL) discovered a perchlorate salt in the Phoenix soils and a mass 32 peak evolved between 325 and 625 C for one surface sample dubbed Baby Bear [3]. The mass 32 peak is attributed to evolved O2 generated during the thermal decomposition of the perchlorate salt. Perchlorates are very strong oxidizers when heated, so it is possible that organic fragments evolved in the temperature range of 300-600 C were combusted by the O2 released during the thermal decomposition of the perchlorate salt. The byproduct of the combustion of organic molecules is CO2. There is a prominent release of CO2 between 200-600 C for several of the Phoenix soils analyzed by TEGA. This low temperature release of CO2 might be any combination of 1) desorption of adsorbed CO2, 2) thermal decomposition of Fe- and Mg-carbonates, and 3) combustion of organic molecules [2].

Ming, D.W.↗
NASA NTRS2020

Titan's Ionospheric Chemistry, Fullerenes, Oxygen, Galactic Cosmic Rays and the Formation of Exobiological Molecules on and Within Its Surfaces and Lakes

We discuss the formation of aerosols within Titan's thermosphere-ionosphere and the different chemical pathways. Negative ion measurements by the Cassini Plasma Spectrometer (CAPS) Electron Spectrometer (ELS) give evidence for formation of unsaturated anion carbon chains, while positive ion measurements of the Cassini Ion Neutral Mass Spectrometer (INMS) indicate formation of more aromatic cation hydrocarbons. There is presently no direct observational evidence for large neutral molecule growth in Titan's thermosphere-ionosphere. The hydrocarbon cations are expected to form Polycyclic Aromatic Hydrocarbons (PAHs), those with the addition of nitrogen being called PAHNs. We theorize anion carbon chains can eventually become long enough to fold into fullerene C60,70 carbon shells, of various charge states. Based on laboratory data the fullerenes can trap incoming O+ magnetospheric ions that have relatively high energy collisions with the fullerenes and, once trapped, protect the oxygen atom from Titan's reducing thermosphere-ionosphere. The fullerenes can form into larger onion fullerenes and condense into larger embryo aerosols (i.e., m/q (mass-to-charge ratio) greater than 10,000 amu/q (atomic mass unit-to-charge ratio) anions as observed by CAPS/ELS) eventually falling onto Titan's surface and precipitating to the bottom of its hydrocarbon lakes. Molecule production composed of H, C, N is known to occur in Titan's atmosphere with energy input from the magnetosphere, solar UV (ultraviolet), and deep-penetrating irradiation from galactic cosmic rays (GCR). Space radiation effects by GCR irradiation of Titan's surface and lakes can lead to the manufacture of exobiological molecules with oxygen as the new ingredient. We have developed a model of galactic cosmic ray irradiation of Titan's atmosphere, surface, subsurface and bottoms of Titan lakes. GCR would provide further energy for processing of the aerosols into more complex organic forms such as tholins and precursor molecules for amino acids. A second process called hydrolysis then converts the precursor molecules into amino acids. Hydrolysis is provided via meteor impacts with size greater than 10 kilometers and cryovolcanism both which can produce liquid water on Titan's surface for episodic periods more than several 100 to 1000 years. Our model shows that GCR secondary particles can penetrate ~100 meters below the ice surface (including the bottom of Titan's less dense hydrocarbon lakes ~150-meter depths) and produce chemically significant dosages over very long timescales ~450 million years. The GCR model is combined with laboratory data from experiments in which dry methyl ices were irradiated to doses producing prebiotic amino acids such as glycine. The model calculations show glycine can form to ~2.5 parts-per-billion levels near the surface after ~450 million years of GCR proton irradiation and potentially to 5 parts-per-billion if heavy-ion GCRs up through Fe are included. If such molecules were detected, this would not only confirm this model but indicate that life forms different from ours may not be required.

Edward C. Sittler Jr↗
NASA NTRS2019

Titan's Ionospheric Chemistry, Fullerenes, Oxygen, Galactic Cosmic Rays and the Formation of Exobiological Molecules on and within its Surfaces and Lakes

We discuss the formation of aerosols within Titan's thermosphere-ionosphere and the different chemical pathways. Negative ion measurements by the Cassini Plasma Spectrometer (CAPS) Electron Spectrometer (ELS) give evidence for formation of unsaturated anion carbon chains, while positive ion measurements of the Cassini Ion Neutral Mass Spectrometer (INMS) indicate formation of more aromatic cation hydrocarbons. There is presently no direct observational evidence for large neutral molecule growth in Titan's thermosphere-ionosphere. The hydrocarbon cations are expected to form Polycyclic Aromatic Hydrocarbons (PAH), those with the addition of nitrogen being called PAHNs. We theorize anion carbon chains can eventually become long enough to fold into fullerene C(60,70) carbon shells, of various charge states. Based on laboratory data the fullerenes can trap incoming O(sup +) magnetospheric ions that have relatively high energy collisions with the fullerenes and, once trapped, protect the oxygen atom from Titan's reducing thermosphere-ionosphere. The fullerenes can form into larger onion fullerenes and condense into larger embryo aerosols (i.e., m/q > 10,000 amu/q anions as observed by CAPS/ELS) eventually falling onto Titan's surface and precipitating to the bottom of its hydrocarbon lakes. Molecule production composed of H, C, N is known to occur in Titan's atmosphere with energy input from the magnetosphere, solar UV, and deeppenetrating irradiation from galactic cosmic rays (GCR). Space radiation effects by GCR irradiation of Titan's surface and lakes can lead to the manufacture of exobiological molecules with oxygen as the new ingredient. We have developed a model of galactic cosmic ray irradiation of Titan's atmosphere, surface, subsurface and bottoms of Titan lakes. GCR would provide further energy for processing of the aerosols into more complex organic forms such as tholins and precursor molecules for amino acids. A second process called hydrolysis then converts the precursor molecules into amino acids. Hydrolysis is provided via meteor impacts with size > 10 km and cryovolcanism both which can produce liquid water on Titan's surface for episodic periods > several 100 to 1000 years. Our model shows that GCR secondary particles can penetrate ~ 100 m below the ice surface (including the bottom of Titan's less dense hydrocarbon lakes ~ 150 m depths) and produce chemically significant dosages over very long timescales ~ 450 Myrs. The GCR model is combined with laboratory data from experiments in which dry methyl ices were irradiated to doses producing prebiotic amino acids such as glycine. The model calculations show glycine can form to ~ 2.5 ppb levels near the surface after ~450 Myrs of GCR proton irradiation and potentially to 5 ppb if heavy-ion GCRs up through Fe are included. If such molecules were detected, this would not only confirm this model but indicate that life forms different from ours may not be required.

Edward C. Sittler Jr↗
NASA NTRS2021

Identifying Molecules as Biosignatures with Assembly Theory and Mass Spectrometry

The search for evidence of life elsewhere in the universe is hard because it is not obvious what signatures are unique to life. Here we postulate that complex molecules found in high abundance are universal biosignatures as they cannot form by chance. To explore this, we developed the first intrinsic measure of molecular complexity that can be experimentally determined, and this is based upon a new approach called assembly theory which gives the molecular assembly number (MA) of a given molecule. MA allows us to compare the intrinsic complexity of molecules using the minimum number of steps required to construct the molecular graph starting from basic objects, and a probabilistic model shows how the probability of any given molecule forming randomly drops dramatically as its MA increases. To map chemical space, we calculated the MA of ca. 2.5 million compounds, and collected data which showed the complexity of a molecule can be experimentally determined by using three independent techniques including infra-red spectroscopy, nuclear magnetic resonance, and by fragmentation in a mass spectrometer, and this data has an excellent corelation with the values predicted from our assembly theory. We then set out to see if this approach could allow us to identify molecular biosignatures with a set of diverse samples from around the world, outer space, and the laboratory including prebiotic soups. The results show that there is a non-living to living threshold in MA complexity and the higher the MA for a given molecule, the more likely that it had to be produced by a biological process. This work demonstrates it is possible to use this approach to build a life detection instrument that could be deployed on missions to extra-terrestrial locations to detect biosignatures, map the extent of life on Earth, and be used as a molecular complexity scale to quantify the constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital if we are going to find new life elsewhere in the universe or create de-novo life in the lab.

Stuart M Marshall↗
DOE OSTI2020

Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning

Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.

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

Modulating the Electron Affinity of Small Bipyridyl Molecules on Single Gold Nanoparticles for Plasmon-Driven Electron Transfer

Developing controlled platforms for plasmon-driven chemistry is of great importance in catalytic reactions at the nanoscale. We report anion radical formation for five bipyridyl complexes of varying degrees of electron affinity utilizing optically fo-cused intraband (594 nm) and interband (532 nm) pump excitation of single gold nanoparticles. The surface-enhanced Raman scattering (SERS) of anion radicals for the five non-resonant adsorbed molecules 2,2’-bipyridine (22BPY), 4,4’-bipyridine (44BPY), trans-1,2-bis(4-pyridyl)ethylene (BPE), 1,2-bis(4-pyridyl)acetylene (BPA), and 1,2-bis(4-pyridyl)ethane (BPEt) were detected using localized surface-plasmon resonance (LSPR) excitation with 785 nm. The electron affinity of the five bipyridyl complexes were determined using electrochemistry. Molecules with low electron affinity experienced high-er instances of radical anion formation under a plasmon-coupled intraband electron transfer excitation (594 nm) whereas molecules with high electron affinity showed a preference for anion radical formation under direct interband electron trans-fer excitation (532 nm). The lowest unoccupied molecular orbital (LUMO) energy levels for low electron affinity surface-bound molecules (22BPY, BPEt) are on average ~0.43 eV higher for high electron affinity surface-bound molecules (BPA, BPE, 44BPY) as calculated using time-dependent density functional theory, elucidating the importance of plasmon coupling to energy levels that facilitate charge transfer pathways. We also show the ability to ‘activate’ high vs low electron affinity single nanoparticles with the choice of pump excitation wavelength. The findings show the complex interplay between molecular electron affinity, orbital overlap with the density of states of the plasmonic metal, and excitation energetics of the pump laser wavelength. Potential applications of this work include enhanced control over molecular scale catalysis, biosensor design, and solar energy capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

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

Abnormal Slow Phonon Dynamics Toward Prolonging Excited States Dynamics Enabled by Crystalline‐Assembling Donor–Acceptor Molecules

Phonon dynamics are a critical factor to control the optical properties of excited states in light-emitting materials. Here, we report an extremely slow relaxation of photoexcited lattice vibrations enabled by assembling the donor-acceptor (D–A) molecules [2-(9,9-dimethylacridin-10(9H)-yl)-9,9-dimethyl-9H-thioxanthene 10,10-dioxide], namely AC molecules, into dipolar crystal. By using photoexcitation-modulated Raman spectroscopy, we find that the crystalline-lattice vibrations monitored by Raman-scattering laser beam of 785 nm demonstrate an un-usual slow relaxation in the time scale of seconds after ceasing photoexcitation beam of 343 nm in such dipolar crystal. This presents extremely slow phonon dynamics enabled by crystalline-assembling the D–A molecules into a dipolar crystal. Simultaneously, the photoluminescence (PL) exhibits a prolonged behavior, lasting 10 ms after ceasing photoexcitation in dipolar AC crystal. This phenomenon provides an experimental hypothesis that the slow phonon dynamics function as an important mechanism to unusually prolong excited states dynamics upon crystalline-assembling the D–A molecules into dipolar crystal. Here, this hypothesis can be verified by directly suppressing the phonon dynamics through freezing D–A molecular liquid into dipolar crystalline solid at 77 K to largely prolong the PL to 1 s- after removing photoexcitation. Clearly, crystalline-assembling D–A molecules provide the necessary conditions to enable slow phonon dynamics toward prolonging excited states dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Single-Molecule Tracking Measurements Reveal the Detailed Mechanisms of Molecular Diffusion in Solvent Mixtures under Nanoconfinement

Understanding mass transport mechanisms in nanopores is important for developing advanced materials for chemical separations, chemical sensing, and energy storage. This paper reports a novel imaging platform that is employed for the first time to investigate the detailed diffusion dynamics of single rhodamine B (RhB) dye molecules confined within solution-filled cylindrical anodic aluminum oxide (AAO) nanopores. The imaging platform relies on illumination of horizontally-oriented AAO nanopores in a highly inclined and laminated optical (HILO) light sheet microscopy geometry. The method was used to investigate the translational and orientational dynamics of single rhodamine B (RhB) molecules within horizontally-oriented 5- and 10-nm diameter AAO nanopores filled with water–ethanol mixtures. The established platform enabled the observation of one-dimensional motion along the pore axis involving occasional short- or long-term immobilization at the single-molecule level. Analysis of cumulative squared-displacement distributions revealed fast (5 – 30 µm²/s), intermediate (1 – 5 µm²/s), and slow (< 1 µm²/s) diffusion components. From the effects of mixture composition and pore size on the contributions of these three components, we inferred that the fast, intermediate, and slow components could be assigned to desorption-mediated hopping, crawling, and wiggling motions, respectively. The platform based on the horizontally-oriented AAO nanopores also permitted single-molecule emission polarization measurements that revealed the negligible steric confinement of individual diffusing RhB molecules within the AAO nanopores. The imaging platform based on AAO membranes and HILO microscopy provided a unique means to investigate how solvation-mediated surface interactions and nanoconfinement govern molecular transport in nanoporous environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Revisiting Competitive Adsorption of Small Molecules in the Metal–Organic Framework Ni-MOF-74

To precisely evaluate the potential of metal-organic frameworks (MOFs) for gas separation and purification applications, it is crucial to understand how various molecules competitively adsorb inside MOFs. In this paper, we combine in situ infrared spectroscopy with ab initio calculations to investigate the mechanisms associated with co-adsorption of a number of small molecules including CO, NO, and CO 2 inside the prototypical framework Ni-MOF-74. Surprisingly, we find that the displacement of CO bound inside Ni-MOF-74 (binding energy of 53 kJ/mol) is readily driven by CO 2 exposure, even though CO 2 has a noticeably weaker binding energy of only 41 kJ/mol; meanwhile, the significantly more strongly binding NO molecule (90 kJ/mol) is not able to easily displace bound CO inside Ni-MOF74. These results show that single-phase binding energies of a molecule inside the MOF cannot completely describe their interaction with the MOF in the presence of other guest molecules. Here, we unveil a number of crucial factors such as the kinetic barrier, partial pressure, secondary binding sites, and guest-host/lateral interactions that control the co-adsorption process and combined with the binding energy are better descriptors of the behavior and adsorption of gas mixtures inside MOFs.

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

3D-Scaffold: A Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds

The prerequisite of therapeutic drug design is to identify novel molecules with desired biophysical and biochemical properties. Deep generative models have demonstrated their ability to find such molecules by exploring a huge chemical space efficiently. An effective way to obtain molecules with desired target properties is the preservation of critical scaffolds in the generation process. To this end, we propose a domain aware generative framework called 3D-Scaffold that takes 3D coordinates of a desired scaffold as an input and generates 3D coordinates of novel therapeutic candidates as an output while always preserving the desired scaffolds in generated structures. We show that our framework generates predominantly valid, unique, novel, and experimentally synthesizable molecules that have drug-like properties similar to the molecules in the training set. Using domain specific datasets, we generate covalent and non-covalent antiviral inhibitors. Therefore, to measure the success of our framework in generating therapeutic candidates, generated structures were subjected to high throughput virtual screening via docking simulations, which shows favorable interaction against SARS-CoV-2 main protease and non-structural protein endoribonuclease (NSP15) targets. Most importantly, our model performs well with relatively small volumes of training data and generalizes to new scaffolds, making it applicable to other domain.

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

Probing Dipolar Interactions between Rydberg Atoms and Ultracold Polar Molecules

Here, we probe resonant dipolar interactions between ultracold 40 K ⁢ 87 Rb molecules and Rydberg 87 Rb atoms in an optically trapped ensemble. Through state-selective ionization detection of the KRb molecules, we observe resonant energy transfer at 2.227 GHz from Rydberg atoms to molecules under a tunable external electric field. We measure a broadening up to 3.5 MHz, for the Rb Rydberg excitation spectrum, which matches a Monte Carlo simulation that describes a Rydberg atom and neighboring molecules evolving under a dipole-dipole interacting Hamiltonian. The demonstrated interspecies dipolar interaction is a key ingredient for hybrid Rydberg-polar molecule systems, where the advantages of each system can be leveraged and combined.

dipolar Rydberg atoms↗