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At least 523 records · Page 29

Organic Molecules On the Surfaces of Iapetus and Phoebe

Absorption bands of both aliphatic and aromatic organic molecules are found in the reflectance spectra of Saturn satellites Iapetus, Phoebe, and Hyperion obtained with the Cassini Visible-Infrared Mapping Spectrometer (VIMS). The VIMS data do not fully resolve the individual bands of C-H functional groups specific to particular molecules, but instead show absorption envelopes representing blended clusters of the bands of aromatic (approximately 3.28 microns) and aliphatic (approximately 3.4 microns) hydrocarbons known in spectra of interstellar dust. In Cruikshank et al. (2014), we matched components of the unresolved hydrocarbon band envelopes with clusters of bands of a range of functional groups in specific types of organic compounds (e.g., normal and N-substituted polycyclic aromatic hydrocarbons, olefins, cycloalkanes, and molecules with lone-pair interactions of N and O with CH3+). In the work reported here, we revisit the spectra of Iapetus and Phoebe using VIMS data processed with improved radiometric and wavelength calibration (denoted RC19). The band envelopes of both aromatic and aliphatic hydrocarbons are now more clearly defined, corroborating the provisional assignment of specific classes of molecules in Cruikshank et al. 2014, but permitting a more reliable quantitative assessment of the relative contributions of those classes, and a revision to the earlier estimate of the ratio of the abundances of aromatic to aliphatic molecules.

Phoeb↗

Polycyclic Aromatic Hydrocarbons and Dust Particle Surface Interactions: Catalytic Hydrogenation of Polycyclic Aromatic Hydrocarbon Molecules under Vacuum Conditions

This work reports experiments on the catalytic interaction occurring between polycyclic aromatic hydrocarbon (PAH) molecules and TiO2 dust grain surfaces under vacuum conditions. The investigation sheds light on the potential catalytic pathways that TiO2 dust surfaces provide in the hydrogenation of PAH molecules and the chemistry that can be driven by PAH-dust interactions under vacuum conditions. Naphthalene, anthracene, and coronene were chosen as the PAH molecules, while titanium dioxide was selected as the dust analog. PAH samples and dust analog mixtures were studied under vacuum for 24 h while monitored via diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). The acquired spectra show that PAH molecules are hydrogenated when in contact with TiO2 dust particles without the need for external energy or hydrogen sources. Our results suggest that linear PAHs undergo a similar hydrogenation process where the dominant species are fully hydrogenated PAHs. For larger condensed PAHs, the hydrogenation process yields partially hydrogenated molecules. Fully hydrogenated species can be identified by a band around 2960 per cm, while partially hydrogenated species produce a band around 2825 per cm. In the case of the production of hydrogenated species, our results suggest that the smaller the PAH, the faster the hydrogenation rate.

polycyclic aromatic hydrocarbons↗

Neutral–neutral synthesis of organic molecules in cometary comae

Remote and in situ observations of cometary gases have revealed the presence of a wealth of complex organic molecules, including carbon chains, alcohols, imines, and the amino acid glycine. Such chemical complexity in cometary material implies that impacts by comets could have supplied reagents for prebiotic chemistry to young planetary surfaces. However, the assumption that some of the molecules observed in cometary comae at millimetre wavelengths originate from ices stored inside the nucleus has not yet been proven. In fact, the comae of moderately-active comets reach sufficient densities within a few thousand kilometres of the nucleus for an active (solar radiation-driven) photochemistry to ensue. Here, we present results from our latest chemical-hydrodynamic models incorporating an updated reaction network, and show that the commonly-observed HC3N (cyanoacetylene) and NH2CHO (formamide) molecules can be efficiently produced in cometary comae as a result of two-body, neutral–neutral, gas-phase reactions involving well-known coma species. In the presence of a near-nucleus distributed source of CN (similar to that observed by the Rosetta spacecraft at comet 67P), we find that sufficient HC3N and NH2CHO can be synthesized to match the abundances of these molecules observed previously in Oort cloud comets. The precise coma origins of these (and other) complex organic molecules can be verified through radio interferometric mapping observations, for example using the Atacama Large Millimeter/submillimeter Array.

Comets↗

Diverse organic molecules on Mars revealed by the first SAM TMAH experiment

The search for organic matter on Mars has rapidly evolved in the past decade with simple aromatic, S-heterocycles, and aliphatic organic molecules detected in Gale crater. We report the in situ detection of >20 organic molecules from clay-bearing sandstones in the ~3.5-billion-year-old Knockfarrill Hill member of Glen Torridon, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. These molecules were liberated by the onboard tetramethylammonium hydroxide wet chemistry experiment. Diverse thermochemolysis products, including benzothiophene, methyl benzoate, and single and dicyclic aromatic molecules were released and detected by evolved gas analysis and gas chromatography-mass spectrometry. Results indicate the experiment successfully released molecules preserved in ancient macromolecular or free organic matter within Martian bedrock despite ~3.5 billion years of diagenesis and radiation exposure.

Amy J Williams↗

Computer systems for annotation of single molecule fragments

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated nitrogen atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. Furthermore, these results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular packing modulation enabling optimized blend morphology and efficient all small molecule organic solar cells

The molecular planarity of a small molecule donor is one of the key factors affecting its molecular packing behavior, the morphology of the related active blend and thus the photovoltaic properties of all small molecule organic solar cells (ASM-OSCs). Here, a series of new benzodithiophene (BDT)-based A-π-D-π-A type small molecules were developed, namely SD1, SD2 and SD3, by combining the chemical modification of side chain (sulfuration), π-bridge (alkoxy groups introducing) and end group (different type or different alkyl chain). The sulfuration of the BDT side chains and introducing alkoxy group to the π-bridge could induce intermolecular S … S and intramolecular S … O non-covalent interactions for higher planarity of these small molecules. The rhodanine and cyanoacetate end groups showed less effect on the optical and electronic properties but significantly affected the molecular packing behavior and blend morphology. From SD1:Y6-T to SD2:Y6-T and SD3:Y6-T, the face-to-face packing was gradually reduced, while the face-to-edge packing was increased, which resulted in lowered exciton dissociation efficiency, further decreased the device performance. SD1:Y6-T blend exhibited more favorable face-to-face packing and ideal morphology for efficient charge dissociation and transport, contributing to a champion PCE of 10.12%. This work provided a deep insight of the donor and acceptor packing behavior effect on the photovoltaic property by molecular design.

36 MATERIALS SCIENCE↗

Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction

We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determination of local concentration of H{sub 2}O molecules and gas temperature in the process of hydrogen - oxygen gas mixture heating by means of linear and nonlinear laser spectroscopy

Employing the methods of linear absorption spectroscopy and nonlinear four-wave mixing spectroscopy using laserinduced gratings we have simultaneously measured the local concentrations of H{sub 2}O molecules and the gas temperature in the process of the H{sub 2} - O{sub 2} mixture heating. During the measurements of the deactivation rates of pulsed-laser excited singlet oxygen O{sub 2} (b {sup 1}{Sigma}{sup +}{sub g}) in collisions with H{sub 2} in the range 294 - 850 K, the joint use of the two methods made it possible to determine the degree of hydrogen oxidation at a given temperature. As the mixture is heated, H{sub 2}O molecules are formed by 'dark' reactions of H{sub 2} with O{sub 2} in the ground state. The experiments have shown that the measurements of tunable diode laser radiation absorption along an optical path through the inhomogeneously heated gas mixture in a cell allows high-accuracy determination of the local H{sub 2}O concentration in the O{sub 2} laser excitation volume, if the gas temperature in this volume is known. When studying the collisional deactivation of O{sub 2} (b {sup 1}{Sigma}{sup +}{sub g}) molecules, the necessary measurements of the local temperature can be implemented using laser-induced gratings, arising due to spatially periodic excitation of O{sub 2} (X{sup 3}{Sigma}{sup -}{sub g}) molecules to the b {sup 1}{Sigma}{sup +}{sub g} state by radiation of the pump laser of the four-wave mixing spectrometer. (laser spectroscopy)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ultracold spin-polarized mixtures of {sup 2}{Sigma} molecules with S-state atoms: Collisional stability and implications for sympathetic cooling

The prospects of sympathetic cooling of polar molecules with magnetically cotrapped alkali-metal atoms are generally considered poor due to strongly anisotropic atom-molecule interactions leading to large spin relaxation rates. Using rigorous quantum scattering calculations based on ab initio interaction potentials, we show that inelastic spin relaxation in low-temperature collisions of CaH({sup 2}{Sigma}) molecules with Li and Mg atoms occurs at a slow rate despite the strongly anisotropic interactions. This unexpected result, which we rationalize using multichannel quantum-defect theory, opens up the possibility of sympathetic cooling of polar {sup 2}{Sigma} molecules with alkali-metal atoms in a magnetic trap and with alkaline-earth-metal atoms in an optical dipole trap.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Observation of cold Rb{sub 2} molecules trapped in an optical dipole trap using a laser-pulse-train technique

In this work, we have developed and characterized a laser-pulse-train technique to observe cold Rb{sub 2} molecules trapped in an optical dipole trap. The molecules are produced in a magneto-optical trap, and then loaded into a crossed optical dipole trap. The time evolution of the molecular population is obtained by applying a laser pulse train, which photoionizes the ground-state molecules through intermediate molecular bands. Our results show that this technique allows us to obtain a faster data acquisition rate of the time evolution of the molecule population than other techniques.

74 ATOMIC AND MOLECULAR PHYSICS↗

Modifying molecule-surface scattering by ultrashort laser pulses

In recent years it has become possible to align molecules in free space using ultrashort laser pulses. Here we explore two schemes for controlling molecule-surface scattering processes and which are based on laser-induced molecular alignment. In the first scheme, a single ultrashort nonresonant laser pulse is applied to a molecular beam hitting the surface. This pulse modifies the angular distribution of the incident molecules and causes the scattered molecules to rotate with a preferred sense of rotation (clockwise or counterclockwise). In the second scheme, two properly delayed laser pulses are applied to a molecular beam composed of two chemically close molecular species (isotopes, or nuclear-spin isomers). As the result of the double-pulse excitation, these species are selectively scattered to different angles after the collision with the surface. These effects may provide new means for the analysis and separation of molecular mixtures.

74 ATOMIC AND MOLECULAR PHYSICS↗

Measurements of the number density of water molecules in plasma by using a combined spectral−probe method

A novel method for measuring the number density of water molecules in low-temperature plasma is developed. The absolute intensities of rotational lines of the (0,0) band of the OH(A{sup 2}Σ–X{sup 2}Π) transition are used. Lines with sufficiently large rotational quantum numbers referring to the so-called “hot” group of molecules produced by electron-impact dissociative excitation of water molecules are chosen for measurements. The excitation rate of a process with a known cross section is determined by measuring the parameters of plasma electrons by means of the probe method. The measured number densities of molecules are compared with those in the initial plasma-forming mixture. The time evolution of the particle densities in plasma is investigated. The problems of the sensitivity and applicability of the absolute spectral method are considered.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Production and trapping of ultracold polar molecules

We report a set of experiments aimed at the production and trapping of ultracold polar molecules. We begin with samples of laser-cooled and trapped Rb and Cs atoms, and bind them together to form polar RbCs molecules. The binding is accomplished via photoassociation, which uses a laser to catalyze the sticking process. We report results from investigation of a new pathway for photoassociation that can produce molecules in their absolute ground state of vibrational and rotational motion. We also report preliminary observations of collisions between these ground-state molecules and co-trapped atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗

Single-Molecule Interfacial Electron Transfer

Interfacial electron transfer (ET) plays an important role in many chemical and biological processes. Specifically, interfacial ET in TiO 2 -based systems is important to solar energy technology, catalysis, and environmental remediation technology. However, the microscopic mechanism of interfacial ET is not well understood with regard to atomic surface structure, molecular structure, bonding, orientation, and motion. In this project, we used two complementary methodologies; single-molecule fluorescence spectroscopy, and scanning-tunneling microscopy and spectroscopy (STM and STS) to address this scientific need. The goal of this project was to integrate these techniques and measure the molecular dependence of ET between adsorbed molecules and TiO 2 semiconductor surfaces and the ET induced reactions such as the splitting of water. The scanning probe techniques, STM and STS, are capable of providing the highest spatial resolution but not easily time-resolved data. Single-molecule fluorescence spectroscopy is capable of good time resolution but requires further development to match the spatial resolution of the STM. The integrated approach involving Peter Lu at Bowling Green State University (BGSU) and Wilson Ho at the University of California, Irvine (UC Irvine) produced methods for time and spatially resolved chemical imaging of interfacial electron transfer dynamics and photocatalytic reactions. An integral aspect of the joint research was a significant exchange of graduate students to work at the two institutions. This project bridged complementary approaches to investigate a set of common problems by working with the same molecules on a variety of solid surfaces, but using appropriate techniques to probe under ambient (BGSU) and ultrahigh vacuum (UCI) conditions. The molecular level understanding of the fundamental interfacial electron transfer processes obtained in this joint project will be important for developing efficient light harvesting, solar energy conversion, and broadly applicable to problems in interface chemistry and surface physics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

High-throughput screening identifies small molecules that bind to the RAS:SOS:RAS complex and perturb RAS signaling

K-RAS is mutated in approximately 30% of human cancers, resulting in increased RAS signaling and tumor growth. Thus, RAS is a highly validated therapeutic target, especially in tumors of the pancreas, lung and colon. Although directly targeting RAS has proven to be challenging, it may be possible to target other proteins involved in RAS signaling, such as the guanine nucleotide exchange factor Son of Sevenless (SOS). We have previously reported on the discovery of small molecules that bind to SOS1, activate SOS-mediated nucleotide exchange on RAS, and paradoxically inhibit ERK phosphorylation. In this paper, we describe the discovery of additional, structurally diverse small molecules that also bind to SOS1 in the same pocket and elicit similar biological effects. We tested>160,000 compounds in a fluorescence-based assay to assess their effects on SOS-mediated nucleotide exchange. X-Ray structures revealed that these small molecules bind to the CDC25 domain of SOS1. Compounds that elicited high levels of nucleotide exchange activity in vitro increased RAS-GTP levels in cells, and inhibited phospho ERK levels at higher treatment concentrations. The identification of structurally diverse SOS1 binding ligands may assist in the discovery of new molecules designed to target RASdriven tumors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single molecule characterization of anomalous transport in a thin, anisotropic film

Here, the diffusion of small, charged molecules incorporated in an anisotropic polyelectrolyte multilayers (PEMs) was tracked in three dimensions by combining single-molecule fluorescence localization (to characterize lateral diffusion) with Förster resonance energy transfer (FRET) between diffusing molecules and the supporting surface (to measure diffusion in the surface-normal direction). Analysis of the surface-normal diffusion required model-based statistical analysis to account for the inherently noisy FRET signal. Combining these distinct single-molecule methods, which are inherently sensitive to different length scales, permitted simultaneous characterization of severely anisotropic diffusion, which was more than three orders of magnitude slower in the surface-normal direction. We hypothesize that the anomalously slow surface-normal diffusion was related to the periodic distribution of charge in the PEM, which created electrostatic barriers. The motion was strongly subdiffusive, with anomalous temporal scaling exponents in lateral and normal directions, suggesting a connection to the transient, random fractal conformation of polymer chains in the film’s matrix.

36 MATERIALS SCIENCE↗

miR-9 modulates the expression of interferon-regulated genes and MHC class I molecules in human nasopharyngeal carcinoma cells

Highlights: ► miR-9 can negatively or positively modulate interferon-induced gene expression. ► miR-9 can up-regulate major histocompatibility complex class I molecule expression. ► miR-9 can down-regulate the expression of interleukin-related genes. -- Abstract: The functions of miR-9 in some cancers are recently implicated in regulating proliferation, epithelial–mesenchymal transition (EMT), invasion and metastasis, apoptosis, and tumor angiogenesis, etc. miR-9 is commonly down-regulated in nasopharyngeal carcinoma (NPC), but the exact roles of miR-9 dysregulation in the pathogenesis of NPC remains unclear. Therefore, we firstly used miR-9-expressing CNE2 cells to determine the effects of miR-9 overexpression on global gene expression profile by microarray analysis. Microarray-based gene expression data unexpectedly demonstrated a significant number of up- or down-regulated immune- and inflammation-related genes, including many well-known interferon (IFN)-induced genes (e.g., IFI44L, PSMB8, IRF5, PSMB10, IFI27, PSB9{sub H}UMAN, IFIT2, TRAIL, IFIT1, PSB8{sub H}UMAN, IRF1, B2M and GBP1), major histocompatibility complex (MHC) class I molecules (e.g., HLA-B, HLA-C, HLA-F and HLA-H) and interleukin (IL)-related genes (e.g., IL20RB, GALT, IL7, IL1B, IL11, IL1F8, IL1A, IL6 and IL7R), which was confirmed by qRT-PCR. Moreover, the overexpression of miR-9 with the miRNA mimics significantly up- or down-regulated the expression of above-mentioned IFN-inducible genes, MHC class I molecules and IL-related genes; on the contrary, miR-9 inhibition by anti-miR-9 inhibitor in CNE2 and 5–8F cells correspondingly decreased or increased the aforementioned immune- and inflammation-related genes. Taken together, these findings demonstrate, for the first time, that miR-9 can modulate the expression of IFN-induced genes and MHC class I molecules in human cancer cells, suggesting a novel role of miR-9 in linking inflammation and cancer, which remains to be fully characterized.

60 APPLIED LIFE SCIENCES↗