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Sample records for molecular pattern molecules

  1. Endogenous Molecules Induced by a Pathogen-Associated Molecular Pattern (PAMP) Elicit Innate Immunity in Shrimp

    PubMed Central

    Chen, Yu-Yuan; Chen, Jiann-Chu; Lin, Yong-Chin; Kitikiew, Suwaree; Li, Hui-Fang; Bai, Jia-Chin; Tseng, Kuei-Chi; Lin, Bo-Wei; Liu, Po-Chun; Shi, Yin-Ze; Kuo, Yi-Hsuan; Chang, Yu-Hsuan

    2014-01-01

    Invertebrates rely on an innate immune system to combat invading pathogens. The system is initiated in the presence of cell wall components from microbes like lipopolysaccharide (LPS), ?-1,3-glucan (?G) and peptidoglycan (PG), altogether known as pathogen-associated molecular patterns (PAMPs), via a recognition of pattern recognition protein (PRP) or receptor (PRR) through complicated reactions. We show herein that shrimp hemocytes incubated with LPS, ?G, and PG caused necrosis and released endogenous molecules (EMs), namely EM-L, EM-?, and EM-P, and found that shrimp hemocytes incubated with EM-L, EM-?, and EM-P caused changes in cell viability, degranulation and necrosis of hemocytes, and increased phenoloxidase (PO) activity and respiratory burst (RB) indicating activation of immunity in vitro. We found that shrimp receiving EM-L, EM-?, and EM-P had increases in hemocyte count and other immune parameters as well as higher phagocytic activity toward a Vibrio pathogen, and found that shrimp receiving EM-L had increases in proliferation cell ratio and mitotic index of hematopoietic tissues (HPTs). We identified proteins of EMs deduced from SDS-PAGE and LC-ESI-MS/MS analyses. EM-L and EM-P contained damage-associated molecular patterns (DAMPs) including HMGBa, HMGBb, histone 2A (H2A), H2B, and H4, and other proteins including proPO, Rab 7 GPTase, and Rab 11 GPTase, which were not observed in controls (EM-C, hemocytes incubated in shrimp salt solution). We concluded that EMs induced by PAMPs contain DAMPs and other immune molecules, and they could elicit innate immunity in shrimp. Further research is needed to identify which individual molecule or combined molecules of EMs cause the results, and determine the mechanism of action in innate immunity. PMID:25517999

  2. Cell Death-Associated Molecular-Pattern Molecules: Inflammatory Signaling and Control

    PubMed Central

    Sangiuliano, Beatriz; Pérez, Nancy Marcela; Moreira, Dayson F.; Belizário, José E.

    2014-01-01

    Apoptosis, necroptosis, and pyroptosis are different cellular death programs characterized in organs and tissues as consequence of microbes infection, cell stress, injury, and chemotherapeutics exposure. Dying and death cells release a variety of self-proteins and bioactive chemicals originated from cytosol, nucleus, endoplasmic reticulum, and mitochondria. These endogenous factors are named cell death-associated molecular-pattern (CDAMP), damage-associated molecular-pattern (DAMP) molecules, and alarmins. Some of them cooperate or act as important initial or delayed inflammatory mediators upon binding to diverse membrane and cytosolic receptors coupled to signaling pathways for the activation of the inflammasome platforms and NF-κB multiprotein complexes. Current studies show that the nonprotein thiols and thiol-regulating enzymes as well as highly diffusible prooxidant reactive oxygen and nitrogen species released together in extracellular inflammatory milieu play essential role in controlling pro- and anti-inflammatory activities of CDAMP/DAMP and alarmins. Here, we provide an overview of these emerging concepts and mechanisms of triggering and maintenance of tissue inflammation under massive death of cells. PMID:25140116

  3. Kawasaki Disease-Specific Molecules in the Sera Are Linked to Microbe-Associated Molecular Patterns in the Biofilms

    PubMed Central

    Murata, Kenji; Kanno, Shunsuke; Nishio, Hisanori; Saito, Mitsumasa; Tanaka, Tamami; Yamamura, Kenichiro; Sakai, Yasunari; Takada, Hidetoshi; Miyamoto, Tomofumi; Mizuno, Yumi; Ouchi, Kazunobu; Waki, Kenji; Hara, Toshiro

    2014-01-01

    Background Kawasaki disease (KD) is a systemic vasculitis of unknown etiology. The innate immune system is involved in its pathophysiology at the acute phase. We have recently established a novel murine model of KD coronary arteritis by oral administration of a synthetic microbe-associated molecular pattern (MAMP). On the hypothesis that specific MAMPs exist in KD sera, we have searched them to identify KD-specific molecules and to assess the pathogenesis. Methods We performed liquid chromatography-mass spectrometry (LC-MS) analysis of fractionated serum samples from 117 patients with KD and 106 controls. Microbiological and LC-MS evaluation of biofilm samples were also performed. Results KD samples elicited proinflammatory cytokine responses from human coronary artery endothelial cells (HCAECs). By LC-MS analysis of KD serum samples collected at 3 different periods, we detected a variety of KD-specific molecules in the lipophilic fractions that showed distinct m/z and MS/MS fragmentation patterns in each cluster. Serum KD-specific molecules showed m/z and MS/MS fragmentation patterns almost identical to those of MAMPs obtained from the biofilms formed in vitro (common MAMPs from Bacillus cereus, Yersinia pseudotuberculosis and Staphylococcus aureus) at the 1st study period, and from the biofilms formed in vivo (common MAMPs from Bacillus cereus, Bacillus subtilis/Bacillus cereus/Yersinia pseudotuberculosis and Staphylococcus aureus) at the 2nd and 3rd periods. The biofilm extracts from Bacillus cereus, Bacillus subtilis, Yersinia pseudotuberculosis and Staphylococcus aureus also induced proinflammatory cytokines by HCAECs. By the experiments with IgG affinity chromatography, some of these serum KD-specific molecules bound to IgG. Conclusions We herein conclude that serum KD-specific molecules were mostly derived from biofilms and possessed molecular structures common to MAMPs from Bacillus cereus, Bacillus subtilis, Yersinia pseudotuberculosis and Staphylococcus aureus. Discovery of these KD-specific molecules might offer novel insight into the diagnosis and management of KD as well as its pathogenesis. PMID:25411968

  4. IgG antibodies from dourine infected horses identify a distinctive Trypanosoma equiperdum antigenic pattern of low molecular weight molecules.

    PubMed

    Luciani, M; Di Pancrazio, C; Di Febo, T; Tittarelli, M; Podaliri Vulpiani, M; Puglielli, M O; Naessens, J; Sacchini, F

    2013-01-15

    Diagnosis and control of dourine is strongly based on serological evidence, but knowledge of the humoral response of horses during infection is limited. In this study we developed a chemiluminescent immunoblotting (cIB) assay to characterise the Trypanosoma equiperdum antigen pattern recognised by IgGs from naturally or experimentally dourine-infected horses and analyse the kinetics of IgG humoral response following the infection. One compounding factor is that sera from uninfected animals often cross-react with T. equiperdum antigens. Development of the cIB assay was based on the hypothesis that serum IgGs from healthy and infected animals recognise different T. equiperdum antigen patterns. We used sera from 8 naturally infected horses which had recovered from Italian outbreaks and 2 experimentally infected mares. In addition, sera from 10 healthy control animals, eight of which were CFT positive but IFA negative for dourine, were collected from disease free regions. Sera were compared by the complement fixation test (CFT), indirect immune fluorescence (IFA) and the cIB assay. cIB analysis revealed that IgGs from infected horses, in contrast to IgGs from healthy horses, specifically recognise a T. equiperdum antigenic profile with low molecular weight bands ranging between 16 and 35 kDa. A time course experiment indicated that IgGs specific for the 16-35 kDa parasite protein fraction appear 17 days post-infection. The cIB assay confirmed all ten infected animals as positive and all controls as negative. This study demonstrated that analysis of IgGs by cIB can provide clear confirmation of trypanosome infection in horses, suggesting that this technique can be applied as a confirmatory serological test for dourine infection. PMID:23218944

  5. Molecular cloning, expression pattern, and phylogenetic analysis of a tetraspanin CD82-like molecule in lamprey Lampetra japonica.

    PubMed

    Zhang, Xiaoping; Song, Xueying; Su, Peng; Gou, Meng; Wang, Hao; Liu, Xin; Li, Qingwei

    2016-03-01

    CD82, a member of the tetraspanins, is originally identified as an accessory molecule in T cell activation, and it participates in the formation of immune synapse both in T cells and antigen-presenting cells of jawed vertebrates. In the present study, a CD82 homologous complementary DNA (cDNA) sequence is identified in the lamprey Lampetra japonica. The open reading frame of this sequence is 801 bp long and encodes a 266-amino acid protein. The multialignment of this sequence with several typical CD82s and CD37s of jawed vertebrates shows that it also possesses their conserved four transmembrane domains and a six-cysteine motif Cys-Cys-Gly…Cys-Ser-Cys…Cys…Cys, which is a characteristic motif of CD82 and CD37 vertebrate tetraspanin sequences. Since it is close to CD82s in sequence similarity, we name it as Lja-CD82-like. From the distribution profile of the conserved motifs of CD82-like, CD82, and CD37 molecules from molluscas to mammals, it seems that the CD82s and CD37s evolved from a common ancestral gene through a gene duplication event to their modern forms by a short insertion or substitution approaches. The phylogenetic analysis indicated that CD82 and CD37 molecules of jawed vertebrates originated from a common ancestral gene which is close to agnathan CD82-like and evolved into two distinct paralogous groups maybe after the divergence of jawed and jawless vertebrates. An expression vector with trigger factor (TF) was constructed to ensure that Lja-CD82-like express in prokaryotic expression host. The expressions of Lja-CD82-like messenger RNA (mRNA) and protein in immune-related tissues of lamprey were detected by real-time quantitative polymerase chain reaction and western blotting. Results showed that the mRNA and the protein levels of Lja-CD82-like were significantly upregulated in lymphocyte-like cells, gills, and supraneural myeloid bodies after stimulation with mixed antigens, respectively. Our data provided a foundation for the further study of Lja-CD82-like and its role in immune response process of jawless vertebrates. PMID:26935717

  6. Molecular Cloning, Expression Pattern, and Immunocytochemical Localization of a Gonadotropin-Releasing Hormone-like Molecule in the Gastropod Mollusk, Aplysia californica

    PubMed Central

    Zhang, Lihong; Tello, Javier A.; Zhang, Weimin; Tsai, Pei-San

    2008-01-01

    Successful reproduction in vertebrates depends upon the actions of gonadotropin-releasing hormone (GnRH). Despite the wide presence of GnRH in Phylum Chordata, GnRH has not been isolated in protostomes other than the common octopus. To provide information on the evolution of this critical hormone, we isolated the full-length cDNA of a GnRH-like molecule from the central nervous system of a gastropod mollusk, the sea hare Aplysia californica. The open reading frame of this cDNA encodes a protein of 147 amino acids. The molecular architecture of the deduced protein is highly homologous to that reported for the prepro-octopus GnRH (oct-GnRH) and consists of a putative signal peptide, a GnRH dodecapeptide, a downstream processing site, and a GnRH-associated peptide (GAP). The deduced amino acid sequence of the Aplysia GnRH (ap-GnRH) is QNYHFSNGWYAG and differs from oct-GnRH by only two amino acids. The transcript for ap-GnRH is widely expressed in the central nervous system (CNS), the ovotestis, and the atrial gland, an exocrine gland. Immunocytochemistry (ICC) using an antiserum against oct-GnRH detected immunoreactive neurons in all CNS ganglia examined, and the staining was abolished by the preadsorption of the antiserum with synthetic ap-GnRH. In sum, ap-GnRH sequence is the first gastropod GnRH-like molecule to be elucidated. Further, it represents one of the only two GnRH-like molecules found outside Phylum Chordata. These data refute the possibility that oct-GnRH arose singly in cephalopods by convergent evolution and provide valuable support for an ancient origin of GnRH during metazoan evolution. PMID:18178211

  7. DAMP molecule S100A9 acts as a molecular pattern to enhance inflammation during influenza A virus infection: role of DDX21-TRIF-TLR4-MyD88 pathway.

    PubMed

    Tsai, Su-Yu; Segovia, Jesus A; Chang, Te-Hung; Morris, Ian R; Berton, Michael T; Tessier, Philippe A; Tardif, Mélanie R; Cesaro, Annabelle; Bose, Santanu

    2014-01-01

    Pathogen-associated molecular patterns (PAMPs) trigger host immune response by activating pattern recognition receptors like toll-like receptors (TLRs). However, the mechanism whereby several pathogens, including viruses, activate TLRs via a non-PAMP mechanism is unclear. Endogenous "inflammatory mediators" called damage-associated molecular patterns (DAMPs) have been implicated in regulating immune response and inflammation. However, the role of DAMPs in inflammation/immunity during virus infection has not been studied. We have identified a DAMP molecule, S100A9 (also known as Calgranulin B or MRP-14), as an endogenous non-PAMP activator of TLR signaling during influenza A virus (IAV) infection. S100A9 was released from undamaged IAV-infected cells and extracellular S100A9 acted as a critical host-derived molecular pattern to regulate inflammatory response outcome and disease during infection by exaggerating pro-inflammatory response, cell-death and virus pathogenesis. Genetic studies showed that the DDX21-TRIF signaling pathway is required for S100A9 gene expression/production during infection. Furthermore, the inflammatory activity of extracellular S100A9 was mediated by activation of the TLR4-MyD88 pathway. Our studies have thus, underscored the role of a DAMP molecule (i.e. extracellular S100A9) in regulating virus-associated inflammation and uncovered a previously unknown function of the DDX21-TRIF-S100A9-TLR4-MyD88 signaling network in regulating inflammation during infection. PMID:24391503

  8. Patterns and conformations in molecularly thin films

    NASA Astrophysics Data System (ADS)

    Basnet, Prem B.

    Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn increasing attention because of the richness in phases that they exhibit. Due to the unique coupling between dipole properties and the packing constraints placed by the bent shape, these molecules are emerging as strong candidates in electromechanical devices. However, most applications require that the molecules be aligned, which has proved difficult. Our group has tested such molecules both as Langmuir layers and, when transferred to a solid, as alignment layers with some limited success. However, these molecules do not behave well with the surfaces and the domains at the air/water interface tend to form ill-controlled multilayer structures since attraction with the surfaces is relatively weak. New bent-core molecules obtained from Prof. Dr. C. Tsehiemke from Department of Chemistry Institute of Organic Chemistry, Martin-Luther-University, Germany, have a hydrophilic group at one end. We expect this molecule to behave better on the surface because of the stronger attraction of the hydrophilic group towards the surface than for the bent-core molecules without the hydrophilic group. Polydimethylsiloxane (PDMS) is a polymer which finds many applications in modifying surface properties. It is used in manufacturing lubricants, protective coatings, hair conditioner and glass-coating. However its properties are not well understood. This polymer has been proposed to follow either helical or caterpillar conformations on a surface. The orientational order of CH3 side groups can test for these conformations (they would be predominantly up/down for the caterpillar conformation, but rotating through the entire 360 degree for the helical one). Thus previous work on the Langmuir polymer films at the air/water interface were complemented by deuterium NMR studies to probe their conformations at a surface. These experiments were performed using humid porous solids, in order to provide sufficient surface area for the technique. Previous tests in this group at room temperature were suggestive but inconclusive because of the rapid averaging motion of the molecules. Here, we attempt to freeze the molecules on the surface.

  9. Molecular-beam spectroscopy of interhalogen molecules

    SciTech Connect

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

  10. Rotation and Anisotropic Molecular Orbital Effect in a Single H2TPP Molecule Transistor

    NASA Astrophysics Data System (ADS)

    Sakata, Shuichi; Yoshida, Kenji; Kitagawa, Yuichi; Ishii, Kazuyuki; Hirakawa, Kazuhiko

    2013-12-01

    Electron transport through a single molecule is determined not only by the intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by changes in the configuration. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited negative differential resistance, the magnitude of which changed with the pattern in the Coulomb stability diagram. Such behavior can be explained by the rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stress. Moreover, we find that the energy separations between molecular orbitals are also affected by the rotation, confirming that the metal-molecule interface configuration renormalizes the electronic levels in the molecule.

  11. Rotation and anisotropic molecular orbital effect in a single H2TPP molecule transistor.

    PubMed

    Sakata, Shuichi; Yoshida, Kenji; Kitagawa, Yuichi; Ishii, Kazuyuki; Hirakawa, Kazuhiko

    2013-12-13

    Electron transport through a single molecule is determined not only by the intrinsic properties of the molecule but also by the configuration of the molecule with respect to the lead electrodes. Here, we show how electron transport through a single H2TPP molecule is modulated by changes in the configuration. The Coulomb stability diagram of a single H2TPP molecule transistor exhibited a few different patterns in different measurement scans. Furthermore, the sample exhibited negative differential resistance, the magnitude of which changed with the pattern in the Coulomb stability diagram. Such behavior can be explained by the rotation of the molecule with anisotropic molecular orbitals in the gap electrodes induced by electrical stress. Moreover, we find that the energy separations between molecular orbitals are also affected by the rotation, confirming that the metal-molecule interface configuration renormalizes the electronic levels in the molecule. PMID:24483690

  12. Orientation detection of a single molecule using pupil filter with electrically controllable polarization pattern

    NASA Astrophysics Data System (ADS)

    Hashimoto, Mamoru; Yoshiki, Keisuke; Kurihara, Makoto; Hashimoto, Nobuyuki; Araki, Tsutomu

    2015-12-01

    We have developed a system for measuring the orientation of single molecules using a conventional wide-field fluorescence microscope with a polarization filter consisting of a polarizer and a compact polarization mode converter. The polarization filter electrically controls the pattern of polarization filtering. Since the polarization of the fluorescence from a single molecule highly depends on the angle between the observation direction and the molecular direction, polarization pattern filtering at the pupil plane of the objective lens allows the orientation of a single molecule to be visualized. Using this system, we demonstrated the orientation detection of single molecules.

  13. Molecular cloning, relative expression, and structural analysis of pattern recognition molecule β-glucan binding protein from mangrove crab Episesarma tetragonum.

    PubMed

    Sivakamavalli, Jeyachandran; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Vaseeharan, Baskaralingam

    2015-01-01

    A full-length cDNA of a β-glucan binding protein (β-GBP) gene was identified from the mangrove crab Episesarma tetragonum. The open reading frame of the E. tetragonum β-GBP (Epte β-GBP) is 1,167 bp long, encoding a polypeptide of 389 amino acids. The deduced amino acid sequence of Epte β-GBP gene has conserved a potential recognition motif for β-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites. Phylogenetic analysis of the Epte β-GBP gene showed the similarity with β-GBPs of other crustaceans and arthropods. Quantitative RT-PCR results showed the upregulation of Epte β-GBP gene expression in E. tetragonum hemocytes following a 12-H challenge in response to β-glucan (β-G). Epte β-GBP was involved in the regulation and activation of the prophenoloxidase cascade. A three-dimensional structure of active Epte β-GBP was modeled by homology modeling and refined with molecular dynamics simulations. A structural aspect of the protein is discussed based on experimental and theoretical results obtained. PMID:25066826

  14. Single molecular spectroscopy: identification of individual fullerene molecules.

    PubMed

    Tizei, Luiz H G; Liu, Zheng; Koshino, Masanori; Iizumi, Yoko; Okazaki, Toshiya; Suenaga, Kazu

    2014-10-31

    We report the molecule-by-molecule spectroscopy of individual fullerenes by means of electron spectroscopy based on scanning transmission electron microscopy. Electron energy-loss fine structure analysis of carbon 1s absorption spectra is used to discriminate carbon allotropes with known symmetries. C(60) and C(70) molecules randomly stored inside carbon nanotubes are successfully identified at a single-molecular basis. We show that a single molecule impurity is detectable, allowing the recognition of an unexpected contaminant molecule with a different symmetry. Molecules inside carbon nanotubes thus preserve their intact molecular symmetry. In contrast, molecules anchored at or sandwiched between atomic BN layers show spectral modifications possibly due to a largely degraded structural symmetry. Moreover, by comparing the spectrum from a single C(60) molecule and its molecular crystal, we find hints of the influence of solid-state effects on its electronic structure. PMID:25396379

  15. Single Molecular Spectroscopy: Identification of Individual Fullerene Molecules

    NASA Astrophysics Data System (ADS)

    Tizei, Luiz H. G.; Liu, Zheng; Koshino, Masanori; Iizumi, Yoko; Okazaki, Toshiya; Suenaga, Kazu

    2014-10-01

    We report the molecule-by-molecule spectroscopy of individual fullerenes by means of electron spectroscopy based on scanning transmission electron microscopy. Electron energy-loss fine structure analysis of carbon 1 s absorption spectra is used to discriminate carbon allotropes with known symmetries. C60 and C70 molecules randomly stored inside carbon nanotubes are successfully identified at a single-molecular basis. We show that a single molecule impurity is detectable, allowing the recognition of an unexpected contaminant molecule with a different symmetry. Molecules inside carbon nanotubes thus preserve their intact molecular symmetry. In contrast, molecules anchored at or sandwiched between atomic BN layers show spectral modifications possibly due to a largely degraded structural symmetry. Moreover, by comparing the spectrum from a single C60 molecule and its molecular crystal, we find hints of the influence of solid-state effects on its electronic structure.

  16. Single Molecule Approaches Embrace Molecular Cohorts

    PubMed Central

    Ha, Taekjip

    2013-01-01

    Enormous mechanistic insight has been gained by studying the behavior of single molecules. The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. PMID:23953107

  17. Controlling single-molecule junction conductance by molecular interactions

    PubMed Central

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  18. Controlling single-molecule junction conductance by molecular interactions

    NASA Astrophysics Data System (ADS)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-07-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment.

  19. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center (ESTSC)

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  20. Molecular machines: Molecules bearing robotic arms

    NASA Astrophysics Data System (ADS)

    Aprahamian, Ivan

    2016-02-01

    Mass production at the nanoscale requires molecular machines that can control, with high fidelity, the spatial orientation of other reactive species. The demonstration of a synthetic system in which a molecular robotic arm can be used to manipulate the position of a chemical cargo is a significant step towards achieving this goal.

  1. Mitochondrial damage-associated molecular patterns and vascular function†

    PubMed Central

    Wenceslau, Camilla Ferreira; McCarthy, Cameron G.; Szasz, Theodora; Spitler, Kathryn; Goulopoulou, Styliani; Webb, R. Clinton

    2014-01-01

    Immune system activation occurs not only due to foreign stimuli, but also due to endogenous molecules. As such, endogenous molecules that are released into the circulation due to cell death and/or injury alarm the immune system that something has disturbed homeostasis and a response is needed. Collectively, these molecules are known as damage-associated molecular patterns (DAMPs). Mitochondrial DAMPs (mtDAMPs) are potent immunological activators due to the bacterial ancestry of mitochondria. Mitochondrial DAMPs are recognized by specific pattern recognition receptors of the innate immune system, some of which are expressed in the cardiovascular system. Cell death leads to release of mtDAMPs that may induce vascular changes by mechanisms that are currently not well understood. This review will focus on recently published evidence linking mtDAMPs and immune system activation to vascular dysfunction and cardiovascular disease. PMID:24569027

  2. Advanced molecular self-assemblies facilitated by simple molecules.

    PubMed

    Wu, Zheng; Yan, Yun; Huang, Jianbin

    2014-12-01

    Advanced materials are often based on smart molecular self-assemblies that either respond to external stimuli or have hierarchical structures. Approaches to this goal usually stem from complicated molecular design and difficult organic synthesis. In this invited feature article, we demonstrate that desired molecular self-assemblies can be made conveniently by introducing simple functional molecules into amphiphilic systems. We show that upon introducing specific small molecules which serve as responders, modulators, or even building blocks, smart supramolecular architectures can be achieved which avoid complicated organic synthesis. We expect that this could be a general and economical way to produce advanced materials in the near future. PMID:24870151

  3. Regular and anomalous torsional splitting patterns: a trend in ethane-like molecules and general perspectives

    NASA Astrophysics Data System (ADS)

    Lattanzi, F.; di Lauro, C.

    2004-01-01

    It is shown that torsional Coriolis coupling can alter the torsional splittings in molecules with hindered internal rotation. Splitting patterns that would occur in the absence of any vibrational contribution to the torsional angular momentum, with reference to a molecular axis system (IAM), are called regular. It is shown that different sets of vibrational coordinates, corresponding to vibrational states with different splitting patterns, can be defined for modes normal to the internal rotation axis. The forms of normal coordinates appropriate to basis vibrational states with regular and inverted splitting patterns are identified. It is found that in normal coordinates appropriate to vibrational states with regular torsional splitting patterns, the relative orientation of the displacements of pairs of atoms belonging to different molecular moieties is independent of the internal rotation angle, and relative displacements normal to the internal rotation axis can be cis or trans at any conformation. On the contrary, in normal coordinates appropriate to vibrational states with inverted torsional splitting patterns the relative orientation of such displacements changes by ?(cis-trans interchange) upon half the internal rotation converting two neighbor equivalent conformations (as in a staggered-eclipsed conformational conversion). The formation of the actual torsional splitting patterns in degenerate vibrational states of CH3CH3-type molecules depends on the joint effect of torsional Coriolis and head-tail coupling. The torsional Coriolis operator can tune pairs of levels to resonance for the action of typical head-tail coupling operators (torsion-dependent vibrational operators), depending on the values of the torsional Coriolis coefficients, generating vibrational states with either regular or inverted torsional splitting patterns and affecting the splitting magnitude. It is shown that operators with a sin3?-type torsional dependence favor the formation of inverted splitting patterns. In less symmetric molecules torsional Coriolis coupling affects the torsional splitting patterns by the same mechanism as in CH3CH3-type molecules, but the torsion-dependent operators are different and their action is expected to be less effective. Typical anomalous perpendicular splitting patterns can be predicted for non-degenerate modes localized in a single molecular moiety, normal or with a component normal to the internal rotation axis, having fixed orientation in that moiety (as the C=O or C-H stretchings of acetaldehyde). Adopting a barrier-hindered torsional basis, where the lower torsional levels can be seen as vibrational states with quantum numbers v? exhibiting tunneling splitting, one finds that all operators generating matrix elements with ?v?=+/-1, or in general odd, work toward the formation of inverted splitting patterns, generating anomalous patterns.

  4. Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules

    SciTech Connect

    Jordan, Jacob L.; Arndt, Joseph W.; Hanf, Karl; Li, Guohui; Hall, Janine; Demarest, Stephen; Huang, Flora; Wu, Xiufeng; Miller, Brian; Glaser, Scott; Fernandez, Erik J.; Wang, Deping; Lugovskoy, Alexey

    2010-01-12

    Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LT{beta}R) binding Fv domain of an anti-LT{beta}R/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability.

  5. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution.

    PubMed

    Deniz, Ashok A

    2016-01-29

    The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects. PMID:26707199

  6. A random rotor molecule: Vibrational analysis and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

    2012-12-01

    Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

  7. Photocleavable linker for the patterning of bioactive molecules.

    PubMed

    Wegner, Seraphine V; Sentürk, Oya I; Spatz, Joachim P

    2015-01-01

    Herein, we report the use of a versatile photocleavable nitrobenzyl linker to micropattern a wide variety of bioactive molecules and photorelease them on demand. On one end, the linker has an NHS group that can be coupled with any amine, such as peptides, proteins or amine-linkers, and on the other end an alkyne for convenient attachment to materials with an azide functional group. This linker was conjugated with NTA-amine or the cell adhesion peptide cRGD to enable straightforward patterning of His6-tagged proteins or cells, respectively, on PEGylated glass surfaces. This approach provides a practical way to control the presentation of a wide variety of bioactive molecules with high spatial and temporal resolution. The extent of photocleavage can also be controlled to tune the biomolecule density and degree of cell attachment to the surface. PMID:26670693

  8. Photocleavable linker for the patterning of bioactive molecules

    PubMed Central

    Wegner, Seraphine V.; Sentürk, Oya I.; Spatz, Joachim P.

    2015-01-01

    Herein, we report the use of a versatile photocleavable nitrobenzyl linker to micropattern a wide variety of bioactive molecules and photorelease them on demand. On one end, the linker has an NHS group that can be coupled with any amine, such as peptides, proteins or amine-linkers, and on the other end an alkyne for convenient attachment to materials with an azide functional group. This linker was conjugated with NTA-amine or the cell adhesion peptide cRGD to enable straightforward patterning of His6-tagged proteins or cells, respectively, on PEGylated glass surfaces. This approach provides a practical way to control the presentation of a wide variety of bioactive molecules with high spatial and temporal resolution. The extent of photocleavage can also be controlled to tune the biomolecule density and degree of cell attachment to the surface. PMID:26670693

  9. Photocleavable linker for the patterning of bioactive molecules

    NASA Astrophysics Data System (ADS)

    Wegner, Seraphine V.; Sentürk, Oya I.; Spatz, Joachim P.

    2015-12-01

    Herein, we report the use of a versatile photocleavable nitrobenzyl linker to micropattern a wide variety of bioactive molecules and photorelease them on demand. On one end, the linker has an NHS group that can be coupled with any amine, such as peptides, proteins or amine-linkers, and on the other end an alkyne for convenient attachment to materials with an azide functional group. This linker was conjugated with NTA-amine or the cell adhesion peptide cRGD to enable straightforward patterning of His6-tagged proteins or cells, respectively, on PEGylated glass surfaces. This approach provides a practical way to control the presentation of a wide variety of bioactive molecules with high spatial and temporal resolution. The extent of photocleavage can also be controlled to tune the biomolecule density and degree of cell attachment to the surface.

  10. Resolution-associated molecular patterns (RAMP): RAMParts defending immunological homeostasis?

    PubMed Central

    Shields, A M; Panayi, G S; Corrigall, V M

    2011-01-01

    The resolution of inflammation is central to the maintenance of good health and immune homeostasis. Recently, several intracellular stress proteins have been described as having extracellular properties that are anti-inflammatory or favour the resolution of inflammation. We propose that these molecules should be defined as resolution-associated molecular patterns (RAMPs). RAMPs are released at times of cellular stress and help to counterbalance the inflammatory effects of pathogen-associated (PAMPs) and damage-associated (DAMPs) molecular patterns. We propose that heat shock protein 10 (HSP10), ?B-crystallin (?BC), HSP27 and binding immunoglobulin protein (BiP) should be considered founding members of the RAMP family. A greater understanding of RAMP biology may herald the development of novel immunotherapies. PMID:21671907

  11. Molecular Rotation Signals: Molecule Chemistry and Particle Physics

    NASA Astrophysics Data System (ADS)

    Grabow, Jens-Uwe

    2015-06-01

    Molecules - large or small - are attractive academic resources, with numerous questions on their chemical behaviour as well as problems in fundamental physics now (or still) waiting to be answered: Targeted by high-resolution spectroscopy, a rotating molecular top can turn into a laboratory for molecule chemistry or a laboratory for particle physics. Once successfully entrained (many species - depending on size and chemical composition - have insufficient vapour pressures or are of transient nature, such that specifically designed pulsed-jet sources are required for their transfer into the gas phase or in-situ generation) into the collision-free environment of a supersonic-jet expansion, each molecular top comes with its own set of challenges, theoretically and experimentally: Multiple internal interactions are causing complicated energy level schemes and the resulting spectra will be rather difficult to predict theoretically. Experimentally, these spectra are difficult to assess and assign. With today's broad-banded chirp microwave techniques, finding and identifying such spectral features have lost their major drawback of being very time consuming for many molecules. For other molecules, the unrivalled resolution and sensitivity of the narrow-banded impulse microwave techniques provide a window to tackle - at the highest precision available to date - fundamental questions in physics, even particle physics - potentially beyond the standard model. Molecular charge distribution, properties of the chemical bond, details on internal dynamics and intermolecular interaction, the (stereo-chemical) molecular structure (including the possibility of their spatial separation) as well as potential evidence for tiny yet significant interactions encode their signature in pure molecular rotation subjected to time-domain microwave spectroscopic techniques. Ongoing exciting technical developments promise rapid progress. We present recent examples from Hannover, new directions, and an outlook at the future of molecular rotation spectroscopy.

  12. Molecular surface analysis by laser ionization of desorbed molecules

    SciTech Connect

    Pellin, M.J.; Lykke, K.R.; Wurz, P.; Parker, D.H.

    1992-07-01

    While elemental analysis of surfaces has progressed dramatically over the past ten years, quantitative molecular surface analysis remains difficult. This is particularly true in the analysis of complex materials such as polymers and rubbers which contain a wide compliment of additives and pigments to enhance their material characteristics. For mass spectrometric analysis the difficulty is two fold. First, desorption of surface molecules must be accompanied with minimal fragmentation and collateral surface damage. Second, the desorbed molecules must be ionized for subsequent mass analysis with high efficiency and without significant cracking. This paper focuses on the second of these problems.

  13. Molecular surface analysis by laser ionization of desorbed molecules

    SciTech Connect

    Pellin, M.J.; Lykke, K.R.; Wurz, P.; Parker, D.H.

    1992-01-01

    While elemental analysis of surfaces has progressed dramatically over the past ten years, quantitative molecular surface analysis remains difficult. This is particularly true in the analysis of complex materials such as polymers and rubbers which contain a wide compliment of additives and pigments to enhance their material characteristics. For mass spectrometric analysis the difficulty is two fold. First, desorption of surface molecules must be accompanied with minimal fragmentation and collateral surface damage. Second, the desorbed molecules must be ionized for subsequent mass analysis with high efficiency and without significant cracking. This paper focuses on the second of these problems.

  14. Molecular Dynamics Simulation on Calcium Silicate Hydrate Doped Organic Molecules

    NASA Astrophysics Data System (ADS)

    Dai, Wei; Shui, Zhonghe; Duan, Ping

    The interactions between organic molecules and calcium silicate hydrate were studied using molecular simulation techniques. Representative model of calcium silicate hydrate-Hamid model was selected as the initial structure of this simulation. Method of molecular mechanics (MM) and molecular dynamics (MD) were employed for simulation and calculation of C-S-H doped with styrene-acrylate, and the most stable conformation with lowest energy was obtained. Solubility parameters were calculated by analyzing the data of molecular trajectory combined with cohesive energy density (CED) of the structure. The results show that: doped calcium silicate hydrate have significant growth in the bulk modulus, compressibility and other mechanical performance parameters, compatibility of styrene-acrylate and calcium silicate hydrate is better, that is unanimous with test results.

  15. The computation of molecular properties of flexible molecules

    NASA Astrophysics Data System (ADS)

    Dunmur, David A.; Grayson, Martin; Pickup Mark, Barry T.; Wilson, R.

    Temperature dependent molecular properties have been calculated using a combination of classical molecular dynamics and Monte Carlo methods and semiempirical quantum techniques. Sample geometries from stochastic dynamics and Metropolis Monte Carlo calculations have been fed into the AM1 Hamiltonian in MOPAC-5 to produce estimates of dipole moments, polarizabilities and hyperpolarizabilities at a variety of temperatures for the molecules butane, 4-cyanoaniline, dopamine (3,4-dihydroxyphenylethylamine) and 1,2-di-(4-cyanophenyl)ethane. Reasonably reliable results can be produced with only a modest use of computer time.

  16. Reconstruction of three-dimensional molecular structure from diffraction of laser-aligned molecules.

    PubMed

    Yang, Jie; Makhija, Varun; Kumarappan, Vinod; Centurion, Martin

    2014-07-01

    Diffraction from laser-aligned molecules has been proposed as a method for determining 3-D molecular structures in the gas phase. However, existing structural retrieval algorithms are limited by the imperfect alignment in experiments and the rotational averaging in 1-D alignment. Here, we demonstrate a two-step reconstruction comprising a genetic algorithm that corrects for the imperfect alignment followed by an iterative phase retrieval method in cylindrical coordinates. The algorithm was tested with simulated diffraction patterns. We show that the full 3-D structure of trifluorotoluene, an asymmetric-top molecule, can be reconstructed with atomic resolution. PMID:26798781

  17. Molecular Design of Branched and Binary Molecules at Ordered Interfaces

    SciTech Connect

    Kirsten Larson Genson

    2005-12-27

    This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

  18. Behavior of molecules and molecular ions near a field emitter

    NASA Astrophysics Data System (ADS)

    Gault, Baptiste; Saxey, David W.; Ashton, Michael W.; Sinnott, Susan B.; Chiaramonti, Ann N.; Moody, Michael P.; Schreiber, Daniel K.

    2016-03-01

    The cold emission of particles from surfaces under intense electric fields is a process which underpins a variety of applications including atom probe tomography (APT), an analytical microscopy technique with near-atomic spatial resolution. Increasingly relying on fast laser pulsing to trigger the emission, APT experiments often incorporate the detection of molecular ions emitted from the specimen, in particular from covalently or ionically bonded materials. Notably, it has been proposed that neutral molecules can also be emitted during this process. However, this remains a contentious issue. To investigate the validity of this hypothesis, a careful review of the literature is combined with the development of new methods to treat experimental APT data, the modeling of ion trajectories, and the application of density-functional theory simulations to derive molecular ion energetics. It is shown that the direct thermal emission of neutral molecules is extremely unlikely. However, neutrals can still be formed in the course of an APT experiment by dissociation of metastable molecular ions. This work is a partial contribution of the US Government and therefore is not subject to copyright in the United States.

  19. Apparatus and method of determining molecular weight of large molecules

    DOEpatents

    Fuerstenau, Stephen; Benner, W. Henry; Madden, Norman; Searles, William

    1998-01-01

    A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e.sup.- are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation.

  20. Apparatus and method of determining molecular weight of large molecules

    DOEpatents

    Fuerstenau, S.; Benner, W.H.; Madden, N.M.; Searles, W.

    1998-06-23

    A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e{sup {minus}} are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation. 14 figs.

  1. Molecular evolution of hemojuvelin and the repulsive guidance molecule family.

    PubMed

    Camus, Laura Marie; Lambert, Lisa A

    2007-07-01

    Repulsive guidance molecules (RGMs) are found in vertebrates and chordates and are involved in embryonic development and iron homeostasis. Members of this family are GPI-linked membrane proteins that contain an N-terminal signal peptide, a C-terminal propeptide, and a conserved RGD motif. Vertebrates are known to possess three paralogues; RGMA and RGMB (sometimes called Dragon) are expressed in the nervous system and are thought to play various roles in neural development. Hemojuvelin (HJV; also called repulsive guidance molecule c, RGMC) is the third member of this family, and mutations in this gene result in a form of juvenile hemochromatosis (type 2A). Phylogenetic analyses of 55 different RGM family sequences from 21 different species support the existence of a novel gene, found only in fish, which we have labeled RGMD. The pattern of conserved residues in each family identifies new candidates for important functional roles, including ligand binding. PMID:17593421

  2. Maskless RGB color patterning of vacuum-deposited small molecule OLED displays by diffusion of luminescent dopant molecules.

    PubMed

    Kajiyama, Yoshitaka; Kajiyama, Koichi; Aziz, Hany

    2015-06-29

    A maskless RGB color patterning technique based on diffusion of luminescent dopant molecules is proposed here for vacuum-deposited small molecule OLED displays. The proposed maskless color patterning technique enables us to overcome challenging issues in OLED display manufacturing arising from shadow mask limitations. This approach utilizes selective diffusion of luminescent dopant molecules from a donor substrate to an acceptor substrate. Results show that sufficiently high doping levels can be achieved through this technique and that devices with performance similar to those produced by standard co-deposition can be easily produced. Red, green and blue OLEDs are successfully fabricated side by side on one substrate using this technique. PMID:26191677

  3. Molecular dynamics simulation of paracetamol molecules ordering around glycogen

    NASA Astrophysics Data System (ADS)

    Lim, Wilber; Feng, Yuan Ping; Liu, X. Y.

    2005-05-01

    By the use of classical atomistic molecular dynamics simulations, we demonstrate that paracetamol molecules exist in a highly ordered phase in the presence of a glycogen substrate at 317K whereas the paracetamol fluid exists in an isotropic phase in the absence of the glycogen substrate at the same temperature. This result further validates the studies made on polysaccharide regarding its abilities to promote nucleation of paracetamol via liquid preordering. As little is known regarding liquid ordering induced by a polymeric substrate, we seek to explore the ordering mechanism from an energy perspective. This is accomplished using conformation mappings. Our analysis shows that the conformation space accessible to the paracetamol molecule at 317K in the vicinity of glycogen is smaller than the one in the absence of glycogen. An investigation on the orientation of the dipole moments of the glycogen monomers and paracetamol molecules were carried out as well. From the investigations, we show that dipolar interactions play an important role in the ordering process. These studies bear significance to the understanding of the ordering process as well as the promotion and effective control of the nucleation rate.

  4. Small-Molecule Hormones: Molecular Mechanisms of Action

    PubMed Central

    Budzińska, Monika

    2013-01-01

    Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30–60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes. PMID:23533406

  5. The molecular origins of species-specific facial pattern.

    PubMed

    Brugmann, Samantha A; Tapadia, Minal D; Helms, Jill A

    2006-01-01

    The prevailing approach within the field of craniofacial development is focused on finding a balance between tissues (e.g., facial epithelia, neuroectoderm, and neural crest) and molecules (e.g., bone morphogenetic proteins, fibroblast growth factors, Wnts) that play a role in sculpting the face. We are rapidly learning that neither these tissues nor molecular signals are able to act in isolation; in fact, molecular cues are constantly reciprocating signals between the epithelia and the neural crest in order to pattern and mold facial structures. More recently, it has been proposed that this crosstalk is often mediated and organized by discrete organizing centers within the tissues that are able to act as a self-contained unit of developmental potential (e.g., the rhombomere and perhaps the ectomere). Whatever the molecules are and however they are interpreted by these tissues, it appears that there is a remarkably conserved mechanism for setting up the initial organization of the facial prominences between species. Regardless of species, all vertebrates appear to have the same basic bauplan. However, sometime during mid-gestation, the vertebrate face begins to exhibit species-specific variations, in large part due to differences in the rates of growth and differentiation of cells comprising the facial prominences. How do these differences arise? Are they due to late changes in molecular signaling within the facial prominences themselves? Or are these late changes a reflection of earlier, more subtle alterations in boundaries and fields that are established at the earliest stages of head formation? We do not have clear answers to these questions yet, but in this chapter we present new studies that shed light on this age-old question. This chapter aims to present the known signals, both on a molecular and cellular level, responsible for craniofacial development while bringing to light the events that may serve to create difference in facial morphology seen from species to species. PMID:16782454

  6. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

    PubMed Central

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W.

    2011-01-01

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems. PMID:22022236

  7. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

    PubMed

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W

    2011-10-11

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems. PMID:22022236

  8. GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

    SciTech Connect

    MUCKERMAN,J.T.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

  9. Libraries of Extremely Localized Molecular Orbitals. 1. Model Molecules Approximation and Molecular Orbitals Transferability.

    PubMed

    Meyer, Benjamin; Guillot, Benoît; Ruiz-Lopez, Manuel F; Genoni, Alessandro

    2016-03-01

    Despite more and more remarkable computational ab initio results are nowadays continuously obtained for large macromolecular systems, the development of new linear-scaling techniques is still an open and stimulating field of research in theoretical chemistry. In this family of methods, an important role is occupied by those strategies based on the observation that molecules are generally constituted by recurrent functional units with well-defined intrinsic features. In this context, we propose to exploit the notion of extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, or functional groups), are in principle transferable from one molecule to another. Accordingly, the construction of orbital libraries to almost instantaneously build up approximate wave functions and electron densities of very large systems becomes conceivable. In this work, the ELMOs transferability is further investigated in detail and, furthermore, suitable rules to construct model molecules for the computation of ELMOs to be stored in future databanks are also defined. The obtained results confirm the reliable transferability of the ELMOs and show that electron densities obtained from the transfer of extremely localized molecular orbitals are very close to the corresponding Hartree-Fock ones. These observations prompt us to construct new ELMOs databases that could represent an alternative/complement to the already popular pseudoatoms databanks both for determining electron densities and for refining crystallographic structures of very large molecules. PMID:26799516

  10. Simple molecular model for the binding of antibiotic molecules to bacterial ion channels

    NASA Astrophysics Data System (ADS)

    Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

    2003-10-01

    A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill's theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of interacting sites facilitates drug binding. The dependence of the number of ampicillin binding events per second with the solution pH and salt concentration is explained qualitatively using a reduced number of fundamental concepts.

  11. Application of Machine Learning tools to recognition of molecular patterns in STM images

    NASA Astrophysics Data System (ADS)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kalinin, Sergei; Sumpter, Bobby

    The ability to utilize individual molecules and molecular assemblies as data storage elements has motivated scientist for years, concurrent with the continuous effort to shrink a size of data storage devices in microelectronics industry. One of the critical issues in this effort lies in being able to identify individual molecular assembly units (patterns), on a large scale in an automated fashion of complete information extraction. Here we present a novel method of applying machine learning techniques for extraction of positional and rotational information from scanning tunneling microscopy (STM) images of π-bowl sumanene molecules on gold. We use Markov Random Field (MRF) model to decode the polar rotational states for each molecule in a large scale STM image of molecular film. We further develop an algorithm that uses a convolutional Neural Network combined with MRF and input from density functional theory to classify molecules into different azimuthal rotational classes. Our results demonstrate that a molecular film is partitioned into distinctive azimuthal rotational domains consisting typically of 20-30 molecules. In each domain, the ``bowl-down'' molecules are generally surrounded by six nearest neighbor molecules in ``bowl-up'' configuration, and the resultant overall structure form a periodic lattice of rotational and polar states within each domain. Research was supported by the US Department of Energy.

  12. ION AND MOLECULE SENSORS USING MOLECULAR RECOGNITION IN LUMINESCENT, CONDUCTIVE POLYMERS

    EPA Science Inventory

    This program integrates three individual, highly interactive projects that will use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecul...

  13. MAMP (microbe-associated molecular pattern) triggered immunity in plants

    PubMed Central

    Newman, Mari-Anne; Sundelin, Thomas; Nielsen, Jon T.; Erbs, Gitte

    2013-01-01

    Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and β-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants. PMID:23720666

  14. Sensing of protein molecules through nanopores: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kannam, Sridhar Kumar; Kim, Sung Cheol; Rogers, Priscilla R.; Gunn, Natalie; Wagner, John; Harrer, Stefan; Downton, Matthew T.

    2014-04-01

    Solid-state nanopores have been shown to be suitable for single molecule detection. While numerous modeling investigations exist for DNA within nanopores, there are few simulations of protein translocations. In this paper, we use atomistic molecular dynamics to investigate the translocation of proteins through a silicon nitride nanopore. The nanopore dimensions and profile are representative of experimental systems. We are able to calculate the change in blockade current and friction coefficient for different positions of the protein within the pore. The change in ionic current is found to be negligible until the protein is fully within the pore and the current is lowest when the protein is in the pore center. Using a simple theory that gives good quantitative agreement with the simulation results we are able to show that the variation in current with position is a function of the pore shape. In simulations that guide the protein through the nanopore we identify the effect that confinement has on the friction coefficient of the protein. This integrated view of translocation at the nanoscale provides useful insights that can be used to guide the design of future devices.

  15. Signatures of molecular magnetism in single-molecule transport spectroscopy.

    PubMed

    Jo, Moon-Ho; Grose, Jacob E; Baheti, Kanhayalal; Deshmukh, Mandar M; Sokol, Jennifer J; Rumberger, Evan M; Hendrickson, David N; Long, Jeffrey R; Park, Hongkun; Ralph, D C

    2006-09-01

    We report single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. PMID:16968018

  16. Site-selective patterning of organic luminescent molecules via gas phase deposition.

    PubMed

    Hao, Juanyuan; Lu, Nan; Wu, Qiong; Hu, Wei; Chen, Xiaodong; Zhang, Hongyu; Wu, Ying; Wang, Yue; Chi, Lifeng

    2008-05-20

    In this paper, we present a bottom-up approach to pattern organic luminescent molecules with a feature size down to sub-100 nm over wafer-sized areas. This method is based on the selective gas deposition of organic molecules on self-organized patterned structures, which consist of an organic monolayer with two different phases rather than different materials. The site selectivity is controllable by deposition rate and the pattern features. The reason for the site selectivity may be due to the nucleation and diffusion behaviors of the deposited organic molecules on different monolayer phases. PMID:18370416

  17. Exploration of target molecules for molecular imaging of inflammatory bowel disease

    SciTech Connect

    Higashikawa, Kei; Akada, Naoki; Yagi, Katsuharu; Watanabe, Keiko; Kamino, Shinichiro; Kanayama, Yousuke; Hiromura, Makoto; Enomoto, Shuichi; Multiple Molecular Imaging Research Laboratory, RIKEN Center for Molecular Imaging Science, Kobe 650-0047

    2011-07-08

    Highlights: {sup {yields}18}F-FDG PET could discriminate each inflamed area of IBD model mice clearly. {sup {yields}18}F-FDG PET could not discriminate the difference of pathogenic mechanism. {yields} Cytokines and cytokine receptors expression was different by pathogenic mechanism. {yields} Cytokines and cytokine receptors would be new target molecules for IBD imaging. -- Abstract: Molecular imaging technology is a powerful tool for the diagnosis of inflammatory bowel disease (IBD) and the efficacy evaluation of various drug therapies for it. However, it is difficult to elucidate directly the relationships between the responsible molecules and IBD using existing probes. Therefore, the development of an alternative probe that is able to elucidate the pathogenic mechanism and provide information on the appropriate guidelines for treatment is earnestly awaited. In this study, we investigated pathognomonic molecules in the intestines of model mice. The accumulation of fluorine-18 fluorodeoxyglucose ({sup 18}F-FDG) in the inflamed area of the intestines of dextran sulfate sodium (DSS)- or indomethacin (IND)-induced IBD model mice was measured by positron emission tomography (PET) and autoradiography to confirm the inflamed area. The results suggested that the inflammation was selectively induced in the colons of mice by the administration of DSS, whereas it was induced mainly in the ilea and the proximal colons of mice by the administration of IND. To explore attractive target molecules for the molecular imaging of IBD, we evaluated the gene expression levels of cytokines and cytokine receptors in the inflamed area of the intestines of both model mice. We found that the expression levels of cytokines and cytokine receptors were significantly increased during the progression of IBD, whereas the expression levels were decreased as the mucosa began to heal. In particular, the expression levels of these molecules had already changed before the symptoms of IBD appeared. In addition, the alterations of cytokine and cytokine receptor expression levels indicated differences in the expression pattern depending on the pathogenic mechanism or the region of inflammation (e.g., TNF-{alpha}). Our results suggest that these cytokines or cytokine receptors participate in the pathogenesis of IBD and are valuable biomarkers for the detection of the different circumstances underlying inflammation by the molecular imaging method. Finally, the development of an imaging probe for our target molecules is expected to improve our understanding of the inflammatory conditions of IBD.

  18. From Molecular Oxygen to Primordial Molecules with the Odin Satellite

    NASA Astrophysics Data System (ADS)

    Persson, C.; Encrenaz, P.; Hjalmarson, .; Sandqvist, Aa.

    2008-08-01

    Odin is a mm/submm-wave-spectroscopy Astronomy and Aeronomy satellite. Its design life time was two years, but it has now operated successfully for more than six years. Its 1.1 m high-precision telescope, with a beam efficiency of 90%, has beamwidths of 10 arcmin and 2 arcmin at mm and submm wavelengths, respectively. It is equipped with a cryogenic receiver package of four tunable, SSB, submm Schottky mixers covering the 486-504 and 541-581 GHz frequency range, and a fixed-tuned HEMT receiver at a frequency of 118-119 GHz. Odin has discovered the elusive oxygen (O2) molecule at 119 GHz---the detection was made in the ? Oph A molecular-cloud core. The O2 abundance, X(O2), is ? 5 10-8---Larsson et al. (2007: A&A, 466, 999). Odin has also discovered water (H2O) at 557 GHz in the core of the Milky Way Galaxy---the Sgr A CircumNuclear Disk (CND)---and mapped its distribution in the Sgr A Complex including the +20 and +50 km s-1 Molecular Clouds---Sandqvist et al. (2006: J.Phys. Conf.Ser., 54, 72). Furthermore, devoting about 1,100 orbits (each of which contains 1 hour of observable astronomy time) Odin has performed a spectral-line survey of Orion KL in the ranges 487-492 and 542-577 GHz. There are 280 identified spectral lines from 38 species and 64 unidentified lines [Olofsson et al. (2007: A&A, 476, 791) and Persson et al. (2007: A&A, 476, 807)]. Odin has searched for emission from the 557 GHz ortho-H2O line in six nearby starburst galaxies yielding three-sigma upper limits to the water abundance relative to H2 (NGC253 - <2.0 10-9; IC342 - <2.6 10-9; M82 - <1.7 10-9; NGC 4258 - <1.3 10-8; CenA - <7.8 10-9 and M51 - <2.4 10-9) [Wilson et al. (2007: A&A, 469, 121)]. Odin has an ongoing project for studying the first phases of structure formation in the early universe. The presence of primordial molecules (e.g., HD, H2+, LiH, HeH+) is investigated by searching for spectral lines produced by resonant scattering of the cosmic microwave background (CMB). During the summer of 2004, Odin performed a spectral scan (547-578 GHz, 1 MHz resolution) towards two Wilkinson Microwave Anisotropy Probe CMB Hot Spots using 350 orbits (5 orbits per LO setting and point). No lines were detected down to an rms level of 65 mK. A new observing strategy was developed for a second observing session (430 orbits) during the winter of 2006/7 to accommodate for the spatial uncertainty of primordial clouds. The spectral range is 486.5-492.0 and 542.0-547.5 GHz (10 orbits per LO setting and point, 1 MHz resolution yielding an rms of about 30 mK). Analysis of these data is ongoing. This is a pilot programme for GTO time on ESA's Herschel Space Observatory, planned for launch in late 2008.

  19. Information theory, atoms in molecules, and molecular similarity

    PubMed Central

    Nalewajski, Roman F.; Parr, Robert G.

    2000-01-01

    Using information theory, it is argued that from among possible definitions of what an atom is when it is in a molecule, a particular one merits special attention. Namely, it is the atom defined by the stockholders partitioning of a molecule invented by Hirshfeld [(1977) Theor. Chim. Acta 44, 129]. The theoretical tool used is the minimum entropy deficiency principle (minimum missing information principle) of Kullback and Liebler [(1951) Ann. Math. Stat. 22, 79]. A corresponding analysis is given of the problem of assessing similarity between molecules or pieces of molecules. PMID:10922049

  20. The long pentraxin PTX3: a paradigm for humoral pattern recognition molecules.

    PubMed

    Mantovani, Alberto; Valentino, Sonia; Gentile, Stefania; Inforzato, Antonio; Bottazzi, Barbara; Garlanda, Cecilia

    2013-05-01

    Pattern recognition molecules (PRMs) are components of the humoral arm of innate immunity; they recognize pathogen-associated molecular patterns (PAMP) and are functional ancestors of antibodies, promoting complement activation, opsonization, and agglutination. In addition, several PRMs have a regulatory function on inflammation. Pentraxins are a family of evolutionarily conserved PRMs characterized by a cyclic multimeric structure. On the basis of structure, pentraxins have been operationally divided into short and long families. C-reactive protein (CRP) and serum amyloid P component are prototypes of the short pentraxin family, while pentraxin 3 (PTX3) is a prototype of the long pentraxins. PTX3 is produced by somatic and immune cells in response to proinflammatory stimuli and Toll-like receptor engagement, and it interacts with several ligands and exerts multifunctional properties. Unlike CRP, PTX3 gene organization and regulation have been conserved in evolution, thus allowing its pathophysiological roles to be evaluated in genetically modified animals. Here we will briefly review the general properties of CRP and PTX3 as prototypes of short and long pentraxins, respectively, emphasizing in particular the functional role of PTX3 as a prototypic PRM with antibody-like properties. PMID:23527487

  1. Elements of the theory of molecular spectra. [multiatomic molecules

    NASA Technical Reports Server (NTRS)

    Gribov, L. A.

    1979-01-01

    The basic aspects of the theory concerning the spectra of multiatomic molecules are presented. The classification of the forms of motions in a molecule, the methods for determining the corresponding Schroudinger levels, the spectral types and the selection rules are discussed in order to identify their presence and state in outer space.

  2. Speckle Patterns with Atomic and Molecular de Broglie Waves

    SciTech Connect

    Patton, Forest S.; Deponte, Daniel P.; Kevan, Stephen D.; Elliott, Greg S.

    2006-07-07

    We have developed a nozzle source that delivers a continuous beam of atomic helium or molecular hydrogen having a high degree of transverse coherence and with adequate optical brightness to enable new kinds of experiments. Using this source we have measured single slit diffraction patterns and the first ever speckle-diffraction patterns using atomic and molecular de Broglie waves. Our results suggest fruitful application of coherent matter beams in dynamic scattering and diffractive imaging at short wavelength and with extreme surface sensitivity.

  3. Organic molecules as chemical fossils - The molecular fossil record

    NASA Technical Reports Server (NTRS)

    Eglinton, G.

    1983-01-01

    The study of biochemical clues to the early earth and the origin of life is discussed. The methods used in such investigation are described, including the extraction, fractionation, and analysis of geolipids and the analysis of kerogen. The occurrence of molecular fossils in the geological record is examined, discussing proposed precursor-product relationships and the molecular assessment of deep sea sediments, ancient sediments, and crude petroleums. Alterations in the molecular record due to diagenesis and catagenesis are considered, and the use of microbial lipids as molecular fossils is discussed. The results of searches for molecular fossils in Precambrian sediments are assessed.

  4. Alignment and Patterning of Ordered Small-Molecule Organic Semiconductor Micro-/Nanocrystals for Device Applications.

    PubMed

    Zhang, Xiujuan; Jie, Jiansheng; Deng, Wei; Shang, Qixun; Wang, Jincheng; Wang, Hui; Chen, Xianfeng; Zhang, Xiaohong

    2016-04-01

    Large-area alignment and patterning of small-molecule organic semiconductor micro-/nanocrystals (SMOSNs) at desired locations is a prerequisite for their practical device applications. Recent strategies for alignment and patterning of ordered SMOSNs and their corresponding device applications are highlighted. PMID:26813697

  5. Time-Resolved Molecular Frame Dynamics of Fixed-in-Space CS2 Molecules

    SciTech Connect

    Bisgaard, Christer; Clarkin, Owen; Wu, Guorong; Lee, Anthony; Gessner, Oliver; Hayden, Carl; Stolow, Albert

    2009-04-02

    Random orientation of molecules within a sample leads to blurred observationsof chemical reactions studied from the laboratory perspective. Methodsdeveloped for the dynamic imaging of molecular structures and processesstruggle with this, as measurements are optimally made in the molecular frame.Here we uselaser alignment to transiently fix CS2 molecules in space longenough to elucidate, in the molecular reference frame, details of ultrafast electronic vibrationaldynamics during a photochemical reaction. These three-dimensional photoelectron imaging results, combined with ongoing efforts in molecular alignment and orientation, presage a wide range of insights obtainable fromtime-resolved studies in the molecular frame.

  6. Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules.

    PubMed

    Schweitzer, Mary Higby; Zheng, Wenxia; Cleland, Timothy P; Bern, Marshall

    2013-01-01

    The discovery of soft, transparent microstructures in dinosaur bone consistent in morphology with osteocytes was controversial. We hypothesize that, if original, these microstructures will have molecular features in common with extant osteocytes. We present immunological and mass spectrometry evidence for preservation of proteins comprising extant osteocytes (Actin, Tubulin, PHEX, Histone H4) in osteocytes recovered from two non-avian dinosaurs. Furthermore, antibodies to DNA show localized binding to these microstructures, which also react positively with DNA intercalating stains propidium iodide (PI) and 4',6'-diamidino-2-phenylindole dihydrochloride (DAPI). Each antibody binds dinosaur cells in patterns similar to extant cells. These data are the first to support preservation of multiple proteins and to present multiple lines of evidence for material consistent with DNA in dinosaurs, supporting the hypothesis that these structures were part of the once living animals. We propose mechanisms for preservation of cells and component molecules, and discuss implications for dinosaurian cellular biology. PMID:23085295

  7. Resonant excitation of trapped molecules in a molecular synchrotron

    NASA Astrophysics Data System (ADS)

    Zieger, Peter C.; Eyles, Chris J.; Meijer, Gerard; Bethlem, Hendrick L.

    2013-04-01

    We characterize a synchrotron for polar molecules that consists of forty straight hexapoles arranged in a circle. By modulating either the voltages or the duration of the high-voltage pulses that are applied to the hexapoles, we shake the transverse and longitudinal well. If the frequency of the modulation matches a characteristic frequency of a stored molecule, the amplitude of the motion is resonantly excited, leading to a decrease in the number of molecules that are stored. From this, we determine the longitudinal, vertical, and radial frequencies that characterize the motion of the molecules inside the synchrotron and obtain knowledge about the couplings between the longitidinal and transverse motion. The measured frequencies are in good agreement with those obtained from three-dimensional trajectory calculations.

  8. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    SciTech Connect

    Iancu, Violeta

    2006-08-01

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  9. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  10. Chains of quantum dot molecules grown on Si surface pre-patterned by ion-assisted nanoimprint lithography

    SciTech Connect

    Smagina, Zh. V.; Stepina, N. P. Zinovyev, V. A.; Kuchinskaya, P. A.; Novikov, P. L.; Dvurechenskii, A. V.

    2014-10-13

    An original approach based on the combination of nanoimprint lithography and ion irradiation through mask has been developed for fabrication of large-area periodical pattern on Si(100). Using the selective etching of regions amorphized by ion irradiation ordered structures with grooves and ridges were obtained. The shape and depth of the relief were governed by ion energy and by the number of etching stages as well. Laterally ordered chains of Ge quantum dots were fabricated by molecular beam epitaxy of Ge on the pre-patterned Si substrates. For small amount of Ge deposited chains contain separate quantum dot molecules. The increase of deposition amount leads to overlapping of quantum dot molecules with formation of dense homogeneous chains of quantum dots. It was shown that the residual irradiation-induced bulk defects underneath the grooves suppress nucleation of Ge islands at the bottom of grooves. On pre-patterned substrates with whole defect regions, etched quantum dots grow at the bottom of grooves. The observed location of Ge quantum dots is interpreted in terms of local strain-mediated surface chemical potential which controls the sites of islands nucleation. The local chemical potential is affected by additional strain formed by the residual defects. It was shown by molecular dynamics calculations that these defects form the compressive strain at the bottom of grooves.

  11. Three-dimensional molecular modeling with single molecule FRET.

    PubMed

    Brunger, Axel T; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R

    2011-03-01

    Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes. PMID:20837146

  12. Three-dimensional Molecular Modeling with Single Molecule FRET

    PubMed Central

    Brunger, Axel T.; Strop, Pavel; Vrljic, Marija; Chu, Steven; Weninger, Keith R.

    2011-01-01

    Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes. PMID:20837146

  13. Complexity of Danger: The Diverse Nature of Damage-associated Molecular Patterns*

    PubMed Central

    Schaefer, Liliana

    2014-01-01

    In reply to internal or external danger stimuli, the body orchestrates an inflammatory response. The endogenous triggers of this process are the damage-associated molecular patterns (DAMPs). DAMPs represent a heterogeneous group of molecules that draw their origin either from inside the various compartments of the cell or from the extracellular space. Following interaction with pattern recognition receptors in cross-talk with various non-immune receptors, DAMPs determine the downstream signaling outcome of septic and aseptic inflammatory responses. In this review, the diverse nature, structural characteristics, and signaling pathways elicited by DAMPs will be critically evaluated. PMID:25391648

  14. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

    NASA Astrophysics Data System (ADS)

    Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

    2015-11-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods.

  15. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

    PubMed Central

    Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

    2015-01-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

  16. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection.

    PubMed

    Zheng, Yuanhui; Soeriyadi, Alexander H; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J

    2015-01-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

  17. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale.

    PubMed

    Juette, Manuel F; Terry, Daniel S; Wasserman, Michael R; Altman, Roger B; Zhou, Zhou; Zhao, Hong; Blanchard, Scott C

    2016-04-01

    Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis. PMID:26878382

  18. A Novel Pictorial Approach to Teaching Molecular Motions in Polyatomic Molecules.

    ERIC Educational Resources Information Center

    Verkade, John G.

    1987-01-01

    Describes a procedure for teaching the "generator orbital" (GO) approach of molecular orbital bonding in polyatomic molecules. Explains how the GO can be utilized with students in generating the vibrational, rotational, and translational modes of molecules in a completely pictorial manner. (ML)

  19. The Virtual Museum of Minerals and Molecules: Molecular Visualization in a Virtual Hands-On Museum

    ERIC Educational Resources Information Center

    Barak, Phillip; Nater, Edward A.

    2005-01-01

    The Virtual Museum of Minerals and Molecules (VMMM) is a web-based resource presenting interactive, 3-D, research-grade molecular models of more than 150 minerals and molecules of interest to chemical, earth, plant, and environmental sciences. User interactivity with the 3-D display allows models to be rotated, zoomed, and specific regions of

  20. The Virtual Museum of Minerals and Molecules: Molecular Visualization in a Virtual Hands-On Museum

    ERIC Educational Resources Information Center

    Barak, Phillip; Nater, Edward A.

    2005-01-01

    The Virtual Museum of Minerals and Molecules (VMMM) is a web-based resource presenting interactive, 3-D, research-grade molecular models of more than 150 minerals and molecules of interest to chemical, earth, plant, and environmental sciences. User interactivity with the 3-D display allows models to be rotated, zoomed, and specific regions of…

  1. Molecular polarizability in quantum defect theory: polar molecules

    SciTech Connect

    Akindinova, E. V.; Chernov, V. E.; Kretinin, I. Yu.; Zon, B. A.

    2010-04-15

    The reduced-added Green's function technique in the quantum defect theory combines the advantages of analytical and ab initio methods in calculating frequency-dependent (dynamic) polarizabilities of atoms and molecules, providing an exact account for the high-excited and continuum electronic states. In the present paper this technique is modified to take into account the long-range dipole potential of a polar molecule core. The method developed is applied to calculation of the dynamic polarizability tensors of alkali-metal hydrides LiH and NaH as well as to some fluorides (CaF and BF) in the frequency range up to the first resonances. The results are in good agreement with ab initio calculations available for some frequencies.

  2. Laser Induced Molecular Spectroscopy of Zn{sub 2} Molecule

    SciTech Connect

    Singh, Subhash C.; Gopal, Ram

    2008-11-14

    Laser produced spectra of zinc molecule have been recorded in the region of 540-670 nm using second harmonics of Nd: YAG laser, computer--controlled TRIAX 320 M monochromator with a reciprocal linear dispersion 2.64 nm/mm fitted with ICCD detector. The spectrum consists of 35 bands, which are classified into D ({sup 1} product {sub u}){yields}A({sup 3} product {sub g}) and C ({sup 1}{sigma}{sub u}{sup +}){yields}A({sup 3} product {sub g}) systems. We have recorded the florescence spectrum of zinc dimer by pumping and probing with the same laser, which proves that produced molecules are stable for more than 0.1 seconds.

  3. Role of hydrogen interaction in two-dimensional molecular packing with strong molecule-substrate bonding

    SciTech Connect

    Langlais, V.; Torrelles, X.; Gauthier, Y.; De Santis, M.

    2007-07-15

    Calixarene molecules deposited on Au(110) self-organize giving rise to a (19x6) coincidence cell with the substrate. Using grazing incidence x-ray diffraction, the structure has been completely resolved: gold reconstructs with a (1x3) missing-row structure while the molecules form a (19/6x6) surface cell containing two molecules. This study opens perspectives to create long-range ordered molecular templates to be used as receptors for other species providing an example of collaborative self-arrangement through a metallic substrate acting as guide and molecular flexibility.

  4. Are Molecular Vibration Patterns of Cell Structural Elements Used for Intracellular Signalling?

    PubMed Central

    Jaross, Werner

    2016-01-01

    Background: To date the manner in which information reaches the nucleus on that part within the three-dimensional structure where specific restorative processes of structural components of the cell are required is unknown. The soluble signalling molecules generated in the course of destructive and restorative processes communicate only as needed. Hypothesis: All molecules show temperature-dependent molecular vibration creating a radiation in the infrared region. Each molecule species has in its turn a specific frequency pattern under given specific conditions. Changes in their structural composition result in modified frequency patterns of the molecules in question. The main structural elements of the cell membrane, of the endoplasmic reticulum, of the Golgi apparatus, and of the different microsomes representing the great variety of polar lipids show characteristic frequency patterns with peaks in the region characterised by low water absorption. These structural elements are very dynamic, mainly caused by the creation of signal molecules and transport containers. By means of the characteristic radiation, the area where repair or substitution services are needed could be identified; this spatial information complements the signalling of the soluble signal molecules. Based on their resonance properties receptors located on the outer leaflet of the nuclear envelope should be able to read typical frequencies and pass them into the nucleus. Clearly this physical signalling must be blocked by the cell membrane to obviate the flow of information into adjacent cells. Conclusion: If the hypothesis can be proved experimentally, it should be possible to identify and verify characteristic infrared frequency patterns. The application of these signal frequencies onto cells would open entirely new possibilities in medicine and all biological disciplines specifically to influence cell growth and metabolism. Similar to this intracellular system, an extracellular signalling system with many new therapeutic options has to be discussed. PMID:27073582

  5. Selective inner-valence ionization of aligned polyatomic molecules for controlling molecular fragmentation

    NASA Astrophysics Data System (ADS)

    Xie, X.; Doblhoff-Dier, K.; Xu, H.; Roither, S.; Iwasaki, A.; Schöffler, M.; Kartashov, D.; Yamanouchi, K.; Baltuška, A.; Gräfe, S.; Kitzler, M.

    2014-04-01

    We show experimentally and theoretically, using acetylene as an example, that the strong preponderance of ionization from specific molecular orbitals to the alignment of the molecular axis with respect to the laser polarization direction allows implementing a method for controlling fragmentation reactions of polyatomic molecules.

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

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René Kumar, Avijit; Zandvliet, Harold J. W.; Geskin, Victor

    2014-01-01

    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.

  7. Evidence on single-molecule transport in electrostatically-gated molecular transistors

    NASA Astrophysics Data System (ADS)

    Bldea, Ioan; Kppel, Horst

    2012-03-01

    We show that, if adequately formulated for molecular electronics, the barrier picture can quantitatively reproduce the currents and describe the orbital gating in the molecular transistors fabricated by Song et al. [H. Song, Y. Kim, Y.H. Jang, H. Jeong, M.A. Reed, T. Lee, Nature 462 (2009) 1039]. Based on our results, we demonstrate (i) that the measured current represents the contribution of a single molecule, and (ii) the linear dependence of the molecular orbital energy offset ?g on the voltage Vt at the Fowler-Nordheim minimum, validating thereby the transition voltage spectroscopy for the gated single molecule devices of Song et al.

  8. Molecular assembly of highly symmetric molecules under a hydrogen bond framework controlled by alkyl building blocks: a simple approach to fine-tune nanoscale structures.

    PubMed

    Tanphibal, Pimsai; Tashiro, Kohji; Chirachanchai, Suwabun

    2016-01-14

    To date, molecular assemblies under the contribution of hydrogen bond in combination with weak interactions and their consequent morphologies have been variously reported; however, how the systematic variation of the structure can fine-tune the morphologies has not yet been answered. The present work finds an answer through highly symmetric molecules, i.e. diamine-based benzoxazine dimers. This type of molecule develops unique molecular assemblies with their networks formed by hydrogen bonds at the terminal, while, at the same time, their hydrogen bonded frameworks are further controlled by the hydrophobic segment at the center of the molecule. When this happens, slight differences in hydrophobic alkyl chain lengths (, , and ) bring a significant change to the molecular assemblies, thus resulting in tunable morphologies, i.e. spheres, needles and dendrites. The superimposition between the crystal lattice obtained from X-ray single crystal analysis and the electron diffraction pattern obtained from transmission electron microscopy allows us to identify the molecular alignment from single molecules to self-assembly until the morphologies developed. The present work, for the first time, shows the case of symmetric molecules, where the hydrophobic building block controls the hydrogen bond patterns, leading to the variation of molecular assemblies with tunable morphologies. PMID:26482133

  9. Metagenes and molecular pattern discovery using matrix factorization.

    PubMed

    Brunet, Jean-Philippe; Tamayo, Pablo; Golub, Todd R; Mesirov, Jill P

    2004-03-23

    We describe here the use of nonnegative matrix factorization (NMF), an algorithm based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to a handful of metagenes. Coupled with a model selection mechanism, adapted to work for any stochastic clustering algorithm, NMF is an efficient method for identification of distinct molecular patterns and provides a powerful method for class discovery. We demonstrate the ability of NMF to recover meaningful biological information from cancer-related microarray data. NMF appears to have advantages over other methods such as hierarchical clustering or self-organizing maps. We found it less sensitive to a priori selection of genes or initial conditions and able to detect alternative or context-dependent patterns of gene expression in complex biological systems. This ability, similar to semantic polysemy in text, provides a general method for robust molecular pattern discovery. PMID:15016911

  10. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations.

    PubMed

    Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F

    2016-04-13

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. PMID:26953616

  11. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  12. Tracking molecular resonance forms of donor-acceptor push-pull molecules by single-molecule conductance experiments.

    PubMed

    Lissau, Henriette; Frisenda, Riccardo; Olsen, Stine T; Jevric, Martyn; Parker, Christian R; Kadziola, Anders; Hansen, Thorsten; van der Zant, Herre S J; Brøndsted Nielsen, Mogens; Mikkelsen, Kurt V

    2015-01-01

    The ability of molecules to change colour on account of changes in solvent polarity is known as solvatochromism and used spectroscopically to characterize charge-transfer transitions in donor-acceptor molecules. Here we report that donor-acceptor-substituted molecular wires also exhibit distinct properties in single-molecule electronics under the influence of a bias voltage, but in absence of solvent. Two oligo(phenyleneethynylene) wires with donor-acceptor substitution on the central ring (cruciform-like) exhibit remarkably broad conductance peaks measured by the mechanically controlled break-junction technique with gold contacts, in contrast to the sharp peak of simpler molecules. From a theoretical analysis, we explain this by different degrees of charge delocalization and hence cross-conjugation at the central ring. Thus, small variations in the local environment promote the quinoid resonance form (off), the linearly conjugated (on) or any form in between. This shows how the conductance of donor-acceptor cruciforms is tuned by small changes in the environment. PMID:26667583

  13. Tracking molecular resonance forms of donor–acceptor push–pull molecules by single-molecule conductance experiments

    PubMed Central

    Lissau, Henriette; Frisenda, Riccardo; Olsen, Stine T.; Jevric, Martyn; Parker, Christian R.; Kadziola, Anders; Hansen, Thorsten; van der Zant, Herre S. J.; Brøndsted Nielsen, Mogens; Mikkelsen, Kurt V.

    2015-01-01

    The ability of molecules to change colour on account of changes in solvent polarity is known as solvatochromism and used spectroscopically to characterize charge-transfer transitions in donor–acceptor molecules. Here we report that donor–acceptor-substituted molecular wires also exhibit distinct properties in single-molecule electronics under the influence of a bias voltage, but in absence of solvent. Two oligo(phenyleneethynylene) wires with donor–acceptor substitution on the central ring (cruciform-like) exhibit remarkably broad conductance peaks measured by the mechanically controlled break-junction technique with gold contacts, in contrast to the sharp peak of simpler molecules. From a theoretical analysis, we explain this by different degrees of charge delocalization and hence cross-conjugation at the central ring. Thus, small variations in the local environment promote the quinoid resonance form (off), the linearly conjugated (on) or any form in between. This shows how the conductance of donor–acceptor cruciforms is tuned by small changes in the environment. PMID:26667583

  14. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

    NASA Astrophysics Data System (ADS)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  15. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    PubMed

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules. PMID:26156491

  16. Microbes, molecular mimicry and molecules of mood and motivation.

    PubMed

    Morris, J A; Broughton, S J; Wessels, Q

    2016-02-01

    The hypothesis proposed is that functional disorders, such as irritable bowel syndrome, chronic fatigue syndrome and anorexia nervosa are caused by auto-antibodies to neuronal proteins induced by molecular mimicry with microbial antigens. The age incidence of these conditions, the marked female excess, increase with economic and technological advance, precipitation by infection, and the paucity of histological changes are all consistent with the hypothesis. It can be tested directly using human sera to search for cross reaction with brain proteins in model systems such as Drosophila melanogaster. The conditions might be amenable to treatment using pooled immunoglobulin. Identification and elimination from the microbial flora of the bacteria that express the cross reacting antigens should be possible. PMID:26826639

  17. MoFlow: visualizing conformational changes in molecules as molecular flow improves understanding

    PubMed Central

    2015-01-01

    Background Current visualizations of molecular motion use a Timeline-analogous representation that conveys "first the molecule was shaped like this, then like this...". This scheme is orthogonal to the Pathline-like human understanding of motion "this part of the molecule moved from here to here along this path". We present MoFlow, a system for visualizing molecular motion using a Pathline-analogous representation. Results The MoFlow system produces high-quality renderings of molecular motion as atom pathlines, as well as interactive WebGL visualizations, and 3D printable models. In a preliminary user study, MoFlow representations are shown to be superior to canonical representations for conveying molecular motion. Conclusions Pathline-based representations of molecular motion are more easily understood than timeline representations. Pathline representations provide other advantages because they represent motion directly, rather than representing structure with inferred motion. PMID:26361501

  18. Conventional, molecular methods and biomarkers molecules in detection of septicemia

    PubMed Central

    Arabestani, Mohammad Reza; Rastiany, Sahar; Kazemi, Sima; Mousavi, Seyed Masoud

    2015-01-01

    Sepsis is a leading cause of morbidity and mortality in hospitalized patients worldwide and based on studies, 30–40% of all cases of severe sepsis and septic shock results from the blood stream infections (BSIs). Identifying of the disease, performing laboratory tests, and consequently treatment are factors that required for optimum management of BSIs. In addition, applying precise and immediate identification of the etiologic agent is a prerequisite for specific antibiotic therapy of pathogen and thereby decreasing mortality rates. The diagnosis of sepsis is difficult because clinical signs of sepsis often overlap with other noninfectious cases of systemic inflammation. BSIs are usually diagnosed by performing a series of techniques such as blood cultures, polymerase chain reaction-based methods, and biomarkers of sepsis. Extremely time-consuming even to take up to several days is a major limitation of conventional methods. In addition, yielding false-negative results due to fastidious and slow-growing microorganisms and also in case of antibiotic pretreated samples are other limitations. In comparison, molecular methods are capable of examining a blood sample obtained from suspicious patient with BSI and gave the all required information to prescribing antimicrobial therapy for detected bacterial or fungal infections immediately. Because of an emergency of sepsis, new methods are being developed. In this review, we discussed about the most important sepsis diagnostic methods and numbered the advantage and disadvantage of the methods in detail. PMID:26261822

  19. Molecular properties from conformational ensembles. 1. Dipole moments of molecules with multiple internal rotations.

    PubMed

    Lavy, Tal; Harries, Daniel; Goldblum, Amiram

    2011-06-16

    We present a novel method for constructing the stable conformational space of small molecules with many rotatable bonds that uses our iterative stochastic elimination (ISE) algorithm, a robust stochastic search method capable of finding ensembles of best solutions for large combinatorial problems. To validate the method, we show that ISE reproduces the best conformers found in a fully exhaustive search, as well as compare computed dipole moments to experimental values, based on molecular ensembles and their Boltzmann distributions. Results were also compared to the alternative molecular dynamics and simulated annealing methods. Our results clarify that many low energy conformations may be required to reproduce molecular properties, while single low energy conformers or ensembles of low energy conformers cannot account for the experimental properties of flexible molecules. Whereas ISE well reproduces conformations that are not separated by very large energy barriers, it has not been successful in reproducing conformations of strained molecules. PMID:21210653

  20. Origins of entropy change for the amphiphilic molecule in micellization: a molecular dynamics study.

    PubMed

    Liu, Guokui; Wei, Yaoyao; Gao, Fengfeng; Yuan, Shiling; Liu, Chengbu

    2016-04-20

    The micellization of amphiphilic molecules is an important phenomenon in the natural world. However, the origin of entropy change during micellization is still unclear. Molecular dynamics simulation was applied to study configurational entropy change of amphiphilic molecules in micellization. The entropy change of polar heads, hydrophobic chains, vibration, translation and rotation are discussed. Analyses provide a clear physical picture of the entropy increase in micellization, and thus foundations for further study. PMID:27056091

  1. Millimeter-Wave Spectroscopic and Collisional Studies of Molecules and Molecular Ions

    NASA Astrophysics Data System (ADS)

    Pearson, John Christoffersen

    1995-01-01

    Molecular spectroscopy in the millimeter- and submillimeter-wave regions is an important tool in molecular physics. Information on molecular motions and interactions is obtained from spectroscopic studies of energy levels and collisions. This information and the data from which it is derived are essential in remote sensing of the atmosphere and the interstellar medium. Remote sensing at submillimeter wavelengths is now possible, making higher frequency and quantum number measurements of known interstellar species like water, propionitrile and ethyl alcohol necessary. Remote sensing improvements have also facilitated the need for spectral data on suspected interstellar molecules like propylene. The desire to extract quantitative information from atmospheric remote sensing has resulted in the need for a better understanding of the molecular interactions that cause pressure broadening. The use of a cold molecular ion to magnify the effects of intermolecular interactions has serious implications for pressure broadening theory. The measurement and analysis of rotational spectra of the asymmetric rotors water and propionitrile and the internal rotors propylene and ethyl alcohol are presented. These investigations provide the data and analysis necessary for astronomical observation. The ethyl alcohol investigation is the first experimental millimeter-wave study of a molecule with an asymmetric internal rotor. This study provides the data necessary for detailed theoretical modeling of this type of problem. A novel new experimental technique for generating and studying molecular ions is presented. The first temperature dependent microwave pressure broadening study of a molecular ion colliding with a neutral molecule, HCO^{+} on H_2 , is presented.

  2. Molecular level studies on binding modes of labeling molecules with polyalanine peptides

    NASA Astrophysics Data System (ADS)

    Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen

    2011-04-01

    In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00782j

  3. Laser Field Alignment of Organic Molecules on Semiconductor Surfaces: Toward Ultrafast Molecular Switches

    SciTech Connect

    Reuter, Matthew G.; Sukharev, Maxim; Seideman, Tamar

    2008-11-14

    An ultrafast, nanoscale molecular switch is proposed, based on extension of the concept of nonadiabatic alignment to surface-adsorbed molecules. The switch consists of a conjugated organic molecule adsorbed onto a semiconducting surface and placed near a scanning tunneling microscope tip. A low-frequency, polarized laser field is used to switch the system by orienting the molecule with the field polarization axis, enabling conductance through the junction. Enhancement and spatial localization of the incident field by the metallic tip allow operation at low intensities. The principles of nonadiabatic alignment lead to switch on and off time scales far below rotational time scales.

  4. A quantum mechanical/molecular mechanical approach to the investigation of particle-molecule interactions

    NASA Astrophysics Data System (ADS)

    Sloth, Marianne; Bilde, Merete; Mikkelsen, Kurt V.

    2003-06-01

    A quantum mechanical/molecular mechanical aerosol model is developed to describe the interaction between gas phase molecules and atmospheric particles. The model enables the calculation of interaction energies and time-dependent properties. We use the model to investigate how a succinic acid molecule interacts with an aqueous particle. We show how the interaction energies and linear response properties (excitation energies, transition moments, and polarizabilities) depend on the distance between aerosol particle and molecule and on their relative orientation. The results are compared with those obtained previously using a dielectric continuum model [Sloth et al., J. Phys. Chem. (submitted)].

  5. Super-Resolution Imaging of Molecular Emission Spectra and Single Molecule Spectral Fluctuations

    PubMed Central

    Mlodzianoski, Michael J.; Curthoys, Nikki M.; Gunewardene, Mudalige S.; Carter, Sean; Hess, Samuel T.

    2016-01-01

    Localization microscopy can image nanoscale cellular details. To address biological questions, the ability to distinguish multiple molecular species simultaneously is invaluable. Here, we present a new version of fluorescence photoactivation localization microscopy (FPALM) which detects the emission spectrum of each localized molecule, and can quantify changes in emission spectrum of individual molecules over time. This information can allow for a dramatic increase in the number of different species simultaneously imaged in a sample, and can create super-resolution maps showing how single molecule emission spectra vary with position and time in a sample. PMID:27002724

  6. Paramagnetic molecule induced strong antiferromagnetic exchange coupling on a magnetic tunnel junction based molecular spintronics device

    NASA Astrophysics Data System (ADS)

    Tyagi, Pawan; Baker, Collin; D'Angelo, Christopher

    2015-07-01

    This paper reports our Monte Carlo (MC) studies aiming to explain the experimentally observed paramagnetic molecule induced antiferromagnetic coupling between ferromagnetic (FM) electrodes. Recently developed magnetic tunnel junction based molecular spintronics devices (MTJMSDs) were prepared by chemically bonding the paramagnetic molecules between the FM electrodes along the tunnel junction’s perimeter. These MTJMSDs exhibited molecule-induced strong antiferromagnetic coupling. We simulated the 3D atomic model analogous to the MTJMSD and studied the effect of molecule’s magnetic couplings with the two FM electrodes. Simulations show that when a molecule established ferromagnetic coupling with one electrode and antiferromagnetic coupling with the other electrode, then theoretical results effectively explained the experimental findings. Our studies suggest that in order to align MTJMSDs’ electrodes antiparallel to each other, the exchange coupling strength between a molecule and FM electrodes should be ˜50% of the interatomic exchange coupling for the FM electrodes.

  7. Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

    NASA Technical Reports Server (NTRS)

    Han, Jie

    2001-01-01

    Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

  8. Dynamic expression patterns of ECM molecules in the developing mouse olfactory pathway

    PubMed Central

    Shay, Elaine L.; Greer, Charles A.; Treloar, Helen B.

    2009-01-01

    Olfactory sensory neuron (OSN) axons follow stereotypic spatio-temporal paths in the establishment of the olfactory pathway. Extracellular matrix (ECM) molecules are expressed early in the developing pathway and are proposed to have a role in its initial establishment. During later embryonic development, OSNs sort out and target specific glomeruli to form precise, complex topographic projections. We hypothesized that ECM cues may help to establish this complex topography. The aim of this study was to characterize expression of ECM molecules during the period of glomerulogenesis, when synaptic contacts are forming. We examined expression of laminin-1, perlecan, tenascin-C and CSPGs and found a coordinated pattern of expression of these cues in the pathway. These appear to restrict axons to the pathway while promoting axon outgrowth within. Thus, ECM molecules are present in dynamic spatio-temporal positions to affect OSN axons as they navigate to the olfactory bulb and establish synapses. PMID:18570250

  9. A molecular full-adder and full-subtractor, an additional step toward a moleculator.

    PubMed

    Margulies, David; Melman, Galina; Shanzer, Abraham

    2006-04-12

    Over the past decade, there has been remarkable progress in the development of molecular logic and arithmetic systems, which has brought chemists closer to the realization of a molecular scale calculator (a Moleculator). This paper describes a significant step in this direction. By integrating past and new approaches for molecular logic reconfiguration, we were able to load advanced arithmetic calculations onto a single molecular species. Exchanging chemical inputs, monitoring at several wavelengths simultaneously, as well as using negative logic for the transmittance mode significantly increase the input and output information channels of the processing molecule. Changing the initial state of the processor is an additional approach used for altering the logical output of the device. Finally, introducing degeneracy to the chemical inputs or, alternatively, controlling their interactions to form identical chemical states minimizes the complexity of realizing three-bits addition and subtraction at the molecular scale. Consequently, using a commercially available fluorescein molecule, acid and base chemical inputs, and a simple UV-vis measurement setup, integration of a full-adder and, for the first time, a full-subtractor is now possible within individual molecules. PMID:16594723

  10. A new graph-based molecular descriptor using the canonical representation of the molecule.

    PubMed

    Hentabli, Hamza; Saeed, Faisal; Abdo, Ammar; Salim, Naomie

    2014-01-01

    Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried. PMID:25140330

  11. A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule

    PubMed Central

    Hentabli, Hamza; Abdo, Ammar; Salim, Naomie

    2014-01-01

    Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried. PMID:25140330

  12. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies.

    PubMed

    Dauga, Catherine

    2002-03-01

    Phylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships. PMID:11931166

  13. Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Technical report, January 1990--December 1990

    SciTech Connect

    1997-07-01

    The objective of our effort is to carry out theoretical studies of resonance enhanced multiphoton ionization processes in molecules and molecular fragments. These studies are designed to provide a quantitatively robust analysis and prediction of key spectral features of interest in several ongoing experimental studies and applications of this technique.

  14. Molecular isomerization and fragmentation of polyatomic molecules controlled by inner-valence recollision-ionization

    NASA Astrophysics Data System (ADS)

    Xie, X.; Doblhoff-Dier, K.; Roither, S.; Schöffler, M.; Kartashov, D.; Xu, H.; Rathje, T.; Paulus, G. G.; Baltuška, A.; Gräfe, S.; Kitzler, M.

    2014-04-01

    Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets.

  15. Tris-thiourea tripodal-based molecules as chloride transmembrane transporters: insights from molecular dynamics simulations.

    PubMed

    Marques, Igor; Colaço, Ana R; Costa, Paulo J; Busschaert, Nathalie; Gale, Philip A; Félix, Vítor

    2014-05-28

    The interaction of six tripodal synthetic chloride transmembrane transporters with a POPC bilayer was investigated by means of molecular dynamics simulations using the general Amber force field (GAFF) for the transporters and the LIPID11 force field for phospholipids. These transporters are structurally simple molecules, based on the tris(2-aminoethyl)amine scaffold, containing three thiourea binding units coupled with three n-butyl (1), phenyl (2), fluorophenyl (3), pentafluorophenyl (4), trifluoromethylphenyl (5), or bis(trifluoromethyl)phenyl (6) substituents. The passive diffusion of 1-6⊃ Cl(-) was evaluated with the complexes initially positioned either in the water phase or inside the bilayer. In the first scenario the chloride is released in the water solution before the synthetic molecules achieve the water-lipid interface and permeate the membrane. In the latter one, only when the chloride complex reaches the interface is the anion released to the water phase, with the transporter losing the initial ggg tripodal shape. Independently of the transporter used in the membrane system, the bilayer structure is preserved and the synthetic molecules interact with the POPC molecules at the phosphate headgroup level, via N-H···O hydrogen bonds. Overall, the molecular dynamics simulations' results indicate that the small tripodal molecules in this series have a low impact on the bilayer and are able to diffuse with chloride inside the lipid environment. Indeed, these are essential conditions for these molecules to promote the transmembrane transport as anion carriers, in agreement with experimental efflux data. PMID:24663079

  16. Renormalization of Molecular Energy Levels in Single-Molecule Nanojunctions: An Ab-initio Approach

    NASA Astrophysics Data System (ADS)

    Parashar, Sweta; Srivastava, Pankaj; Pattanaik, Manisha

    2015-02-01

    Using first-principle calculations based on Density Functional Theory (DFT) in conjunction with the Non-Equilibrium Greens Functions (NEGF) technique, we have studied the effect of electrostatic environment in molecular energy levels of single-molecule transistors. This approach is applied to three polycyclic aromatic hydrocarbons (PAHs) anthracene, tetracene and pentacene, for calculating charging energies of molecular systems weakly coupled to an electrostatic environment. The result shows renormalization of molecular energy levels in an electrostatic environment. Further, it is observed that on increasing the number of aromatic rings, the addition energy value decreases which increases the conductivity of the system. Subsequently charge stability diagram for PAHs has been obtained.

  17. Ultra high resolution molecular beam cars spectroscopy with application to planetary atmospheric molecules

    NASA Technical Reports Server (NTRS)

    Byer, R. L.

    1982-01-01

    The measurement of high resolution pulsed and continuous wave (CW) coherent anti-Stokes Raman spectroscopy (CARS) measurements in pulsed and steady state supersonic expansions were demonstrated. Pulsed molecular beam sources were characterized, and saturation of a Raman transition and, for the first time, the Raman spectrum of a complex molecular cluster were observed. The observation of CW CARS spectra in a molecular expansion and the effects of transit time broadening is described. Supersonic expansion is established as a viable technique for high resolution Raman spectroscopy of cold molecules with resolutions of 100 MH2.

  18. Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.

    PubMed

    Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W

    2003-10-01

    Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101

  19. Molecular Nanoshearing: An Innovative Approach to Shear off Molecules with AC-Induced Nanoscopic Fluid Flow

    NASA Astrophysics Data System (ADS)

    Shiddiky, Muhammad J. A.; Vaidyanathan, Ramanathan; Rauf, Sakandar; Tay, Zhikai; Trau, Matt

    2014-01-01

    Early diagnosis of disease requires highly specific measurement of molecular biomarkers from femto to pico-molar concentrations in complex biological (e.g., serum, blood, etc.) samples to provide clinically useful information. While reaching this detection limit is challenging in itself, these samples contain numerous other non-target molecules, most of which have a tendency to adhere to solid surfaces via nonspecific interactions. Herein, we present an entirely new methodology to physically displace nonspecifically bound molecules from solid surfaces by utilizing a newly discovered ``tuneable force'', induced by an applied alternating electric field, which occurs within few nanometers of an electrode surface. This methodology thus offers a unique ability to shear-off loosely bound molecules from the solid/liquid interface. Via this approach, we achieved a 5-fold reduction in nonspecific adsorption of non-target protein molecules and a 1000-fold enhancement for the specific capture of HER2 protein in human serum.

  20. Observation of CS Trilobite Molecules with Kilo-Debye Molecular Frame Permanent Electric Dipole Moments

    NASA Astrophysics Data System (ADS)

    Shaffer, James P.

    2015-06-01

    We present results on Cs ultracold Rydberg atom experiments involving trilobite and butterfly molecules. Trilobite molecules are predicted to have giant, body-fixed permanent dipole moments, on the order of 1000 Debye. We present spectra for nS1/2+6S1/2 ^3σ^+ molecules, where n=37, 39 and 40, and measurements of the Stark broadenings of selected trilobite states in Cs due to the application of a constant external electric field. These results show that for Cs, because of its near integer s-state quantum defect, it is possible to photoassociate molecules whose wavefunction is predominantly of trilobite character yielding molecular frame dipole moments of around 2000 Debye. In addition, we have also recently observed states whose spectra show characteristics of p-wave dominated butterfly states. The work on what we believe to be the butterfly states will be compared and contrasted to the measurements of the trilobite states.

  1. Energy-Level Related Nuclear-Spin Effects and Super-Hyperfine Spectral Patterns: how Molecules do Self-Nmr

    NASA Astrophysics Data System (ADS)

    Harter, William; Mitchell, Justin

    2009-06-01

    At several points in his defining works on molecular spectroscopy, Herzberg notes that ``because nuclear moments ldots are so very slight ldots transitions between species ldots are very strictly forbiddenldots '' Herzberg's most recent statement of such selection rules pertained to spherical top spin-species. It has since been shown that spherical top species (as well as those of lower symmetry molecules) converge exponentially with momentum quanta J and K to degenerate level clusters wherein even ``very slight'' nuclear fields and moments cause pervasive resonance and total spin species mixing. Ultra-high resolution spectra of Borde, et .al and Pfister et .al shows how SF_6 and SiF_4 Fluorine nuclear spin levels rearrange from total-spin multiplets to NMR-like patterns as their superfine structure converges. Similar super-hyperfine effects are anticipated for lower symmetry molecules exhibiting converging superfine level-clusters. Examples include PH_3 molecules and asymmetric tops. Following this we consider models that treat nuclear spins as coupled rotors undergoing generalized Hund-case transitions from spin-lab-momentum coupling to various spin-rotor correlations. G. A. Herzberg, Electronic Spectra of Polyatomic Molecules, (Von Norstrand Rheinhold 1966) p. 246. W G. Harter and C. W Patterson, Phys. Rev. A 19, 2277 (1979) W. G. Harter, Phys. Rev. A 24, 192 (1981). Ch. J. Borde, J. Borde, Ch. Breant, Ch. Chardonnet, A. Van Lerberghe, and Ch. Salomon, in Laser Spectroscopy VII, T. W Hensch and Y. R. Shen, eds. (Springer-Verlag, Berlin, 1985). O. Pfister, F. Guernet, G. Charton, Ch. Chardonnet, F. Herlemont, and J. Legrand, J. Opt. Soc. Am. B 10, 1521 (1993). O. Pfister, Ch. Chardonnet, and Ch. J. Bordè, Phys. Rev. Lett. 76, 4516 (1996) S. N. Yurchenko, W. Thiel, S. Patchkovskii, and P. Jensen, Phys. Chem. Chem. Phys.7, 573 (2005)

  2. Spin-split antibonding molecular ground state in manganese-doped quantum dot molecules

    NASA Astrophysics Data System (ADS)

    Qu, Fanyao; Villegas-Lelovsky, L.; Morais, P. C.

    2015-09-01

    Tunnel coupling between two dots in manganese-doped InAs/GaAs quantum dot molecules (QDMs), valence band mixing, and p -d exchange interaction between holes and localized d electrons give rise to a tunability of charge, spin, and molecular orbitals. The interplay among them determines the nature of the molecular ground state. Remarkably, unlike usual diatomic molecules in which the bonding (BD) state is always the ground state, we found that the molecular ground state in Mn-doped QDMs is of antibonding (AB) character. Furthermore, it is a spin-split state and can be switched into the spin-split BD type. We also demonstrate that this unusual behavior can be tuned by the lateral confinement strength of the QDMs, the concentration, and the distribution of manganese as well as the electric field applied along the direction of the QDM axis.

  3. Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface

    PubMed Central

    Kemmish, Kent; Hamalainen, Mark; Bowell, Charlotte; Bleloch, Andrew; Klejwa, Nathan; Lehrach, Wolfgang; Schatz, Ken; Stark, Heather; Marblestone, Adam; Church, George; Own, Christopher S.; Andregg, William

    2013-01-01

    We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers. PMID:23935923

  4. A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Kleppmann, Nicola; Klapp, Sabine H. L.

    2015-02-01

    Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase.

  5. Recognition of damage-associated molecular patterns related to nucleic acids during inflammation and vaccination

    PubMed Central

    Jounai, Nao; Kobiyama, Kouji; Takeshita, Fumihiko; Ishii, Ken J.

    2012-01-01

    All mammalian cells are equipped with large numbers of sensors for protection from various sorts of invaders, who, in turn, are equipped with molecules containing pathogen-associated molecular patterns (PAMPs). Once these sensors recognize non-self antigens containing PAMPs, various physiological responses including inflammation are induced to eliminate the pathogens. However, the host sometimes suffers from chronic infection or continuous injuries, resulting in production of self-molecules containing damage-associated molecular patterns (DAMPs). DAMPs are also responsible for the elimination of pathogens, but promiscuous recognition of DAMPs through sensors against PAMPs has been reported. Accumulation of DAMPs leads to massive inflammation and continuous production of DAMPs; that is, a vicious circle leading to the development of autoimmune disease. From a vaccinological point of view, the accurate recognition of both PAMPs and DAMPs is important for vaccine immunogenicity, because vaccine adjuvants are composed of several PAMPs and/or DAMPs, which are also associated with severe adverse events after vaccination. Here, we review as the roles of PAMPs and DAMPs upon infection with pathogens or inflammation, and the sensors responsible for recognizing them, as well as their relationship with the development of autoimmune disease or the immunogenicity of vaccines. PMID:23316484

  6. Molecular Pathways: Co-Expression of Immune Checkpoint Molecules: Signaling Pathways and Implications for Cancer Immunotherapy

    PubMed Central

    Nirschl, Christopher J.; Drake, Charles G.

    2014-01-01

    The expression of immune checkpoint molecules on T cells represents an important mechanism that the immune system uses to regulate responses to self-proteins. Checkpoint molecules include CTLA-4 (Cytotoxic T Lymphocyte Antigen-4), PD-1 (Programmed Death-1), LAG-3 (Lymphocyte Activation Gene-3), TIM-3 (T cell Immunoglobulin and Mucin protein-3) and several others. Previous studies have identified individual roles for each of these molecules, but more recent data show that co-expression of checkpoint molecules occurs frequently on cancer-specific T cells, as well as on pathogen-specific T cells in chronic infections. While the signaling pathways associated with each checkpoint molecule have not been fully elucidated, blocking multiple checkpoints with specific monoclonal antibodies results in improved outcomes in several chronic viral infections as well as in a wide array of pre-clinical models of cancer. Recent clinical data suggest similar effects in patients with metastatic melanoma. These findings support the concept that individual immune checkpoint molecules may function through non-overlapping molecular mechanisms. Here we review current data regarding immune checkpoint molecule signaling and co-expression, both in cancer and infectious disease, as well as the results of preclinical and clinical manipulations of checkpoint proteins. PMID:23868869

  7. Xylan decoration patterns and the plant secondary cell wall molecular architecture.

    PubMed

    Busse-Wicher, Marta; Grantham, Nicholas J; Lyczakowski, Jan J; Nikolovski, Nino; Dupree, Paul

    2016-02-15

    The molecular architecture of plant secondary cell walls is still not resolved. There are several proposed structures for cellulose fibrils, the main component of plant cell walls and the conformation of other molecules is even less well known. Glucuronic acid (GlcA) substitution of xylan (GUX) enzymes, in CAZy family glycosyl transferase (GT)8, decorate the xylan backbone with various specific patterns of GlcA. It was recently discovered that dicot xylan has a domain with the side chain decorations distributed on every second unit of the backbone (xylose). If the xylan backbone folds in a similar way to glucan chains in cellulose (2-fold helix), this kind of arrangement may allow the undecorated side of the xylan chain to hydrogen bond with the hydrophilic surface of cellulose microfibrils. MD simulations suggest that such interactions are energetically stable. We discuss the possible role of this xylan decoration pattern in building of the plant cell wall. PMID:26862191

  8. Microbe Associated Molecular Pattern Signaling in Guard Cells.

    PubMed

    Ye, Wenxiu; Murata, Yoshiyuki

    2016-01-01

    Stomata, formed by pairs of guard cells in the epidermis of terrestrial plants, regulate gas exchange, thus playing a critical role in plant growth and stress responses. As natural openings, stomata are exploited by microbes as an entry route. Recent studies reveal that plants close stomata upon guard cell perception of molecular signatures from microbes, microbe associated molecular patterns (MAMPs), to prevent microbe invasion. The perception of MAMPs induces signal transduction including recruitment of second messengers, such as Ca(2+) and H2O2, phosphorylation events, and change of transporter activity, leading to stomatal movement. In the present review, we summarize recent findings in signaling underlying MAMP-induced stomatal movement by comparing with other signalings. PMID:27200056

  9. Microbe Associated Molecular Pattern Signaling in Guard Cells

    PubMed Central

    Ye, Wenxiu; Murata, Yoshiyuki

    2016-01-01

    Stomata, formed by pairs of guard cells in the epidermis of terrestrial plants, regulate gas exchange, thus playing a critical role in plant growth and stress responses. As natural openings, stomata are exploited by microbes as an entry route. Recent studies reveal that plants close stomata upon guard cell perception of molecular signatures from microbes, microbe associated molecular patterns (MAMPs), to prevent microbe invasion. The perception of MAMPs induces signal transduction including recruitment of second messengers, such as Ca2+ and H2O2, phosphorylation events, and change of transporter activity, leading to stomatal movement. In the present review, we summarize recent findings in signaling underlying MAMP-induced stomatal movement by comparing with other signalings. PMID:27200056

  10. An acidic microenvironment sets the humoral pattern recognition molecule PTX3 in a tissue repair mode.

    PubMed

    Doni, Andrea; Musso, Tiziana; Morone, Diego; Bastone, Antonio; Zambelli, Vanessa; Sironi, Marina; Castagnoli, Carlotta; Cambieri, Irene; Stravalaci, Matteo; Pasqualini, Fabio; Laface, Ilaria; Valentino, Sonia; Tartari, Silvia; Ponzetta, Andrea; Maina, Virginia; Barbieri, Silvia S; Tremoli, Elena; Catapano, Alberico L; Norata, Giuseppe D; Bottazzi, Barbara; Garlanda, Cecilia; Mantovani, Alberto

    2015-06-01

    Pentraxin 3 (PTX3) is a fluid-phase pattern recognition molecule and a key component of the humoral arm of innate immunity. In four different models of tissue damage in mice, PTX3 deficiency was associated with increased fibrin deposition and persistence, and thicker clots, followed by increased collagen deposition, when compared with controls. Ptx3-deficient macrophages showed defective pericellular fibrinolysis in vitro. PTX3-bound fibrinogen/fibrin and plasminogen at acidic pH and increased plasmin-mediated fibrinolysis. The second exon-encoded N-terminal domain of PTX3 recapitulated the activity of the intact molecule. Thus, a prototypic component of humoral innate immunity, PTX3, plays a nonredundant role in the orchestration of tissue repair and remodeling. Tissue acidification resulting from metabolic adaptation during tissue repair sets PTX3 in a tissue remodeling and repair mode, suggesting that matrix and microbial recognition are common, ancestral features of the humoral arm of innate immunity. PMID:25964372

  11. An acidic microenvironment sets the humoral pattern recognition molecule PTX3 in a tissue repair mode

    PubMed Central

    Doni, Andrea; Musso, Tiziana; Morone, Diego; Bastone, Antonio; Zambelli, Vanessa; Sironi, Marina; Castagnoli, Carlotta; Cambieri, Irene; Stravalaci, Matteo; Pasqualini, Fabio; Laface, Ilaria; Valentino, Sonia; Tartari, Silvia; Ponzetta, Andrea; Maina, Virginia; Barbieri, Silvia S.; Tremoli, Elena; Catapano, Alberico L.; Norata, Giuseppe D.; Bottazzi, Barbara; Garlanda, Cecilia

    2015-01-01

    Pentraxin 3 (PTX3) is a fluid-phase pattern recognition molecule and a key component of the humoral arm of innate immunity. In four different models of tissue damage in mice, PTX3 deficiency was associated with increased fibrin deposition and persistence, and thicker clots, followed by increased collagen deposition, when compared with controls. Ptx3-deficient macrophages showed defective pericellular fibrinolysis in vitro. PTX3-bound fibrinogen/fibrin and plasminogen at acidic pH and increased plasmin-mediated fibrinolysis. The second exon-encoded N-terminal domain of PTX3 recapitulated the activity of the intact molecule. Thus, a prototypic component of humoral innate immunity, PTX3, plays a nonredundant role in the orchestration of tissue repair and remodeling. Tissue acidification resulting from metabolic adaptation during tissue repair sets PTX3 in a tissue remodeling and repair mode, suggesting that matrix and microbial recognition are common, ancestral features of the humoral arm of innate immunity. PMID:25964372

  12. Detecting differential patterns of interaction in molecular pathways

    PubMed Central

    Yajima, Masanao; Telesca, Donatello; Ji, Yuan; Müller, Peter

    2015-01-01

    We consider statistical inference for potentially heterogeneous patterns of association characterizing the expression of bio-molecular pathways across different biologic conditions. We discuss a modeling approach based on Gaussian-directed acyclic graphs and provide computational and methodological details needed for posterior inference. Our application finds motivation in reverse phase protein array data from a study on acute myeloid leukemia, where interest centers on contrasting refractory versus relapsed patients. We illustrate the proposed method through both synthetic and case study data. PMID:25519431

  13. Electron transport in asymmetric biphenyl molecular junctions: effects of conformation and molecule-electrode distance

    NASA Astrophysics Data System (ADS)

    Parashar, Sweta; Srivastava, Pankaj; Pattanaik, Manisha; Jain, Sandeep Kumar

    2014-09-01

    On the basis of ab-initio calculations, we predict the effect of conformation and molecule-electrode distance on transport properties of asymmetric molecular junctions for different electrode materials M (M = Au, Ag, Cu, and Pt). The asymmetry in these junctions is created by connecting one end of the biphenyl molecule to conjugated double thiol (model A) and single thiol (model B) groups, while the other end to Cu atom. A variety of phenomena viz. rectification, negative differential resistance (NDR), switching has been observed that can be controlled by tailoring the interface state properties through molecular conformation and molecule-electrode distance for various M. These properties are further analyzed by calculating transmission spectra, molecular orbitals, and orbital energy. It is found that Cu electrode shows significantly enhanced rectifying performance with change in torsion angles, as well as with increase in molecule-electrode distances than Au and Ag electrodes. Moreover, Pt electrode manifests distinctive multifunctional behavior combining switch, diode, and NDR. Thus, the Pt electrode is suggested to be a good potential candidate for a novel multifunctional electronic device. Our findings are compared with available experimental and theoretical results. Supplementary material in the form of one pdf file available from the Journal web page at http://http//dx.doi.org/10.1140/epjb/e2014-50133-2

  14. Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis

    PubMed Central

    Torella, Joseph P.; Holden, Seamus J.; Santoso, Yusdi; Hohlbein, Johannes; Kapanidis, Achillefs N.

    2011-01-01

    Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics. PMID:21402040

  15. Carbon Electrode-Molecule Junctions: A Reliable Platform for Molecular Electronics.

    PubMed

    Jia, Chuancheng; Ma, Bangjun; Xin, Na; Guo, Xuefeng

    2015-09-15

    The development of reliable approaches to integrate individual or a small collection of molecules into electrical nanocircuits, often termed "molecular electronics", is currently a research focus because it can not only overcome the increasing difficulties and fundamental limitations of miniaturization of current silicon-based electronic devices, but can also enable us to probe and understand the intrinsic properties of materials at the atomic- and/or molecular-length scale. This development might also lead to direct observation of novel effects and fundamental discovery of physical phenomena that are not accessible by traditional materials or approaches. Therefore, researchers from a variety of backgrounds have been devoting great effort to this objective, which has started to move beyond simple descriptions of charge transport and branch out in different directions, reflecting the interdisciplinarity. This Account exemplifies our ongoing interest and great effort in developing efficient lithographic methodologies capable of creating molecular electronic devices through the combination of top-down micro/nanofabrication with bottom-up molecular assembly. These devices use nanogapped carbon nanomaterials (such as single-walled carbon nanotubes (SWCNTs) and graphene), with a particular focus on graphene, as point contacts formed by electron beam lithography and precise oxygen plasma etching. Through robust amide linkages, functional molecular bridges terminated with diamine moieties are covalently wired into the carboxylic acid-functionalized nanogaps to form stable carbon electrode-molecule junctions with desired functionalities. At the macroscopic level, to improve the contact interface between electrodes and organic semiconductors and lower Schottky barriers, we used SWCNTs and graphene as efficient electrodes to explore the intrinsic properties of organic thin films, and then build functional high-performance organic nanotransistors with ultrahigh responsivities. At the molecular level, to form robust covalent bonds between electrodes and molecules and improve device stability, we developed a reliable system to immobilize individual molecules within a nanoscale gap of either SWCNTs or graphene through covalent amide bond formation, thus affording two classes of carbon electrode-molecule single-molecule junctions. One unique feature of these devices is the fact that they contain only one or two molecules as conductive elements, thus forming the basis for building new classes of chemo/biosensors with ultrahigh sensitivity. We have used these approaches to reveal the dependence of the charge transport of individual metallo-DNA duplexes on π-stacking integrity, and fabricate molecular devices capable of realizing label-free, real-time electrical detection of biological interactions at the single-event level, or switching their molecular conductance upon exposure to external stimuli, such as ion, pH, and light. These investigations highlight the unique advantages and importance of these universal methodologies to produce functional carbon electrode-molecule junctions in current and future researches toward the development of practical molecular devices, thus offering a reliable platform for molecular electronics and the promise of a new generation of multifunctional integrated circuits and sensors. PMID:26190024

  16. Molecules, cancer, and the surgeon. A review of molecular biology and its implications for surgical oncology.

    PubMed Central

    Arbeit, J M

    1990-01-01

    Interactions between molecules control intra- and intercellular physiology. Cancer is emerging as a disease in which individual molecules are either overproduced, mutated, expressed at inappropriate stages of development, or lost due to inheritance or aberrant mitotic division. The major players in this contest of cellular control are growth factors, growth factor receptors (GFRs), signal transducers, and dominant or suppressor/recessive oncogenes. The tumors most frequently removed by surgeons have been reported to have changes in one or another of these types of molecules. The concept of multistage carcinogenesis, whereby malignancy arises after a sequence of changes that are cumulative, and passed from progenitor to daughter cells, is also being defined as a sequence of molecular, genetic, and chromosomal alterations. Molecular antineoplastic therapy is in early stages of development at the laboratory bench. The future may see patients screened for cancer susceptibility, evaluated for adjuvant therapy, and chosen for particular treatment based on molecular analysis. The types of cancer operations and the scope of surgical resection may change as molecular techniques enhance oncologic treatment. PMID:2194440

  17. Molecular release from patterned nanoporous gold thin films

    NASA Astrophysics Data System (ADS)

    Kurtulus, Ozge; Daggumati, Pallavi; Seker, Erkin

    2014-05-01

    Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 μg cm-2 and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features.Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 μg cm-2 and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01288g

  18. Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Mu, Yuguang; Nordenskild, Lars; van der Maarel, Johan R. C.

    2008-03-01

    All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

  19. Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule.

    PubMed

    Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W

    2015-05-22

    A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j=0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom. PMID:26047242

  20. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Kim, Yu Jin; Park, Chan Eon

    2016-03-01

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control.In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00775a

  1. Proposed Molecular Beam Determination of Energy Partition in the Photodissociation of Polyatomic Molecules

    DOE R&D Accomplishments Database

    Zare, P. N.; Herschbach, D. R.

    1964-01-29

    Conventional photochemical experiments give no information about the partitioning of energy between translational recoil and internal excitation of the fragment molecules formed in photodissociation of a polyatomic molecule. In a molecular beam experiment, it becomes possible to determine the energy partition from the form of the laboratory angular distribution of one of the photodissociation products. A general kinematic analysis is worked out in detail, and the uncertainty introduced by the finite angular resolution of the apparatus and the velocity spread in the parent beam is examined. The experimental requirements are evaluated for he photolysis of methyl iodide by the 2537 angstrom Hg line.

  2. Resonant multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, October 1987--September 1988

    SciTech Connect

    1988-12-31

    The objective of the research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n+1)-REMPI process of interest an atom or molecule in a specific initial state absorbs n photons making a transition to an intermediate state from which it is subsequently ionized by absorption of an additional photon. The studies are designed to provide a quantitatively robust analysis and prediction of key spectral features in several ongoing experimental studies and potentially practical applications of this technique. The specific problems of interest to the authors in these studied are (1) the vibrational distributions of ions that can be expected in REMPI of small molecules and molecular fragments with particular emphasis on their non-Franck-Condon behavior. Such non-Franck-Condon behavior introduces serious complications in the use of the technique for state-specific production of ions, e.g., O{sub 2}{sup +}({nu}) and OH{sup +}({nu}), and in the extraction of state populations from REMPI signals, (2) rotational distributions of ions that can be produced in various REMPI schemes and how these distributions can be tuned by choice of the resonant state and influenced by the molecular character of the photoelectron, and (3) the circular dichroism in photoelectron angular distributions, i.e., the difference in photoelectron angular distributions produced by right- and left-circularly polarized, and their use as a probe of molecular alignment. Here the author will summarize the progress that has been made to date in the studies of these features and applications of REMPI of molecules and molecular fragments. A significant feature of these studies, which will be explicitly assumed throughout the discussion below, is that they are carried out using quantitatively reliable molecular photoelectron orbitals.

  3. Novel Vein Patterns in Arabidopsis Induced by Small Molecules1[OPEN

    PubMed Central

    Cutler, Sean

    2016-01-01

    The critical role of veins in transporting water, nutrients, and signals suggests that some key regulators of vein formation may be genetically redundant and, thus, undetectable by forward genetic screens. To identify such regulators, we screened more than 5000 structurally diverse small molecules for compounds that alter Arabidopsis (Arabidopsis thaliana) leaf vein patterns. Many compound-induced phenotypes were observed, including vein networks with an open reticulum; decreased or increased vein number and thickness; and misaligned, misshapen, or nonpolar vascular cells. Further characterization of several individual active compounds suggests that their targets include hormone cross talk, hormone-dependent transcription, and PIN-FORMED trafficking. PMID:26574596

  4. Molecular Dynamics Simulations of RNA: An In Silico Single Molecule Approach

    PubMed Central

    McDowell, S. Elizabeth; pa?kov, Nad'a; poner, Ji?; Walter, Nils G.

    2007-01-01

    RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNAsmall molecule and RNAprotein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structurefunction relationships in diverse and complex RNA molecules. PMID:17080418

  5. Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

    PubMed

    Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

    2016-02-01

    Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions. PMID:26728229

  6. Beyond Tissue Injury—Damage-Associated Molecular Patterns, Toll-Like Receptors, and Inflammasomes Also Drive Regeneration and Fibrosis

    PubMed Central

    2014-01-01

    Tissue injury initiates an inflammatory response through the actions of immunostimulatory molecules referred to as damage-associated molecular patterns (DAMPs). DAMPs encompass a group of heterogenous molecules, including intracellular molecules released during cell necrosis and molecules involved in extracellular matrix remodeling such as hyaluronan, biglycan, and fibronectin. Kidney-specific DAMPs include crystals and uromodulin released by renal tubular damage. DAMPs trigger innate immunity by activating Toll-like receptors, purinergic receptors, or the NLRP3 inflammasome. However, recent evidence revealed that DAMPs also trigger re-epithelialization upon kidney injury and contribute to epithelial-mesenchymal transition and, potentially, to myofibroblast differentiation and proliferation. Thus, these discoveries suggest that DAMPs drive not only immune injury but also kidney regeneration and renal scarring. Here, we review the data from these studies and discuss the increasingly complex connection between DAMPs and kidney diseases. PMID:24762401

  7. Molecular release from patterned nanoporous gold thin films.

    PubMed

    Kurtulus, Ozge; Daggumati, Pallavi; Seker, Erkin

    2014-06-21

    Nanostructured materials have shown significant potential for biomedical applications that require high loading capacity and controlled release of drugs. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a promising novel material that benefits from compatibility with microfabrication, tunable pore morphology, electrical conductivity, well-established gold-thiol conjugate chemistry, and biocompatibility. While np-Au's non-biological applications are abundant, its performance in the biomedical field is nascent. In this work, we employ a combination of techniques including nanoporous thin film synthesis, quantitative electron microscopy, fluorospectrometry, and electrochemical surface characterization to study loading capacity and molecular release kinetics as a function of film properties and discuss underlying mechanisms. The sub-micron-thick sputter-coated nanoporous gold films provide small-molecule loading capacities up to 1.12 μg cm(-2) and molecular release half-lives between 3.6 hours to 12.8 hours. A systematic set of studies reveals that effective surface area of the np-Au thin films on glass substrates plays the largest role in determining loading capacity. The release kinetics on the other hand depends on a complex interplay of micro- and nano-scale morphological features. PMID:24842586

  8. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    SciTech Connect

    Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

    2014-10-14

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW₁₂O₄₀³⁻, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  9. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  10. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    NASA Astrophysics Data System (ADS)

    Balliou, A.; Douvas, A. M.; Normand, P.; Tsikritzis, D.; Kennou, S.; Argitis, P.; Glezos, N.

    2014-10-01

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW12O403-, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  11. A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

    PubMed Central

    2016-01-01

    Summary This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples. PMID:26877815

  12. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    NASA Astrophysics Data System (ADS)

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; Asai, Yoshihiro; Tao, Nongjian

    2016-04-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelectric effect is large and sensitive to the length in the tunnelling regime. These findings indicate that one may control the thermoelectric effect in DNA by varying its sequence and length. We describe the experimental results in terms of hopping and tunnelling charge transport models.

  13. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    PubMed Central

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; Asai, Yoshihiro; Tao, Nongjian

    2016-01-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelectric effect is large and sensitive to the length in the tunnelling regime. These findings indicate that one may control the thermoelectric effect in DNA by varying its sequence and length. We describe the experimental results in terms of hopping and tunnelling charge transport models. PMID:27079152

  14. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules.

    PubMed

    Li, Yueqi; Xiang, Limin; Palma, Julio L; Asai, Yoshihiro; Tao, Nongjian

    2016-01-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelectric effect is large and sensitive to the length in the tunnelling regime. These findings indicate that one may control the thermoelectric effect in DNA by varying its sequence and length. We describe the experimental results in terms of hopping and tunnelling charge transport models. PMID:27079152

  15. Femtosecond photoelectron diffraction on laser-aligned molecules: Towards time-resolved imaging of molecular structure

    NASA Astrophysics Data System (ADS)

    Boll, R.; Anielski, D.; Bostedt, C.; Bozek, J. D.; Christensen, L.; Coffee, R.; De, S.; Decleva, P.; Epp, S. W.; Erk, B.; Foucar, L.; Krasniqi, F.; Küpper, J.; Rouzée, A.; Rudek, B.; Rudenko, A.; Schorb, S.; Stapelfeldt, H.; Stener, M.; Stern, S.; Techert, S.; Trippel, S.; Vrakking, M. J. J.; Ullrich, J.; Rolles, D.

    2013-12-01

    We demonstrate an experimental method to record snapshot diffraction images of polyatomic gas-phase molecules, which can, in a next step, be used to probe time-dependent changes in the molecular geometry during photochemical reactions with femtosecond temporal and angstrom spatial resolution. Adiabatically laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) molecules were imaged by diffraction of photoelectrons with kinetic energies between 31 and 62 eV, created from core ionization of the fluorine (1s) level by ≈80 fs x-ray free-electron-laser pulses. Comparison of the experimental photoelectron angular distributions with density functional theory calculations allows relating the diffraction images to the molecular structure.

  16. Theoretical estimation of the electron molecular vibration coupling in several organic donor molecules

    NASA Astrophysics Data System (ADS)

    Taniguchi, M.; Misaki, Y.; Tanaka, K.

    2000-03-01

    The electron-molecular vibration (EMV) coupling constants and the accompanying vibronic energy values of five kinds of organic donor molecules (TTF +1, TTP +1, TTPY +1, TOF +1 and TSF +1) are crucial ingredients of metallic organic salts, and have been theoretically estimated in order to systematically investigate their dependencies on the molecular structures. The effect of the replacement of sulfur atoms in TTF +1 with oxygen and selenium atoms (TOF +1 and TSF +1) has been paid particular attention. It has been found that the EMV coupling constant decreases in the order of TOF +1>TTF +1>TSF +1>TTP +1>TTPY +1. That is, the smaller coupling constants appear in the larger-sized molecule with heavier atoms.

  17. Nonadiabatic molecular high-order harmonic generation from polar molecules: Spectral redshift

    SciTech Connect

    Bian Xuebin; Bandrauk, Andre D.

    2011-04-15

    Molecular high-order harmonic generation (MHOHG) from the polar diatomic molecule HeH{sup 2+} in short intense laser fields is studied numerically. Due to the nonadiabatic response of the molecular dipole to the rapid change of laser intensity, a spectral redshift is predicted in high-intensity and ultrashort laser pulses, contrary to the blueshift observed in the harmonics generated from atoms in long laser pulses. The MHOHG temporal structures are investigated by a wavelet time-frequency analysis, which shows that the enhanced excitation of localized long lifetime excited states shifts the harmonic generation spectrum in the falling part of short laser pulses, due to the presence of a permanent dipole moment, and thus is unique to polar molecules.

  18. Polar molecules engaged in pendular states captured by molecular-beam scattering experiments

    NASA Astrophysics Data System (ADS)

    Roncaratti, Luiz F.; Cappelletti, David; Candori, Pietro; Pirani, Fernando

    2014-07-01

    We demonstrate that when two polar molecules as those of water, ammonia, and hydrogen sulfide encounter each other at a distance much larger than their dimensions they engage a synchronous motion that promotes the transformation of free rotations into coupled pendular states. This discovery has been prompted by high-resolution molecular beam scattering experiments presented here, addressed to the measure of the total integral cross section changes as a consequence of molecular rotation couplings. The experimental observations and the theoretical treatment developed to shed light on the details of the phenomenon suggest that the interplay among free rotations and pendular states depends on the relative velocity, on the rotational levels, and on the dipole moments of the interacting molecules. The features of this intriguing phenomenon may be crucial for the interpretation and the control of basic chemical and biological processes.

  19. Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery

    PubMed Central

    Ji, Hong-Fang; Kong, De-Xin; Shen, Liang; Chen, Ling-Ling; Ma, Bin-Guang; Zhang, Hong-Yu

    2007-01-01

    Background Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. Results By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super ligands (shared by three or more folds) from others. Conclusion These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products. PMID:17727706

  20. The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

    PubMed Central

    Kronforst, Marcus R.; Papa, Riccardo

    2015-01-01

    Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

  1. The functional basis of wing patterning in Heliconius butterflies: the molecules behind mimicry.

    PubMed

    Kronforst, Marcus R; Papa, Riccardo

    2015-05-01

    Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

  2. Photodissociation of laboratory oriented molecules: Revealing molecular frame properties of nonaxial recoil

    SciTech Connect

    Brom, Alrik J. van den; Rakitzis, T. Peter; Janssen, Maurice H.M.

    2004-12-15

    We report the photodissociation of laboratory oriented OCS molecules. A molecular beam of OCS molecules is hexapole state-selected and spatially oriented in the electric field of a velocity map imaging lens. The oriented OCS molecules are dissociated at 230 nm with the linear polarization set at 45 deg. to the orientation direction of the OCS molecules. The CO({nu}=0,J) photofragments are quantum state-selectively ionized by the same 230 nm pulse and the angular distribution is measured using the velocity map imaging technique. The observed CO({nu}=0,J) images are strongly asymmetric and the degree of asymmetry varies with the CO rotational state J. From the observed asymmetry in the laboratory frame we can directly extract the molecular frame angles between the final photofragment recoil velocity and the permanent dipole moment and the transition dipole moment. The data for CO fragments with high rotational excitation reveal that the dissociation dynamics is highly nonaxial, even though conventional wisdom suggests that the nearly limiting {beta} parameter results from fast axial recoil dynamics. From our data we can extract the relative contribution of parallel and perpendicular transitions at 230 nm excitation.

  3. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells.

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-03-31

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as that contain the alkylthio group and that does not. The improved performance of the -based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control. PMID:26987868

  4. Mechanics and Chemistry: Sinle Molecule Bond Rupture Forces Correlate with Molecular Backbone Structure

    SciTech Connect

    Frei, M.; Hybertsen, M.; Aradhya, S.V.; Koentopp, M.; Venkataraman, L.

    2011-03-02

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 {+-} 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

  5. SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

    PubMed

    Wei, Ning-Ning; Hamza, Adel

    2014-01-27

    We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request. PMID:24328054

  6. Manipulating the motion of large molecules: Information from the molecular frame

    NASA Astrophysics Data System (ADS)

    Küpper, Jochen

    2011-05-01

    Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (~1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) at the LCLS (operated by Stanford University on behalf of the US DOE).

  7. Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast

    PubMed Central

    Li, Chunquan; Hao, Dapeng; Zhang, Shaojun; Zhou, Meng; Su, Fei; Chen, Xi; Zhi, Hui; Li, Xia

    2013-01-01

    The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast. PMID:23308257

  8. Exploring the aqueous vertical ionization of organic molecules by molecular simulation and liquid microjet photoelectron spectroscopy.

    PubMed

    Tentscher, Peter R; Seidel, Robert; Winter, Bernd; Guerard, Jennifer J; Arey, J Samuel

    2015-01-01

    To study the influence of aqueous solvent on the electronic energy levels of dissolved organic molecules, we conducted liquid microjet photoelectron spectroscopy (PES) measurements of the aqueous vertical ionization energies (VIEaq) of aniline (7.49 eV), veratrole alcohol (7.68 eV), and imidazole (8.51 eV). We also reanalyzed previously reported experimental PES data for phenol, phenolate, thymidine, and protonated imidazolium cation. We then simulated PE spectra by means of QM/MM molecular dynamics and EOM-IP-CCSD calculations with effective fragment potentials, used to describe the aqueous vertical ionization energies for six molecules, including aniline, phenol, veratrole alcohol, imidazole, methoxybenzene, and dimethylsulfide. Experimental and computational data enable us to decompose the VIEaq into elementary processes. For neutral compounds, the shift in VIE upon solvation, ΔVIEaq, was found to range from ≈-0.5 to -0.91 eV. The ΔVIEaq was further explained in terms of the influence of deforming the gas phase solute into its solution phase conformation, the influence of solute hydrogen-bond donor and acceptor interactions with proximate solvent molecules, and the polarization of about 3000 outerlying solvent molecules. Among the neutral compounds, variability in ΔVIEaq appeared largely controlled by differences in solute-solvent hydrogen-bonding interactions. Detailed computational analysis of the flexible molecule veratrole alcohol reveals that the VIE is strongly dependent on molecular conformation in both gas and aqueous phases. Finally, aqueous reorganization energies of the oxidation half-cell ionization reaction were determined from experimental data or estimated from simulation for the six compounds aniline, phenol, phenolate, veratrole alcohol, dimethylsulfide, and methoxybenzene, revealing a surprising constancy of 2.06 to 2.35 eV. PMID:25516011

  9. Cancer molecular pattern discovery by subspace consensus kernel classification.

    PubMed

    Han, Xiaoxu

    2007-01-01

    Cancer molecular pattern efficient discovery is essential in the molecular diagnostics. The characteristics of the gene/protein expression data are challenging traditional unsupervised classification algorithms. In this work, we describe a subspace consensus kernel clustering algorithm based on the projected gradient nonnegative matrix factorization (PG-NMF). The algorithm is a consensus kernel hierarchical clustering (CKHC) method in the subspace generated by the PG-NMF. It integrates convergence-soundness parts-based learning, subspace and kernel space clustering in the microarray and proteomics data classification. We first integrated subspace methods and kernel methods by following our framework of the input space, subspace and kernel space clustering. We demonstrate more effective classification results from our algorithm by comparison with those of the classic NMF, sparse-NMF classifications and supervised classifications (KNN and SVM) for the four benchmark cancer datasets. Our algorithm can generate a family of classification algorithms in machine learning by selecting different transforms to generate subspaces and different kernel clustering algorithms to cluster data. PMID:17951812

  10. Distance-dependent patterns of molecular divergences in tuatara mitogenomes

    PubMed Central

    Subramanian, Sankar; Mohandesan, Elmira; Millar, Craig D.; Lambert, David M.

    2015-01-01

    Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection. PMID:25731894

  11. Distance-dependent patterns of molecular divergences in Tuatara mitogenomes.

    PubMed

    Subramanian, Sankar; Mohandesan, Elmira; Millar, Craig D; Lambert, David M

    2015-01-01

    Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection. PMID:25731894

  12. How, when, and where in pattern formation: Spying on embryonic development one molecule at a time

    NASA Astrophysics Data System (ADS)

    Garcia, Hernan

    An abiding mystery in the study of living matter is how a single cell develops into a multicellular organism. As this cell divides, its progeny read the program encoded on their DNA and adopt different fates becoming familiar cell types such as those found in muscle, liver and our brains. We now know that the decisions that cells make during development are not so much based on which genes to express, but rather on when, where and how to express them. Despite advances in determining the identities of the molecules that mediate these decisions we are still incapable of predicting how simple physical parameters such as the number, position and affinity of binding sites for these molecules on the DNA determine developmental fates. Using the fruit fly, one of the classic model systems for embryonic development, I will show how a combination of new technologies, quantitative experiments, and statistical mechanics is providing new insights about cellular decision making during development. In particular, I will describe how the specification of macroscopic body parts in an organism is linked to the non-equilibrium molecular-scale processes inside single cells. The goal of this interdisciplinary research is to produce a predictive understanding of developmental programs which will enable the rational control of biological size, shape and function.

  13. Symmetry of extremely floppy molecules: Molecular states beyond rotation-vibration separation

    NASA Astrophysics Data System (ADS)

    Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per

    2015-10-01

    Traditionally, molecules are theoretically described as near-static structures rotating in space. Vibrational motion causing small structural deformations induces a perturbative treatment of the rotation-vibration interaction, which fails in highly fluxional molecules, where all vibrational motions have amplitudes comparable in size to the linear dimensions of the molecule. An example is protonated methane (CH 5+ ) [P. Kumar and D. Marx, Phys. Chem. Chem. Phys. 8, 573 (2006); Z. Jin et al., J. Phys. Chem. A 110, 1569 (2006); and A. S. Petit et al., J. Phys. Chem. A 118, 7206 (2014)]. For these molecules, customary theory fails to simulate reliably even the low-energy spectrum [T. Oka, Science 347, 1313-1314 (2015) and O. Asvany et al., Science 347, 1346-1349 (2015)]. Within the traditional view of rotation and vibration being near-separable, rotational and vibrational wavefunctions can be symmetry classified separately in the molecular symmetry (MS) group [P. Bunker and P. Jensen, Molecular Symmetry and Spectroscopy, NRC Monograph Publishing Program (NRC Research Press, 2006)]. In this article, we discuss a fundamental group theoretical approach to the problem of determining the symmetries of molecular rotation-vibration states. We will show that all MS groups discussed so far are isomorphic to subgroups of the special orthogonal group in three dimensions SO(3). This leads to a group theoretical foundation of the technique of equivalent rotations [H. Longuet-Higgins, Mol. Phys. 6, 445 (1963)]. The group G240 (the MS group of protonated methane) represents, to the best of our knowledge, the first example of a MS group which is not isomorphic to a subgroup of SO(3) (nor of O(3) or of SU(2)). Because of this, a separate symmetry classification of vibrational and rotational wavefunctions becomes impossible in this MS group, consistent with the fact that a decoupling of vibrational and rotational motion is impossible. We discuss here the consequences of this. In conclusion, we show that the prototypical, extremely floppy molecule CH 5+ represents a new class of molecules, where customary group theoretical methods for determining selection rules and spectral assignments fail so that new methods have to be developed.

  14. CSO Broadband Molecular Line Surveys II: Intial Correlation Analysis Results for Complex Organic Molecules

    NASA Astrophysics Data System (ADS)

    Sanders, James L. Sanders, Iii; Radhuber, Mary L.; Laas, Jacob C.; Hays, Brian M.; Lis, Darek C.; Weaver, Susanna L. Widicus

    2013-06-01

    As was presented in the previous talk, we have conducted 25 broadband line surveys of interstellar sources in the λ=1.3 mm band using the Caltech Submillimeter Observatory. Using the results from the spectral analysis of these observations, the influence of physical environment on molecular complexity can be examined. Our broader research goal is to improve astrochemical models to the point where accurate predictions of complex molecular inventory can be made based on the physical and chemical environment of a given source. The CSO observations include a statistically-significant sample of sources, cover a range of physical environments, and target selected frequency windows containing transitions from a set of known complex organic molecules. We are now analyzing these line surveys to search for correlations between the relative abundances of organic molecules and the physical properties of the source (i.e. temperature, density, mass, etc.), as well as correlations between sets of molecules. Here we present the results from the initial quantitative analysis of these surveys, as well as chemical trends that have been determiend. The implications of these results for astrochemical models will also be discussed.

  15. Vibrational spectra and molecular dynamics of hydrogen peroxide molecules at quartz/water interfaces

    NASA Astrophysics Data System (ADS)

    Lv, Ye-qing; Zheng, Shi-li; Wang, Shao-na; Yan, Wen-yi; Zhang, Yi; Du, Hao

    2016-06-01

    The influence of H2O2 on the water vibration at quartz interface was examined using sum-frequency generation (SFG) spectroscopy, and the effect of H2O2 concentration has been systematically studied. Further, the number density and radical distribution of water molecules, H2O2 molecules, and quartz surface silanol groups were calculated using molecular dynamics (MD) simulation to provide molecular level interpretation for the SFG spectra. It is concluded from this study that the hydrogen peroxide molecules prefers to donate H-bonds to the in-plane silanol groups rather than accepting H-bonds from out-of-plane silanol groups, as evidenced by the strengthening of the peak located at 3400 cm-1 assigned to "liquid-like" hydrogen-bonding network. The SFG results have been supported by the MD calculation results, which demonstrate that the relative intensity of the peak located at 3400 cm-1 to that of located at 3200 cm-1 increases monotonously with the increase in the number of hydrogen peroxide in the first hydration shell of silanol.

  16. Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

    PubMed

    Buslaev, Pavel; Gordeliy, Valentin; Grudinin, Sergei; Gushchin, Ivan

    2016-03-01

    Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers. PMID:26765212

  17. Ab initio molecular dynamics simulations on the hydrolysis of methyl chloride with explicit consideration of three water molecules

    NASA Astrophysics Data System (ADS)

    Aida, Misako; Yamataka, Hiroshi; Dupuis, Michel

    1998-08-01

    Ab initio molecular dynamics (MD) simulations were performed on the hydrolysis of methyl chloride (CH 3Cl) with explicit consideration of three water molecules to understand the dynamics of the reaction and the role of solvent molecules in S N2 reactions in solution. The simulations clearly showed the existence and dynamical characteristics of two nearly concerted proton transfers involving the attacking water molecule and the solvent water molecules on the way to formation of the products. Observation of these proton transfers points clearly to the need for an explicit quantum chemical treatment of at least a few solvent water molecules to describe methyl chloride solvolysis.

  18. Resonant multiphoton ionization spectra of molecules and molecular fragments. Technical report, October 1987--September 1988

    SciTech Connect

    1997-07-01

    The objective of our research under this contract is to carry out studies of resonant enhanced multiphoton ionization (REMPI) processes in molecules. In the (n + 1) - REMPI process of interest an atom or molecule in a specific initial state absorbs n photons making a transition to an intermediate state from which it is subsequently ionized by absorption of an additional photon. A remarkable feature of resonant enhanced multiphoton ionization is that the narrow bandwidth radiation of lasers makes it possible (i) to select a specific rovibrational level in the initial state of a molecule or fragment, (ii) to resonantly pump this level up to a selected rotational-vibrational level of an excited electronic state, and (iii) to subsequently photoionize the state that has been resonantly excited. The extreme state-selectivity and sensitivity make REMPI both a tool with several practical applications and an important technique for probing the photoionization dynamics of vibrationally and electronically excited states. Some significant applications of this technique include its use for state-specific detection of species and diagnostics in combustion and chemical etching media and plasmas, (ii) for state-specific generation of molecular ions for use in ion-molecule reaction studies, and (iii) as a probe of photofragmentation and gas-surface scattering including alignment and orientation effects in these processes.

  19. Biological carrier molecules of radiopharmaceuticals for molecular cancer imaging and targeted cancer therapy.

    PubMed

    Aerts, A; Impens, N R E N; Gijs, M; D'Huyvetter, M; Vanmarcke, H; Ponsard, B; Lahoutte, T; Luxen, A; Baatout, S

    2014-01-01

    Many tumors express one or more proteins that are either absent or hardly present in normal tissues, and which can be targeted by radiopharmaceuticals for either visualization of tumor cells or for targeted therapy. Radiopharmaceuticals can consist of a radionuclide and a carrier molecule that interacts with the tumor target and as such guides the attached radionuclide to the right spot. Radiopharmaceuticals hold great promise for the future of oncology by providing early, precise diagnosis and better, personalized treatment. Most advanced developments with marketed products are based on whole antibodies or antibody fragments as carrier molecules. However, a substantial number of (pre)clinical studies indicate that radiopharmaceuticals based on other carrier molecules, such as peptides, nonimmunoglobulin scaffolds, or nucleic acids may be valuable alternatives. In this review, we discuss the biological molecules that can deliver radionuclide payloads to tumor cells in terms of their structure, the selection procedure, their (pre)clinical status, and advantages or obstacles to their use in a radiopharmaceutical design. We also consider the plethora of molecular targets existing on cancer cells that can be targeted by radiopharmaceuticals, as well as how to select a radionuclide for a given diagnostic or therapeutic product. PMID:24606796

  20. Bond orientation properties in lipid molecules of membranes: molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Lyubartsev, Alexander P.

    2014-05-01

    Atomistic molecular dynamics simulations have been carried out for 16 different fully hydrated phosphatidylcholine lipid bilayers, having 16 or 18 carbon atoms in fully saturated sn - 1 chain and from 18 to 22 carbon atoms in sn - 2 chain with different degree of unsaturation, with the purpose to investigate the effect of unsaturation on physical properties of lipid bilayers. Special attention has been paid to profiles of C-C and C-H bond order parameters of lipid molecules and the orientational fluctuations of these bond vectors. It was shown that the study of anisotropy degree of bond orientations probability distributions allows distinguishing extended regions with different types of angular fluctuations of bonds in a membrane formed by lipid molecules with unsaturated chains.

  1. Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

  2. Achieving ground-state polar molecular condensates by chainwise atom-molecule adiabatic passage

    SciTech Connect

    Qian Jing; Zhang Weiping; Ling, Hong Y.

    2010-01-15

    We generalize the idea of chainwise stimulated Raman adiabatic passage (STIRAP) [Kuznetsova et al., Phys. Rev. A 78, 021402(R) (2008)] to a photoassociation-based chainwise atom-molecule system, with the goal of directly converting two-species atomic Bose-Einstein condensates (BEC) into a ground polar molecular BEC. We pay particular attention to the intermediate Raman laser fields, a control knob inaccessible to the usual three-level model. We find that an appropriate exploration of both the intermediate laser fields and the stability property of the atom-molecule STIRAP can greatly reduce the power demand on the photoassociation laser, a key concern for STIRAPs starting from free atoms due to the small Franck-Condon factor in the free-bound transition.

  3. A molecular dynamics study on slow ion interactions with the polycyclic aromatic hydrocarbon molecule anthracene

    SciTech Connect

    Postma, J.; Hoekstra, R.; Schlathölter, T.; Tielens, A. G. G. M.

    2014-03-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C{sub 14}H{sub 10}) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

  4. Molecular Spectra of RbSr: Helium Droplet Assisted Preparation of a Diatomic Molecule

    NASA Astrophysics Data System (ADS)

    Lackner, Florian; Krois, Günter; Buchsteiner, Thomas; Pototschnig, Johann V.; Ernst, Wolfgang E.

    2014-06-01

    We report on the first spectroscopic investigation of the ground and excited states of RbSr. The molecules are prepared in their vibronic ground state (X^2Σ^+1/2, ν" = 0) in a sequential pickup process on the surface of helium nanodroplets, confined in a cold (0.38 K) and weakly perturbing superfluid environment. Utilizing resonance-enhanced multi-photon ionization time-of-flight (REMPI-TOF) spectroscopy and laser induced fluorescence (LIF) spectroscopy our investigations cover the spectral regime of 11500 cm-1 - 23000 cm-1. The weak interaction between molecules and helium droplets causes a broadening of the observed transitions. For spectrally resolved band systems the helium droplet isolation approach facilitates the determination of molecular constants. Our assignment is assisted by theoretical calculations of potential energy curves based on a multireference configuration interaction (MRCI) approach. Several strong transitions could be identified; the most prominent spectral feature is a vibrational resolved band system at 14000 cm-1. In contrast to the excitation spectra, dispersed fluorescence (DF) spectra are not influenced by the helium environment, because the molecules leave the droplets upon photoexcitation, revealing detailed insights into the electronic structure of the free RbSr molecule. G. Krois, J.V. Pototschnig, F. Lackner and W.E. Ernst, J. Phys. Chem. A, 117 (50), 13719-13731 (2013) C. Callegari and W. E. Ernst, Helium Droplets as Nanocryostats for Molecular Spectroscopy - from the Vacuum Ultraviolet to the Microwave Regime, in: Handbook of High-Resolution Spectroscopy, eds. M. Quack and F. Merkt, John Wiley & Sons, Chichester, (2011) P.S. Żuchowski, R. Guerout, and O. Dulieu, arXiv preprint arXiv:1402.0702 (2014) B. Pasquiou, A. Bayerle, S.M. Tzanova, S. Stellmer, J. Szczepkowski, M. Parigger, R. Grimm, and F. Schreck, Phys. Rev. A, 88 (2), 023601 (2013).

  5. Attached molecular motor in a trapped single molecule assay as a bidimensional Brownian multistable system.

    PubMed

    Marcucci, L; Yanagida, T

    2013-06-01

    To elucidate the physical properties of the force generation mechanism in molecular motors, we have obtained an analytical solution of the bidimensional Fokker-Plank equation which describes a common setup used in single molecule experiments. As a first application of this general result, we have shown that the size of the trapping system affects the dwell time of a multistable particle linearly. A quantitative application to skeletal actomyosin complex, using direct observation of force generation dynamics in the literature, shows that the size of the trapping system used was important for increasing the dwell time of the myosin head stable states to an observable time scale. PMID:23848719

  6. High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular details of DNA aptamer-ricin interactions were investigated. The toxic protein ricin molecules were immobilized on Au(111) surface using N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in ...

  7. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    PubMed Central

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  8. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules.

    PubMed

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R R; Lin, C D

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  9. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    NASA Astrophysics Data System (ADS)

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-03-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

  10. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  11. Signatures of the molecular potential in the ellipticity of high-order harmonics from aligned molecules

    SciTech Connect

    Sherratt, Paul A. J.; Ramakrishna, S.; Seideman, Tamar

    2011-05-15

    We explore the information content of the polarization of high-order harmonics emitted from aligned molecules driven by a linearly polarized field. The study builds upon our previous work [Ramakrishna et al., Phys. Rev. A 81, 021802(R) (2010)], which illustrated that the phase of the continuum electronic wave function, and hence the underlying molecular potential, is responsible, at least in part, for the ellipticity observed in harmonic spectra. We use a simple model potential and systematically vary the potential parameters to investigate the sense in which, and the degree to which, the shape of the molecular potential is imprinted onto the polarization of the emitted harmonics. Strong ellipticity is observed over a wide range of potential parameters, suggesting that the emission of elliptically polarized harmonics is a general phenomenon, yet qualitatively determined by the molecular properties. The sensitivity of the ellipticity to the model parameters invites the use of ellipticity measurements as a probe of the continuum wave function and the underlying molecular potential.

  12. LC-MS with electron ionization of cold molecules in supersonic molecular beams

    NASA Astrophysics Data System (ADS)

    Granot, Ori; Amirav, Aviv

    2005-06-01

    A new approach is described for the combination of electron ionization and LC-MS based on sample ionization as vibrationally cold molecules in a supersonic molecular beam (Cold EI). Cold EI of sample compounds in liquid solutions (methanol, acetonitrile, water, etc.) is achieved through spray formation, followed by soft thermal vaporization of the sample particles prior to their supersonic expansion and direct electron ionization of the sample compounds while they are contained in a supersonic molecular beam (SMB). Cold EI mass spectra were demonstrated to combine an enhanced molecular ion and improved mass spectral information (in comparison with standard EI), plus all the library searchable fragments. Cold EI enables the ionization of a broad range of compounds, including the full range of non-polar samples. Four orders of magnitude linear dynamic range is demonstrated and a detection limit of 2 pg was achieved for a 774 amu compound in single ion monitoring mode at m/z = 774. The method and apparatus are under continuous development and we feel that it can excel particularly in the analysis of unknown samples, while enabling fast LC-MS analysis through automated mass spectral deconvolution of coeluting LC peaks. In addition, the same MS system can also serve as an advanced GC-MS with supersonic molecular beams.

  13. The immunoproteasome controls the availability of the cardioprotective pattern recognition molecule Pentraxin3.

    PubMed

    Paeschke, Anna; Possehl, Anna; Klingel, Karin; Voss, Martin; Voss, Karolin; Kespohl, Meike; Sauter, Martina; Overkleeft, Hermen S; Althof, Nadine; Garlanda, Cecilia; Voigt, Antje

    2016-03-01

    Cardiomyocyte death as a result of viral infection is an excellent model for dissecting the inflammatory stress response that occurs in heart tissue. We reported earlier that a specific proteasome isoform, the immunoproteasome, prevents exacerbation of coxsackievirus B3 (CVB3)-induced myocardial destruction and preserves cell vitality in heart tissue inflammation. Following the aim to decipher molecular targets of immunoproteasome-dependent proteolysis, we investigated the function and regulation of the soluble PRR Pentraxin3 (PTX3). We show that the ablation of PTX3 in mice aggravated CVB3-triggered inflammatory injury of heart tissue, without having any significant effect on viral titers. Thus, there might be a role of PTX3 in preventing damage-associated molecular pattern-induced cell death. We found that the catalytic activity of the immunoproteasome subunit LMP7 regulates the timely availability of factors controlling PTX3 production. We report on immunoproteasome-dependent alteration of ERK1/2 and p38MAPKs, which were both found to be involved in PTX3 expression control. Our finding of a cardioprotective function of immunoproteasome-dependent PTX3 expression revealed a crucial mechanism of the stress-induced damage response in myocardial inflammation. In addition to antigen presentation and cytokine production, proteolysis by the immunoproteasome can also regulate the innate immune response during viral infection. PMID:26578407

  14. Critical Roles of Metal-Molecule Contacts in Electron Transport Through Molecular-wire Junctions

    NASA Astrophysics Data System (ADS)

    Grigoriev, Anton; Crljen, Zeljko

    2005-03-01

    We use non-equilibrium Green's function DFT methods (TranSIESTA) to study the bonding-site dependence of the transmission through metal-molecule contacts in molecular junctions of type M-S-mol-S-M for a number of different molecular systems, mainly short molecules with DTB as a reference system, and also OPVn, n=3-5. For all systems on Au(111) surfaces the transmission is quite insensitive to the bonding site. However, if S is adsorbed in an Au vacancy, or on- top of a small (3-Au-atom) island, the transmission can drop very substantially due to mismatch and changes of the HOMO structure in the contacts. However, we do not find any examples of several orders-of-magnitude reductions of the conductivity. In several systems with low zero-bias transmission at the Fermi level, we found that buried Au-S contacts (S adsorbed in Au vacancy) are associated with very sharp LUMO levels just above the Fermi level. Such a system will show extremely strong non-linear effects and might work as uni- or bi-directional voltage-controlled 2-terminal switches.

  15. High energy sources and materials: High-temperature molecules and molecular energy storage

    NASA Astrophysics Data System (ADS)

    Weltner, W., Jr.

    1980-10-01

    The objective of this research was the characterization of molecular species which are important because of (a) their occurrence in high-temperature environments, as for example in the vapor over refractory solids, and in combustion, flames, and propellant burning; (b) their relevance to clarification and/or extension of the basic theory of molecular properties. The molecules studied were usually highly reactive or metastable and often inaccessible by the usual gas-phase spectroscopic methods. They were therefore trapped in a solid matrix, usually neon or orgon, at 4 K and investigated by optical and electron-spin-resonance (ESR) spectroscopies. This isolation procedure is known to produce only small perturbations and to yield information pertinent to the gas-phase species. The species studied included boron and bromine atoms, methylene radicals, diatomic boron, beryllium hydroxide, diatomic chlorine anion, carbonyl silene, diazasilene, the first-row transition-metal mono, di, and trifluorides and their corresponding hydrides and oxides, and a few rare-earth hydrides and fluorides. Vibrational frequencies, electronic transitions, g factors, spin-rotation constants, hyperfine coupling constants, zero-field-splittings, ground-state multiplicities, and perhaps some information about structure, were obtained. The molecules contained from one to seven unpaired electrons.

  16. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

    PubMed

    Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

    2015-02-01

    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921

  17. The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics

    SciTech Connect

    Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

    2012-05-01

    MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

  18. Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level.

    PubMed

    Dopfer, Otto; Fujii, Masaaki

    2016-05-11

    Solvation processes play a crucial role in chemical reactions and biomolecular recognition phenomena. Although solvation dynamics of interfacial or biological water has been studied extensively in aqueous solution, the results are generally averaged over several solvation layers and the motion of individual solvent molecules is difficult to capture. This review describes the development and application of a new experimental approach, namely, picosecond time-resolved pump-probe infrared spectroscopy of size- and isomer-selected aromatic clusters, in which for the first time the dynamics of a single individual solvent molecule can be followed in real time. The intermolecular isomerization reaction is triggered by resonant photoionization (pump), and infrared photodissociation (probe) at variable delay generates the spectroscopic signature of salient properties of the reaction, including rates, yields, pathways, branching ratios of competing reactions, existence of reaction intermediates, occurrence of back reactions, and time scales of energy relaxation processes. It is shown that this relevant information can reliably be decoded from the experimental spectra by sophisticated molecular dynamics simulations. This review covers a description of the experimental strategies and spectroscopic methods along with all applications to date, which range from aromatic clusters with nonpolar solvent molecules to aromatic monohydrated biomolecules. PMID:27054835

  19. Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.

    PubMed

    Ray, Andrew D; Hammond, Janet; Major, Hilary

    2010-01-01

    Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism. PMID:20212333

  20. Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants

    PubMed Central

    Tanaka, Kiwamu; Choi, Jeongmin; Cao, Yangrong; Stacey, Gary

    2014-01-01

    As sessile organisms, plants have evolved effective mechanisms to protect themselves from environmental stresses. Damaged (i.e., wounded) plants recognize a variety of endogenous molecules as danger signals, referred to as damage-associated molecular patterns (DAMPs). ATP is among the molecules that are released by cell damage, and recent evidence suggests that ATP can serve as a DAMP. Although little studied in plants, extracellular ATP is well known for its signaling roles in animals, including acting as a DAMP during the inflammatory response and wound healing. If ATP acts outside the cell, then it is reasonable to expect that it is recognized by a plasma membrane-localized receptor. Recently, DORN1, a lectin receptor kinase, was shown to recognize extracellular ATP in Arabidopsis. DORN1 is the founding member of a new purinoceptor subfamily, P2K (P2 receptor kinase), which is plant-specific. P2K1 (DORN1) is required for ATP-induced cellular responses (e.g., cytosolic Ca2+ elevation, MAPK phosphorylation, and gene expression). Genetic analysis of loss-of-function mutants and overexpression lines showed that P2K1 participates in the plant wound response, consistent with the role of ATP as a DAMP. In this review, we summarize past research on the roles and mechanisms of extracellular ATP signaling in plants, and discuss the direction of future research on extracellular ATP as a DAMP signal. PMID:25232361

  1. Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors

    NASA Astrophysics Data System (ADS)

    Zhang, Zhenglong; Sheng, Shaoxiang; Zheng, Hairong; Xu, Hongxing; Sun, Mengtao

    2014-04-01

    The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by `plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply `hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry.The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by `plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply `hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry. Electronic supplementary information (ESI) available: Further experimental spectra and theoretical calculations. See DOI: 10.1039/c3nr06799h

  2. Nanofibers for drug delivery – incorporation and release of model molecules, influence of molecular weight and polymer structure

    PubMed Central

    Hrib, Jakub; Hobzova, Radka; Hampejsova, Zuzana; Bosakova, Zuzana; Munzarova, Marcela; Michalek, Jiri

    2015-01-01

    Summary Nanofibers were prepared from polycaprolactone, polylactide and polyvinyl alcohol using NanospiderTM technology. Polyethylene glycols with molecular weights of 2 000, 6 000, 10 000 and 20 000 g/mol, which can be used to moderate the release profile of incorporated pharmacologically active compounds, served as model molecules. They were terminated by aromatic isocyanate and incorporated into the nanofibers. The release of these molecules into an aqueous environment was investigated. The influences of the molecular length and chemical composition of the nanofibers on the release rate and the amount of released polyethylene glycols were evaluated. Longer molecules released faster, as evidenced by a significantly higher amount of released molecules after 72 hours. However, the influence of the chemical composition of nanofibers was even more distinct – the highest amount of polyethylene glycol molecules released from polyvinyl alcohol nanofibers, the lowest amount from polylactide nanofibers. PMID:26665065

  3. Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor: Linear molecules

    NASA Astrophysics Data System (ADS)

    Xiao, Yunlong; Liu, Wenjian

    2013-07-01

    The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)], 10.1063/1.4797496. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR.

  4. Surface-mounted altitudinal molecular rotors in alternating electric field: single-molecule parametric oscillator molecular dynamics.

    PubMed

    Horinek, Dominik; Michl, Josef

    2005-10-01

    Molecular dynamics simulations of the response to oscillating electric field elicited from an altitudinal dipolar molecular rotor mounted on the Au(111) surface and previously studied experimentally in static fields show unidirectional rotation in one of the three pairs of conformational enantiomers. The simulations are based on the universal force field and take into account electronic friction in the metal through its effect on the image charges. The rotor consists of two cobalt sandwich posts whose upper decks carry a biphenyl-like rotator with a dipole moment perpendicular to the rotation axle, mounted parallel to the surface. A phase diagram of rotor performance at 10 K as a function of field frequency and amplitude contains five unidirectional rotation regions: synchronous, half-synchronous (every other cycle skipped), quarter-synchronous (only indistinctly), asynchronous, and essentially no response. The nature of the subharmonic "single-molecule parametric oscillator" behavior is understood in mechanistic detail. Simulations at higher temperatures distinguish the thermal ("Brownian") and driven regimes of rotation, elucidated in terms of time-dependent potential energy surfaces for the rotation. PMID:16186490

  5. Dressed-bound-state molecular strong-field approximation: Application to above-threshold ionization of heteronuclear diatomic molecules

    SciTech Connect

    Hasovic, E.; Busuladzic, M.; Becker, W.; Milosevic, D. B.

    2011-12-15

    The molecular strong-field approximation (MSFA), which includes dressing of the molecular bound state, is introduced and applied to above-threshold ionization of heteronuclear diatomic molecules. Expressions for the laser-induced molecular dipole and polarizability as functions of the laser parameters (intensity and frequency) and molecular parameters [molecular orientation, dipole, and parallel and perpendicular polarizabilities of the highest occupied molecular orbital (HOMO)] are presented. Our previous MSFA theory, which incorporates the rescattering effects, is generalized from homonuclear to heteronuclear diatomic molecules. Angle- and energy-resolved high-order above-threshold ionization spectra of oriented heteronuclear diatomic molecules, exemplified by the carbon monoxide (CO) molecule, exhibit pronounced minima, which can be related to the shape of their HOMO-electron-density distribution. For the CO molecule we have found an analytical condition for the positions of these minima. We have also shown that the effect of the dressing of the HOMO is twofold: (i) the laser-induced Stark shift decreases the ionization yield and (ii) the laser-induced time-dependent dipole and polarizability change the oscillatory structure of the spectra.

  6. Structure of the F-spondin Domain of Mindin an Integrin Ligand and Pattern Recognition Molecule

    SciTech Connect

    Y Li; C Cao; W Jia; L Yu; M Mo; Q Wang; Y Huang; J Lim; M Ishihara; et. al.

    2011-12-31

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-A resolution. The structure revealed an eight-stranded antiparallel beta-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses.

  7. Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule

    PubMed Central

    Li, Yili; Cao, Chunzhang; Jia, Wei; Yu, Lily; Mo, Min; Wang, Qian; Huang, Yuping; Lim, Jae-Min; Ishihara, Mayumi; Wells, Lance; Azadi, Parastoo; Robinson, Howard; He, You-Wen; Zhang, Li; Mariuzza, Roy A

    2009-01-01

    Mindin (spondin-2) is an extracellular matrix protein of unknown structure that is required for efficient T-cell priming by dendritic cells. Additionally, mindin functions as a pattern recognition molecule for initiating innate immune responses. These dual functions are mediated by interactions with integrins and microbial pathogens, respectively. Mindin comprises an N-terminal F-spondin (FS) domain and C-terminal thrombospondin type 1 repeat (TSR). We determined the structure of the FS domain at 1.8-Å resolution. The structure revealed an eight-stranded antiparallel β-sandwich motif resembling that of membrane-targeting C2 domains, including a bound calcium ion. We demonstrated that the FS domain mediates integrin binding and identified the binding site by mutagenesis. The mindin FS domain therefore represents a new integrin ligand. We further showed that mindin recognizes lipopolysaccharide (LPS) through its TSR domain, and obtained evidence that C-mannosylation of the TSR influences LPS binding. Through these dual interactions, the FS and TSR domains of mindin promote activation of both adaptive and innate immune responses. PMID:19153605

  8. The Role of Molecular Dipole Orientation in Single-Molecule Fluorescence Microscopy and Implications for Super-Resolution Imaging

    PubMed Central

    Backlund, Mikael P.; Lew, Matthew D.; Backer, Adam S.; Sahl, Steffen J.

    2014-01-01

    Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules. PMID:24382708

  9. Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams

    SciTech Connect

    Chu, P.M.Y.

    1991-10-01

    The vibrational to translational (V{yields}T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V{yields}T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH{sub 3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.

  10. Nontypable Haemophilus influenzae Displays a Prevalent Surface Structure Molecular Pattern in Clinical Isolates

    PubMed Central

    Mauro, Silvia; Hood, Derek W.; Viadas, Cristina; Calatayud, Laura; Morey, Pau; Servin, Alain; Liñares, Josefina; Oliver, Antonio; Bengoechea, José Antonio; Garmendia, Junkal

    2011-01-01

    Non-typable Haemophilus influenzae (NTHi) is a Gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA−, lic2C+, ompP5+, oapA+) displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells. PMID:21698169

  11. NKp44 and Natural Cytotoxicity Receptors as Damage-Associated Molecular Pattern Recognition Receptors

    PubMed Central

    Horton, Nathan C.; Mathew, Porunelloor A.

    2015-01-01

    Natural killer (NK) cells are a key constituent of the innate immune system, protecting against bacteria, virally infected cells, and cancer. Recognition and protective function against such cells are dictated by activating and inhibitory receptors on the surface of the NK cell, which bind to specific ligands on the surface of target cells. Among the activating receptors is a small class of specialized receptors termed the natural cytotoxicity receptors (NCRs) comprised of NKp30, NKp46, and NKp44. The NCRs are key receptors in the recognition and termination of virally infected and tumor cells. Since their discovery over 10 years ago, ligands corresponding to the NCRs have largely remained elusive. Recent identification of the cellular ligands for NKp44 and NKp30 as exosomal proliferating cell nuclear antigen (PCNA) and HLA-B-associated transcript 3 (BAT3), respectively, implicate that NCRs may function as receptors for damage-associated molecular pattern (DAMP) molecules. In this review, we focus on NKp44, which surprisingly recognizes two distinct ligands resulting in either activation or inhibition of NK cell effector responses in response to tumor cells. The inhibitory function of NKp44 requires further study as it may play a pivotal role in placentation in addition to being exploited by tumors as a mechanism to escape NK cell killing. Finally, we suggest that the NCRs are a class of pattern recognition receptors, which recognize signals of genomic instability and cellular stress via interaction with the c-terminus of DAMP molecules localized to the surface of target cells by various co-ligands. PMID:25699048

  12. Complement activating soluble pattern recognition molecules with collagen-like regions, mannan-binding lectin, ficolins and associated proteins.

    PubMed

    Thiel, Steffen

    2007-09-01

    Mannan-binding lectin (MBL), L-ficolin, M-ficolin and H-ficolin are all complement activating soluble pattern recognition molecules with recognition domains linked to collagen-like regions. All four may form complexes with four structurally related proteins, the three MBL-associated serine proteases (MASPs), MASP-1, MASP-2 and MASP-3, and a smaller MBL-associated protein (MAp19). The four recognition molecules recognize patterns of carbohydrate or acetyl-group containing ligands. After binding to the relevant targets all four are able to activate the complement system. We thus have a system where four different and/or overlapping patterns of microbial origin or patterns of altered-self may be recognized, but in all cases the signalling molecules, the MASPs, are shared. MASP-1 and MASP-3 are formed from one gene, MASP1/3, by alternative splicing generating two different mRNAs from a single primary transcript. Similarly MASP-2 and MAp19 are both generated from one gene, MASP-2/MAp19, by alternative splicing. A number of non-synonymous polymorphisms of the four recognition molecules and of the MASPs are known, and the implications of these alterations are being studied. The clinical impact of deficiencies will be discussed. PMID:17768106

  13. Therapeutic Opportunities in Damage-Associated Molecular Pattern-Driven Metabolic Diseases

    PubMed Central

    Garcia-Martinez, Irma; Shaker, Mohamed E.

    2015-01-01

    Abstract Significance: Sterile inflammation is a common finding present in various metabolic disorders. This type of inflammation is mediated by damage-associated molecular patterns (DAMPs) that are released upon cellular injury to activate pattern recognition receptors on innate immune cells and amplify organ damage. Recent Advances: In the last decade, DAMPs, such as high-mobility group protein B1, nucleic acids (DNA, RNA), adenosine triphosphate, and other metabolites, were found to contribute to the inflammatory response in diabetes, gout, obesity, steatohepatitis, and atherosclerosis. Varied receptors, including Toll-like receptors (TLRs), the purinergic P2X7 receptors, and nucleotide-binding domain, and leucine-rich repeat protein 3 (NLRP3)-inflammasome sense DAMPs and DAMP-like molecules and release the proinflammatory cytokines, interleukin (IL)-1β and IL-18. Critical Issues: Available therapeutic approaches that interfered with the signaling of TLRs, P2X7, NLRP3-inflammasome, and IL-1β showed encouraging results in metabolic diseases, which will be also highlighted in this review. Future Directions: It is important to understand the origination of DAMPs and how they contribute to the inflammatory response in metabolic disorders to develop selective and efficient therapeutics for intervention. Antioxid. Redox Signal. 23, 1305–1315. PMID:26055926

  14. Patterned graphone—a novel template for molecular packing

    NASA Astrophysics Data System (ADS)

    Reddy, C. D.; Zhang, Y. W.; Shenoy, V. B.

    2012-04-01

    Precise positioning and packing of nanoscale building blocks is essential for the fabrication of many nanoelectro-mechanical devices. Carrying out such manipulations at the nanoscale still remains a challenge. Here we propose the use of graphone domain arrays embedded in a graphene sheet as a template to precisely position and pack molecules. Our atomistic simulations show that a graphone domain is able to adopt well-defined three-dimensional geometries, which in turn create ‘energy wells’ to trap molecules by means of physisorption. Using the C60 molecule as a model block, the stable trapping conditions are identified. The present work presents a novel route to position and pack molecules for nanoengineering applications.

  15. Molecular jigsaw: pattern diversity encoded by elementary geometrical features.

    PubMed

    Rohr, C; Balbás Gambra, M; Gruber, K; Constable, E C; Frey, E; Franosch, T; Hermann, B A

    2010-03-10

    Scanning tunneling microscopy (STM) images of self-organized monolayers of Frechet dendrons display a variety of two-dimensional ordering motifs, which are influenced by engineering the molecular interactions. An interaction-site model condenses the essential molecular properties determined by molecular mechanics modeling, which in a Monte Carlo approach successfully predicts the various ordering motifs. This confirms that geometry as well as a few salient weak interaction sites encode these structural motifs. PMID:20158248

  16. Ultraviolet Pretreatment of Titanium Dioxide and Tin-Doped Indium Oxide Surfaces as a Promoter of the Adsorption of Organic Molecules in Dry Deposition Processes: Light Patterning of Organic Nanowires.

    PubMed

    Oulad-Zian, Youssef; Sanchez-Valencia, Juan R; Parra-Barranco, Julian; Hamad, Said; Espinos, Juan P; Barranco, Angel; Ferrer, Javier; Coll, Mariona; Borras, Ana

    2015-08-01

    In this article we present the preactivation of TiO2 and ITO by UV irradiation under ambient conditions as a tool to enhance the incorporation of organic molecules on these oxides by evaporation at low pressures. The deposition of π-stacked molecules on TiO2 and ITO at controlled substrate temperature and in the presence of Ar is thoroughly followed by SEM, UV-vis, XRD, RBS, and photoluminescence spectroscopy, and the effect is exploited for the patterning formation of small-molecule organic nanowires (ONWs). X-ray photoelectron spectroscopy (XPS) in situ experiments and molecular dynamics simulations add critical information to fully elucidate the mechanism behind the increase in the number of adsorption centers for the organic molecules. Finally, the formation of hybrid organic/inorganic semiconductors is also explored as a result of the controlled vacuum sublimation of organic molecules on the open thin film microstructure of mesoporous TiO2. PMID:26168350

  17. Testosterone Induces Molecular Changes in Dopamine Signaling Pathway Molecules in the Adolescent Male Rat Nigrostriatal Pathway

    PubMed Central

    Purves-Tyson, Tertia D.; Owens, Samantha J.; Double, Kay L.; Desai, Reena; Handelsman, David J.; Weickert, Cynthia Shannon

    2014-01-01

    Adolescent males have an increased risk of developing schizophrenia, implicating testosterone in the precipitation of dopamine-related psychopathology. Evidence from adult rodent brain indicates that testosterone can modulate nigrostriatal dopamine. However, studies are required to understand the role testosterone plays in maturation of dopamine pathways during adolescence and to elucidate the molecular mechanism(s) by which testosterone exerts its effects. We hypothesized that molecular indices of dopamine neurotransmission [synthesis (tyrosine hydroxylase), breakdown (catechol-O-methyl transferase; monoamine oxygenase), transport [vesicular monoamine transporter (VMAT), dopamine transporter (DAT)] and receptors (DRD1-D5)] would be changed by testosterone or its metabolites, dihydrotestosterone and 17β-estradiol, in the nigrostriatal pathway of adolescent male rats. We found that testosterone and dihydrotestosterone increased DAT and VMAT mRNAs in the substantia nigra and that testosterone increased DAT protein at the region of the cell bodies, but not in target regions in the striatum. Dopamine receptor D2 mRNA was increased and D3 mRNA was decreased in substantia nigra and/or striatum by androgens. These data suggest that increased testosterone at adolescence may change dopamine responsivity of the nigrostriatal pathway by modulating, at a molecular level, the capacity of neurons to transport and respond to dopamine. Further, dopamine turnover was increased in the dorsal striatum following gonadectomy and this was prevented by testosterone replacement. Gene expression changes in the dopaminergic cell body region may serve to modulate both dendritic dopamine feedback inhibition and reuptake in the dopaminergic somatodendritic field as well as dopamine release and re-uptake dynamics at the presynaptic terminals in the striatum. These testosterone-induced changes of molecular indices of dopamine neurotransmission in males are primarily androgen receptor-driven events as estradiol had minimal effect. We conclude that nigrostriatal responsivity to dopamine may be modulated by testosterone acting via androgen receptors to alter gene expression of molecules involved in dopamine signaling during adolescence. PMID:24618531

  18. Molecular Regulation of Adipogenesis and Potential Anti-Adipogenic Bioactive Molecules

    PubMed Central

    Moseti, Dorothy; Regassa, Alemu; Kim, Woo-Kyun

    2016-01-01

    Adipogenesis is the process by which precursor stem cells differentiate into lipid laden adipocytes. Adipogenesis is regulated by a complex and highly orchestrated gene expression program. In mammalian cells, the peroxisome proliferator-activated receptor γ (PPARγ), and the CCAAT/enhancer binding proteins (C/EBPs) such as C/EBPα, β and δ are considered the key early regulators of adipogenesis, while fatty acid binding protein 4 (FABP4), adiponectin, and fatty acid synthase (FAS) are responsible for the formation of mature adipocytes. Excess accumulation of lipids in the adipose tissue leads to obesity, which is associated with cardiovascular diseases, type II diabetes and other pathologies. Thus, investigating adipose tissue development and the underlying molecular mechanisms is vital to develop therapeutic agents capable of curbing the increasing incidence of obesity and related pathologies. In this review, we address the process of adipogenic differentiation, key transcription factors and proteins involved, adipogenic regulators and potential anti-adipogenic bioactive molecules. PMID:26797605

  19. Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

    NASA Astrophysics Data System (ADS)

    Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

    2013-05-01

    Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

  20. Encaged molecules in external electric fields: a molecular `tug-of-war'

    NASA Astrophysics Data System (ADS)

    Pathak, Rajeev; Gurav, Nalini; Gejji, Shridhar; Bartolotti, Libero

    We investigate applying ab initio theoretical methods, the molecules Hydrogen peroxide, H2O2, and Methanol, CH3OH, encaged in hydrogen-bonded water ``buckyballs'' (H2O)20 , subjected to an externally applied electric field. While the water-cage (host) tends to confine the guest-molecule, the external electric field tends to stretch it along with its labile hydrogen-bonded host, resulting into a molecular `tug-of-war'. We appraise these two competing effects in terms of the extent of `screening' of the host by the cage and compare the response of the composite system in the form of the consequent structural mutations, redistributions in the electron density and the electrostatic potential leading to emergence and suppression of the covalent O-H characteristic frequency shifts in the infra-red vibrational spectrum. This study brings forth the cooperative effect of hydrogen-bonding up to a maximally sustainable threshold electric field, beyond which fragmentation of the water cage occurs. Partial support from The Center for Development in Advanced Computing (C-DAC) in terms of Computer time on the PARAM Supercomputing facility at Pune, MH, India, is gratefully acknowledged.

  1. Interpretation of atomic motion in flexible molecules: Accelerating molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor; Kovalenko, Andriy

    2012-02-01

    We propose a new approach to split up the velocities of atoms of flexible molecules into translational, rotational, and vibrational components. As a result, the kinetic energy of the system can easily be expressed in terms of only three parts related to the above components. This is distinct from the standard Eckart method, where the cumbersome Coriolis contribution to the kinetic energy appears additionally. The absence of such a contribution within the proposed approach allows us to readily extend the microcanonical multiple-time-step dynamics of flexible molecules to the canonical-isokinetic Nosé-Hoover chain ensemble by explicitly integrating the translational, orientational, and vibrational motion. The previous extensions dealt exclusively with translational degrees of freedom of separate atoms, leading to a limitation on the size of the outer time step of 100 femtoseconds. We show on molecular dynamics simulations of the flexible TIP3P water model that the new canonical-isokinetic formulation gives a possibility to significantly overcome this limitation. In particular, huge outer time steps of order from a few hundred femtoseconds up to several picoseconds can now be employed to study conformational properties without loss of accuracy.

  2. Configurational biomimesis in drug delivery: molecular imprinting of biologically significant molecules.

    PubMed

    Hilt, J Zachary; Byrne, Mark E

    2004-09-22

    This review focuses on trends in the macromolecular recognition of biologically significant molecules (e.g., drugs, amino acids, steroids, nucleotide bases, carbohydrates, etc.) via molecular imprinting methods. An extensive list of prior art including type of functional monomers and crosslinkers for each biomolecule imprinted polymer is presented. Representative samples of receptor-ligand dissociation constants and polymer capacities are presented as well as typical values that occur in classes of biological recognition systems. Imprinting technology has direct impact in enhanced drug loading of controlled-release carriers for the sustained release of therapeutic agents as well as robust biosensors for novel therapeutic and diagnostic devices. This review also discusses the future of designed recognition, configurational biomimesis within polymeric gels, and highlights recent efforts toward integrating imprinted polymers in controlled drug delivery systems and sensing devices. In particular, the application of imprinted polymers for sustained release, enhanced loading capacity, and enantioselective loading or release are discussed. This article also highlights the most important problems to be solved in the design of synthetic recognition-based networks for biological molecules. PMID:15350291

  3. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect

    Welch, Gregory C.; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-07-22

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  4. Exploring Molecular Complexity with ALMA: Deuterated complex organic molecules in Sgr B2

    NASA Astrophysics Data System (ADS)

    Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

    2016-05-01

    Apart from the case of methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in high mass star forming regions. We take advantage of the EMoCA spectral line survey to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We report the secure detection of CH2DCN with a deuteration level of 0.4% and tentative detections of CH2DOH, CH2DCH2CN, CH3CHDCN, and DC3N with levels in the range 0.05-0.12%. Except for methyl cyanide, the measured deuteration levels lie at least a factor of four below the predictions of current astrochemical models. They are also lower than in Orion KL by a factor of a few up to a factor ten. These discrepancies and differences may be due to the higher temperatures that prevail in the Galactic Center region compared to nearby clouds, or they may result from a lower overall abundance of deuterium itself in the Galactic Center region by up to a factor ten.

  5. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

    PubMed Central

    Hiatt, Joseph B.; Pritchard, Colin C.; Salipante, Stephen J.; O'Roak, Brian J.; Shendure, Jay

    2013-01-01

    The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10−6 in cell lines and 2.6 × 10−5 in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%–4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%–1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings. PMID:23382536

  6. Femtosecond Time-Resolved Single-Molecule Spectroscopy: Towards Probing Ultrafast Dynamics at Single Molecular Level Under Ambient Conditions

    NASA Astrophysics Data System (ADS)

    Fujiwara, Takashige; Lu, H. Peter

    2015-05-01

    The structure-function relationship is an important fundamental concept in the molecular sciences. Recent applications of ultrafast spectroscopy to single-molecular level provide a direct measurement of the inhomogeneity with respect to the electronic and chemical properties of the molecules in the microenvironment. In this poster, we present detailed experimental setups for the single color time-resolved pump-probe single molecule spectroscopy that we have developed in our laboratory. We demonstrated detections of the excited-state dynamics of electron transfer in interactions of dye molecules with nanoparticles at ambient conditions. Insights obtained and applications to probe single molecular orientations will be discussed. Center for Photochemical Sciences and Department of Chemistry.

  7. A titanosilicate molecular sieve with adjustable pores for size-selective adsorption of molecules

    NASA Astrophysics Data System (ADS)

    Kuznicki, Steven M.; Bell, Valerie A.; Nair, Sankar; Hillhouse, Hugh W.; Jacubinas, Richard M.; Braunbarth, Carola M.; Toby, Brian H.; Tsapatsis, Michael

    2001-08-01

    Zeolites and related crystalline microporous oxides-tetrahedrally coordinated atoms covalently linked into a porous framework-are of interest for applications ranging from catalysis to adsorption and ion-exchange. In some of these materials (such as zeolite rho) adsorbates, ion-exchange, and dehydration and cation relocation can induce strong framework deformations. Similar framework flexibility has to date not been seen in mixed octahedral/tetrahedral microporous framework materials, a newer and rapidly expanding class of molecular sieves. Here we show that the framework of the titanium silicate ETS-4, the first member of this class of materials, can be systematically contracted through dehydration at elevated temperatures to `tune' the effective size of the pores giving access to the interior of the crystal. We show that this so-called `molecular gate' effect can be used to tailor the adsorption properties of the materials to give size-selective adsorbents suitable for commercially important separations of gas mixtures of molecules with similar size in the 4.0 to 3.0Å range, such as that of N2/CH4, Ar/O2 and N2/O2.

  8. Molecular Quantum Spintronics: Supramolecular Spin Valves Based on Single-Molecule Magnets and Carbon Nanotubes

    PubMed Central

    Urdampilleta, Matias; Nguyen, Ngoc-Viet; Cleuziou, Jean-Pierre; Klyatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

    2011-01-01

    We built new hybrid devices consisting of chemical vapor deposition (CVD) grown carbon nanotube (CNT) transistors, decorated with TbPc2 (Pc = phthalocyanine) rare-earth based single-molecule magnets (SMMs). The drafting was achieved by tailoring supramolecular π-π interactions between CNTs and SMMs. The magnetoresistance hysteresis loop measurements revealed steep steps, which we can relate to the magnetization reversal of individual SMMs. Indeed, we established that the electronic transport properties of these devices depend strongly on the relative magnetization orientations of the grafted SMMs. The SMMs are playing the role of localized spin polarizer and analyzer on the CNT electronic conducting channel. As a result, we measured magneto-resistance ratios up to several hundred percent. We used this spin valve effect to confirm the strong uniaxial anisotropy and the superparamagnetic blocking temperature (TB ~ 1 K) of isolated TbPc2 SMMs. For the first time, the strength of exchange interaction between the different SMMs of the molecular spin valve geometry could be determined. Our results introduce a new design for operable molecular spintronic devices using the quantum effects of individual SMMs. PMID:22072910

  9. Room-temperature repositioning of individual C60 molecules at Cu steps: Operation of a molecular counting device

    NASA Astrophysics Data System (ADS)

    Cuberes, M. T.; Schlittler, R. R.; Gimzewski, J. K.

    1996-11-01

    C60 molecules absorbed on a monoatomic Cu step have been reversibly repositioned at room temperature with the tip of a scanning tunneling microscope by performing controlled displacements along the step direction. We demonstrate the feasibility of building an abacus on the nanometer scale using single molecules as ``counters,'' Cu monoatomic steps as ``rods'' that constrain the molecular motion to one dimension, and the scanning tunneling microscope as an ``actuator'' for counting operations.

  10. Surface-bound norbornylogous bridges as molecular rulers for investigating interfacial electrochemistry and as single molecule switches.

    PubMed

    Darwish, Nadim; Paddon-Row, Michael N; Gooding, J Justin

    2014-02-18

    Electron transfer (ET) reactions through molecules attached to surfaces, whether they are through single molecules or ensembles, are the subject of much research in molecular electronics, bioelectronics, and electrochemistry. Therefore, understanding the factors that govern ET is of high importance. The availability of rigid hydrocarbon molecular scaffolds possessing well-defined configurations and lengths that can be systematically varied is crucial to the development of such devices. In this Account, we demonstrate how suitably functionalized norbornylogous (NB) systems can provide important insights into interfacial ET processes and electrical conduction through single molecules. To this end, we created NB bridges with vic-trans-bismethylenethiol groups at one end so they can assemble on gold electrodes and redox species at the distal ends. With these in hand, we then formed mixed self-assembled monolayers (SAMs) containing a small proportion of the NB bridges diluted with alkanethiols. As such, the NB bridges served as molecular rulers for probing the environment above the surface defined by the diluent species. Using this construct, we were able to measure the interfacial potential distribution above the diluent surface, and track how variation in the ionic distribution in the electrical double layer impacts ET kinetics. Using the same construct, but with a redox molecule that remains neutral in both oxidized and reduced states, we could explore the impact of the chemical environment near a surface on ET processes. These results are important, because with conventional surface constructs, ET occurs across this interfacial region. Such knowledge is therefore relevant to the design of molecular systems at surfaces involving ET. With a second family of molecules, we investigated aspects of single-molecule electrical conduction using NB bridges bearing vic-trans-bismethylenethiol groups at both ends of the bridge. This gave us insights into distance-dependent electron transport through single molecules and introduced a method of boosting the conductance of saturated molecules by incorporating aromatic moieties in their backbone. These partially conjugated NB molecules represent a new class of molecular wires with far greater stability than conventional completely conjugated molecular wires. Of particular note was our demonstration of a single molecule switch, using a NB bridge containing an embedded anthraquinone redox group, the switching mechanism being via electrochemically controlled quantum interference. PMID:24160945

  11. Hierarchical protein patterning by meso to molecular scale self-assembly

    NASA Astrophysics Data System (ADS)

    Andersen, Andreas S.; Sutherland, Duncan S.; Ogaki, Ryosuke

    2015-10-01

    Numerous protein patterning methodologies are used extensively for biomedical research and development. We have developed a novel bottom-up protein patterning method using a combination of self-assembly processes in the meso to molecular scale range to allow hierarchical protein patterns to be straightforwardly fabricated with low cost over large areas. As a proof of principle, we patterned vitronectin in various dimensional hierarchies using meso to nanoscale colloids and self-assembled monolayers.

  12. A molecular symmetry analysis of the electronic states and transition dipole moments for molecules with two torsional degrees of freedom

    SciTech Connect

    Obaid, R.; Leibscher, M.

    2015-02-14

    We present a molecular symmetry analysis of electronic states and transition dipole moments for molecules which undergo large amplitude intramolecular torsions. The method is based on the correlation between the point group of the molecule at highly symmetric configurations and the molecular symmetry group. As an example, we determine the global irreducible representations of the electronic states and transition dipole moments for the quinodimethane derivative 2-[4-(cyclopenta-2,4-dien-1-ylidene)cyclohexa-2,5-dien-1-ylidene]-2H-1, 3-dioxole for which two torsional degrees of freedom can be activated upon photo-excitation and construct the resulting symmetry adapted transition dipole functions.

  13. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

    SciTech Connect

    Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh -Thu; Lu, Ruifeng; Lin, C. D.

    2015-10-27

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. Lastly, with picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement.

  14. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

    PubMed Central

    Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh-Thu; Lu, Ruifeng; Lin, C. D.

    2015-01-01

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. With picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement. PMID:26503116

  15. Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

    NASA Astrophysics Data System (ADS)

    Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

    2015-03-01

    Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of these COMs also spreads out. We calculated the temporal variation of the radial profiles of these COMs for different hot core models. These profiles resemble the so-called jump profiles with relative abundances higher than 10-9 within the evaporation font will furthermore be useful to model the observed spectra of hot cores. We present the simulated spectra of these COMs for different hot core models at various evolutionary timescales. A qualitative comparison of the simulated and observed spectra suggests that these self-consistent hot core models can reproduce the notable trends in hot core spectral variation within the typical hot core timescales of 105 year. These models predict that the spatial distribution of various emission line maps will also expand with evolutionary time; this feature can be used to constrain the relative desorption energies of the molecules that mainly form on the grain surface and return to the gas phase via thermal desorption. The detailed modeling of the thermal structure of hot cores with similar masses along with the characterization of the desorption energies of different molecules can be used to constrain the luminosity evolution of the central protostars. The model predictions can be compared with high resolution observation that can probe scales of a few thousand AU in high-mass star forming regions such as from Atacama Large Millimeter/submillimeter Array (ALMA). We used a spectral fitting method to analyze the simulated spectra and find that it significantly underestimates some of the physical parameters such as temperature. The coupling of chemical evolution with radiative transfer models will be particularly useful to decipher the physical structure of hot cores and also to constrain the initial evolutionary stages of high-mass star formation. Appendices are available in electronic form at http://www.aanda.org

  16. Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules

    SciTech Connect

    Cui, Q.; Karplus, M.

    2000-04-20

    A method for calculating the chemical shielding tensor of any atom with the QM/MM approach has been developed. The method is described and applied to a number of model systems including the water dimer, NMA-water complexes, cytosine monophosphate, paired and stacked nucleic acid bases, imidazole-metal complexes, and 1{prime}-deoxyribose-metal ion complexes. The results demonstrate that with an appropriate QM/MM partition, good descriptions of the environmental effects on chemical shift tensors are obtained. The typical error compared to full QM calculations is 1--2 ppm for heavy atoms. At distances below 2.5 {angstrom}, such as occur in hydrogen bonding, larger errors arise due to the lack of Pauli repulsion and magnetic susceptibility of the nearby groups in the current QM/MM model; including the hydrogen bonded molecules as part of the QM region is a way of solving this problem. The method is also applied to a simple model of myoglobin-CO and it is shown that the significant influence from the distal histidine on the shielding of Fe and CO is well reproduced by a QM/MM calculation. Application to the chemical shift of the 1-N nitrogen in nicotinamide adenine dinucleotide (NAD{sup +}), relative to N-methyl nicotinamide, gives good results, indicating that accurate chemical shifts can be obtained for specific atoms in large molecules that cannot be treated by QM at the MP2 level. The effect of solvation on the chemical shift of water was also studied with the QM/MM approach in a molecular dynamics framework. The test calculations described in this paper demonstrate that the QM/MM method for estimating shielding tensors and chemical shifts is a useful approach for large systems.

  17. Pattern Speeds of BIMA SONG Galaxies with Molecule-dominated Interstellar Mediums Using the Tremaine-Weinberg Method

    NASA Astrophysics Data System (ADS)

    Rand, Richard J.; Wallin, John F.

    2004-10-01

    We apply the Tremaine-Weinberg method of pattern speed determination to data cubes of CO emission in six spiral galaxies from the BIMA Survey of Nearby Galaxies, each with an interstellar medium dominated by molecular gas. We compare derived pattern speeds with estimates based on other methods, usually involving the identification of a predicted behavior at one or more resonances of the pattern(s). In two cases (NGC 1068 and NGC 4736), we find evidence for a central bar pattern speed that is greater than that of the surrounding spiral and roughly consistent with previous estimates. However, the spiral pattern speed in both cases is much larger than previous determinations. For the barred spirals NGC 3627 and NGC 4321, the method is insensitive to the bar pattern speed (the bar in each is nearly parallel to the major axis; in this case the method will not work), but for the former galaxy the spiral pattern speed found agrees with previous estimates of the bar pattern speed, suggesting that these two structures are part of a single pattern. For the latter, the spiral pattern speed found is in agreement with several previous determinations. For the flocculent spiral NGC 4414 and the ``Evil Eye'' galaxy NGC 4826, the method does not support the presence of a large-scale coherent pattern. We also apply the method to a simulated barred galaxy in order to demonstrate its validity and to understand its sensitivity to various observational parameters. In addition, we study the results of applying the method to a simulated, clumpy axisymmetric disk with no wave present. The Tremaine & Weinberg method in this case may falsely indicate a well-defined pattern.

  18. Biomimicry issues: the quest for sensing molecules at the origin of life using molecularly imprinter polymer

    NASA Astrophysics Data System (ADS)

    Carbonnier, Benjamin; Chehimi, Mohamed M.; Bakas, Idriss; Salmi, Zakaria; Mazerie, Isabelle; Floner, Didier; Geneste, Florence; Guerrouache, Mohamed

    The use of real time sensing analysis is becoming very popular in many applications and research areas such as, environment and agriculture for in situ monitoring of contaminants and food safety analysis, fundamental biology for studying for example protein-membrane interactions or drug discovery, health research for clinical diagnosis.[1] More recently, chip technology involving antibody-based detection system has been envisioned to search for life outside the Earth with a specific focus on Mars. [2] Sensors using such natural receptors are usually costly and suffer from the unstability of the surface-immobilized receptors. In this respect, the use of synthetic receptors appears as a very promising approach. Molecularly imprinting is undoubtedly one of the most promising approaches for designing biomimetic materials. In this respect, sensing microdevices based on molecularly imprinted polymers (MIPs) have attracted a great deal of interest over the recent years given their ability to recognize specifically and selectively molecules, proteins and even microorganisms, with excellent detection limits. MIPs can be prepared as powders, colloids and ultrathin films. The latter option is particularly interesting because it limits diffusion of the analytes to the artificial receptor sites within the sensing layers [3] and facilitates the making of nanostructured MIP grafts [4]. In addition, MIP sensing ultrathin layers are amenable to the detection of the analytes with varied transducing methods among which electrochemistry, a simple, versatile and easy to implement technique is very appealing to detect analytes concentrations in the picomolar or sub-picomolar range [5]. In this contribution, the important parameters in obtaining molecularly imprinted polymer layers grafted on gold working electrodes and exhibiting high sensitivity towards acid and base molecules are addressed. Square wave voltammetry is demonstrated to be a very powerful electroanalytical while the limit of detection of analytes can be decreased down to sub-nanomolar by controlling the MIP layers thickness. Finally, it is shown that such an approach offers potentials and opportunities for miniaturization to fulfill workspace constraints inherent to space exploration. Indeed, electrode arrays grafted with MIPs are prepared for portable sensor devices design. This work undoubtedly highlights molecularly imprinting in tandem with electrochemical detection as a very promising approach for sensing organic matter in a fast, highly sensitive and specific way. MIP-based biomimetic materials and their applications of as recognition layers within sensors are increasingly considered and it is expected that MIP will become a generic sensing technology This work is funded by the French National Research Agency (ANR) References: [1] C. Ayela, F. Roquet, L. Valera, C. Granier, L. Nicu, M. Pugnière, M. Biosensors and Bioelectronics 22 (2007) 3113. [2] M.A. Sephton, M.R. Sims, R.W. Court, D. Luong, D.C. Cullen, Planetary and Space Science 86 (2013) 66. [3] S. Lepinay, K. Khémara, M.-C. Millot, B. Carbonnier, Chem. Pap. 66 (2012) 340. [4] Y. Fuchs, O. Soppera, K. Haupt, Anal. Chim. Acta, 717 (2012) 7. [5] C. Malitesta, E. Mazzotta, R. A. Picca, A. Poma, I. Chianella, S. A. Piletsky, Anal. Bioanal. Chem. 402 (2012) 1827

  19. PDMS-Glass bonding using grafted polymeric adhesive - Alternative process flow for compatibility with patterned biological molecules

    PubMed Central

    Beh, Cyrus Weijie; Zhou, Weizhuang

    2013-01-01

    We report a novel modification of silicone elastomer, polydimethylsiloxane (PDMS) with a polymer graft that allows interfacial bonding between elastomer and glass substrate to be performed without exposure of said substrate to harsh treatment conditions like oxygen plasma. Organic molecules can thus be patterned within microfluidic channels and still remain functional post-bonding. In addition, after polymer grafting the PDMS can be stored in a desiccator for at least 40 days, and activated upon exposure to acidic buffer for bonding. The bonded devices remain fully bonded in excess of 80 psi driving pressure, with no signs of compromise to the bond integrity. Finally, we demonstrate the compatibility of our method with biological molecules using a proof-of-concept DNA sensing device, in which fluorescently-labelled DNA targets are successfully captured by a patterned probe in a device sealed using our method, while the pattern on a plasma-treated device was completely destroyed. Therefore, this method provides a much-needed alternative bonding process for incorporation of biological molecules in microfluidic devices. PMID:22858861

  20. Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns

    PubMed Central

    Benedetti, Manuel; Pontiggia, Daniela; Raggi, Sara; Cheng, Zhenyu; Scaloni, Flavio; Ferrari, Simone; Ausubel, Frederick M.; Cervone, Felice; De Lorenzo, Giulia

    2015-01-01

    Oligogalacturonides (OGs) are fragments of pectin that activate plant innate immunity by functioning as damage-associated molecular patterns (DAMPs). We set out to test the hypothesis that OGs are generated in planta by partial inhibition of pathogen-encoded polygalacturonases (PGs). A gene encoding a fungal PG was fused with a gene encoding a plant polygalacturonase-inhibiting protein (PGIP) and expressed in transgenic Arabidopsis plants. We show that expression of the PGIP–PG chimera results in the in vivo production of OGs that can be detected by mass spectrometric analysis. Transgenic plants expressing the chimera under control of a pathogen-inducible promoter are more resistant to the phytopathogens Botrytis cinerea, Pectobacterium carotovorum, and Pseudomonas syringae. These data provide strong evidence for the hypothesis that OGs released in vivo act as a DAMP signal to trigger plant immunity and suggest that controlled release of these molecules upon infection may be a valuable tool to protect plants against infectious diseases. On the other hand, elevated levels of expression of the chimera cause the accumulation of salicylic acid, reduced growth, and eventually lead to plant death, consistent with the current notion that trade-off occurs between growth and defense. PMID:25870275

  1. [Participation of damage-associated molecular patterns in conventional treatment of cancer].

    PubMed

    Rojo-León, Verónica; Aguilar-Cázares, Dolores; Prado-García, Heriberto; Carlos-Reyes, Angeles; López-González, José Sullivan

    2012-01-01

    Cells of the innate immune system are involved in discriminating between the innocuous cell death (apoptosis) which occurs in tissues during homeostasis, and the cell death associated to tissue damage (necrosis). Recently, a new variant of apoptosis termed immunogenic apoptosis has been described. In cancer, this type of cell death has acquired great relevance. In vitro and in vivo experimental models support that radiotherapy and some chemotherapeutic drugs induce the immunogenic apoptosis of malignant cells. Dying cells express at cytoplasmic membrane or release several nuclear or intracytoplasmic molecules termed "danger signals" or damage associated molecular patterns (DAMPs). DAMPs alert the organism and play a role inducing an efficient anti-tumor immune response. In this review, the importance of cell death by immunogenic apoptosis, the cytotoxic drugs that induce this type of cell death, the biologic role of some DAMPs and their participation in the activation of the antitumor immune response, in particular in the phagocytic cell, are indicated. The goal of this information should impact in improving the participation of the immune system in the recognition and efficient elimination of the residual tumor cells and to overcome the evasion mechanisms of tumor cells. This knowledge should lead to a better control of the growth of tumors with a concomitant reduction in the tumor recurrence. Also, an increase in the survival of the cancer patients or probably their definitive cure could be reached in the future. PMID:23045951

  2. Limited-projection-angle hybrid fluorescence molecular tomography of multiple molecules.

    PubMed

    Radrich, Karin; Mohajerani, Pouyan; Bussemer, Johanna; Schwaiger, Markus; Beer, Ambros J; Ntziachristos, Vasilis

    2014-04-01

    An advantage of fluorescence methods over other imaging modalities is the ability to concurrently resolve multiple moieties using fluorochromes emitting at different spectral regions. Simultaneous imaging of spectrally separated agents is helpful in interrogating multiple functions or establishing internal controls for accurate measurements. Herein, we investigated multimoiety imaging in the context of a limited-projection-angle hybrid fluorescence molecular tomography (FMT), and x-ray computed tomography implementation and the further registration with positron emission tomography (PET) data. Multichannel FMT systems may image fluorescent probes of varying distribution patterns. Therefore, it is possible that different channels may require different use of priors and regularization parameters. We examined the performance of automatically estimating regularization factors implementing priors, using data-driven regularization specific for limited-projection-angle schemes. We were particularly interested in identifying the implementation variations between hybrid-FMT channels due to probe distribution variation. For this reason, initial validation of the data-driven algorithm on a phantom was followed by imaging different agent distributions in animals, assuming superficial and deep seated activity. We further demonstrate the benefits of combining hybrid FMT with PET to gain multiple readings on the molecular composition of disease. PMID:24770661

  3. A graphene-based affinity nanosensor for detection of low-charge and low-molecular-weight molecules.

    PubMed

    Zhu, Yibo; Hao, Yufeng; Adogla, Enoch A; Yan, Jing; Li, Dachao; Xu, Kexin; Wang, Qian; Hone, James; Lin, Qiao

    2016-03-10

    This paper presents a graphene nanosensor for affinity-based detection of low-charge, low-molecular-weight molecules, using glucose as a representative. The sensor is capable of measuring glucose concentration in a practically relevant range of 2 μM to 25 mM, and can potentially be used in noninvasive glucose monitoring. PMID:26912374

  4. Laser guiding of cold molecules in a hollow optical fiber and continuous-wave cold molecular beam generation

    NASA Astrophysics Data System (ADS)

    Liu, Run-Qin; Yin, Ya-Ling; Yin, Jian-Ping

    2012-03-01

    A novel scheme for guiding arbitrary buffer-gas cooled neutral molecules in a hollow optical fiber (HOF) using a red-detuned HE11 mode is proposed and analysed theoretically. We give the electromagnetic field distribution of the HE11 mode in the HOF and calculate the optical potential of an I2 molecule, and study the molecule guiding mechanism using a classical Monte Carlo simulation. Using a 6 kW input laser, an S-shape HOF with a 2 cm curvature radius for both bends, and an input molecular beam with a transverse temperature of 0.5 K and longitudinal temperature of 5 K, we obtain a guiding efficiency of ~0.126% for the scheme, and the transverse and longitudinal temperatures of the guided molecular beam are 1.9 mK and 0.5 K, respectively.

  5. Pattern Formations in Polymer-Molecular Motor Networks

    NASA Astrophysics Data System (ADS)

    Smith, David; Humphrey, David; Duggan, Cynthia; Käs, Josef

    2001-03-01

    In previous studies with the microtubule-kinesin system, organized patterns such as asters and rotating vortices have been seen (Nedelec et al, Nature 1997), which were of a dynamic nature and dependent on active motors. A similar system was constructed using actin and myosin, which displays similar patterns, however, with drastically different dynamics. These patterns arise independent of the initial amount of immediate use energy (in the form of ATP), assembling only upon the near exhaustion of available ATP. Further studies have clearly shown that in fact these patterns are not dependent upon the motor activity of the myosin but its propensity to serve as a cross-linking element in an actin network, with the motor activity serving to prevent the arising of order in the system. We believe the dynamic differences inherent between the two polymer-motor systems studied lies primarily in the structural nature of the motor complexes, with the kinesin complex ordering the system by pushing multiple filaments in a parallel direction, and the myosin complexes disordering the system by pushing filaments in an antiparallel manner.

  6. Angle-Resolved High-Order Above-Threshold Ionization of a Molecule: Sensitive Tool for Molecular Characterization

    SciTech Connect

    Busuladzic, M.; Gazibegovic-Busuladzic, A.; Milosevic, D. B.; Becker, W.

    2008-05-23

    The strong-field approximation for ionization of diatomic molecules by an intense laser field is generalized to include rescattering of the ionized electron off the various centers of its molecular parent ion. The resulting spectrum and its interference structure strongly depend on the symmetry of the ground state molecular orbital. For N{sub 2}, if the laser polarization is perpendicular to the molecular axis, we observe a distinct minimum in the emission spectrum, which survives focal averaging and allows determination of, e.g., the internuclear separation. In contrast, for O{sub 2}, rescattering is absent in the same situation.

  7. Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

    PubMed

    Gladich, Ivan; Rodriguez, Alex; Hong Enriquez, Rolando P; Guida, Filomena; Berti, Federico; Laio, Alessandro

    2015-10-15

    Short peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature. PMID:26398715

  8. Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report

    SciTech Connect

    1997-07-01

    Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. A remarkable feature of REMPI, and one that is very basic to many of its applications and uses, is that the very narrow bandwidth of the {open_quotes}pump{close_quotes} laser makes it possible to select a specific vibrational and rotational level in the initial state and to prepare the excited state of interest in a single vibrational and rotational level. Thus, by suitable choice of the photon pump transition, it is possible to selectively ionize a species of interest without ionizing any other species that might be present. This feature makes REMPI one of the most powerful tools for ultrasensitive detection of species. With REMPI it is also possible to study the photoionization dynamics of a single rotational level of an excited electronic state. Such state-resolved studies can certainly be expected to provide significant insight into the underlying dynamics of molecular photoionization.

  9. Molecular dynamics of host-guest complexes of small gas molecules with calix[4]arenes.

    PubMed

    Adams, John E; Cox, Jack R; Christiano, Andrew J; Deakyne, Carol A

    2008-07-31

    The unexpected sorption of gases by a low-density p-tert-butylcalix[4]arene crystal polymorph raises fundamental questions about differential gas transport and sequestration in the organic solid state. To gain insight into the processes underlying these observations, we have used molecular dynamics simulations, augmented with calculations of potentials of mean force, to investigate the stability of isolated host-guest complexes and the relationship between the dynamics of these complexes and the dynamics of a solvated host molecule. Thermal fluctuations of the calixarenes themselves are found to be consistent with proposed mechanisms for gas entry into the host cavities, while relative host-guest stabilities correlate well with experimental absorption-desorption isotherms in some cases (CO2 and CH4) but not in others (C2H2). In these isolated systems, stable complexes characteristically form when the attractive interactions of the guest with the ring of negative charge density on the inner surface of the host cavity are not disrupted by thermal motion. The experimentally observed efficient uptake of gases such as C2H2 by the host crystals suggests, however, that stabilization of host-guest complexes in some systems may derive from dynamical constraints imposed by the crystal lattice. PMID:18593133

  10. Small molecule kinase inhibitors alleviate different molecular features of myotonic dystrophy type 1

    PubMed Central

    Wojciechowska, Marzena; Taylor, Katarzyna; Sobczak, Krzysztof; Napierala, Marek; Krzyzosiak, Wlodzimierz J

    2014-01-01

    Expandable (CTG)n repeats in the 3′ UTR of the DMPK gene are a cause of myotonic dystrophy type 1 (DM1), which leads to a toxic RNA gain-of-function disease. Mutant RNAs with expanded CUG repeats are retained in the nucleus and aggregate in discrete inclusions. These foci sequester splicing factors of the MBNL family and trigger upregulation of the CUGBP family of proteins resulting in the mis-splicing of their target transcripts. To date, many efforts to develop novel therapeutic strategies have been focused on disrupting the toxic nuclear foci and correcting aberrant alternative splicing via targeting mutant CUG repeats RNA; however, no effective treatment for DM1 is currently available. Herein, we present results of culturing of human DM1 myoblasts and fibroblasts with two small-molecule ATP-binding site-specific kinase inhibitors, C16 and C51, which resulted in the alleviation of the dominant-negative effects of CUG repeat expansion. Reversal of the DM1 molecular phenotype includes a reduction of the size and number of foci containing expanded CUG repeat transcripts, decreased steady-state levels of CUGBP1 protein, and consequent improvement of the aberrant alternative splicing of several pre-mRNAs misregulated in DM1. PMID:24824895

  11. Specific features of propagation of femtosecond laser pulses through a molecular gaseous medium under conditions of efficient alignment of molecules

    SciTech Connect

    Gulyaev, A V; Tikhonova, O V

    2013-07-31

    The propagation of femtosecond laser pulses in a molecular gaseous medium is studied with the rotational dynamics of molecules under the action of these pulses taken into account. Based on the simultaneous numerical solution of the wave equation describing the laser pulse evolution and the Schroedinger equation that determines the quantum state evolution of the medium molecules, the rotational dynamics of molecules in the laser field and the laser pulse evolution are analysed with their mutual influence taken into account. Efficient dynamic alignment of molecules along the direction of laser radiation polarisation is observed, which causes variation in the spatiotemporal pulse profile, as well as significant broadening and deformation of its spectrum in the course of propagation through the medium. The physical mechanisms of the observed phenomena are analysed by using the approximate analytical solution of the problem, derived for the case of preliminary excitation of the medium by a pump pulse (the pump-probe scheme). (nonlinear optical phenomena)

  12. Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report

    SciTech Connect

    Wasielewski, M.R.

    1997-01-01

    'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

  13. Continuously Adjustable, Molecular-Sieving “Gate” on 5A Zeolite for Distinguishing Small Organic Molecules by Size

    PubMed Central

    Song, Zhuonan; Huang, Yi; Xu, Weiwei L.; Wang, Lei; Bao, Yu; Li, Shiguang; Yu, Miao

    2015-01-01

    Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. This novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation. PMID:26358480

  14. Mosaic cellular patterning in the nose: Adhesion molecules give their two scents.

    PubMed

    Beaudoin, Gerard M J

    2016-02-29

    The sense of smell is mediated by the olfactory epithelium, which is composed of a mosaic pattern of olfactory sensory cells surrounded by supporting cells. In this issue, Katsunuma et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201509020) show that the differential expression of nectins and cadherins establishes this pattern. PMID:26929448

  15. Practical Approaches for Mining Frequent Patterns in Molecular Datasets

    PubMed Central

    Naulaerts, Stefan; Moens, Sandy; Engelen, Kristof; Berghe, Wim Vanden; Goethals, Bart; Laukens, Kris; Meysman, Pieter

    2016-01-01

    Pattern detection is an inherent task in the analysis and interpretation of complex and continuously accumulating biological data. Numerous itemset mining algorithms have been developed in the last decade to efficiently detect specific pattern classes in data. Although many of these have proven their value for addressing bioinformatics problems, several factors still slow down promising algorithms from gaining popularity in the life science community. Many of these issues stem from the low user-friendliness of these tools and the complexity of their output, which is often large, static, and consequently hard to interpret. Here, we apply three software implementations on common bioinformatics problems and illustrate some of the advantages and disadvantages of each, as well as inherent pitfalls of biological data mining. Frequent itemset mining exists in many different flavors, and users should decide their software choice based on their research question, programming proficiency, and added value of extra features. PMID:27168722

  16. Real-Space Imaging of Molecular Structure by Single-Molecule Inelastic Tunneling Probe

    NASA Astrophysics Data System (ADS)

    Han, Zhumin; Chiang, Chi-Lun; Xu, Chen; Ho, Wilson

    2014-03-01

    The scanning tunneling microscope is one of the most powerful tools to perform real space imaging of the electronic, magnetic, optical, and vibrational signatures of a single molecule. However, the spatial distributions of these signatures do not always relate directly to the geometric structures of the molecules. In this study, a CO molecule is transferred from the surface to a STM tip. The energy and intensity of the hindered translational mode of the CO vary when the tip is scanned across an adsorbed molecule (such as cobalt phthalocyanine). By monitoring these variations in space, we are able to resolve the geometric structure of the molecule and even subtle intramolecular and intermolecular interactions.

  17. Single-molecule imaging of organic semiconductors: Toward nanoscale insights into photophysics and molecular packing

    NASA Astrophysics Data System (ADS)

    Shepherd, W. E. B.; Grollman, R.; Robertson, A.; Paudel, K.; Hallani, R.; Loth, M. A.; Anthony, J. E.; Ostroverkhova, O.

    2015-06-01

    Photophysical properties of functionalized anthradithiophene (ADT) and pentacene (Pn) derivatives, as well as energy and charge transfer properties of donor-acceptor (D/A) pairs of these derivatives, are presented. The molecules studied were imaged on the single-molecule level in a polymeric and in a functionalized benzothiophene (BTBTB) crystalline host using room-temperature wide-field epifluorescence microscopy. The BTBTB host imposed orientational constraints on the guest molecules, depending on their functionalization. Flexibility of functionalization of both guest (ADT, Pn) and host (BTBTB) molecules can be used for systematic studies of nanoscale morphology and photophysics of D/A organic semiconductor bulk heterojunctions using single-molecule fluorescence microscopy.

  18. Opening the way to molecular cycloaddition of large molecules on supported silicene

    NASA Astrophysics Data System (ADS)

    Stephan, Régis; Hanf, Marie-Christine; Sonnet, Philippe

    2015-10-01

    Within density functional theory, the adsorption of the H2Pc molecule on the (3 × 3) silicene/(4 × 4) Ag(111) surface has been investigated. We observe an electronic redistribution in the central macrocycle of the H2Pc molecule and the formation of two Si - N covalent bonds between the molecule and the silicene, in agreement with a cycloaddition reaction. However, while on SiC(0001)(3 × 3) or Si ( 111 ) ( √{ 3 } × √{ 3 } ) R 30 °-boron, the H2Pc molecule remains planar, and the H2Pc molecule takes a butterfly conformation on the silicene/Ag substrate due to an electrostatic or a polarization repulsion between the molecule and the silicene. Our study opens a way to the experimental adsorption of large organic molecules on supported silicene.

  19. A Purification Method for a Molecular Complex in Which a Scaffold Molecule Is Fully Loaded with Heterogeneous Molecules

    PubMed Central

    Ohuchi, Shoji J.; Sagawa, Fumihiko; Ohno, Hirohisa; Inoue, Tan

    2015-01-01

    An affinity resin-based pull-down method is convenient for the purification of biochemical materials. However, its use is difficult for the isolation of a molecular complex fully loaded with multiple components from a reaction mixture containing the starting materials and intermediate products. To overcome this problem, we have developed a new purification procedure that depends on sequential elimination of the residues. In practice, two affinity resins were used for purifying a triangular-shaped RNP (RNA-protein complex) consisting of three ribosomal proteins (L7Ae) bound to an RNA scaffold. First, a resin with immobilized L7Ae protein captured the incomplete RNP complexes and the free RNA scaffold. Next, another resin with an immobilized chemically modified RNA of a derivative of Box C/D motif, the binding partner of L7Ae, was used to capture free protein. The complete triangular RNP was successfully purified from the mixture by these two steps. Obviously, the purified triangular RNP displaying three protein-binding peptides exhibited an improved performance when compared with the unrefined product. Conceptually, this purification procedure should be applicable for the purification of a variety of complexes consisting of multiple components other than RNP. PMID:25781936

  20. Hunting complex differential gene interaction patterns across molecular contexts

    PubMed Central

    Song, Mingzhou; Zhang, Yang; Katzaroff, Alexia J.; Edgar, Bruce A.; Buttitta, Laura

    2014-01-01

    Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CPχ2) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets for conserved and differential interactions. CPχ2 decomposes interactions across conditions to assess homogeneity and heterogeneity. Theoretically, we prove an asymptotic chi-square null distribution for the interaction heterogeneity statistic. Empirically, on synthetic yeast cell cycle data, CPχ2 achieved much higher statistical power in detecting differential networks than alternative approaches. We applied CPχ2 to Drosophila melanogaster wing gene expression arrays collected under normal conditions, and conditions with overexpressed E2F and Cabut, two transcription factor complexes that promote ectopic cell cycling. The resulting differential networks suggest a mechanism by which E2F and Cabut regulate distinct gene interactions, while still sharing a small core network. Thus, CPχ2 is sensitive in detecting network rewiring, useful in comparing related biological systems. PMID:24482443

  1. A tripodal molecule on a gold surface: orientation-dependent coupling and electronic properties of the molecular legs.

    PubMed

    Lukas, Maya; Dössel, Kerrin; Schramm, Alexandrina; Fuhr, Olaf; Stroh, Christophe; Mayor, Marcel; Fink, Karin; v Löhneysen, Hilbert

    2013-07-23

    The realization of molecular electronics demands a detailed knowledge of the correlation between chemical groups and electronic function. It has become obvious during the last years that the conformation of a molecule and its coupling to the connecting electrodes plays a crucial role in its conductance behavior and its electronic function, e.g., as a switch. Knowledge about these relationships is therefore essential for future design of molecular electronic building blocks. We present a new three-dimensional molecule, consisting of three identical molecular wires connected to a headgroup. Due to the well-defined spatial arrangement of the molecule in a nonplanar geometry, it is possible to investigate the conductance behavior of these wires with respect to their position and coupling to the surface electrode with the submolecular resolution of a scanning tunneling microscope. The experimental findings are supported by calculations of the electronic structure and conformation of the molecule on the surface by density functional theory with dispersion corrections. PMID:23790078

  2. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules.

    PubMed

    Borek, Bartłomiej; Hasty, Jeff; Tsimring, Lev

    2016-01-01

    The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems. PMID:27148743

  3. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules

    PubMed Central

    Hasty, Jeff; Tsimring, Lev

    2016-01-01

    The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems. PMID:27148743

  4. Dynamical behavior of one-dimensional water molecule chains in zeolites: Nanosecond time-scale molecular dynamics simulations of bikitaite

    NASA Astrophysics Data System (ADS)

    Demontis, Pierfranco; Stara, Giovanna; Suffritti, Giuseppe B.

    2004-05-01

    Nanosecond scale molecular dynamics simulations of the behavior of the one-dimensional water molecule chains adsorbed in the parallel nanochannels of bikitaite, a rare lithium containing zeolite, were performed at different temperatures and for the fully and partially hydrated material. New empirical potential functions have been developed for representing lithium-water interactions. The structure and the vibrational spectrum of bikitaite were in agreement both with experimental data and Car-Parrinello molecular dynamics results. Classical molecular dynamics simulations were extended to the nanosecond time scale in order to study the flip motion of water molecules around the hydrogen bonds connecting adjacent molecules in the chains, which has been observed by NMR experiments, and the dehydration mechanism at high temperature. Computed relaxation times of the flip motion follow the Arrhenius behavior found experimentally, but the activation energy of the simulated system is slightly underestimated. Based on the results of the simulations, it may be suggested that the dehydration proceeds by a defect-driven stepwise diffusion. The diffusive mechanism appears as a single-file motion: the molecules never pass one another, even at temperatures as high as about 1000 K, nor can they switch between different channels. However, the mean square displacement (MSD) of the molecules, computed with respect to the center of mass of the simulated system, shows an irregular trend from which the single-file diffusion cannot be clearly evidenced. If the MSDs are evaluated with respect to the center of mass of the molecules hosted in each channel, the expected dependence on the square root of time finally appears.

  5. Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

    PubMed Central

    2009-01-01

    Background A method to estimate ease of synthesis (synthetic accessibility) of drug-like molecules is needed in many areas of the drug discovery process. The development and validation of such a method that is able to characterize molecule synthetic accessibility as a score between 1 (easy to make) and 10 (very difficult to make) is described in this article. Results The method for estimation of the synthetic accessibility score (SAscore) described here is based on a combination of fragment contributions and a complexity penalty. Fragment contributions have been calculated based on the analysis of one million representative molecules from PubChem and therefore one can say that they capture historical synthetic knowledge stored in this database. The molecular complexity score takes into account the presence of non-standard structural features, such as large rings, non-standard ring fusions, stereocomplexity and molecule size. The method has been validated by comparing calculated SAscores with ease of synthesis as estimated by experienced medicinal chemists for a set of 40 molecules. The agreement between calculated and manually estimated synthetic accessibility is very good with r2 = 0.89. Conclusion A novel method to estimate synthetic accessibility of molecules has been developed. This method uses historical synthetic knowledge obtained by analyzing information from millions of already synthesized chemicals and considers also molecule complexity. The method is sufficiently fast and provides results consistent with estimation of ease of synthesis by experienced medicinal chemists. The calculated SAscore may be used to support various drug discovery processes where a large number of molecules needs to be ranked based on their synthetic accessibility, for example when purchasing samples for screening, selecting hits from high-throughput screening for follow-up, or ranking molecules generated by various de novo design approaches. PMID:20298526

  6. Molecular Characterisation of Small Molecule Agonists Effect on the Human Glucagon Like Peptide-1 Receptor Internalisation

    PubMed Central

    Thompson, Aiysha; Stephens, Jeffrey W.; Bain, Stephen C.

    2016-01-01

    The glucagon-like peptide receptor (GLP-1R), which is a G-protein coupled receptor (GPCR), signals through both Gαs and Gαq coupled pathways and ERK phosphorylation to stimulate insulin secretion. The aim of this study was to determine molecular details of the effect of small molecule agonists, compounds 2 and B, on GLP-1R mediated cAMP production, intracellular Ca2+ accumulation, ERK phosphorylation and its internalisation. In human GLP-1R (hGLP-1R) expressing cells, compounds 2 and B induced cAMP production but caused no intracellular Ca2+ accumulation, ERK phosphorylation or hGLP-1R internalisation. GLP-1 antagonists Ex(9–39) and JANT-4 and the orthosteric binding site mutation (V36A) in hGLP-1R failed to inhibit compounds 2 and B induced cAMP production, confirming that their binding site distinct from the GLP-1 binding site on GLP-1R. However, K334A mutation of hGLP-1R, which affects Gαs coupling, inhibited GLP-1 as well as compounds 2 and B induced cAMP production, indicating that GLP-1, compounds 2 and B binding induce similar conformational changes in the GLP-1R for Gαs coupling. Additionally, compound 2 or B binding to the hGLP-1R had significantly reduced GLP-1 induced intracellular Ca2+ accumulation, ERK phosphorylation and hGLP-1R internalisation. This study illustrates pharmacology of differential activation of GLP-1R by GLP-1 and compounds 2 and B. PMID:27100083

  7. Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level

    NASA Astrophysics Data System (ADS)

    Okholm, A. H.; Aslan, H.; Besenbacher, F.; Dong, M.; Kjems, J.

    2015-06-01

    DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth.DNA origami has been used to orchestrate reactions with nano-precision using a variety of biomolecules. Here, the dynamics of albumin-assisted, localized single-molecule DNA polymerization by terminal deoxynucleotidyl transferase on a 2D DNA origami are monitored using AFM in liquid. Direct visualization of the surface activity revealed the mechanics of growth. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01945a

  8. Molecule-pharmacophore superpositioning and pattern matching in computational drug design.

    PubMed

    Wolber, Gerhard; Seidel, Thomas; Bendix, Fabian; Langer, Thierry

    2008-01-01

    Three-dimensional (3D) pharmacophore modeling is a technique for describing the interaction of a small molecule ligand with a macromolecular target. Since chemical features in a pharmacophore model are well known and highly transparent for medicinal chemists, these models are intuitively understandable and have been increasingly successful in computational drug discovery in the past few years. The performance and applicability of pharmacophore modeling depends on two main factors: the definition and placement of pharmacophoric features and the alignment techniques used to overlay 3D pharmacophore models and small molecules. An overview of key technologies and latest developments in the area of 3D pharmacophores is given and provides insight into different approaches as implemented by the 3D pharmacophore modeling packages like Catalyst, MOE, Phase and LigandScout. PMID:18190860

  9. Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality

    SciTech Connect

    Brito Silva, C. A. Jr.; Granhen, E. R.; Silva, S. J. S. da; Leal, J. F. P.; Del Nero, J.; Pinheiro, F. A.

    2010-08-15

    We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

  10. Directional crystallization of polymer molecules through solvent annealing on a patterned substrate.

    PubMed

    Li, Hongwei; Zhang, Xinping

    2015-04-01

    Multi-crystalline fibers of poly (3-hexylthiophene) (P3HT) have been grown on a patterned substrate through annealing the spin-coated film in the solvent of 1,5-pentanediol at 120 °C. The large-area patterns of photoresist grating have been fabricated by interference lithography, enabling growth of crystal fibers in a length scale of centimeters. The produced organic crystal fibers were characterized by microscopic, spectroscopic, and electrical conductivity performances. Mechanisms for the crystallization processes were investigated. PMID:25968681

  11. Genetic basis of dental agenesis - molecular genetics patterning clinical dentistry

    PubMed Central

    Goswami, Mridula; Chhabra, Anuj

    2014-01-01

    Tooth agenesis is one of the most common congenital malformations in humans. Hypodontia can either occur as an isolated condition (non-syndromic hypodontia) or can be associated with a syndrome (syndromic hypodontia), highlighting the heterogeneity of the condition. Though much progress has been made to identify the developmental basis of tooth formation, knowledge of the etiological basis of inherited tooth loss is still lacking. To date, the mutation spectra of non-syndromic form of familial and sporadic tooth agenesis in humans have revealed defects in various such genes that encode transcription factors, MSX1 and PAX9 or genes that code for a protein involved in canonical Wnt signaling (AXIN2), and a transmembrane receptor of fibroblast growth factors (FGFR1). The aim of this paper is to review the current literature on the molecular mechanisms responsible for selective hypodontia in humans and to present a detailed overview of causative genes and syndromes associated with hypodontia. Key words:Tooth agenesis, hypodontia, growth factors, mutations. PMID:24121910

  12. A molecular-beam apparatus with a spray-jet technique for studying neutral non-volatile molecules

    NASA Astrophysics Data System (ADS)

    Yamada, Toshiki; Shinohara, Hidenori; Maofa, Ge; Mashiko, Shinro; Kimura, Katsumi

    2003-03-01

    A molecular-beam apparatus has been newly constructed for studying neutral non-volatile molecules, consisting of (1) a sample inlet system with a supersonic nebulizer, an inlet chamber, and a pulsed nozzle, (2) a set of skimmers, and (3) a high-vacuum chamber in which pulsed-laser photoionization and mass detection are carried out. A heavy mist of sample solution is initially prepared with the nebulizer, and then stored in the inlet chamber, from which a molecular beam is ejected into vacuum through the pulsed nozzle and skimmers. In this report we want to emphasize several advantages of this technique and its broad applicability.

  13. Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups

    NASA Astrophysics Data System (ADS)

    Gorkunov, M. V.; Osipov, M. A.; Kocot, A.; Vij, J. K.

    2010-06-01

    Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry.

  14. A graphene-based affinity nanosensor for detection of low-charge and low-molecular-weight molecules

    NASA Astrophysics Data System (ADS)

    Zhu, Yibo; Hao, Yufeng; Adogla, Enoch A.; Yan, Jing; Li, Dachao; Xu, Kexin; Wang, Qian; Hone, James; Lin, Qiao

    2016-03-01

    This paper presents a graphene nanosensor for affinity-based detection of low-charge, low-molecular-weight molecules, using glucose as a representative. The sensor is capable of measuring glucose concentration in a practically relevant range of 2 μM to 25 mM, and can potentially be used in noninvasive glucose monitoring.This paper presents a graphene nanosensor for affinity-based detection of low-charge, low-molecular-weight molecules, using glucose as a representative. The sensor is capable of measuring glucose concentration in a practically relevant range of 2 μM to 25 mM, and can potentially be used in noninvasive glucose monitoring. Electronic supplementary information (ESI) available: Further details on experiments, materials, fabrication, and data analysis. See DOI: 10.1039/c5nr08866f

  15. Resonance enhanced multiphoton ionization spectra of molecules and molecular fragments. Annual technical report, March 1991--February 1992

    SciTech Connect

    1993-12-31

    Resonance Enhanced Multiphoton Ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that state before it can decay. The overall objective of this effort is to carry out theoretical studies of these REMPI processes in molecules and molecular fragments which are designed to provide a robust analysis and prediction of key spectral features of interest in several experimental studies and applications of this technique. A specific and very important objective of the effort is to predict the vibrational and rotational ion distributions which result from REMPI of representative molecules and to understand the underlying mechanisms that give use to these ion distributions. The author highlights progress made during this period.

  16. Single Molecule PCR Reveals Similar Patterns of Non-Homologous DSB Repair in Tobacco and Arabidopsis

    PubMed Central

    Lloyd, Andrew H.; Wang, Dong; Timmis, Jeremy N.

    2012-01-01

    DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (120 bp) deletions occurred at a minority (2545%) of repair junctions. Approximately ?1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ. PMID:22389691

  17. Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm

    NASA Astrophysics Data System (ADS)

    Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Markevicius, Augustinas; Solà, Jordi

    2016-02-01

    Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

  18. Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm.

    PubMed

    Kassem, Salma; Lee, Alan T L; Leigh, David A; Markevicius, Augustinas; Solà, Jordi

    2016-02-01

    Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk. PMID:26791896

  19. High-order harmonic generation in diatomic molecules: A quantum-orbit analysis of the interference patterns

    SciTech Connect

    Figueira de Morisson Faria, C.

    2007-10-15

    We perform a detailed analysis of high-order harmonic generation in diatomic molecules within the strong-field approximation (SFA), with emphasis on quantum-interference effects. Specifically, we investigate how the different types of electron orbits, involving one or two centers, affect the interference patterns in the spectra. We also briefly address the influence of the choice of gauge and of the initial and final electronic bound states on such patterns. For the length-gauge SFA and undressed bound states, there exist additional terms, which can be interpreted as potential energy shifts. If, on the one hand, such shifts alter the potential barriers through which the electron initially tunnels, and may lead to a questionable physical interpretation of the features encountered, on the other hand, they seem to be necessary in order to reproduce the overall maxima and minima in the spectra. Indeed, for dressed electronic bound states in the length gauge, or undressed bound states in the velocity gauge, for which such shifts are absent, there is a breakdown of the interference patterns. In order to avoid such a problem, we provide an alternative pathway for the electron to reach the continuum, by means of an additional attosecond-pulse train. A comparison of the purely monochromatic case with the situation for which the attosecond pulses are present suggests that the patterns are due to the interference between the electron orbits which finish at different centers, regardless of whether one or two centers are involved.

  20. De novo design of drug-like molecules by a fragment-based molecular evolutionary approach.

    PubMed

    Kawai, Kentaro; Nagata, Naoya; Takahashi, Yoshimasa

    2014-01-27

    This paper describes a similarity-driven simple evolutionary approach to producing candidate molecules of new drugs. The aim of the method is to explore the candidates that are structurally similar to the reference molecule and yet somewhat different in not only peripheral chains but also their scaffolds. The method employs a known active molecule of our interest as a reference molecule which is used to navigate a huge chemical space. The reference molecule is also used to obtain seed fragments. An initial set of individual structures is prepared with the seed fragments and additional fragments using several connection rules. The fragment library is preferably prepared from a collection of known molecules related to the target of the reference molecule. Every fragment of the library can be used for fragment-based mutation. All the fragments are categorized into three classes; rings, linkers, and side chains. New individuals are produced by the crossover and the fragment-based mutation with the fragment library. Computer experiments with our own fragment library prepared from GPCR SARfari verified the feasibility of our approach to drug discovery. PMID:24372539

  1. In situ formation and photo patterning of emissive quantum dots in small organic molecules.

    PubMed

    Bansal, Ashu K; Sajjad, Muhammad T; Antolini, Francesco; Stroea, Lenuta; Gečys, Paulius; Raciukaitis, Gediminas; André, Pascal; Hirzer, Andreas; Schmidt, Volker; Ortolani, Luca; Toffanin, Stefano; Allard, Sybille; Scherf, Ullrich; Samuel, Ifor D W

    2015-07-01

    Nanostructured composites of inorganic and organic materials are attracting extensive interest for electronic and optoelectronic device applications. Here we report a novel method for the fabrication and patterning of metal selenide nanoparticles in organic semiconductor films that is compatible with solution processable large area device manufacturing. Our approach is based upon the controlled in situ decomposition of a cadmium selenide precursor complex in a film of the electron transporting material 1,3,5-tris(N-phenyl-benzimidazol-2-yl)-benzene (TPBI) by thermal and optical methods. In particular, we show that the photoluminescence quantum yield (PLQY) of the thermally converted CdSe quantum dots (QDs) in the TPBI film is up to 15%. We also show that laser illumination can form the QDs from the precursor. This is an important result as it enables direct laser patterning (DLP) of the QDs. DLP was performed on these nanocomposites using a picosecond laser. Confocal microscopy shows the formation of emissive QDs after laser irradiation. The optical and structural properties of the QDs were also analysed by means of UV-Vis, PL spectroscopy and transmission electron microscopy (TEM). The results show that the QDs are well distributed across the film and their emission can be tuned over a wide range by varying the temperature or irradiated laser power on the blend films. Our findings provide a route to the low cost patterning of hybrid electroluminescent devices. PMID:26062105

  2. In situ formation and photo patterning of emissive quantum dots in small organic molecules

    NASA Astrophysics Data System (ADS)

    Bansal, Ashu K.; Sajjad, Muhammad T.; Antolini, Francesco; Stroea, Lenuta; Gečys, Paulius; Raciukaitis, Gediminas; André, Pascal; Hirzer, Andreas; Schmidt, Volker; Ortolani, Luca; Toffanin, Stefano; Allard, Sybille; Scherf, Ullrich; Samuel, Ifor D. W.

    2015-06-01

    Nanostructured composites of inorganic and organic materials are attracting extensive interest for electronic and optoelectronic device applications. Here we report a novel method for the fabrication and patterning of metal selenide nanoparticles in organic semiconductor films that is compatible with solution processable large area device manufacturing. Our approach is based upon the controlled in situ decomposition of a cadmium selenide precursor complex in a film of the electron transporting material 1,3,5-tris(N-phenyl-benzimidazol-2-yl)-benzene (TPBI) by thermal and optical methods. In particular, we show that the photoluminescence quantum yield (PLQY) of the thermally converted CdSe quantum dots (QDs) in the TPBI film is up to 15%. We also show that laser illumination can form the QDs from the precursor. This is an important result as it enables direct laser patterning (DLP) of the QDs. DLP was performed on these nanocomposites using a picosecond laser. Confocal microscopy shows the formation of emissive QDs after laser irradiation. The optical and structural properties of the QDs were also analysed by means of UV-Vis, PL spectroscopy and transmission electron microscopy (TEM). The results show that the QDs are well distributed across the film and their emission can be tuned over a wide range by varying the temperature or irradiated laser power on the blend films. Our findings provide a route to the low cost patterning of hybrid electroluminescent devices.

  3. PTX3, a humoral pattern recognition molecule at the interface between microbe and matrix recognition.

    PubMed

    Garlanda, Cecilia; Jaillon, Sebastien; Doni, Andrea; Bottazzi, Barbara; Mantovani, Alberto

    2016-02-01

    Innate immunity consists of a cellular and a humoral arm. PTX3 is a fluid patter recognition molecule (PRM) with antibody-like properties. Gene targeted mice and genetic associations in humans suggest that PTX3 plays a non-redundant role in resistance against selected pathogens (e.g. Aspergillus fumigatus, Pseudomonas aeruginosa, uropathogenic Escherichia coli) and in the regulation of inflammation. PTX3 acts as an extrinsic oncosuppressor by taming complement elicited tumor-promoting inflammation. Recent results indicate that, by interacting with provisional matrix components, PTX3 contributes to the orchestration of tissue repair. An acidic pH sets PTX3 in a tissue repair mode, while retaining anti-microbial recognition. Based on these data and scattered information on humoral PRM and matrix components, we surmise that matrix and microbial recognition are related functions in evolution. PMID:26650391

  4. A molecular dynamics study of Hras-GTP and GDP complexes: The properties of water molecules around guanine nucleotide

    NASA Astrophysics Data System (ADS)

    Miyakawa, T.; Morikawa, R.; Takasu, M.; Sugimori, K.; Kawaguchi, K.; Saito, H.; Nagao, H.

    2013-02-01

    We study the structures of Hras-GTP and Hras-GDP complexes in water in order to investigate the mechanism of hydrolysis of GTP in the Hras-GTP complex. Understanding of the mechanism of hydrolysis of GTP in the Hras-GTP complex plays a key role in overcoming the human cancer. We performed molecular dynamics (MD) simulations of Hras-GTP complex and Hras-GDP complex in water using AMBER03 parameters and our calculated parameters around Mg2+. Using the trajectories of the MD simulations, we calculated the radial distribution functions of water molecules around the phosphorus atoms in guanine nucleotide in each complex. We also calculated the radius of the first hydration sphere, the averaged number of water molecules in the first hydration sphere, and the distribution of duration time of water molecules in the first hydration sphere. We also calculated the distribution of water molecules with respect to the angle around the PG in GTP and PB in GDP. It is suggested that the hydrolysis is triggered by water molecules attacking ?-phosphate from the direction rotated 35 to the O1B from the axis defined by PG and O3B.

  5. Molecular Combing of Single DNA Molecules on the 10 Megabase Scale.

    PubMed

    Kaykov, Atanas; Taillefumier, Thibaud; Bensimon, Aaron; Nurse, Paul

    2016-01-01

    DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200-500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions. PMID:26781994

  6. Molecular Combing of Single DNA Molecules on the 10 Megabase Scale

    PubMed Central

    Kaykov, Atanas; Taillefumier, Thibaud; Bensimon, Aaron; Nurse, Paul

    2016-01-01

    DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200–500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions. PMID:26781994

  7. The Distribution of Complex Organic Molecules in the Orion KL Molecular Core

    NASA Technical Reports Server (NTRS)

    Kuan, Yi-Jehng; Hsu, Yu-Sen; Charnley, Steven B.; Wang, Kuo-Song

    2011-01-01

    We conducted high angular-resolution observations toward the massive star-forming region Orion KL at 1.3 mm using the Submillimeter Array (SMA). Spectral emission from twelve complex organic molecules was simultaneously imaged. We discuss the distinct chemical characteristics among four sub- regions in Orion KL by comparing the spatial distributions and fractional abundances of these complex molecules. These observations will allow us to test and constrain chemical models of interstellar organic synthesis.

  8. Extracting physics of life at the molecular level: A review of single-molecule data analyses.

    PubMed

    Colomb, Warren; Sarkar, Susanta K

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. PMID:25660417

  9. Oxidation-Specific Epitopes are Danger Associated Molecular Patterns Recognized by Pattern Recognition Receptors of Innate Immunity

    PubMed Central

    Miller, Yury I.; Choi, Soo-Ho; Wiesner, Philipp; Fang, Longhou; Harkewicz, Richard; Hartvigsen, Karsten; Boullier, Agns; Gonen, Ayelet; Diehl, Cody J.; Que, Xuchu; Montano, Erica; Shaw, Peter X.; Tsimikas, Sotirios; Binder, Christoph J.; Witztum, Joseph L.

    2010-01-01

    Oxidation reactions are vital parts of metabolism and signal transduction. However, they also produce reactive oxygen species, which damage lipids, proteins and DNA, generating oxidation-specific epitopes. In this review, we will discuss the hypothesis that such common oxidation-specific epitopes are a major target of innate immunity, recognized by a variety of pattern recognition receptors (PRRs). By analogy with microbial pathogen associated molecular patterns (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent danger (or damage) associated molecular patterns (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Further, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation-specific epitopes, such PAMPs provided a strong secondary selecting pressure for the same set of oxidation-specific PRRs as well. Because lipid peroxidation is ubiquitous and a major component of the inflammatory state associated with atherosclerosis, the understanding that oxidation-specific epitopes are DAMPs, and thus the target of multiple arcs of innate immunity, provides novel insights into the pathogenesis of atherosclerosis. As examples, we show that both cellular and soluble PRRs, such as CD36, toll-like receptor-4, natural antibodies, and CRP recognize common oxidation-specific DAMPs, such as oxidized phospholipids and oxidized cholesteryl esters, and mediate a variety of immune responses, from expression of proinflammatory genes to excessive intracellular lipoprotein accumulation to atheroprotective humoral immunity. These insights may lead to improved understanding of inflammation and atherogenesis and suggest new approaches to diagnosis and therapy. PMID:21252151

  10. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope.

    PubMed

    Green, Matthew F B; Esat, Taner; Wagner, Christian; Leinen, Philipp; Grötsch, Alexander; Tautz, F Stefan; Temirov, Ruslan

    2014-01-01

    One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. PMID:25383304

  11. Differential adhesiveness between blood and marrow leukemic cells having similar pattern of VLA adhesion molecule expression.

    PubMed

    Thomas, X; Anglaret, B; Bailly, M; Maritaz, O; Magaud, J P; Archimbaud, E

    1998-10-01

    Functional adhesion of blood and marrow leukemic cells from 14 acute myeloid leukemia patients presenting with hyperleukocytosis was evaluated by performing cytoadhesion assays on purified (extracellular matrix proteins) and non-purified supports (MRC5 fibroblastic cell line). Results, in 30-min chromium release assay, show a mean +/- S.D. adhesion to fibronectin, collagen, and laminin respectively of 30 +/- 17%, 20 +/- 13%, 25 +/- 17% for blood leukemic cells and 18 +/- 11%, 11 +/- 10%, 11 +/- 8% for marrow leukemic cells. These differences between blood and marrow cells were statistically significant (respectively P = 0.005, P = 0.01 and P = 0.002), while no difference was noted regarding adhesion to non-purified supports. The higher adhesion of blood blast cells to purified supports was observed regardless of CD34 expression. No significant difference was observed in the expression of cell surface VLA-molecules (CD29, CD49b, CD49d, CD49e, CD49f) between blood and marrow blast cells. The addition of GM-CSF or G-CSF induced increased adhesion of marrow blasts and decreased adhesion of blood blasts leading to a loss of the difference between blood and marrow cells. In a 60-min chromium release assay, marrow blasts adhered even more than blood leukemic cells to fibronectin. In contrast, marrow blasts from 'aleukemic' acute myeloid leukemia patients did not show any modification regarding their adhesion to extracellular matrix proteins when co-cultured with growth factors. PMID:9766756

  12. LARGE SCALE EVALUATION OF A PATTERN RECOGNITION/EXPERT SYSTEM FOR MASS SPECTRAL MOLECULAR WEIGHT ESTIMATION

    EPA Science Inventory

    A fast, personal-computer based method of estimating molecular weights of organic compounds from low resolution mass I spectra has been thoroughly evaluated. he method is based on a rule-based pattern,recognition/expert system approach which uses empirical linear corrections whic...

  13. Excitation of Ultracold Molecules to ``TRILOBITE-LIKE" Long-Range Molecular Rydberg States

    NASA Astrophysics Data System (ADS)

    Bellos, M. A.; Carollo, R.; Banerjee, J.; Eyler, E. E.; Gould, P. L.; Stwalley, W. C.

    2013-06-01

    A class of long-range Rydberg molecules, sometimes called ``trilobite states", occurs when a ground-state atom is embedded in the electronic cloud of a Rydberg atom. The bond between the Rydberg atom and the ground-state atom originates from the low-energy scattering of the Rydberg electron from the ground-state atom. We produce trilobite-like states of ultracold Rb_2 at low principal quantum numbers and at internuclear separations less than 40 bohr. We populate these states through single-photon ultraviolet transitions starting from molecules in high-lying vibrational levels of the lowest triplet state. This demonstrates that long-range Rydberg molecules can also be excited through bound-bound transitions, in addition to previous studies that used free-bound transitions. We also discuss the advantages of a bound-bound pathway. C. H. Greene, A. S. Dickinson, and H. R. Sadeghpour, Phys. Rev. Lett. 85, 2458 (2000).

  14. Self-assembly and separation of nematic colloids through photo-patterned molecular orientation

    NASA Astrophysics Data System (ADS)

    Peng, Chenhui; Guo, Yubing; Conklin, Christopher; Viñals, Jorge; Shiyanovskii, Sergij; Wei, Qi-Huo; Lavrentovich, Oleg; Oleg D. Lavrentovich Team; Jorge Viñals Collaboration

    Design and control of particles self-assembly is an important theme in colloidal science. Dispersions of colloids in a nematic liquid crystal (LC) show a diversity of self-assembled structures guided by long-range interactions. Here we describe a versatile approach to control colloidal structures through surface-patterned molecular orientation and dynamic processes of LC-enabled electrokinetics (LCEK). In presence of the electric field, the surface-imprinted pattern of molecular orientation triggers LCEK flows which transport the colloidal aggregates to specified locations. The aggregation is directed by the director gradients. Colloids that differ in surface anchoring or shape are guided into different areas of the cell, thus being sorted. The dynamic approach to control colloidal systems through LCEK in cells with patterned director field opens the opportunities in the microfluidic and lab on a chip applications. This work was supported by NSF grants DMR-1507637 , DMS-1434185 and CMMI-1436565.

  15. RNA:DNA hybrids are a novel molecular pattern sensed by TLR9

    PubMed Central

    Rigby, Rachel E; Webb, Lauren M; Mackenzie, Karen J; Li, Yue; Leitch, Andrea; Reijns, Martin A M; Lundie, Rachel J; Revuelta, Ailsa; Davidson, Donald J; Diebold, Sandra; Modis, Yorgo; MacDonald, Andrew S; Jackson, Andrew P

    2014-01-01

    The sensing of nucleic acids by receptors of the innate immune system is a key component of antimicrobial immunity. RNA:DNA hybrids, as essential intracellular replication intermediates generated during infection, could therefore represent a class of previously uncharacterised pathogen-associated molecular patterns sensed by pattern recognition receptors. Here we establish that RNA:DNA hybrids containing viral-derived sequences efficiently induce pro-inflammatory cytokine and antiviral type I interferon production in dendritic cells. We demonstrate that MyD88-dependent signalling is essential for this cytokine response and identify TLR9 as a specific sensor of RNA:DNA hybrids. Hybrids therefore represent a novel molecular pattern sensed by the innate immune system and so could play an important role in host response to viruses and the pathogenesis of autoimmune disease. PMID:24514026

  16. Molecular locks and keys: the role of small molecules in phytohormone research

    PubMed Central

    Fonseca, Sandra; Rosado, Abel; Vaughan-Hirsch, John; Bishopp, Anthony; Chini, Andrea

    2014-01-01

    Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds. PMID:25566283

  17. Direct observation of molecularly-aligned molecules in the second physisorbed layer-CO/Ag(110)

    SciTech Connect

    Lee, J.-G.; Hong, S.-H.; Ahner, J.; Zhao, X.; Chen, L.; Johnson, J.K.; Yates, J.T., Jr.

    2006-01-25

    We report the direct observation of oriented second-layer physisorbed molecules on a single crystal surface by electron stimulated desorption. Experiments and simulations show that the orientation of the second-layer physisorbed CO molecules on Ag(110) is the result of both electrostatic and dispersion forces from the underlying chemisorbed CO and Ag atoms. At 25 K, the physisorbed C-O bond is tilted and azimuthally oriented with the C-O bond axis inclined in an azimuthal plane at 45° to the principal Ag( 110) azimuthal crystallographic directions. The O atom in CO is directed outward, giving an O+ beam at 43° to the normal.

  18. Secretion pattern, ultrastructural localization and function of extracellular matrix molecules involved in eggshell formation.

    PubMed

    Soledad Fernandez, M; Moya, A; Lopez, L; Arias, J L

    2001-01-01

    The chicken eggshell is a composite bioceramic containing organic and inorganic phases. The organic phase contains, among other constituents, type X collagen and proteoglycans (mammillan, a keratan sulfate proteoglycan, and ovoglycan, a dermatan sulfate proteoglycan), whose localization depends on a topographically defined and temporally regulated deposition. Although the distribution of these macromolecules in the eggshell has been well established, little is known about their precise localization within eggshell substructures and oviduct cells or their pattern of production and function during eggshell formation. By using immunofluorescent and immuno-ultrastructural analyses, we examined the distribution of these macromolecules in oviduct cells at different post-oviposition times. To understand the role of proteoglycan sulfation on eggshell formation, we studied the effects of inhibition of proteoglycan sulfation by treatment with sodium chlorate. We showed that these macromolecules are produced by particular oviduct cell populations and at precise post-oviposition times. Based on the precise ultrastructural localization of these macromolecules in eggshell substructures, the timing of the secretion of these macromolecules by oviduct cells and the effects on eggshell formation caused by the inhibition of proteoglycan sulfation, the putative role of mammillan is in the nucleation of the first calcite crystals, while that of ovoglycan is to regulate the growth and orientation of the later forming crystals of the chicken eggshell. PMID:11223339

  19. Array formatting of the heat-transfer method (HTM) for the detection of small organic molecules by molecularly imprinted polymers.

    PubMed

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-01-01

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

  20. Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers

    PubMed Central

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-01-01

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

  1. Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: formulation in a rectangular coordinate system.

    PubMed

    Ishizuka, Ryosuke; Yoshida, Norio

    2013-08-28

    An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics. PMID:24006986

  2. Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: Formulation in a rectangular coordinate system

    NASA Astrophysics Data System (ADS)

    Ishizuka, Ryosuke; Yoshida, Norio

    2013-08-01

    An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the truncation of spherical harmonic expansion with respect to solute orientation. In order to show its applicability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approximation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ theory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics.

  3. Binding site identification and role of permanent water molecule of PIM-3 kinase: A molecular dynamics study.

    PubMed

    Ul-Haq, Zaheer; Gul, Sana; Usmani, Saman; Wadood, Abdul; Khan, Waqasuddin

    2015-11-01

    The kinome is a protein kinase complement of the human genome, categorized as serine/threonine and tyrosine kinases. These kinases catalyze phosphorylation reaction by using ATP as phosphoryl donor. Proviral Integration Site for Moloney Murine Leukemia Virus (PIM) kinase encodes serine/threonine protein kinases that recognized as proto-oncogene, responsible for rapid growth of cancerous cells. It is implicated in cell survival and function via cell cycle progression and its metabolism. PIM-3, sub-member of PIM kinases is a proto-oncogene, its overexpression inhibits apoptosis, and results in progression of hepatocellular carcinoma. PIM-3 is considered as a promising drug target but attempts to develop its specific inhibitors is slowed down due to the lack of 3D structure by any experimental technique. In silico techniques generally facilitate scientist to explore hidden structural features in order to improve drug discovery. In the present study, homology modeling, molecular docking and MD simulation techniques were utilized to explore the structure and dynamics of PIM-3 kinase. Induction of water molecules during molecular docking simulation explored differences in the hinge region between PIM-1 and PIM-3 kinases that may be responsible for specificity. Furthermore, role of water molecules in the active site was also explored via radial distribution function (RDF) after a 10ns molecular dynamics (MD) simulations. Generated RDF plots exhibited the importance of water for inhibitor binding through their bridging capability that links the ligand with binding site residues. PMID:26529487

  4. The inherent dynamics of a molecular liquid: geodesic pathways through the potential energy landscape of a liquid of linear molecules.

    PubMed

    Jacobson, Daniel; Stratt, Richard M

    2014-05-01

    Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape. PMID:24811642

  5. The Frontier of Molecular Spintronics Based on Multiple-Decker Phthalocyaninato Tb(III) Single-Molecule Magnets.

    PubMed

    Katoh, Keiichi; Komeda, Tadahiro; Yamashita, Masahiro

    2016-04-01

    Ever since the first example of a double-decker complex (SnPc2 ) was discovered in 1936, MPc2 complexes with π systems and chemical and physical stabilities have been used as components in molecular electronic devices. More recently, in 2003, TbPc2 complexes were shown to be single-molecule magnets (SMMs), and researchers have utilized their quantum tunneling of the magnetization (QTM) and magnetic relaxation behavior in spintronic devices. Herein, recent developments in Ln(III) -Pc-based multiple-decker SMMs on surfaces for molecular spintronic devices are presented. In this account, we discuss how dinuclear Tb(III) -Pc multiple-decker complexes can be used to elucidate the relationship between magnetic dipole interactions and SMM properties, because these complexes contain two TbPc2 units in one molecule and their intramolecular Tb(III) -Tb(III) distances can be controlled by changing the number of stacks. Next, we focus on the switching of the Kondo signal of Tb(III) -Pc-based multiple-decker SMMs that are adsorbed onto surfaces, their characterization using STM and STS, and the relationship between the molecular structure, the electronic structure, and the Kondo resonance of Tb(III) -Pc multiple-decker complexes. PMID:26991524

  6. Resonant multiphoton ionization spectra of molecules and molecular fragments. Technical progress report

    SciTech Connect

    1997-07-01

    objectives of this research are the development and application of theoretical techniques for studying several resonant multiphoton ionization processes in molecules. Specific problems of interest pertain to experimental studies of such spectra in which the photoelectron energy and angular distributions are determined.

  7. Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

    ERIC Educational Resources Information Center

    Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

    2008-01-01

    We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

  8. Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

    ERIC Educational Resources Information Center

    Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

    2008-01-01

    We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked

  9. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    DOE PAGESBeta

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

  10. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    SciTech Connect

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology.

  11. Templating effects in molecular growth of blended films for efficient small-molecule photovoltaics.

    PubMed

    Wang, Zhiping; Miyadera, Tetsuhiko; Yamanari, Toshihiro; Yoshida, Yuji

    2014-05-14

    A strategy to control the molecular growth of coevaporated zinc phthalocyanine (ZnPc) and fullerene (C60) blended films for efficient organic photovoltaic (OPV) cells was demonstrated. Introduction of a 2,5-bis(4-biphenylyl)-bithiophene (BP2T) film or a ZnPc film on BP2T as nanostructured templates not only results in phase-separated domains in blended films with clear interpenetrating networks but also improves the crystallinity of ZnPc domains, both of which enhance photocurrent generation and charge carrier transport. Such morphology is strongly associated with the molecular growth of the templating layers. Roughness and adhesion of the templating layers are of great importance for the molecular growth of the blended films and in turn for cell characteristics. By carefully regulating the molecular growth of the blended films, the power conversion efficiency was improved by 125%, from 1.85 to 4.15% under 1 sun. PMID:24712371

  12. Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1

    PubMed Central

    Contreras, F.-Xabier; Rodriguez-Plata, Maria T.; Glass, Bärbel; Erkizia, Itziar; Prado, Julia G.; Casas, Josefina; Fabriàs, Gemma; Kräusslich, Hans-Georg; Martinez-Picado, Javier

    2012-01-01

    HIV-1 is internalized into mature dendritic cells (mDCs) via an as yet undefined mechanism with subsequent transfer of stored, infectious virus to CD4+ T lymphocytes. Thus, HIV-1 subverts a DC antigen capture mechanism to promote viral spread. Here, we show that gangliosides in the HIV-1 membrane are the key molecules for mDC uptake. HIV-1 virus-like particles and liposomes mimicking the HIV-1 lipid composition were shown to use a common internalization pathway and the same trafficking route within mDCs. Hence, these results demonstrate that gangliosides can act as viral attachment factors, in addition to their well known function as cellular receptors for certain viruses. Furthermore, the sialyllactose molecule present in specific gangliosides was identified as the determinant moiety for mDC HIV-1 uptake. Thus, sialyllactose represents a novel molecular recognition pattern for mDC capture, and may be crucial both for antigen presentation leading to immunity against pathogens and for succumbing to subversion by HIV-1. PMID:22545022

  13. Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers†

    PubMed Central

    Emory, Jason M.; Peng, Zhiyong; Young, Brandon; Hupert, Mateusz L.; Rousselet, Arnold; Patterson, Donald; Ellison, Brad; Soper, Steven A.

    2012-01-01

    Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use. PMID:22005669

  14. Musical molecules: the molecular junction as an active component in audio distortion circuits

    NASA Astrophysics Data System (ADS)

    Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Semple, Mitchell; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L.

    2016-03-01

    Molecular junctions that have a non-linear current-voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities.

  15. Musical molecules: the molecular junction as an active component in audio distortion circuits.

    PubMed

    Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Semple, Mitchell; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L

    2016-03-01

    Molecular junctions that have a non-linear current-voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities. PMID:26871885

  16. Ionization of Na(3P) atoms by collisions with vibrationally excited nitrogen molecules in crossed molecular beams

    NASA Astrophysics Data System (ADS)

    De Jong, A. A.; Kircz, J. G.; Alkemade, C. Th. J.; van der Valk, F.

    1981-06-01

    A crossed molecular beam experiment is described in which the rate of ionization of Na(3P) atoms in collision with vibrationally excited N 2 molecul has been measured as a function of the N 2 temperature up to 3050 K. The activation energy in the experiment appears to be close to the ionization energy of the 3P level. An ionization cross section of about 100 »A 2 (excluding the activation energy factor) is derived with the help of a theoretical model. The limitations of the experiments as well as of the model are discussed.

  17. Strong-field approximation for above-threshold ionization of polyatomic molecules. II. The role of electron rescattering off the molecular centers

    NASA Astrophysics Data System (ADS)

    Hasović, E.; Milošević, D. B.

    2014-05-01

    We consider high-order above-threshold ionization of polyatomic molecules by a strong laser field. An improved molecular strong-field approximation which takes into account the electron rescattering off the molecular centers is developed. The presented theory is applied to calculate the photoelectron energy and angular distributions for the ozone molecule. The obtained spectra exhibit pronounced minima, and this is explained as a three-point destructive interference of the rescattered electron wave packets.

  18. Sulphur-bearing molecules in diffuse molecular clouds: new results from SOFIA/GREAT and the IRAM 30 m telescope

    NASA Astrophysics Data System (ADS)

    Neufeld, D. A.; Godard, B.; Gerin, M.; Pineau des Forêts, G.; Bernier, C.; Falgarone, E.; Graf, U. U.; Güsten, R.; Herbst, E.; Lesaffre, P.; Schilke, P.; Sonnentrucker, P.; Wiesemeyer, H.

    2015-05-01

    We have observed five sulphur-bearing molecules in foreground diffuse molecular clouds lying along the sight-lines to five bright continuum sources. We have used the GREAT instrument on SOFIA to observe the SH 1383 GHz 2Π3/2 J = 5/2 ← 3/2 lambda doublet toward the star-forming regions W31C, G29.96-0.02, G34.3+0.1, W49N and W51, detecting foreground absorption towards all five sources; and the EMIR receivers on the IRAM 30 m telescope at Pico Veleta to detect the H2S 110-101 (169 GHz), CS J = 2-1 (98 GHz) and SO 32-21 (99 GHz) transitions. Upper limits on the H3S+10-00 (293 GHz) transition were also obtained at the IRAM 30 m. In nine foreground absorption components detected towards these sources, the inferred column densities of the four detected molecules showed relatively constant ratios, with N(SH) /N(H2S) in the range 1.1-3.0, N(CS) /N(H2S) in the range 0.32-0.61, and N(SO) /N(H2S) in the range 0.08-0.30. The column densities of the sulphur-bearing molecules are very well correlated amongst themselves, moderately well correlated with CH (a surrogate tracer for H2), and poorly correlated with atomic hydrogen. The observed SH/H2 ratios - in the range 5 to 26 × 10-9 - indicate that SH (and other sulphur-bearing molecules) account for ≪ 1% of the gas-phase sulphur nuclei. The observed abundances of sulphur-bearing molecules, however, greatly exceed those predicted by standard models of cold diffuse molecular clouds, providing further evidence for the enhancement of endothermic reaction rates by elevated temperatures or ion-neutral drift. We have considered the observed abundance ratios in the context of shock and turbulent dissipation region (TDR) models. Using the TDR model, we find that the turbulent energy available at large scale in the diffuse ISM is sufficient to explain the observed column densities of SH and CS. Standard shock and TDR models, however, fail to reproduce the column densities of H2S and SO by a factor of about 10; more elaborate shock models - in which account is taken of the velocity drift, relative to H2, of SH molecules produced by the dissociative recombination of H3S+ - reduce this discrepancy to a factor ~3. Appendices are available in electronic form at http://www.aanda.org

  19. Healthy dietary patterns and risk of breast cancer by molecular subtype.

    PubMed

    Hirko, Kelly A; Willett, Walter C; Hankinson, Susan E; Rosner, Bernard A; Beck, Andrew H; Tamimi, Rulla M; Eliassen, A Heather

    2016-02-01

    We examined associations between dietary quality indices and breast cancer risk by molecular subtype among 100,643 women in the prospective Nurses' Health Study (NHS) cohort, followed from 1984 to 2006. Dietary quality scores for the Alternative Healthy Eating Index (AHEI), alternate Mediterranean diet (aMED), and Dietary Approaches to Stop Hypertension (DASH) dietary patterns were calculated from semi-quantitative food frequency questionnaires collected every 2-4 years. Breast cancer molecular subtypes were defined according to estrogen receptor (ER), progesterone receptor, human epidermal growth factor 2 (HER2), cytokeratin 5/6 (CK5/6), and epidermal growth factor receptor status from immunostained tumor microarrays in combination with histologic grade. Cox proportional hazards models, adjusted for age and breast cancer risk factors, were used to estimate hazard ratios (HRs) and 95 % confidence intervals (CIs). Competing risk analyses were used to assess heterogeneity by subtype. We did not observe any significant associations between the AHEI or aMED dietary patterns and risk of breast cancer by molecular subtype. However, a significantly reduced risk of HER2-type breast cancer was observed among women in 5th versus 1st quintile of the DASH dietary pattern [n = 134 cases, Q5 vs. Q1 HR (95 % CI) = 0.44 (0.25-0.77)], and the inverse trend across quintiles was significant (p trend = 0.02). We did not observe any heterogeneity in associations between AHEI (p het = 0.25), aMED (p het = 0.71), and DASH (p het = 0.12) dietary patterns and breast cancer by subtype. Adherence to the AHEI, aMED, and DASH dietary patterns was not strongly associated with breast cancer molecular subtypes. PMID:26872903

  20. Phospholipid Membrane Protection by Sugar Molecules during Dehydration-Insights into Molecular Mechanisms Using Scattering Techniques

    SciTech Connect

    Garvey, Christopher J.; Lenné, Thomas; Koster, Karen L.; Kent, Ben; Bryant, Gary

    2014-09-24

    Scattering techniques have played a key role in our understanding of the structure and function of phospholipid membranes. These techniques have been applied widely to study how different molecules (e.g., cholesterol) can affect phospholipid membrane structure. However, there has been much less attention paid to the effects of molecules that remain in the aqueous phase. One important example is the role played by small solutes, particularly sugars, in protecting phospholipid membranes during drying or slow freezing. In this paper, we present new results and a general methodology, which illustrate how contrast variation small angle neutron scattering (SANS) and synchrotron-based X-ray scattering (small angle (SAXS) and wide angle (WAXS)) can be used to quantitatively understand the interactions between solutes and phospholipids. Specifically, we show the assignment of lipid phases with synchrotron SAXS and explain how SANS reveals the exclusion of sugars from the aqueous region in the particular example of hexagonal II phases formed by phospholipids.

  1. Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

    PubMed

    Chowdhury, Debashish

    2013-06-01

    A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505

  2. Molecular Mechanics of Single Protein Molecules Measured with the Atomic Force Microscope

    NASA Astrophysics Data System (ADS)

    Hansma, Paul K.

    2000-03-01

    After a short history of AFM development in our lab, including recent developments with small cantilevers, this talk will focus on 1) pulling single protein molecules to explore the forces involved in unfolding and 2) watching single protein molecules in action to learn how they function mechanically. 1) Pulling experiments on proteins used as marine adhesives in abalone shells and other biological composite materials reveal modules bound together by sacrificial bonds that are weaker than the backbone bonds in the polypeptide chain.1 These self-healing modules provide effective energy absorption and appear to be a real key to understanding the impressive fracture resistance of biological composite materials. For example, the abalone shell is 3000 times more fracture resistant than a single crystal of calcium carbonate, despite the fact that 97% of the mass of the shell is crystalline calcium carbonate. 2) It is becoming possible, again with AFMs, to learn how some enzymes, nature's nanomachines, do their exquisite materials synthesis and processing. The talk will focus on the chaperonin system of GroEL and GroES that processes incorrectly folded proteins and assists them in refolding correctly. It is becoming possible not only to see single molecule events such as the association and disassociation of the GroEL-Gro-ES complex, but also to measure potential energy functions for the molecules in various conformational states. These new measurements, together with detailed structural measurements from other techniques, give new clues about how these proteins use the energy of ATP to do their work. Since the AFMs of today are very far from fundamental limits, this is only the beginning. 1. B. L. Smith, T. E. Schaffer, M. Viani, J. B. Thompson, N. A. Frederick, J. Kindt, A. Belcher, G. D. Stucky, D. E. Morse and P. K. Hansma, Nature 399, 761 (1999)

  3. Multicomponent redox catalysts for reduction of large biological molecules using molecular hydrogen as the reductant

    SciTech Connect

    Chao, S.; Simon, R.A.; Mallouk, T.E.; Wrighton, M.S.

    1988-03-30

    One-electron reduction of the large biological molecules horse heart cytochrome c, sperm whale myoglobin, and horseradish peroxidase using H/sub 2/ as the reductant can be catalyzed by two-component, high surface area heterogeneous catalysts. The catalysts can be prepared by first functionalizing high surface area SiO/sub 2/ with a polycationic polymer into which is dispersed MCl/sub 4//sup 2 -/ (M = Pd, Pt). Reduction with H/sub 2/ yields elemental Pd or Pt dispersed in the polymer. The particles are finally functionalized with a redox polymer derived from hydrolysis of Si(OR)/sub 3/ groups of an N,N'-dialkyl-4,4'-bipyridinium- or from a cobalticenium-based monomer. The two components of the heterogeneous catalysts are the buried noble metal capable of activating the H/sub 2/ and the redox polymer, which can equilibrate both with the noble metal and with the large biological molecule. Reduction of the large biological molecules in aqueous solution can be effected at room temperature and 1 atm H/sub 2/ using the catalysts under conditions where the biological materials would not be reducible with H/sub 2/ alone or when the noble metal alone would be used as the catalyst.

  4. Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules

    NASA Technical Reports Server (NTRS)

    Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

    2011-01-01

    A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.

  5. Tissue organization by cadherin adhesion molecules: dynamic molecular and cellular mechanisms of morphogenetic regulation

    PubMed Central

    Niessen, Carien M.; Leckband, Deborah; Yap, Alpha S.

    2013-01-01

    This review addresses the cellular and molecular mechanisms of cadherin-based tissue morphogenesis. Tissue physiology is profoundly influenced by the distinctive organizations of cells in organs and tissues. In metazoa, adhesion receptors of the classical cadherin family play important roles in establishing and maintaining such tissue organization. Indeed, it is apparent that cadherins participate in a range of morphogenetic events that range from support of tissue integrity to dynamic cellular rearrangements. A comprehensive understanding of cadherin-based morphogenesis must then define the molecular and cellular mechanisms that support these distinct cadherin biologies. Here we focus on four key mechanistic elements: the molecular basis for adhesion through cadherin ectodomains; the regulation of cadherin expression at the cell surface; cooperation between cadherins and the actin cytoskeleton; and regulation by cell signaling. We discuss current progress and outline issues for further research in these fields. PMID:21527735

  6. A Recombinant Horseshoe Crab Plasma Lectin Recognizes Specific Pathogen-Associated Molecular Patterns of Bacteria through Rhamnose

    PubMed Central

    Ng, Sim-Kun; Huang, Yu-Tsyr; Lee, Yuan-Chuan; Low, Ee-Ling; Chiu, Cheng-Hsun; Chen, Shiu-Ling; Mao, Liang-Chi; Chang, Margaret Dah-Tsyr

    2014-01-01

    Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens. PMID:25541995

  7. The dance of molecules: new dynamical perspectives on highly excited molecular vibrations.

    PubMed

    Kellman, Michael E; Tyng, Vivian

    2007-04-01

    At low energies, molecular vibrational motion is described by the normal modes model. This model breaks down at higher energy, with strong coupling between normal modes and onset of chaotic dynamics. New anharmonic modes are born in bifurcations, or branchings of the normal modes. Knowledge of these new modes is obtained through the window of frequency-domain spectroscopy, using techniques of nonlinear classical dynamics. It may soon be possible to "watch" molecular rearrangement reactions spectroscopically. Connections are being made with reaction rate theories, condensed phase systems, and motions of electrons in quantum dots. PMID:17256881

  8. Single molecule force spectroscopy reveals the molecular mechanical anisotropy of the FeS4 metal center in rubredoxin.

    PubMed

    Zheng, Peng; Chou, Chih-Chung; Guo, Ying; Wang, Yanyan; Li, Hongbin

    2013-11-27

    Mechanical anisotropy is an important feature of materials. Depending on the direction it is pulled, a material can exhibit very different mechanical properties. Mechanical anisotropy on the microscopic scale has also been observed for individual elastomeric proteins. Depending upon the direction along which it is stretched, a protein can unfold via different mechanical unfolding pathways and exhibit vastly different mechanical stability. However, it remains to be demonstrated if the concept of mechanical anisotropy can be extended to the molecular scale for small molecular objects containing only a few chemical bonds. Here, we choose the iron-sulfur center FeS4 in the simplest iron-sulfur protein rubredoxin as a model system to demonstrate the molecular level mechanical anisotropy. We used single molecule atomic force spectroscopy to investigate the mechanical rupture of the FeS4 center along different pulling directions. The FeS4 cluster is a simple molecular object with defined three-dimensional structure, where a ferric ion and four coordinating cysteinyl ligands are arranged into a distorted tetrahedral geometry. Mutating two specific residues in rubredoxin to cysteines provides anchoring points that enable us to stretch and rupture the FeS4 center along five distinct and precisely controlled directions. Our results showed that the mechanical stability as well as the rupture mechanism and kinetics of the FeS4 center are strongly dependent upon the direction along which it is stretched, suggesting that the very small and simple FeS4 center exhibits considerable mechanical anisotropy. It is likely that structural asymmetry in the FeS4 cluster and the modulation of the local environment due to partial unfolding of rubredoxin are responsible for the observed mechanical anisotropy. Our results suggest that mechanical anisotropy is a universal feature for any asymmetrical three-dimensional structure, even down to a molecular scale, and such mechanical anisotropy can be potentially utilized to control the mechanochemical reactivity of molecular objects. PMID:24171546

  9. Studying functional dynamics in bio-molecules using accelerated molecular dynamics.

    PubMed

    Markwick, Phineus R L; McCammon, J Andrew

    2011-12-01

    Many biologically important processes such as enzyme catalysis, signal transduction, ligand binding and allosteric regulation occur on the micro- to millisecond time-scale. Despite the sustained and rapid increase in available computational power and the development of efficient simulation algorithms, molecular dynamics (MD) simulations of proteins and bio-machines are generally limited to time-scales of tens to hundreds of nano-seconds. In this perspective article we present a comprehensive review of Accelerated Molecular Dynamics (AMD), an extended biased potential molecular dynamics approach that allows for the efficient study of bio-molecular systems up to time-scales several orders of magnitude greater than those accessible using standard classical MD methods, whilst still maintaining a fully atomistic representation of the system. Compared to many other approaches, AMD affords efficient enhanced conformational space sampling without any a priori understanding of the underlying free energy surface, nor does it require the specific prior definition of a reaction coordinate or a set of collective variables. Successful applications of the AMD method, including the study of slow time-scale functional dynamics in folded proteins and the conformational behavior of natively unstructured proteins are discussed and an outline of the different variants and extensions to the standard AMD approach is presented. PMID:22015376

  10. Meet the Molecules in Chocolate: Informal Opportunities for Building Thematic Molecular Models with Children

    ERIC Educational Resources Information Center

    Amey, Jennifer R.; Fletcher, Matthew D.; Fletcher, Rachael V.; Jones, Alison; Roberts, Erica W.; Roberts, Ieuan O.

    2008-01-01

    We describe the development and use of a molecular model building activity with a chocolate theme, suitable for a public presentation of chemistry through interaction with visitors to science festivals and museums, and as a special classroom activity during science weeks, and so forth. (Contains 3 figures.)

  11. Red Fluorescent Line Emission from Hydrogen Molecules in Diffuse Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Neufeld, David A.; Spaans, Marco

    1996-01-01

    We have modeled the fluorescent pumping of electronic and vibrational emissions of molecular hydrogen (H2) within diffuse molecular clouds that are illuminated by ultraviolet continuum radiation. Fluorescent line intensities are predicted for transitions at ultraviolet, infrared, and red visible wavelengths as functions of the gas density, the visual extinction through the cloud, and the intensity of the incident UV continuum radiation. The observed intensity in each fluorescent transition is roughly proportional to the integrated rate of H2 photodissociation along the line of sight. Although the most luminous fluorescent emissions detectable from ground-based observatories lie at near-infrared wavelengths, we argue that the lower sky brightness at visible wavelengths makes the red fluorescent transitions a particularly sensitive probe. Fabry-Perot spectrographs of the type that have been designed to observe very faint diffuse Ha emissions are soon expected to yield sensitivities that will be adequate to detect H2 vibrational emissions from molecular clouds that are exposed to ultraviolet radiation no stronger than the mean radiation field within the Galaxy. Observations of red H2 fluorescent emission together with cospatial 21 cm H I observations could serve as a valuable probe of the gas density in diffuse molecular clouds.

  12. Molecular entomology: analyzing tiny molecules to answer big questions about disease vectors and their biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The entomologists at the Arthropod-Borne Animal Diseases Research Unit at USDA-Agricultural Research Service are tasked with protecting the nation’s livestock from domestic, foreign and emerging vector-borne diseases. To accomplish this task, a vast array of molecular techniques are being used in pr...

  13. Total π-Electron Energy of Conjugated Molecules with Non-bonding Molecular Orbitals

    NASA Astrophysics Data System (ADS)

    Gutman, Ivan

    2016-02-01

    Lower and upper bounds for the total π-electron energy are obtained, which are applicable to conjugated π-electron systems with non-bonding molecular orbitals (NBMOs). These improve the earlier estimates, in which the number of NBMOs has not been taken into account.

  14. Resonance enhanced multiphoton and single-photon ionization of molecules and molecular fragments. Final report, May 1993--April 1997

    SciTech Connect

    McKoy, V.

    1998-09-01

    Resonance enhanced multiphoton ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that level before it decays. A remarkable feature of REMPI is that the very narrow bandwidth of laser radiation makes it possible to select a specific rotational level in the initial (ground) state and to prepare the excited state of interest in a single rotational level. Thus, by suitable choice of the excitation step, it is possible to selectively ionize a species that may be present. The key objective of the effort is to carry out quantitative studies of REMPI of molecules and molecular fragments, as well as of single-photon ionization of these species by coherent VUV radiation, in order to provide a robust description of significant spectral features of interest in related experiments and needed insight into the underlying dynamics of these spectra. A major focus of the effort is joint theoretical and experimental studies of these ion rotational distributions which are being widely studied by the zero-kinetic-energy (ZEKE) technique. This technique, which is based on the detection of photoelectrons resulting from pulsed-field ionization of very high Rydberg states lying just below an ion threshold, makes it possible to obtain cation distributions with subwavenumber resolution. The unprecedented resolution of this ZEKE technique is opening up entirely new vistas in studies of photoionization dynamics, ion spectroscopy, and state-selected ion-molecule reactions. Emerging applications built on the ultra-high resolution of this technique include its use for accurate determination of thermochemically important ionization energies, for characterization of ion rovibrational level structure of large organic molecules, of elemental clusters, and of weakly bound molecular complexes, for probing reactive fragments, and for pump-probe photoelectron studies of wavepacket dynamics. This surge of experimental activity in ultra-high resolution studies of molecular photoelectron spectra continues to raise new theoretical challenges and has provided the stimulus for several of the collaborations with experimental groups in North America and Europe.

  15. Crossed molecular beams study of O({sup 1}D) reactions with H{sub 2} molecules

    SciTech Connect

    Miau, T.T.

    1995-05-01

    Reaction dynamics of O({sup 1}D) atoms with H{sub 2} molecules was reinvestigated using the crossed molecular beams technique with pulsed beams. The O({sup 1}D) beam was generated by photodissociating O{sub 3} molecules at 248 nm. Time-of-flight spectra and the laboratory angular distribution of the OH products were measured. The derived OH product center-of-mass flux-velocity contour diagram shows more backward scattered intensity with respect to the O({sup 1}D) beam. In contrast to previous studies which show that the insertion mechanism is the dominant process, our results indicate that the contribution from the collinear approach of the O({sup 1}D) atom to the H{sub 2} molecule on the first excited state potential energy surface is significant and the energy barrier for the collinear approach is therefore minimal. Despite the increased time resolution in this experiment, no vibrational structure in the OH product time-of-flight spectra was resolved. This is in agreement with LIF studies, which have shown that the rotational distributions of the OH products in all vibrational states are broad and highly inverted.

  16. The hydrogen molecule and the H+2 molecular ion inside padded prolate spheroidal cavities with arbitrary nuclear positions

    NASA Astrophysics Data System (ADS)

    Coln-Rodrguez, R.; Daz-Garca, C.; Cruz, S. A.

    2011-12-01

    A generalization of previous theoretical studies of molecular confinement based on the molecule-in-a-box model for the H+2 and H2 systems whereby the confining cavity is assumed to be prolate spheroidal in shape is presented. A finite height for the confining barrier potential is introduced and the independent variation of the nuclear positions from the cavity size and shape is allowed. Within this scheme, the non-separable Schrdinger problem for the confined H+2 and H2 molecules in their ground states is treated variationally. In both cases, an important dependence of the equilibrium bond length and total energy on the confining barrier height is observed for fixed cavity sizes and shapes. It is also shown thatgiven a barrier heightas the cavity size is reduced, the limit of stability of the confined molecule is attained for a critical size. The results of this work suggest the adequacy of the proposed method for more realistic studies of electronic and vibrational properties of confined one- and two-electron diatomics for proper comparison with experiment.

  17. Mechanical Operation and Intersubunit Coordination of Ring-Shaped Molecular Motors: Insights from Single-Molecule Studies

    PubMed Central

    Liu, Shixin; Chistol, Gheorghe; Bustamante, Carlos

    2014-01-01

    Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation—often through regulation by other cofactors—to suit their unique biological functions. PMID:24806916

  18. Proton Donor/acceptor Propensities of Ammonia: Rotational Studies of its Molecular Complexes with Organic Molecules

    NASA Astrophysics Data System (ADS)

    Giuliano, Barbara M.; Maris, Assimo; Melandri, Sonia; Favero, Laura B.; Evangelisti, Luca; Caminati, Walther

    2009-06-01

    We studied the rotational spectra of the adducts of ammonia with several organic molecules, namely tert-butanol, glycidol, ethyl alcohol, anisol and 1,4-difluorobenzene. The adducts with glycidol and ethanol have been observed for both conformers of the substrate molecule. Based on the rotational and ^{14}N quadrupole coupling constants of the various complexes, we found a considerably different behaviour of ammonia, with respect to water, in its proton donor/acceptor double role. In the interaction with the three alcohol molecules, NH_{3} acts as a proton acceptor and the OH groups as a proton donor. However, in the case of glycidol-NH_{3}, a secundary N-H\\cdotsO interaction occurrs between ammonia and the ether oxygen. This interaction generates a sizable V_{3} barrier to the internal rotation of the NH_{3} moiety, while NH_{3} undergoes a free rotation in tert-butanol-NH_{3} and in ethanol-NH_{3}. As to the anisole-NH_{3} and 1,4-difluorobenzene-NH_{3} complexes, the NH_{3} group explicits its double proton donor/acceptor role, although through two weak (C_{Me}-H\\cdotsN and N-H\\cdotsπ) H-bonds. There is, however, an important difference between the two complexes, because in the first one NH_{3} lies out of the aromatic plane, while in the second one it is in the plane of the aromatic ring. B. M. Giuliano, M. C. Castrovilli, A. Maris, S. Melandri, W. Caminati and E. A. Cohen, Chem.Phys.Lett., 2008, 463, 330 B. M. Giuliano, S. Melandri, A. Maris, L. B. Favero and W. Caminati, Angew.Chem.Int.Ed., 2009, 48, 1102

  19. Nanopore Analysis of Nucleic Acids: Single-Molecule Studies of Molecular Dynamics, Structure, and Base Sequence

    NASA Astrophysics Data System (ADS)

    Olasagasti, Felix; Deamer, David W.

    Nucleic acids are linear polynucleotides in which each base is covalently linked to a pentose sugar and a phosphate group carrying a negative charge. If a pore having roughly the crosssectional diameter of a single-stranded nucleic acid is embedded in a thin membrane and a voltage of 100 mV or more is applied, individual nucleic acids in solution can be captured by the electrical field in the pore and translocated through by single-molecule electrophoresis. The dimensions of the pore cannot accommodate anything larger than a single strand, so each base in the molecule passes through the pore in strict linear sequence. The nucleic acid strand occupies a large fraction of the pore's volume during translocation and therefore produces a transient blockade of the ionic current created by the applied voltage. If it could be demonstrated that each nucleotide in the polymer produced a characteristic modulation of the ionic current during its passage through the nanopore, the sequence of current modulations would reflect the sequence of bases in the polymer. According to this basic concept, nanopores are analogous to a Coulter counter that detects nanoscopic molecules rather than microscopic [1,2]. However, the advantage of nanopores is that individual macromolecules can be characterized because different chemical and physical properties affect their passage through the pore. Because macromolecules can be captured in the pore as well as translocated, the nanopore can be used to detect individual functional complexes that form between a nucleic acid and an enzyme. No other technique has this capability.

  20. The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology

    PubMed Central

    Goodsell, David S.; Dutta, Shuchismita; Zardecki, Christine; Voigt, Maria; Berman, Helen M.; Burley, Stephen K.

    2015-01-01

    The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general introduction to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org. PMID:25942442

  1. The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology.

    PubMed

    Goodsell, David S; Dutta, Shuchismita; Zardecki, Christine; Voigt, Maria; Berman, Helen M; Burley, Stephen K

    2015-05-01

    The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general introduction to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org. PMID:25942442

  2. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

    PubMed Central

    Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

    2016-01-01

    The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

  3. Orbital tomography: Molecular band maps, momentum maps and the imaging of real space orbitals of adsorbed molecules

    PubMed Central

    Offenbacher, Hannes; Lüftner, Daniel; Ules, Thomas; Reinisch, Eva Maria; Koller, Georg; Puschnig, Peter; Ramsey, Michael G.

    2015-01-01

    The frontier orbitals of molecules are the prime determinants of their chemical, optical and electronic properties. Arguably, the most direct method of addressing the (filled) frontier orbitals is ultra-violet photoemission spectroscopy (UPS). Although UPS is a mature technique from the early 1970s on, the angular distribution of the photoemitted electrons was thought to be too complex to be analysed quantitatively. Recently angle resolved UPS (ARUPS) work on conjugated molecules both, in ordered thick films and chemisorbed monolayers, has shown that the angular (momentum) distribution of the photocurrent from orbital emissions can be simply understood. The approach, based on the assumption of a plane wave final state is becoming known as orbital tomography. Here we will demonstrate, with selected examples of pentacene (5A) and sexiphenyl (6P), the potential of orbital tomography. First it will be shown how the full angular distribution of the photocurrent (momentum map) from a specific orbital is related to the real space orbital by a Fourier transform. Examples of the reconstruction of 5A orbitals will be given and the procedure for recovering the lost phase information will be outlined. We then move to examples of sexiphenyl where we interrogate the original band maps of thick sexiphenyl in the light of our understanding of orbital tomography that has developed since then. With comparison to theoretical simulations of the molecular band maps, the molecular conformation and orientation will be concluded. New results for the sexiphenyl monolayer on Al(1 1 0) will then be presented. From the band maps it will be concluded that the molecule is planarised and adopts a tilted geometry. Finally the momentum maps down to HOMO-11 will be analysed and real space orbitals reconstructed. PMID:26752804

  4. Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors.

    PubMed

    Rietz, Anne; Petrov, Dino P; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V Jo; Androphy, Elliot J

    2016-01-01

    The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

  5. How do molecular marker patterns of BC change at increasing age of chars?

    NASA Astrophysics Data System (ADS)

    Schneider, M. P. W.; Hilf, M.; Schmidt, M. W. I.

    2009-04-01

    Black carbon (BC) is considered to be a relatively stable form of organic carbon. However, previous results have shown that the physical and chemical properties of BC can vary considerably with formation temperature. Thus, to understand the long-term carbon sink potential of BC there is increasing interest to gain more information about i) the conditions under which BC was formed, and ii) the resulting degradability of BC under natural conditions. In a first step, we synthesised chars from two different sources of biomass (chestnut wood, rice straw) under well-defined conditions as model substances to analyse the changes in their molecular structure at increasing formation temperature. Results are presented obtained from a set of laboratory produced char samples pyrolysed at increasing temperatures with a high resolution between 200 and 1000 °C. The chars were characterized by a molecular marker method for pyrogenic carbon quantification, which additionally provides information about the degree of condensation of chars. At temperatures between 275 and 500°C, which typically are observed during wildfires and thus are relevant for natural char formation, the molecular marker pattern of the chars remains almost constant. In a next step, we analysed changes in the molecular marker patterns of chars from a chronosequence, with BC deposited between 0 and 100 years ago. Based on the data obtained from the laboratory char series, we compare changes in the molecular marker patterns of the chars from the chronosequence over time. These results show if less condensed forms of BC are degraded preferentially and more condensed, aromatic backbone of BC becomes enriched in the soils with time of degradation. Our results provide information about the fate of BC in the environment, which has important implications in the context of carbon sequestration strategies.

  6. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    NASA Astrophysics Data System (ADS)

    Makarov, G. N.; Petin, A. N.

    2016-03-01

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF6 and CF3I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF6 molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation.

  7. Optimization of molecular design in the evolution of metabolism: the glycogen molecule.

    PubMed Central

    Meléndez-Hevia, E; Waddell, T G; Shelton, E D

    1993-01-01

    The animal glycogen molecule has to be designed in accordance with its metabolic function as a very effective fuel store allowing quick release of large amounts of glucose. In addition, the design should account for a high capacity of glucose storage in the least possible space. We have studied the optimization of these variables by means of a mathematical model of the glycogen molecule. Our results demonstrate that the structure is optimized to maximize (a) the total glucose stored in the smallest possible volume, (b) the proportion of it that can be directly released by phosphorylase before any debranching occurs, and (c) the number of non-reducing ends (points of attack for phosphorylase), which maximizes the speed of fuel release. The optimization of these four variables is achieved with appropriate values for two key parameters in glycogen design: the degree of branching and the length of the chains. The optimal values of these two parameters are precisely those found in cellular glycogen. PMID:8240246

  8. Effect of molecular structure on fragmentation of isolated organic molecules in solid rare gas matrices

    NASA Astrophysics Data System (ADS)

    Kobzarenko, A. V.; Sukhov, F. F.; Orlov, A. Yu.; Kovalev, G. V.; Baranova, I. A.; Feldman, V. I.

    2012-09-01

    The effect of excess energy on the primary radical cations of bifunctional carbonyl compounds and aliphatic alkynes was simulated by matrix isolation method using rare gas matrices with various ionization potentials. The formation of fragmentation products was monitored by EPR and FTIR spectroscopy. It was shown that the radical cations of bifunctional compounds (CH3OCH2COCH3 and CH3COCOCH3) dissociated effectively yielding rad CH3 radicals upon irradiation in solid argon matrix at T≤16 K. In addition to isolated methyl radicals, the radical pairs consisting of two methyl radicals separated by two CO molecules were detected in the case of diacetyl. The probability of fragmentation decreases with the decreasing excess energy by switching from Ar to Xe. In general, bifunctional molecules were found to be less stable to "hot" ionic fragmentation in low-temperature solids in comparison with simple prototype compounds. In the case of alkynes of the RCCH type, a noticeable yield of fragmentation products was observed when R=-C(CH3)3, but it was negligible for R=-CH3. The mechanisms of "hot" reactions and excess energy relaxation are discussed.

  9. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules

    PubMed Central

    Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K.; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J.; Dunne, Eimear M.; Flagan, Richard C.; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P.; Rondo, Linda; Santos, Filipe D.; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S.; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M.; Worsnop, Douglas R.

    2013-01-01

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions. PMID:24101502

  10. Quantitative surface analysis of molecular overlayers by resonantly enhanced multiphoton ionization of sputtered molecules

    NASA Astrophysics Data System (ADS)

    Schnieders, A.; Rüschenschmidt, K.; Schröder, M.; Benninghoven, A.; Arlinghaus, H. F.

    2001-08-01

    Laser postionization of sputtered neutrals in combination with resonantly enhanced multiphoton ionization is a more quantitative analytical technique for organic surface analysis than secondary ion mass spectrometry due to the reduced matrix effect. Nevertheless, we observed a remaining sputter-induced matrix effect. We have investigated this matrix effect by comparing the secondary neutral and ion emissions from UHV-deposited molecular overlayers of adenine and β-alanine on Ag substrates under Ar+, Xe+, and SF5+ primary ion bombardment.

  11. Universal scaling behavior of molecular electronic stopping cross section for protons colliding with small molecules and nucleobases

    NASA Astrophysics Data System (ADS)

    Trujillo-Lpez, L. N.; Martnez-Flores, C.; Cabrera-Trujillo, R.

    2013-10-01

    The electronic stopping cross section and mean excitation energy for molecules and 5 nucleobases have been calculated within the first Born approximation in terms of an orbital decomposition to take into account the molecular structure. The harmonic oscillator (HO) description of the stopping cross section together with a Floating Spherical Gaussian Orbital (FSGO) model is implemented to account for the chemical composition of the target. This approach allows us to use bonds, cores, and lone pairs as HO basis to describe the ground state molecular structure. In the HO model, the orbital angular frequency is the only parameter that connects naturally with the mean excitation energy. As a result, we obtain a simple expression for the equivalent mean excitation energy in terms of the orbital radius parameter, as well as an analytical expression of the stopping cross section. For gas phase molecular targets, we provide HO based orbital mean excitation energies to describe any molecule containing C, N, O, H, and P atoms. We present results for protons colliding with H2, N2, O2, H2O, CO2, propylene (C3H6), methane (CH4), ethylene (C2H4) and the nucleobases - guanine (C5H5N5O), cytosine (C4H5N2O2), thymine (C5H6N2O2), adenine (C5H5N5) and uracil (C4H4N2O2). The results for the stopping cross section are compared with available experimental and theoretical data showing good to excellent agreement in the region of validity of the model. The HO approach allows us to obtain a universal stopping cross section formula to describe a universal scaling behavior for the energy loss process. The universal scaled curve is confirmed by the experimental data.

  12. Exploring molecular complexity with ALMA (EMoCA): Deuterated complex organic molecules in Sagittarius B2(N2)

    NASA Astrophysics Data System (ADS)

    Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

    2016-03-01

    Context. Deuteration is a powerful tracer of the history of the cold prestellar phase in star-forming regions. Apart from methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in regions forming high-mass stars. Aims: Our goal is to detect deuterated complex organic molecules toward the high mass star-forming region Sagittarius B2 (Sgr B2) and derive the level of deuteration for these molecules. Methods: We use a complete 3-mm spectral line survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA) to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We constructed population diagrams and integrated intensity maps to fit rotational temperatures and emission sizes for each molecule. Column densities are derived by modeling the full spectrum under the assumption of local thermodynamic equilibrium. We compare the results to predictions of two astrochemical models that treat the deuteration process. Results: We report the detection of CH2DCN toward Sgr B2(N2) with a deuteration level of 0.4%, and tentative detections of CH2DOH, CH2DCH2CN, the chiral molecule CH3CHDCN, and DC3N with levels in the range 0.05%-0.12%. A stringent deuteration upper limit is obtained for CH3OD (<0.07%). Upper limits in the range 0.5-1.8% are derived for the three deuterated isotopologues of vinyl cyanide, the four deuterated species of ethanol, and CH2DOCHO. Ethyl cyanide is less deuterated than methyl cyanide by at least a factor five. The [CH2DOH]/[CH3OD] abundance ratio is higher than 1.8. It may still be consistent with the value obtained in Orion KL. Except for methyl cyanide, the measured deuteration levels lie at least a factor four below the predictions of current astrochemical models. The deuteration levels in Sgr B2(N2) are also lower than in Orion KL by a factor of a few up to a factor ten. Conclusions: The discrepancy between the deuteration levels of Sgr B2(N2) and the predictions of chemical models, and the difference between Sgr B2(N2) and Orion KL may both be due to the higher kinetic temperatures that characterize the Galactic center region compared to nearby clouds. Alternatively, they may result from a lower overall abundance of deuterium itself in the Galactic center region by up to a factor ten.

  13. Dual reorientation relaxation routes of water molecules in oxyanion's hydration shell: A molecular geometry perspective

    NASA Astrophysics Data System (ADS)

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin

    2015-12-01

    In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion's hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a "structure breaker" in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.

  14. Dual reorientation relaxation routes of water molecules in oxyanion's hydration shell: A molecular geometry perspective.

    PubMed

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin

    2015-12-14

    In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion's hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a "structure breaker" in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics. PMID:26671387

  15. A unique feature of chiral transition of a difluorobenzo[c]phenanthrene molecule confined in a boron-nitride nanotube based on molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Meng, Yan; Xiu, Peng; Huang, Bolong; Wang, Zhigang; Zhang, Rui-Qin; Zhou, Ruhong

    2014-01-01

    Reliable structural information of extremal points in a reaction is important but difficult to achieve in molecular chiral transitions under confinement due to the complex molecular interactions. In this Letter, based on statistical results of a number of classical molecular dynamics simulations, we found that a complete chiral transition process of a difluorobenzo[c]phenanthrene molecule (C18H12F2, called D molecule) within a single-walled boron-nitride nanotube involves at least five extremal point structures, showing a unique feature of chiral transition in the confined environment and suggesting an alternative to conventional first-principles calculations to determine the complex potential energy surface of intermolecular interactions.

  16. Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations.

    PubMed

    Lach, Joanna; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-01

    Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum. PMID:26774981

  17. Small molecule interactions with lipid bilayers: a molecular dynamics study of chlorhexidine

    NASA Astrophysics Data System (ADS)

    van Oosten, Brad; Marquardt, Drew; Sternin, Edward; Harroun, Thad

    2013-03-01

    Chlorhexidine presents an interesting modelling challenge with a hydrophobic hexane connecting two biguanides (arginine analogues) and two aromatic rings. We conducted molecular dynamic simulations using the GROMACS simulation software to reproduce the experimental environment of chlorhexidine in a 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) bilayer to produce atomic-level information. We constructed an all-atom force field of chlorhexidine from the CHARMM36 force field using well established parameters of certain amino acids. Partial charges were treated differently, which were calculated using GAUSSIAN software. We will compare and contrast the results of our model to that of our neutron scattering experiments previously done in our lab.

  18. The humoral pattern recognition molecule PTX3 is a key component of innate immunity against urinary tract infection.

    PubMed

    Jaillon, Sbastien; Moalli, Federica; Ragnarsdottir, Bryndis; Bonavita, Eduardo; Puthia, Manoj; Riva, Federica; Barbati, Elisa; Nebuloni, Manuela; Cvetko Krajinovic, Lidija; Markotic, Alemka; Valentino, Sonia; Doni, Andrea; Tartari, Silvia; Graziani, Giorgio; Montanelli, Alessandro; Delneste, Yves; Svanborg, Catharina; Garlanda, Cecilia; Mantovani, Alberto

    2014-04-17

    Immunity in the urinary tract has distinct and poorly understood pathophysiological characteristics and urinary tract infections (UTIs) are important causes of morbidity and mortality. We investigated the role of the soluble pattern recognition molecule pentraxin 3 (PTX3), a key component of the humoral arm of innate immunity, in UTIs. PTX3-deficient mice showed defective control of UTIs and exacerbated inflammation. Expression of PTX3 was induced in uroepithelial cells by uropathogenic Escherichia coli (UPEC) in a Toll-like receptor 4 (TLR4)- and MyD88-dependent manner. PTX3 enhanced UPEC phagocytosis and phagosome maturation by neutrophils. PTX3 was detected in urine of UTI patients and amounts correlated with disease severity. In cohorts of UTI-prone patients, PTX3 gene polymorphisms correlated with susceptibility to acute pyelonephritis and cystitis. These results suggest that PTX3 is an essential component of innate resistance against UTIs. Thus, the cellular and humoral arms of innate immunity exert complementary functions in mediating resistance against UTIs. PMID:24745336

  19. Molecular phylogeny of the phylum Gastrotricha: new data brings together molecules and morphology.

    PubMed

    Paps, Jordi; Riutort, Marta

    2012-04-01

    Gastrotricha is a species-rich phylum of microscopical animals that contains two main orders, Chaetonotida and Macrodasyida. Gastrotrichs are important members of the aquatic environment and significant players in the study of animal evolution. In spite of their ecological and evolutionary importance, their internal relationships are not yet well understood. We have produced new sequences for the 18S rDNA gene to improve both the quality and quantity of taxon sampling for the gastrotrichs. Our phylogeny recovers the monophyly of the two main Gastrotricha clades, in contrast to recent studies with similar sampling, but in agreement with morphology based analyses. However, our topology is not able to resolve the first branches of the macrodasyidans or settle the position of the puzzling Neodasys, a controversial genus classified as a chaetonotidan on morphological grounds but placed within macrodasyidans by molecular studies. This analysis is the most exhaustive molecular phylogeny of the phylum to date, and significantly increases our knowledge of gastrotrich evolution. PMID:22198640

  20. Conserved molecular mechanisms underlying the effects of small molecule xenobiotic chemotherapeutics on cells

    PubMed Central

    SARIN, HEMANT

    2016-01-01

    For proper determination of the apoptotic potential of chemoxenobiotics in synergism, it is important to understand the modes, levels and character of interactions of chemoxenobiotics with cells in the context of predicted conserved biophysical properties. Chemoxenobiotic structures are studied with respect to atom distribution over molecular space, the predicted overall octanol-to-water partition coefficient (Log OWPC; unitless) and molecular size viz a viz van der Waals diameter (vdWD). The Log OWPC-to-vdWD (nm−1) parameter is determined, and where applicable, hydrophilic interacting moiety/core-to-vdWD (nm−1) and lipophilic incorporating hydrophobic moiety/core-to-vdWD (nm−1) parameters of their part-structures are determined. The cellular and sub-cellular level interactions of the spectrum of xenobiotic chemotherapies have been characterized, for which a classification system has been developed based on predicted conserved biophysical properties with respect to the mode of chemotherapeutic effect. The findings of this study are applicable towards improving the effectiveness of existing combination chemotherapy regimens and the predictive accuracy of personalized cancer treatment algorithms as well as towards the selection of appropriate novel xenobiotics with the potential to be potent chemotherapeutics for dendrimer nanoparticle-based effective transvascular delivery. PMID:26998284

  1. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation.

    PubMed

    Wang, Anhui; Song, Ting; Wang, Ziqian; Liu, Yubo; Fan, Yudan; Zhang, Yahui; Zhang, Zhichao

    2016-04-01

    Inhibition of interactions between Mcl-1 and proapoptotic proteins is considered to be a therapeutic strategy to induce apoptosis in cancer cells. Here, we adopted molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to study the inhibition mechanism of three Mcl-1 inhibitors, compounds 1, 2 and 3. Analysis of energy components shows that the better binding free energy of compound 3 than compounds 1 and 2 is attributable to the van der Waals energy (ΔEvdw ) and non-polar solvation energy (ΔGnp ) upon binding. In addition to the excellent agreement with previous experimentally determined affinities, our simulation results further show a bend of helix 4 on Mcl-1 upon compound 3 binding, which is driven by hydrophobic interaction with residue Val(253) , leading to a narrowed BH3-binding groove to impede Puma(BH) (3) binding. The computational result is consistent with our competitive isothermal titration calorimetry (ITC) assays, which shows that the competitive ability of compound 3 toward Mcl-1/Puma(BH) (3) complex is improved beyond its direct binding affinity toward Mcl-1 itself, and compound 3 exhibits much more efficiency to compete with Puma(BH) (3) than compound 2. Our study provides a new strategy to improve inhibitory activity on Mcl-1 based on the conformational dynamic change. PMID:26518611

  2. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    SciTech Connect

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-07

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  3. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    NASA Astrophysics Data System (ADS)

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding - a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  4. SI-BEARING MOLECULES TOWARD IRC+10216: ALMA UNVEILS THE MOLECULAR ENVELOPE OF CWLEO

    PubMed Central

    Prieto, L. Velilla; Cernicharo, J.; Quintana–Lacaci, G.; Agúndez, M.; Castro–Carrizo, A.; Fonfŕia, J. P.; Marcelino, N.; Zúñiga, J.; Requena, A.; Bastida, A.; Lique, F.; Guélin, M.

    2015-01-01

    We report the detection of SiS rotational lines in high-vibrational states as well as SiO and SiC2 lines in their ground vibrational state toward IRC+10216 during the Atacama Large Millimeter Array Cycle 0. The spatial distribution of these molecules shows compact emission for SiS and a more extended emission for SiO and SiC2, and also proves the existence of an increase in the SiC2 emission at the outer shells of the circumstellar envelope. We analyze the excitation conditions of the vibrationally excited SiS using the population diagram technique, and we use a large velocity gradient model to compare with the observations. We found moderate discrepancies between the observations and the models that could be explained if SiS lines detected are optically thick. Additionally, the line profiles of the detected rotational lines in the high energy vibrational states show a decreasing linewidth with increasing energy levels. This may be evidence that these lines could be excited only in the inner shells, i.e., the densest and hottest, of the circumstellar envelope of IRC+10216. PMID:26688711

  5. Manipulating photogenerated radical ion pair lifetimes in wirelike molecules using microwave pulses: molecular spintronic gates.

    PubMed

    Miura, Tomoaki; Wasielewski, Michael R

    2011-03-01

    We have studied spin-dependent charge transfer dynamics in wirelike donor-bridge-acceptor (D-B-A) molecules comprising a phenothiazine (PTZ) donor, an oligo(2,7-fluorene) (FL(n)) bridge, and a perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptor, PTZ-FL(3)-PDI (1) and PTZ-FL(4)-PDI (2), dissolved in the magnetic field-aligned nematic phase of 4-cyano-4'-n-pentylbiphenyl (5CB) at 295 K. Time-resolved EPR spectroscopy using both continuous wave and pulsed microwaves shows that the photogenerated radical pairs (RPs), PTZ(+•)-FL(3)-PDI(-•) and PTZ(+•)-FL(4)-PDI(-•), recombine much faster from the singlet RP manifold than the triplet RP manifold. When a strong resonant microwave π pulse is applied following RP photogeneration in 1 and 2, the RP lifetimes increase about 50-fold as indicated by electron spin-echo detection. This result shows that the RP lifetime can be greatly extended by rapidly switching off fast triplet RP recombination. PMID:21319821

  6. Excited-State Structure Modifications Due to Molecular Substituents and Exciton Scattering in Conjugated Molecules.

    PubMed

    Li, Hao; Catanzaro, Michael J; Tretiak, Sergei; Chernyak, Vladimir Y

    2014-02-20

    Attachment of chemical substituents (such as polar moieties) constitutes an efficient and convenient way to modify physical and chemical properties of conjugated polymers and oligomers. Associated modifications in the molecular electronic states can be comprehensively described by examining scattering of excitons in the polymer's backbone at the scattering center representing the chemical substituent. Here, we implement effective tight-binding models as a tool to examine the analytical properties of the exciton scattering matrices in semi-infinite polymer chains with substitutions. We demonstrate that chemical interactions between the substitution and attached polymer are adequately described by the analytical properties of the scattering matrices. In particular, resonant and bound electronic excitations are expressed via the positions of zeros and poles of the scattering amplitude, analytically continued to complex values of exciton quasi-momenta. We exemplify the formulated concepts by analyzing excited states in conjugated phenylacetylenes substituted by perylene. PMID:26270830

  7. UCLA's Molecular Screening Shared Resource: enhancing small molecule discovery with functional genomics and new technology.

    PubMed

    Damoiseaux, Robert

    2014-05-01

    The Molecular Screening Shared Resource (MSSR) offers a comprehensive range of leading-edge high throughput screening (HTS) services including drug discovery, chemical and functional genomics, and novel methods for nano and environmental toxicology. The MSSR is an open access environment with investigators from UCLA as well as from the entire globe. Industrial clients are equally welcome as are non-profit entities. The MSSR is a fee-for-service entity and does not retain intellectual property. In conjunction with the Center for Environmental Implications of Nanotechnology, the MSSR is unique in its dedicated and ongoing efforts towards high throughput toxicity testing of nanomaterials. In addition, the MSSR engages in technology development eliminating bottlenecks from the HTS workflow and enabling novel assays and readouts currently not available. PMID:24661210

  8. Organic molecules in the atmosphere of Jupiter. [low molecular weight hydrocarbons

    NASA Technical Reports Server (NTRS)

    Ponnamperuma, C. A.

    1978-01-01

    Organic synthesis in the primitive solar system was simulated by Fischer Tropsch type experiments. Particular attention was given to the formation of lower molecular weight hydrocarbons. In a gas flow experiment, a gas mixture of H2 and CO was introduced into a heated reaction tube at a constant flow rate and passed through a catalyst (powdered Canyon Diablo). The products that emerged were directly analyzed by gas chromatography. The results of 21 runs under various gas mixing rations, reaction temperatures, and gas-catalyst contact times showed the predominance of the saturated hydrocarbon formation at C sub 4 and C sub 5 over the unsaturated ones. Saturate/unsaturate ratios were mostly less than 0.4 and none showed over 0.7.

  9. Features in the electronic structure and photoemission spectra of organic molecular semiconductors: The molecules of metal-phthalocyanines and PTCDA

    NASA Astrophysics Data System (ADS)

    Tikhonov, E. V.; Uspenskii, Yu. A.; Khokhlov, D. R.

    2013-09-01

    The role of many-electron effects in the formation of electronic quasiparticle spectra in organic molecular semiconductors (OMS) is analyzed. Many-body perturbation theory, ab initio calculations of metal phthalocyanines and PTCDA molecules, and experimental photoemission spectra are applied to this analysis. It is shown that density functional theory (DFT) poorly reproduces the electronic spectra of OMS. The use of a hybrid functional method (HFM) provides precise reproduction of both valence and conducting bands, while the HOMO-LUMO gap remains underestimated. The correct gap width is obtained in both DFT and HFM, when it is calculated through ionization and affinity energies. It is shown that such an approach gives a formula for gap correction due to electron correlations, which is close to an expression derived from the GW approximation.

  10. Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage

    PubMed Central

    Rychel, Amanda L.; Garrick, Jacqueline M.; Kawaguchi, Masayoshi; Peterson, Kylee M.; Torii, Keiko U.

    2015-01-01

    Stomata, valves on the plant epidermis, are critical for plant growth and survival, and the presence of stomata impacts the global water and carbon cycle. Although transcription factors and cell-cell signaling components regulating stomatal development have been identified, it remains unclear as to how their regulatory interactions are translated into two-dimensional patterns of stomatal initial cells. Using molecular genetics, imaging, and mathematical simulation, we report a regulatory circuit that initiates the stomatal cell-lineage. The circuit includes a positive feedback loop constituting self-activation of SCREAMs that requires SPEECHLESS. This transcription factor module directly binds to the promoters and activates a secreted signal, EPIDERMAL PATTERNING FACTOR2, and the receptor modifier TOO MANY MOUTHS, while the receptor ERECTA lies outside of this module. This in turn inhibits SPCH, and hence SCRMs, thus constituting a negative feedback loop. Our mathematical model accurately predicts all known stomatal phenotypes with the inclusion of two additional components to the circuit: an EPF2-independent negative-feedback loop and a signal that lies outside of the SPCH•SCRM module. Our work reveals the intricate molecular framework governing self-organizing two-dimensional patterning in the plant epidermis. PMID:26203655

  11. Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo

    PubMed Central

    Levin, Michael

    2014-01-01

    In addition to biochemical gradients and transcriptional networks, cell behavior is regulated by endogenous bioelectrical cues originating in the activity of ion channels and pumps, operating in a wide variety of cell types. Instructive signals mediated by changes in resting potential control proliferation, differentiation, cell shape, and apoptosis of stem, progenitor, and somatic cells. Of importance, however, cells are regulated not only by their own Vmem but also by the Vmem of their neighbors, forming networks via electrical synapses known as gap junctions. Spatiotemporal changes in Vmem distribution among nonneural somatic tissues regulate pattern formation and serve as signals that trigger limb regeneration, induce eye formation, set polarity of whole-body anatomical axes, and orchestrate craniofacial patterning. New tools for tracking and functionally altering Vmem gradients in vivo have identified novel roles for bioelectrical signaling and revealed the molecular pathways by which Vmem changes are transduced into cascades of downstream gene expression. Because channels and gap junctions are gated posttranslationally, bioelectrical networks have their own characteristic dynamics that do not reduce to molecular profiling of channel expression (although they couple functionally to transcriptional networks). The recent data provide an exciting opportunity to crack the bioelectric code, and learn to program cellular activity at the level of organs, not only cell types. The understanding of how patterning information is encoded in bioelectrical networks, which may require concepts from computational neuroscience, will have transformative implications for embryogenesis, regeneration, cancer, and synthetic bioengineering. PMID:25425556

  12. Patterns of cryptic host specificity in duck lice based on molecular data.

    PubMed

    Escalante, G C; Sweet, A D; McCracken, K G; Gustafsson, D R; Wilson, R E; Johnson, K P

    2016-06-01

    Documenting patterns of host specificity in parasites relies on the adequate definition of parasite species. In many cases, parasites have simplified morphology, making species delimitation based on traditional morphological characters difficult. Molecular data can help in assessing whether widespread parasites harbour cryptic species and, alternatively, in guiding further taxonomic revision in cases in which there is morphological variation. The duck louse genus Anaticola (Phthiraptera: Philopteridae), based on current taxonomy, contains both host-specific and widespread species. Mitochondrial and nuclear DNA sequences of samples from this genus were used to document patterns of host specificity. The comparison of these patterns with morphological variations in Anaticola revealed a general correspondence between the groups identified by DNA sequences and morphology, respectively. These results suggest that a more thorough taxonomic review of this genus is needed. In general, the groups identified on the basis of molecular data were associated with particular groups of waterfowl (e.g. dabbling ducks, sea ducks, geese) or specific biogeographic regions (e.g. North America, South America, Australia, Eurasia). PMID:26753998

  13. Magnetic interaction between a radical spin and a single-molecule magnet in a molecular spin-valve.

    PubMed

    Urdampilleta, Matias; Klayatskaya, Svetlana; Ruben, Mario; Wernsdorfer, Wolfgang

    2015-04-28

    Molecular spintronics using single molecule magnets (SMMs) is a fast growing field of nanoscience that proposes to manipulate the magnetic and quantum information stored in these molecules. Herein we report evidence of a strong magnetic coupling between a metallic ion and a radical spin in one of the most extensively studied SMMs: the bis(phtalocyaninato)terbium(III) complex (TbPc2). For that we use an original multiterminal device comprising a carbon nanotube laterally coupled to the SMMs. The current through the device, sensitive to magnetic interactions, is used to probe the magnetization of a single Tb ion. Combining this electronic read-out with the transverse field technique has allowed us to measure the interaction between the terbium ion, its nuclear spin, and a single electron located on the phtalocyanine ligands. We show that the coupling between the Tb and this radical is strong enough to give extra resonances in the hysteresis loop that are not observed in the anionic form of the complex. The experimental results are then modeled by diagonalization of a three-spins Hamiltonian. This strong coupling offers perspectives for implementing nuclear and electron spin resonance techniques to perform basic quantum operations in TbPc2. PMID:25858088

  14. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.

    PubMed

    Ellis, Christopher R; Tsai, Cheng-Chieh; Hou, Xinjun; Shen, Jana

    2016-03-17

    Targeting β-secretase (BACE1) with small-molecule inhibitors offers a promising route for treatment of Alzheimer's disease. However, the intricate pH dependence of BACE1 function and inhibitor efficacy has posed major challenges for structure-based drug design. Here we investigate two structurally similar BACE1 inhibitors that have dramatically different inhibitory activity using continuous constant pH molecular dynamics (CpHMD). At high pH, both inhibitors are stably bound to BACE1; however, within the enzyme active pH range, only the iminopyrimidinone-based inhibitor remains bound, while the aminothiazine-based inhibitor becomes partially dissociated following the loss of hydrogen bonding with the active site and change of the 10s loop conformation. The drastically lower activity of the second inhibitor is due to the protonation of a catalytic aspartate and the lack of a propyne tail. This work demonstrates that CpHMD can be used for screening pH-dependent binding profiles of small-molecule inhibitors, providing a new tool for structure-based drug design and optimization. PMID:26905811

  15. Computer-aided molecular modeling study on antibody recognition of small molecules: an immunoassay for triazine herbicides.

    PubMed

    Yuan, Meng; Na, Yu; Li, Lingling; Liu, Bing; Sheng, Wei; Lu, Xiaonan; Kennedy, Ivan; Crossan, Angus; Wang, Shuo

    2012-10-24

    Most immunoassays for determination of small molecules are still designed on the basis of the "trial and error" method, due to the lack of understanding of antibody recognition. In the present study, we developed a heterologous indirect competitive enzyme-linked immunosorbent assay for determination of triazine herbicides, with limits of detection for 11 triazines ranging from 0.05 to 29.4 μg/L. Mechanisms of the antigen-antibody interaction were studied by computer-aided molecular modeling (CAMM)-based quantitative structure-activity relationship analyses. Co-effects of the analytes' substructural hydrophobic, electrostatic, and steric fields on antibody recognition were further revealed. Hydrophobicity of the antigens was demonstrated to have the most important impact. Even less exposed substituents provided hydrophobic force to the antigen-antibody interaction. Dislocated orientation of analyte functional groups could lead to steric hindrance and hydrophobic misleading of antibody recognition. This may happen even when the antigens contained the same substituent as the hapten. Frontier orbital energies also affect the reaction significantly. This study highlights of the power of CAMM-based analyses, providing insights into antibody recognition of small molecules. PMID:23043348

  16. Molecular magnetic resonance imaging of acute vascular cell adhesion molecule-1 expression in a mouse model of cerebral ischemia

    PubMed Central

    Hoyte, Lisa C; Brooks, Keith J; Nagel, Simon; Akhtar, Asim; Chen, Ruoli; Mardiguian, Sylvie; McAteer, Martina A; Anthony, Daniel C; Choudhury, Robin P; Buchan, Alastair M; Sibson, Nicola R

    2010-01-01

    The pathogenesis of stroke is multifactorial, and inflammation is thought to have a critical function in lesion progression at early time points. Detection of inflammatory processes associated with cerebral ischemia would be greatly beneficial in both designing individual therapeutic strategies and monitoring outcome. We have recently developed a new approach to imaging components of the inflammatory response, namely endovascular adhesion molecule expression on the brain endothelium. In this study, we show specific imaging of vascular cell adhesion molecule (VCAM)-1 expression in a mouse model of middle cerebral artery occlusion (MCAO), and a reduction in this inflammatory response, associated with improved behavioral outcome, as a result of preconditioning. The spatial extent of VCAM-1 expression is considerably greater than the detectable lesion using diffusion-weighted imaging (25% versus 3% total brain volume), which is generally taken to reflect the core of the lesion at early time points. Thus, VCAM-1 imaging seems to reveal both core and penumbral regions, and our data implicate VCAM-1 upregulation and associated inflammatory processes in the progression of penumbral tissue to infarction. Our findings indicate that such molecular magnetic resonance imaging (MRI) approaches could be important clinical tools for patient evaluation, acute monitoring of therapy, and design of specific treatment strategies. PMID:20087364

  17. Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids.

    PubMed

    Palmer, David S; Mišin, Maksim; Fedorov, Maxim V; Llinas, Antonio

    2015-09-01

    We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction. PMID:26212723

  18. Evaluation of 99mTc-peptide-ZHER2:342 Affibody® molecule for in vivo molecular imaging

    PubMed Central

    Zhang, J-M; Zhao, X-M; Ren, X-C; Wang, N; Han, J-Y; Jia, L-Z

    2014-01-01

    Objective: The aim of this study was to develop an improved method for labelling ZHER2:342 with Technetium-99m (99mTc) using Gly-(d) Ala-Gly-Gly as a chelator and to evaluate the feasibility of its use for visualization of HER2 expression in vivo. Methods: The Affibody® molecule ZHER2:342 was synthesized by Fmoc/tBu solid phase synthesis. The chelator, Gly-(d) Ala-Gly-Gly, was introduced by manual synthesis as the N-terminal extensions of ZHER2:342. ZHER2:342 was labelled with 99mTc. The labelling efficiency, radiochemical purity and in vitro stability of the labelled molecular probe were analysed by reversed-phase high performance liquid chromatography. Biodistribution and molecular imaging using 99mTc-peptide-ZHER2:342 were performed. Results: The molecular probe was successfully synthesized and labelled with 99mTc with the labelling efficiency of 98.10 ± 1.73% (n = 5). The radiolabelled molecular probe remained highly stable in vitro. The molecular imaging showed high uptake in HER2-expressing SKOV-3 xenografts, whereas the MDA-MB-231 xenografts with low HER2 expression were not clearly imaged at any time after the injection of 99mTc-peptide-ZHER2:342. The predominant clearance pathway for 99mTc-peptide-ZHER2:342 was through the kidneys. Conculsion: 99mTc-peptide-ZHER2:342 using Gly-(d) Ala-Gly-Gly as a chelator is a promising tracer agent with favourable biodistribution and imaging properties that may be developed as a radiopharmaceutical for the detection of HER2-positive malignant tumours. Advances in knowledge: The 99mTc-peptide-ZHER2:342 molecular probe is a promising tracer agent, and the results in this study provide a foundation for future development of protocols for earlier visual detection of cancer in the clinical setting. PMID:24273251

  19. Molecular Population Genetics of the Male and Female Mitochondrial DNA Molecules of the California Sea Mussel, Mytilus californianus

    PubMed Central

    Ort, Brian S.; Pogson, Grant H.

    2007-01-01

    The presence of two gender-associated mitochondrial genomes in marine mussels provides a unique opportunity to investigate the dynamics of mtDNA evolution without complications inherent in interspecific comparisons. Here, we assess the relative importance of selection, mutation, and differential constraint in shaping the patterns of polymorphism within and divergence between the male (M) and female (F) mitochondrial genomes of the California sea mussel, Mytilus californianus. Partial sequences were obtained from homologous regions of four genes (nad2, cox1, atp6, and nad5) totaling 2307 bp in length. The M and F mtDNA molecules of M. californianus exhibited extensive levels of nucleotide polymorphism and were more highly diverged than observed in other mytilids (overall Tamura–Nei distances >40%). Consistent with previous studies, the M molecule had significantly higher levels of silent and replacement polymorphism relative to F. Both genomes possessed large numbers of singleton and low-frequency mutations that gave rise to significantly negative Tajima's D values. Mutation-rate scalars estimated for silent and replacement mutations were elevated in the M genome but were not sufficient to account for its higher level of polymorphism. McDonald–Kreitman tests were highly significant at all loci due to excess numbers of fixed replacement mutations between molecules. Strong purifying selection was evident in both genomes in keeping the majority of replacement mutations at low population frequencies but appeared to be slightly relaxed in M. Our results suggest that a reduction in selective constraint acting on the M genome remains the best explanation for its greater levels of polymorphism and faster rate of evolution. PMID:17720935

  20. A Molecular Dynamics Study on the Confinement of Carbon Dioxide Molecules in Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Lazor, Meagan; Rende, Deniz; Baysal, Nihat; Ozisik, Rahmi

    2012-02-01

    The influence of atmospheric carbon dioxide (CO2) concentration on global warming is considered as one of the primary environmental issues of the past two decades. The main source of CO2 emission is human activity, such as the use of fossil fuels in transportation and industrial plants. Following the release of Kyoto Protocol in 1997, effective ways of controlling CO2 emissions received much attention. As a result, various materials such as activated carbon, zeolites, and carbon nanotubes (CNTs) were investigated for their CO2 adsorbing properties. CNTs were reported to have CO2 adsorption capability twice that of activated carbon, hence they received the most attention. In the current study, single walled carbon nanotubes (SWNTs) were used as one dimensional nanoporous materials and their CO2 adsorption capacity was analyzed with Molecular Dynamics simulations. Results indicated that SWNTs are excellent CO2 adsorbers and their effectiveness increase at low CO2 concentrations. In addition, we showed that by varying temperature, CO2 can be removed from the SWNTs, providing a simple method to reuse SWNTs.

  1. Oxidation of nickel surfaces through the energetic impacts of oxygen molecules: Reactive molecular dynamics simulations.

    PubMed

    Amiri, Negar; Behnejad, Hassan

    2016-04-14

    Molecular dynamics approach accompanied by reactive force field is used to study the characteristics of the oxide growth process on Ni(100) and Ni(111) surfaces at the temperatures of 300, 600, and 900 K and 5 eV as the energy of the O2 impacts. The exposure of Ni surfaces to the high-energy O2 impacts indicates that the primary oxide nuclei can be formed on any impact site. The results of kinetic studies clarify that the oxide growth kinetics cannot be accurately explained with the island growth model and increasing the surface temperature raises failure of the model. Under the present conditions, the growth kinetics is found to obey a Langmuir growth model. Increasing the surface temperature from 300 to 900 K results in ∼18.75% and ∼23% more oxygen consumption by (100) and (111) surfaces of Ni, respectively. The structure of nickel oxide (NiO) film formed after 200 successive O2 impacts per surface super-cell is investigated utilizing radial distribution functions and oxygen density profiles. These calculations demonstrate that the structure of the formed NiO film is amorphous. Moreover, the charge profiles in Ni/NiO system are illustrated and discussed. PMID:27083743

  2. Dye-laser intracavity absorption spectrum of deuterium molecule and the collisional quenching of molecular hydrogen

    SciTech Connect

    Banerjee, A.K.

    1988-01-01

    The intracavity absorption technique (ICA) in a continuous wave (cw) multimode dye laser has been applied to the study of the molecular spectrum of D{sub 2} in the optical region (6185.28-5797.37 {angstrom}). This work represents the first attempt to directly observe the optical absorption spectrum of D{sub 2} whereas only the emission spectrum in the region was previously available. In the course of an extensive analysis of our data, new transition assignments were given to lines that were not previously observed in emission. Furthermore, some wrong assignments that existed in the previously published literature have been corrected. Besides the expected transitions originating from the 2c{sup {minus}} state ({tau}: 10{sup {minus}3}s), transitions from very short lived states such as 2a, 2c{sup +}, 2C{sup {plus minus}}, 2B ({tau}: 10{sup {minus}8} {yields} 10{sup {minus}9}s) were also observed, which shows ICA to be highly sensitive to detection of very weak absorption lines. In the second part of this research project the proportionality of the ICA signal to number density has been used to investigate the collisional quenching of the 2c{sup 3}{Phi}{sub u} state of H{sub 2} by H{sub 2}, N{sub 2} Ar, Ne, and He over various vibrational and rotational levels. The study was carried out in an rf (radio frequency) produced plasma containing mixtures of the various gases.

  3. Histologic characteristics of non-microsatellite-instable colon adenomas correlate with distinct molecular patterns.

    PubMed

    Neuville, Agnès; Nicolet, Céline; Meyer, Nicolas; Schneider, Anne; Legrain, Michèle; Brigand, Cécile; Duclos, Bernard; Bachellier, Philippe; Oudet, Pierre; Bellocq, Jean-Pierre; Kedinger, Michèle; Gaub, Marie-Pierre; Guenot, Dominique

    2011-02-01

    Colon carcinogenesis encompasses the stepwise accumulation of genomic aberrations correlated with the transition of aberrant crypt-adenoma-carcinoma. Recent data have revealed that, in addition to the microsatellite-instable phenotype, the chromosome instability pathway, representing four fifth of the colon carcinoma, could be involved in heterogeneous molecular alterations. Our project was aimed at determining the existence of distinct molecular subtypes in 159 non-microsatellite-instable colon polyps and their correlation with histology and dysplasia, using allelotyping, MGMT promoter gene methylation status, and K-RAS mutation analyses. Allelic imbalance, MGMT methylation, and K-RAS mutations arise in 62%, 39%, and 32% of polyps, respectively. Only 14% of polyps had no alterations. A 2-way hierarchical clustering analysis of the allelic imbalances identified subgroups of polyps according to their allelic imbalance frequency and distribution. Not only tubulovillous adenoma but also high-grade adenomas were correlated with high global allelic imbalance frequency (P = .005 and P = .003), with allelic imbalance at microsatellites targeting chromosomes 1, 6, and 9. In conclusion, the data presented in this study show that a large heterogeneity exists in the molecular patterns of alterations in precancerous colon lesions, favoring different modes of tumor initiation. Therefore, molecular alterations correlated with tubulovillous-type and high-grade dysplasia could represent targets identifying predictive factors of progression. PMID:21238786

  4. An important impact of the molecule-electrode coupling asymmetry on the efficiency of bias-driven redox processes in molecular junctions.

    PubMed

    Bâldea, Ioan

    2015-06-28

    Two recent experimental and theoretical studies (Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 1282-1287; Phys. Chem. Chem. Phys., 2014, 16, 25942-25949) have addressed the problem of tuning the molecular charge and vibrational properties of single molecules embedded in nanojunctions. These are molecular characteristics escaping so far from an efficient experimental control in broad ranges. Here, we present a general argument demonstrating why, out of various experimental platforms possible, those wherein active molecules are asymmetrically coupled to electrodes are to be preferred to those symmetrically coupled for achieving a(n almost) complete redox process, and why an electrochemical environment has advantages over "dry" setups. This study aims at helping to nanofabricate molecular junctions using the most appropriate platforms allowing the broadest possible bias-driven control over the redox state and vibrational modes of single molecules linked to electrodes. PMID:26018297

  5. Reconstitution of biologically active 50S ribosomal subunits with artificial 5S RNA molecules carrying disturbances in the base pairing within the molecular stalk.

    PubMed Central

    Raué, H A; Lorenz, S; Erdmann, V A; Planta, R J

    1981-01-01

    Bacillus stearothermophilus 50S ribosomal subunits were reconstituted in vitro using artificial 5S RNA molecules constructed by combining parts of major and minor type (Raué et al. (1976) Europ. J. Biochem. 68, 169-176) B. licheniformis 5S RNA. The artificial 5S RNA molecules carry defined disturbances (A.C juxtapositions and extra G.U pairs) in the base pairing between the 5'- and 3'-terminal sequences of the molecule (the molecular stalk region). The biological activity of the reconstituted subunits was determined in an E. coli cell-free system programmed with poly-U. The results show that conservation of the base pairing within the molecular stalk is not required for biological activity of 5S RNA. Disturbances of the base pairing within this region do reduce the rate of reconstitution, however. Normal base pairing in the molecular stalk is thus required to ensure efficient ribosome assembly. PMID:6164987

  6. Diffuse molecular gas at high redshift. Detection of CO molecules and the 2175 Å dust feature at z = 1.64

    NASA Astrophysics Data System (ADS)

    Noterdaeme, P.; Ledoux, C.; Srianand, R.; Petitjean, P.; Lopez, S.

    2009-09-01

    We present the detection of carbon monoxide molecules (CO) at z=1.6408 towards the quasar SDSS J160457.50+220300.5 using the Very Large Telescope Ultraviolet and Visual Echelle Spectrograph. We detected CO absorption in at least two components in the first six A-X bands and one d-X(5-0) interband system. This is the second detection of its kind along a quasar line of sight. The CO absorption profiles are well modelled by assuming rotational excitation of CO in the range 6 < T_ex < 16 K, which is consistent with or higher than the temperature of the cosmic microwave background radiation at this redshift. We derive a total CO column density of N(CO) = 4 × 1014~ cm-2. The measured column densities of S I, Mg I, Zn II, Fe II, and Si II indicate a dust depletion pattern typical of cold gas in the Galactic disc. The background quasar spectrum is significantly reddened (u-K ~ 4.5 mag) and exhibits a pronounced 2175 Å dust absorption feature at the redshift of the CO absorber. Using a control sample of ~500 quasars, we find that the chance probability that this feature is spurious is ~0.3%. We show that the spectral energy distribution (SED) of the quasar is well fitted by a QSO composite spectrum reddened with a Large Magellanic Cloud supershell extinction law at the redshift of the absorber. It is noticeable that this quasar is absent from the colour-selected SDSS quasar sample. This demonstrates that our current view of the Universe may be biased against dusty sightlines. These direct observations of carbonaceous molecules and dust open up the possibility of studying the physical conditions and chemistry of diffuse molecular gas in high redshift galaxies. Based on observations carried out with the Ultraviolet and Visual Echelle Spectrograph, mounted on the ESO Very Large Telescope, under Prgm. ID. 081.A-0334(B).

  7. Characterization of a molecular switch system that regulates gene expression in mammalian cells through a small molecule

    PubMed Central

    2010-01-01

    Background Molecular switch systems that activate gene expression by a small molecule are effective technologies that are widely used in applied biological research. Nuclear receptors are valuable candidates for these regulation systems due to their functional role as ligand activated transcription factors. Previously, our group engineered a variant of the retinoid × receptor to be responsive to the synthetic compound, LG335, but not responsive to its natural ligand, 9-cis-retinoic acid. Results This work focuses on characterizing a molecular switch system that quantitatively controls transgene expression. This system is composed of an orthogonal ligand/nuclear receptor pair, LG335 and GRQCIMFI, along with an artificial promoter controlling expression of a target transgene. GRQCIMFI is composed of the fusion of the DNA binding domain of the yeast transcription factor, Gal4, and a retinoid × receptor variant. The variant consists of the following mutations: Q275C, I310M, and F313I in the ligand binding domain. When introduced into mammalian cell culture, the switch shows luciferase activity at concentrations as low as 100 nM of LG335 with a 6.3 ± 1.7-fold induction ratio. The developed one-component system activates transgene expression when introduced transiently or virally. Conclusions We have successfully shown that this system can induce tightly controlled transgene expression and can be used for transient transfections or retroviral transductions in mammalian cell culture. Further characterization is needed for gene therapy applications. PMID:20167077

  8. Collectin liver 1 and collectin kidney 1 and other complement-associated pattern recognition molecules in systemic lupus erythematosus.

    PubMed

    Troldborg, A; Thiel, S; Jensen, L; Hansen, S; Laska, M J; Deleuran, B; Jensenius, J C; Stengaard-Pedersen, K

    2015-11-01

    The objective of this study was to explore the involvement of collectin liver 1 (CL-L1) and collectin kidney 1 (CL-K1) and other pattern recognition molecules (PRMs) of the lectin pathway of the complement system in a cross-sectional cohort of systemic lupus erythematosus (SLE) patients. Concentrations in plasma of CL-L1, CL-K1, mannan-binding lectin (MBL), M-ficolin, H-ficolin and L-ficolin were determined in 58 patients with SLE and 65 healthy controls using time-resolved immunoflourometric assays. The SLE patients' demographic, diagnostic, clinical and biochemical data and collection of plasma samples were performed prospectively during 4 months. CL-L1, CL-K1 and M-ficolin plasma concentrations were lower in SLE patients than healthy controls (P-values < 0.001, 0.033 and < 0.001, respectively). H-ficolin concentration was higher in SLE patients (P < 0.0001). CL-L1 and CL-K1 plasma concentrations in the individuals correlated in both patients and controls. Patients with low complement component 3 (C3) demonstrated a negative correlation between C3 and CL-L1 and CL-K1 (P = 0.022 and 0.031, respectively). Patients positive for anti-dsDNA antibodies had lower levels of MBL in plasma than patients negative for anti-dsDNA antibodies (P = 0.02). In a cross-sectional cohort of SLE patients, we found differences in the plasma concentrations of CL-L1, CL-K1, M-ficolin and H-ficolin compared to a group of healthy controls. Alterations in plasma concentrations of the PRMs of the lectin pathway in SLE patients and associations to key elements of the disease support the hypothesis that the lectin pathway plays a role in the pathogenesis of SLE. PMID:26154564

  9. The relations between recombination rate and patterns of molecular variation and evolution in Drosophila.

    PubMed

    Charlesworth, Brian; Campos, José L

    2014-01-01

    Genetic recombination affects levels of variability and the efficacy of selection because natural selection acting at one site affects evolutionary processes at linked sites. The variation in local recombination rates across the Drosophila genome provides excellent material for testing hypotheses concerning the evolutionary consequences of recombination. The current state of knowledge from studies of Drosophila genomics and population genetics is reviewed here. Selection at linked sites has influenced the relations between recombination rates and patterns of molecular variation and evolution, such that higher rates of recombination are associated with both higher levels of variability and a greater efficacy of selection. It seems likely that background selection against deleterious mutations is a major factor contributing to these patterns in genome regions in which crossing over is rare or absent, whereas selective sweeps of positively selected mutations probably play an important role in regions with crossing over. PMID:25251853

  10. Intramolecular vibrations and noise effects on pattern formation in a molecular helix.

    PubMed

    Fouda, H P Ekobena; Tabi, C B; Mohamadou, A; Kofané, T C

    2011-09-21

    Modulational instability in a biexciton molecular chain is addressed. We show that the model can be reduced to a set of three coupled equations: two nonlinear Schrödinger equations and a Boussinesq equation. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Simulations of the full discrete systems reveal some behaviors of modulational instability, since wave patterns are observed for the excitons and the phonon spectrum. We also take the effect of thermal fluctuations into account and we numerically study both the stability and the instability of the plane waves under 300 K. The plane wave is found to be stable under modulation, but displays a gradual increase of the wave amplitudes. Under modulation, the same behaviors are observed and wave patterns are found to resist thermal fluctuations, which is in agreement with earlier research on localized structure stability under thermal noise. PMID:21878712

  11. Molecular basis of natural variation and environmental control of trichome patterning

    PubMed Central

    Hauser, Marie-Theres

    2014-01-01

    Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

  12. Pro-Coagulant Endothelial Dysfunction Results from EHEC Shiga Toxins and Host Damage-Associated Molecular Patterns

    PubMed Central

    Mayer, Chad L.; Parello, Caitlin S. L.; Lee, Benjamin C.; Itagaki, Kiyoshi; Kurosawa, Shinichiro; Stearns-Kurosawa, Deborah J.

    2015-01-01

    Hemolytic uremic syndrome (HUS) from enterohemorrhagic Escherichia coli infection is a leading cause of kidney failure in otherwise healthy U.S. children. The bacterial Shiga toxins (Stx) induce the characteristic coagulopathy of HUS, but the damage to toxin-receptor expressing cells and organ injury due to ischemia likely also releases inflammatory damage-associated molecular patterns (DAMPs), which may exacerbate injury along with the toxins. To examine this, human aortic and renal glomerular cell anti-coagulant and barrier functions were studied after in vitro challenge with Stx1, Stx2, and DAMPs. There was significant loss of surface anti-coagulant protein C pathway molecules, increased expression of pro-thrombotic PAR1 and reduced protein C activation capability by 1527%. Histones nearly completely prevented the activated protein C protection of endothelial cells from thrombin-induced permeability. In mice, lethal Stx2 challenge elevated plasma HMGB1 (day 2, 321??118%; p?

  13. Mixed-metal molecular complexes: Single-molecule nanomagnets and bioinorganic models of the water oxidizing complex of photosystem II

    NASA Astrophysics Data System (ADS)

    Mishra, Abhudaya

    2006-12-01

    The current burgeoning research in high nuclearity manganese-containing carboxylate clusters is primarily due to their relevance in areas as diverse as magnetic materials and bioinorganic chemistry. In the former, the ability of single molecules to retain, below a critical temperature (T B), their magnetization vector, resulting in the observation of bulk magnetization in the absence of a field and without long-range ordering of the spins, has termed such molecules as Single-Molecule Magnets (SMMs), or molecular nanomagnets. These molecules display superparamagnet like slow magnetization relaxation arising from the combination of a large molecular spin, S, and a large and negative magnetoanisotropy, D. Traditionally, these nanomagnets have been Mn containing species. An out of the box approach towards synthesizing SMMs is engineering mixed-metal Mn-containing compounds. An attractive choice towards this end is the use of Lanthanides (Ln), which possess both a high spin, S, and a large D. A family of related MnIII8Ce IV SMMs has been synthesized. However, the Ce ion of these complexes is diamagnetic (CeIV). Thus, further investigation has led to the isolation of a family of MnIII11Ln III4 complexes in which all but the Ln = Eu complex function as single-molecule nanomagnets. The mixed-metal synthetic effort has been extended to include actinides with the successful isolation of a Mn IV10ThIV6 complex, albeit this homovalent complex is not a SMM. In the bioinorganic research, the Water Oxidizing Complex (WOC) in Photosystem II (PS II) catalyzes the oxidation of H2O to O2 in green plants, algae and cyanobacteria. Recent crystal structures of the WOC confirm it to be a Mn4CaOx cluster with primarily carboxylate ligation. To date, various multinuclear Mn complexes have been synthesized as putative models of the WOC. On the contrary, there have been no synthetic MnCa(Sr) mixed-metal complexes. Thus, in this bioinorganic modeling research of the WOC, various synthetic methods have been developed to prepare a variety of heterometallic MnCa(Sr) complexes, namely, Mn13Ca2, Mn11Ca4, Mn8Ca and Mn14Sr; these are the first of their kind. X-ray absorption spectroscopy has been performed on all of these complexes and the results compared with analogous data on the WOC of PS II. In particular, Ca, Sr, and Mn, EXAFS and XANES reveal a distinct similarity between the sub-units within these complexes and the Mn 4CaOx site of the WOC. The data strongly suggest that a single-atom O bridge exists between the Mn atoms and the Ca atom of the WOC.

  14. The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: peptoid molecular transporters.

    PubMed

    Wender, P A; Mitchell, D J; Pattabiraman, K; Pelkey, E T; Steinman, L; Rothbard, J B

    2000-11-21

    Certain proteins contain subunits that enable their active translocation across the plasma membrane into cells. In the specific case of HIV-1, this subunit is the basic domain Tat(49-57) (RKKRRQRRR). To establish the optimal structural requirements for this translocation process, and thereby to develop improved molecular transporters that could deliver agents into cells, a series of analogues of Tat(49-57) were prepared and their cellular uptake into Jurkat cells was determined by flow cytometry. All truncated and alanine-substituted analogues exhibited diminished cellular uptake, suggesting that the cationic residues of Tat(49-57) play a principal role in its uptake. Charge alone, however, is insufficient for transport as oligomers of several cationic amino acids (histidine, lysine, and ornithine) are less effective than Tat(49-57) in cellular uptake. In contrast, a 9-mer of l-arginine (R9) was 20-fold more efficient than Tat(49-57) at cellular uptake as determined by Michaelis-Menton kinetic analysis. The d-arginine oligomer (r9) exhibited an even greater uptake rate enhancement (>100-fold). Collectively, these studies suggest that the guanidinium groups of Tat(49-57) play a greater role in facilitating cellular uptake than either charge or backbone structure. Based on this analysis, we designed and synthesized a class of polyguanidine peptoid derivatives. Remarkably, the subset of peptoid analogues containing a six-methylene spacer between the guanidine head group and backbone (N-hxg), exhibited significantly enhanced cellular uptake compared to Tat(49-57) and even to r9. Overall, a transporter has been developed that is superior to Tat(49-57), protease resistant, and more readily and economically prepared. PMID:11087855

  15. Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK.

    PubMed

    Arita-Morioka, Ken-ichi; Yamanaka, Kunitoshi; Mizunoe, Yoshimitsu; Ogura, Teru; Sugimoto, Shinya

    2015-01-01

    Biofilms are complex communities of microorganisms that attach to surfaces and are embedded in a self-produced extracellular matrix. Since these cells acquire increased tolerance against antimicrobial agents and host immune systems, biofilm-associated infectious diseases tend to become chronic. We show here that the molecular chaperone DnaK is important for biofilm formation and that chemical inhibition of DnaK cellular functions is effective in preventing biofilm development. Genetic, microbial, and microscopic analyses revealed that deletion of the dnaK gene markedly reduced the production of the extracellular functional amyloid curli, which contributes to the robustness of Escherichia coli biofilms. We tested the ability of DnaK inhibitors myricetin (Myr), telmisartan, pancuronium bromide, and zafirlukast to prevent biofilm formation of E. coli. Only Myr, a flavonol widely distributed in plants, inhibited biofilm formation in a concentration-dependent manner (50% inhibitory concentration [IC50] = 46.2 μM); however, it did not affect growth. Transmission electron microscopy demonstrated that Myr inhibited the production of curli. Phenotypic analyses of thermosensitivity, cell division, intracellular level of RNA polymerase sigma factor RpoH, and vulnerability to vancomycin revealed that Myr altered the phenotype of E. coli wild-type cells to make them resemble those of the isogenic dnaK deletion mutant, indicating that Myr inhibits cellular functions of DnaK. These findings provide insights into the significance of DnaK in curli-dependent biofilm formation and indicate that DnaK is an ideal target for antibiofilm drugs. PMID:25403660

  16. Liquid crystals with patterned molecular orientation as an electrolytic active medium

    NASA Astrophysics Data System (ADS)

    Peng, Chenhui; Guo, Yubing; Conklin, Christopher; Viñals, Jorge; Shiyanovskii, Sergij V.; Wei, Qi-Huo; Lavrentovich, Oleg D.

    2015-11-01

    Transport of fluids and particles at the microscale is an important theme in both fundamental and applied science. One of the most successful approaches is to use an electric field, which requires the system to carry or induce electric charges. We describe a versatile approach to generate electrokinetic flows by using a liquid crystal (LC) with surface-patterned molecular orientation as an electrolyte. The surface patterning is produced by photoalignment. In the presence of an electric field, the spatially varying orientation induces space charges that trigger flows of the LC. The active patterned LC electrolyte converts the electric energy into the LC flows and transport of embedded particles of any type (fluid, solid, gaseous) along a predesigned trajectory, posing no limitation on the electric nature (charge, polarizability) of these particles and interfaces. The patterned LC electrolyte exhibits a quadratic field dependence of the flow velocities; it induces persistent vortices of controllable rotation speed and direction that are quintessential for micro- and nanoscale mixing applications.

  17. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  18. Intracellular patterns of sialophorin expression define a new molecular classification of breast cancer and represent new targets for therapy

    PubMed Central

    Fu, Q; Cash, S E; Andersen, J J; Kennedy, C R; Madadi, A R; Raghavendra, M; Dietrich, L L; Agger, W A; Shelley, C S

    2014-01-01

    Background: Sialophorin is a transmembrane sialoglycoprotein. Normally, the molecule is only produced by white blood cells where it regulates functions such as intercellular adhesion, intracellular signalling, apoptosis, migration and proliferation. Methods: Normal breast tissue and primary breast tumours were analysed by immunohistochemistry for sialophorin expression. The sialophorin-positive breast cancer cell line MCF7 was engineered to stably express either non-targeted or sialophorin-targeted small interfering RNA (siRNA). Assays were then performed in vitro to assess apoptosis, intracellular adhesion, transendothelial migration and cytotoxicity. An orthotopic mouse model assayed ability to produce tumours in vivo. Results: Normal breast epithelial cells exhibit expression of the N-terminal domain of sialophorin in the cytoplasm but not the nucleus. The majority of these normal cells are also negative for expression of the C-terminal domain. In contrast, malignant breast epithelial cells exhibit N-terminal expression both in the cytoplasm and nucleus and the majority express the C-terminus in the nucleus. Using differential patterns of intracellular expression of the N and C termini of sialophorin, we define six subtypes of breast cancer that are independent of histological and receptor status classification. Targeting sialophorin with siRNA resulted in the MCF7 breast cancer cell line exhibiting increased homotypic adhesion, decreased transendothelial migration, increased susceptibility to apoptosis, increased vulnerability to lysis by natural killer cells and decreased ability to produce tumours in mice. Conclusion: Our results indicate that intracellular patterns of sialophorin expression define a new molecular classification of breast cancer and that sialophorin represents a novel therapeutic target. PMID:24281005

  19. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-12-01

    The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car-Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  20. Molecular Dynamics Simulation of the Aggregation Patterns in Aqueous Solutions of Bile Salts at Physiological Conditions.

    PubMed

    Mustan, Fatmegyul; Ivanova, Anela; Madjarova, Galia; Tcholakova, Slavka; Denkov, Nikolai

    2015-12-24

    Classical molecular dynamics simulations are employed to monitor the aggregation behavior of six bile salts (nonconjugated and glycine- and taurine-conjugated sodium cholate and sodium deoxycholate) with concentration of 10 mM in aqueous solution in the presence of 120 mM NaCl. There are 150 ns trajectories generated to characterize the systems. The largest stable aggregates are analyzed to determine their shape, size, and stabilizing forces. It is found that the aggregation is a hierarchical process and that its kinetics depends both on the number of hydroxyl groups in the steroid part of the molecules and on the type of conjugation. The micelles of all salts are similar in shape-deformed spheres or ellipsoids, which are stabilized by hydrophobic forces, acting between the steroid rings. The differences in the aggregation kinetics of the various conjugates are rationalized by the affinity for hydrogen bond formation for the glycine-modified salts or by the longer time needed to achieve optimum packing for the tauro derivatives. Evidence is provided for the hypothesis from the literature that the entirely hydrophobic core of all aggregates and the enhanced dynamics of the molecules therein should be among the prerequisites for their pronounced solubilization capacity for hydrophobic substances in vivo. PMID:26605858

  1. Application of pattern recognition in molecular spectroscopy: Automatic line search in high-resolution spectra

    NASA Astrophysics Data System (ADS)

    Bykov, A. D.; Pshenichnikov, A. M.; Sinitsa, L. N.; Shcherbakov, A. P.

    2004-07-01

    An expert system has been developed for the initial analysis of a recorded spectrum, namely, for the line search and the determination of line positions and intensities. The expert system is based on pattern recognition algorithms. Object recognition learning allows the system to achieve the needed flexibility and automatically detect groups of overlapping lines, whose profiles should be fit together. Gauss, Lorentz, and Voigt profiles are used as model profiles to which spectral lines are fit. The expert system was applied to processing of the Fourier transform spectrum of the D2O molecule in the region 3200-4200 cm-1, and it detected 4670 lines in the spectrum, which consisted of 439000 dots. No one experimentally observed line exceeding the noise level was missed.

  2. SPARCoC: A New Framework for Molecular Pattern Discovery and Cancer Gene Identification

    PubMed Central

    Ma, Shiqian; Johnson, Daniel; Ashby, Cody; Xiong, Donghai; Cramer, Carole L.; Moore, Jason H.; Zhang, Shuzhong; Huang, Xiuzhen

    2015-01-01

    It is challenging to cluster cancer patients of a certain histopathological type into molecular subtypes of clinical importance and identify gene signatures directly relevant to the subtypes. Current clustering approaches have inherent limitations, which prevent them from gauging the subtle heterogeneity of the molecular subtypes. In this paper we present a new framework: SPARCoC (Sparse-CoClust), which is based on a novel Common-background and Sparse-foreground Decomposition (CSD) model and the Maximum Block Improvement (MBI) co-clustering technique. SPARCoC has clear advantages compared with widely-used alternative approaches: hierarchical clustering (Hclust) and nonnegative matrix factorization (NMF). We apply SPARCoC to the study of lung adenocarcinoma (ADCA), an extremely heterogeneous histological type, and a significant challenge for molecular subtyping. For testing and verification, we use high quality gene expression profiling data of lung ADCA patients, and identify prognostic gene signatures which could cluster patients into subgroups that are significantly different in their overall survival (with p-values < 0.05). Our results are only based on gene expression profiling data analysis, without incorporating any other feature selection or clinical information; we are able to replicate our findings with completely independent datasets. SPARCoC is broadly applicable to large-scale genomic data to empower pattern discovery and cancer gene identification. PMID:25768286

  3. Rapid screening for citrus canker resistance employing pathogen-associated molecular pattern-triggered immunity responses

    PubMed Central

    Pitino, Marco; Armstrong, Cheryl M; Duan, Yongping

    2015-01-01

    Citrus canker, caused by the bacterial pathogen Xanthomonas citri ssp. citri (Xcc), has been attributed to millions of dollars in loss or damage to commercial citrus crops in subtropical production areas of the world. Since identification of resistant plants is one of the most effective methods of disease management, the ability to screen for resistant seedlings plays a key role in the production of a long-term solution to canker. Here, an inverse correlation between reactive oxygen species (ROS) production by the plant and the ability of Xcc to grow and form lesions on infected plants is reported. Based on this information, a novel screening method that can rapidly identify citrus seedlings that are less susceptible to early infection by Xcc was devised by measuring ROS accumulation triggered by a 22-amino acid sequence of the conserved N-terminal part of flagellin (flg22) from X. citri ssp. citri (Xcc-flg22). In addition to limiting disease symptoms, ROS production was also correlated with the expression of basal defense-related genes such as the pattern recognition receptors LRR8 and FLS2, the leucine-rich repeat receptor-like protein RLP12, and the defense-related gene PR1, indicating an important role for pathogen-associated molecular pattern-triggered immunity (PTI) in determining resistance to citrus canker. Moreover, the differential expression patterns observed amongst the citrus seedlings demonstrated the existence of genetic variations in the PTI response among citrus species/varieties. PMID:26504581

  4. Phage display identification of functional binding peptides against 4-acetamidophenol (Paracetamol): an exemplified approach to target low molecular weight organic molecules.

    PubMed

    Smith, Mathew W; Smith, Jonathan W; Harris, Charlotte; Brancale, Andrea; Allender, Christopher J; Gumbleton, Mark

    2007-06-22

    Peptide-phage display has been widely used to explore protein-protein interactions, however, despite the potential range of applications the use of this technology to identify peptides that bind low molecular weight organic molecules has not been explored. In this current study, we identified a phage clone (PARA-061) displaying the cyclic 7-mer peptide sequence N' AC-NPNNLSH-CGGGS C' that binds the low molecular weight organic molecule 4-acetamidophenol (4-AAP; paracetamol). To avoid occupancy of key functional groups on the target 4-AAP molecule our panning strategy was directed against insoluble complexes of 4-AAP rather than against the target linked to a stationary support or bearing an affinity tag. To augment the panning procedure we deleted phage that also bound the 4-AAP isomers, 2-AAP and 3-AAP. The identified PARA-061 peptide-phage clone displayed functional binding properties against 4-AAP in solution, able in a peptide sequence-dependant manner to prevent the in vitro hepatotoxicity of 4-AAP and reduce ( approximately 20%) the permeability of 4-AAP across a semi-permeable membrane. Molecular dynamic simulations generated a stable binding conformation between the PARA-061 peptide sequence and 4-AAP. In conclusion, we show that a phage display library can be used to identify peptide sequence-specific clones able to modulate the functional binding of a low molecular weight organic molecule. Such peptides may be expected to find utility in the next generation of hybrid polymer-based biosensing devices. PMID:17482566

  5. Molecular and structural characterization of dissolved organic matter from the deep ocean by FTICR-MS, including hydrophilic nitrogenous organic molecules

    USGS Publications Warehouse

    Reemtsma, T.; These, A.; Linscheid, M.; Leenheer, J.; Spitzy, A.

    2008-01-01

    Dissolved organic matter isolated from the deep Atlantic Ocean and fractionated into a so-called hydrophobic (HPO) fraction and a very hydrophilic (HPI) fraction was analyzed for the first time by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to resolve the molecular species, to determine their exact masses, and to calculate their molecular formulas. The elemental composition of about 300 molecules was identified. Those in the HPO fraction (14C age of 5100 year) are very similar to much younger freshwater fulvic acids, but less aromatic and more oxygenated molecules are more frequent. This trend continues toward the HPI fraction and may indicate biotic and abiotic aging processes that this material experienced since its primary production thousands of years ago. In the HPI fraction series of nitrogenous molecules containing one, two, or three nitrogens were identified by FTICR-MS. Product ion spectra of the nitrogenous molecules suggest that the nitrogen atoms in these molecules are included in the (alicyclic) backbone of these molecules, possibly in reduced form. These mass spectrometric data suggest that a large set of stable fulvic acids is ubiquitous in all aquatic compartments. Although sources may differ, their actual composition and structure appears to be quite similar and largely independent from their source, because they are the remainder of intensive oxidative degradation processes. ?? 2008 American Chemical Society.

  6. Activation of coherent lattice phonon following ultrafast molecular spin-state photo-switching: A molecule-to-lattice energy transfer.

    PubMed

    Marino, A; Cammarata, M; Matar, S F; Létard, J-F; Chastanet, G; Chollet, M; Glownia, J M; Lemke, H T; Collet, E

    2016-03-01

    We combine ultrafast optical spectroscopy with femtosecond X-ray absorption to study the photo-switching dynamics of the [Fe(PM-AzA)2(NCS)2] spin-crossover molecular solid. The light-induced excited spin-state trapping process switches the molecules from low spin to high spin (HS) states on the sub-picosecond timescale. The change of the electronic state (<50 fs) induces a structural reorganization of the molecule within 160 fs. This transformation is accompanied by coherent molecular vibrations in the HS potential and especially a rapidly damped Fe-ligand breathing mode. The time-resolved studies evidence a delayed activation of coherent optical phonons of the lattice surrounding the photoexcited molecules. PMID:26798836

  7. Activation of coherent lattice phonon following ultrafast molecular spin-state photo-switching: A molecule-to-lattice energy transfer

    PubMed Central

    Marino, A.; Cammarata, M.; Matar, S. F.; Létard, J.-F.; Chastanet, G.; Chollet, M.; Glownia, J. M.; Lemke, H. T.; Collet, E.

    2015-01-01

    We combine ultrafast optical spectroscopy with femtosecond X-ray absorption to study the photo-switching dynamics of the [Fe(PM-AzA)2(NCS)2] spin-crossover molecular solid. The light-induced excited spin-state trapping process switches the molecules from low spin to high spin (HS) states on the sub-picosecond timescale. The change of the electronic state (<50 fs) induces a structural reorganization of the molecule within 160 fs. This transformation is accompanied by coherent molecular vibrations in the HS potential and especially a rapidly damped Fe-ligand breathing mode. The time-resolved studies evidence a delayed activation of coherent optical phonons of the lattice surrounding the photoexcited molecules. PMID:26798836

  8. Phases, line tension and pattern formation in molecularly thin films at the air-water interface

    NASA Astrophysics Data System (ADS)

    Mandal, Pritam

    A Langmuir film, which is a molecularly thin insoluble film on a liquid substrate, is one practical realization of a quasi-two dimensional matter. The major advantages of this system for the study of phase separation and phase co-existence are (a) it allows accurate control of the components and molecular area of the film and (b) it can be studied by various methods that require very flat films. Phase separation in molecularly thin films plays an important role in a range of systems from biomembranes to biosensors. For example, phase-separated lipid nano-domains in biomembranes are thought to play crucial roles in membrane function. I use Brewster Angel Microscopy (BAM) coupled with Fluorescence Microscopy (FM) and static Light Scattering Microscopy (LSM) to image phases and patterns within Langmuir films. The three microscopic techniques --- BAM, FM and LSM --- are complimentary to each other, providing distinct sets of information. They allow direct comparison with literature results in lipid systems. I have quantitatively validated the use of detailed hydrodynamic simulations to determine line tension in monolayers. Line tension decreases as temperature rises. This decrease gives us information on the entropy associated with the line, and thus about line structure. I carefully consider the thermodynamics of line energy and entropy to make this connection. In the longer run, LSM will be exploited to give us further information about line structure. I have also extended the technique by testing it on domains within the curved surface of a bilayer vesicle. I also note that in the same way that the presence of surface-active agents, known as surfactants, affects surface energy, the addiction of line active agents alters the inter-phase line energy. Thus my results set to stage to systematically study the influence of line active agents ---'linactants' --- on the inter-phase line energy. Hierarchal self-assembled chiral patterns were observed as a function of temperature. I found that the appearance of these domains could be explained with a simple uniaxial optical axis in the underlying structure, which is the first critical step to understanding the origin of these patterns.

  9. Difference in Rotational Temperatures between Neutral Molecules and Molecular Ions of Low-Pressure Discharge N2-O2 Plasmas

    NASA Astrophysics Data System (ADS)

    Akatsuka, Hiroshi; Kawano, Hirokazu; Naoi, Koichi; Tan, Hao; Nezu, Atsushi; Matsuura, Haruaki

    2014-10-01

    For a microwave discharge nitrogen plasma with its discharge pressure about 1 Torr, our OES measurement showed that the rotational temperature of N2+ B state by the first negative system (1NS) is about 1.5 times higher than that of N2 C state by the second positive system (2PS). Meanwhile, it is found that the rotational temperature of O2+ b state by 1NS is almost the same as that of O2 b state by the atmospheric absorption band, which is quite different from N2 plasma. We consider that the rotational temperature of the ground state O2+ X ion should be higher than that of O2+ b state due to difference in the internuclear distance, where that of the O2+ b state is much larger than that of the ground state O2+ X. The angular momentum of both X and b states are almost conserved before and after the electron impact excitation due to small mass of an electron. Therefore, the rotational temperature of the X state of O2+ ion should be estimated to be about 1.3 times of that of O2+ b state. This value gives a similar result with that of nitrogen plasma, where the internuclear distances of B and X states of N2+ are almost the same. It is considered that the ground-state molecular ion has higher rotational temperature than neutral molecule.

  10. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    SciTech Connect

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

  11. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  12. Earle K. Plyler Prize for Molecular Spectroscopy Talk: Coherent Ultrafast Multidimensional Spectroscopy of Molecules; From NMR to X-rays

    NASA Astrophysics Data System (ADS)

    Mukamel, Shaul

    2011-03-01

    Multidimensional spectroscopic techniques which originated with NMR in the 1970s have been extended over the past 15 years to the optical regime. NMR spectroscopists have developed methods for the design of pulse sequences that resolve otherwise congested spectra, enhance selected spectral features and reveal desired dynamical events. The major experimental and computational advances required for extending these ideas to study electronic and vibrational motions on the femtosecond timescale will be surveyed. The response of complex molecules and semiconductor nanostructures to sequences of optical pulses provides snapshots of their structure and dynamical processes. Two-dimensional correlation plots of the signals show characteristic cross-peak patterns which carry information about hydrogen bonding, secondary structure fluctuations of proteins and amyloid fibrils, and coherent and incoherent energy and charge transfer in photosynthetic complexes. Double quantum coherence signals that are induced by correlations among electrons or excitons allow the visualization of correlated wavefunctions. Future extensions to the attosecond regime using xray pulses will be discussed. Since core excitations are highly localized at selected atoms, such signals can monitor the motions of valence electron wavepackets in real space with atomic spatial resolution. Common principles underlying coherent spectroscopy techniques for spins, valence electrons, and core electronic excitations, spanning frequencies from radiowaves, infrared, ultraviolet all the way to hard X-rays will be discussed.

  13. Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein

    PubMed Central

    2011-01-01

    Background Pepino mosaic virus (PepMV) is considered one of the most dangerous pathogens infecting tomatoes worldwide. The virus is highly diverse and four distinct genotypes, as well as inter-strain recombinants, have already been described. The isolates display a wide range on symptoms on infected plant species, ranging from mild mosaic to severe necrosis. However, little is known about the mechanisms and pattern of PepMV molecular evolution and about the role of individual proteins in host-pathogen interactions. Methods The nucleotide sequences of the triple gene block 3 (TGB3) from PepMV isolates varying in symptomatology and geographic origin have been analyzed. The modes and patterns of molecular evolution of the TGBp3 protein were investigated by evaluating the selective constraints to which particular amino acid residues have been subjected during the course of diversification. The tridimensional structure of TGBp3 protein has been modeled de novo using the Rosetta algorithm. The correlation between symptoms development and location of specific amino acids residues was analyzed. Results The results have shown that TGBp3 has been evolving mainly under the action of purifying selection operating on several amino acid sites, thus highlighting its functional role during PepMV infection. Interestingly, amino acid 67, which has been previously shown to be a necrosis determinant, was found to be under positive selection. Conclusions Identification of diverse selection events in TGB3p3 will help unraveling its biological functions and is essential to an understanding of the evolutionary constraints exerted on the Potexvirus genome. The estimated tridimensional structure of TGBp3 will serve as a platform for further sequence, structural and function analysis and will stimulate new experimental advances. PMID:21702943

  14. Integrin engagement mediates the human polymorphonuclear leukocyte response to a fungal pathogen-associated molecular pattern.

    PubMed

    Lavigne, Liz M; O'Brien, Xian M; Kim, Minsoo; Janowski, Jessie W; Albina, Jorge E; Reichner, Jonathan S

    2007-06-01

    Extravasation of leukocytes from peripheral blood is required for an effective inflammatory response at sites of tissue infection. Integrins help mediate extravasation and navigate the leukocyte to the infectious source. A novel role for integrins in regulating the effector response to a cell wall component of fungal pathogens is the subject of the current study. Although phagocytosis is useful for clearance of unicellular fungi, the immune response against large, noningestible hyphae is not well-understood. Fungal beta-glucan, a pathogen-associated molecular pattern, activates production of superoxide anion in leukocytes without the need for phagocytosis. To model polymorphonuclear leukocyte (PMN) recognition of fungi under conditions in which phagocytosis cannot occur, beta-glucan was covalently immobilized onto tissue culture plastic. Plasma membrane-associated respiratory burst was measured by reduction of ferricytochrome C. Results show that the human PMN oxidative burst response to immobilized beta-glucan is suppressed by addition of beta(1) integrin ligands to the beta-glucan matrix. Suppression was dose dependent and steric hindrance was ruled out. beta(1) integrin ligands did not affect respiratory burst to ingestible beta-glucan-containing particles, phorbol esters or live yeast hyphae. Furthermore, in the absence of matrix, Ab activation of VLA3 or VLA5, but not other beta(1) integrins, also prevented beta-glucan-induced respiratory burst. beta(1)-induced suppression was blocked and burst response restored by treating neutrophils with either the cell-binding fragment of soluble human Fn, cyclic RGD peptide, or Ab specific to VLA3 or VLA5. Together these findings extend the functional role of beta(1) integrins to include modulating PMN respiratory burst to a pathogen-associated molecular pattern. PMID:17513777

  15. Damage-associated molecular patterns and their pathological relevance in diabetes mellitus.

    PubMed

    Shin, Jung Jae; Lee, Eun Kyung; Park, Tae Joo; Kim, Wook

    2015-11-01

    Diabetes, a group of metabolic and age-related diseases, is a major global health problem, the incidence of which has increased dramatically in recent decades. Type 1 diabetes mellitus (T1DM) is a complex, T cell-mediated autoimmune disease characterized by immune cell infiltration and chronic inflammation in the islets of Langerhans. Type 2 diabetes mellitus (T2DM) is a complex metabolic disease characterized by hyperglycemia (high blood sugar) resulting from insulin resistance and ?-cell dysfunction. The involvement of inflammatory processes, such as immune cell infiltration, and chronic inflammation in the pathogenesis of diabetes is less well understood in T2DM than in T1DM. However, studies conducted in the past decade have shown a strong link between inflammation and metabolic dysfunction. They have also shown that chronic inflammation plays a key role in the pathogenesis of both T1DM and T2DM. Two immunological factors commonly contribute to the pathogenesis of diabetes: the activation of inflammasomes and the release of proinflammatory cytokines in response to damage-associated molecular patterns (DAMPs). Inflammasomes are intracellular multiprotein molecular platforms. DAMPs act as endogenous danger signals. Here, we review current research on the function(s) of inflammasomes and DAMPs and discuss their pathological relevance and therapeutic implications in diabetes. PMID:26197086

  16. Molecular Phylogeny of Echiuran Worms (Phylum: Annelida) Reveals Evolutionary Pattern of Feeding Mode and Sexual Dimorphism

    PubMed Central

    Goto, Ryutaro; Okamoto, Tomoko; Ishikawa, Hiroshi; Hamamura, Yoichi; Kato, Makoto

    2013-01-01

    The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms. PMID:23457618

  17. Identification of Nicotiana benthamiana genes involved in pathogen-associated molecular pattern-triggered immunity.

    PubMed

    Chakravarthy, Suma; Velásquez, André C; Ekengren, Sophia K; Collmer, Alan; Martin, Gregory B

    2010-06-01

    In order to identify components of pathogen-associated molecular pattern-triggered immunity (PTI) pathways in Nicotiana benthamiana, we conducted a large-scale forward-genetics screen using virus-induced gene silencing and a cell-death-based assay for assessing PTI. The assay relied on four combinations of PTI-inducing nonpathogens and cell-death-causing challenger pathogens and was first validated in plants silenced for FLS2 or BAK1. Over 3,200 genes were screened and 14 genes were identified that, when silenced, compromised PTI as judged by the cell-death-based assay. Further analysis indicated that the 14 genes were not involved in a general cell death response. A subset of the genes was found to act downstream of FLS2-mediated PTI induction, and silencing of three genes compromised production of reactive oxygen species in leaves exposed to flg22. The 14 genes encode proteins with potential functions in defense and hormone signaling, protein stability and degradation, energy and secondary metabolism, and cell wall biosynthesis and provide a new resource to explore the molecular basis for the involvement of these processes in PTI. PMID:20459311

  18. [Tuberculosis in Europe and Poland--new molecular families and new resistance patterns].

    PubMed

    Augustynowicz-Kope?, Ewa; Zwolska, Zofia

    2008-01-01

    At present despite methods of fast recognition of the disease and efficient antituberculosis drugs not only we cannot contain the epidemic but we can see an increase in new cases of tuberculosis including its drug resistant variety. Causes of aggravation of the situation are varied and ought to be examined separately in case of any particular region. One of the major ones are bad programmes of fighting against the disease or their inadequate realization, ignoring a problem of tuberculosis in developed countries, lack of money for treatment in developing countries and coincidence with HIV virus. Among the mentioned factors the phenomenon of drug resistance is considered one of most important reasons of expansion of tuberculosis in the modern world. In epidemiological investigations it is important to determine, apart from drug resistance patterns, what molecular families strains belong to. This allows us to track their transmission routes. Genotyping has given us knowledge of the threats connected with transmission of the infection and made it possible to identify a risk factor which is the cause of MDR (multidrug-resistant), XDR (extensively drug-resistant tuberculosis) strains dissemination as well as strains representing new molecular families. Results of some analyses proved to be surprising. For instance high proportion of genetically similar strains has been shown in countries of low incidence. It proves higher than expected transmission in societies of high economic standard. Analyses of DNA of mycobacteria led to distinguishing several genetic families among which M. tuberculosis Beijing is one of most important. PMID:18536233

  19. Imaging of isolated molecules with ultrafast electron pulses.

    PubMed

    Hensley, Christopher J; Yang, Jie; Centurion, Martin

    2012-09-28

    Imaging isolated molecules in three dimensions with atomic resolution is important for elucidating complex molecular structures and intermediate states in molecular dynamics. This goal has so far remained elusive due to the random orientation of molecules in the gas phase. We show that three-dimensional structural information can be retrieved from multiple electron diffraction patterns of aligned molecules. The molecules are aligned impulsively with a femtosecond laser pulse and probed with a femtosecond electron pulse two picoseconds later, when the degree of alignment reaches a maximum. PMID:23030087

  20. Analysis of molecular expression patterns and integration with other knowledge bases using probabilistic Bayesian network models

    SciTech Connect

    Moler, Edward J.; Mian, I.S.

    2000-03-01

    How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss extending our methods to inferring biological pathways and networks using more complex dynamic Bayesian networks.

  1. COPD disease severity and innate immune response to pathogen-associated molecular patterns

    PubMed Central

    Fan, Vincent S; Gharib, Sina A; Martin, Thomas R; Wurfel, Mark M

    2016-01-01

    The airways of COPD patients are often colonized with bacteria leading to increased airway inflammation. This study sought to determine whether systemic cytokine responses to microbial pathogen-associated molecular patterns (PAMPs) are increased among subjects with severe COPD. In an observational cross-sectional study of COPD subjects, PAMP-induced cytokine responses were measured in whole blood ex vivo. We used PAMPs derived from microbial products recognized by toll-like receptors 1, 2, 4, 5, 6, 7, and 8. Patterns of cytokine response to PAMPs were assessed using hierarchical clustering. One-sided Student’s t-tests were used to compare PAMP-induced cytokine levels in blood from patients with and without severe COPD, and for subjects with and without chronic bronchitis. Of 28 male patients, 12 had moderate COPD (FEV1 50%–80%) and 16 severe COPD (FEV1 <50%); 27 participants provided data on self-reported chronic bronchitis, of which 15 endorsed chronic bronchitis symptoms and 12 did not. Cytokine responses to PAMPs in severe COPD were generally lower than in subjects with milder COPD. This finding was particularly strong for PAMP-induced interleukin (IL)-10, granulocyte colony stimulating factor, and IL-1β. Subjects with chronic bronchitis showed higher PAMP-induced IL-1RA responses to most of the PAMPs evaluated. COPD patients with more severe disease demonstrated a diminished cytokine response to PAMPs, suggesting that chronic colonization with bacteria may dampen the systemic innate immune response. PMID:27019597

  2. Vigilant keratinocytes trigger pathogen-associated molecular pattern signaling in response to streptococcal M1 protein.

    PubMed

    Persson, Sandra T; Wilk, Laura; Mörgelin, Matthias; Herwald, Heiko

    2015-12-01

    The human skin exerts many functions in order to maintain its barrier integrity and protect the host from invading microorganisms. One such pathogen is Streptococcus pyogenes, which can cause a variety of superficial skin wounds that may eventually progress into invasive deep soft tissue infections. Here we show that keratinocytes recognize soluble M1 protein, a streptococcal virulence factor, as a pathogen-associated molecular pattern to release alarming inflammatory responses. We found that this interaction initiates an inflammatory intracellular signaling cascade involving the activation of the mitogen-activated protein kinases extracellular signal-regulated kinase (ERK), p38, and Jun N-terminal protein kinase and the subsequent induction and mobilization of the transcription factors NF-κB and AP-1. We also determined the imprint of the inflammatory mediators released, such as interleukin-8 (IL-8), growth-related oncogene alpha, migration inhibitory factor, extracellular matrix metalloproteinase inducer, IL-1α, IL-1 receptor a, and ST2, in response to streptococcal M1 protein. The expression of IL-8 is dependent on Toll-like receptor 2 activity and subsequent activation of the mitogen-activated protein kinases ERK and p38. Notably, this signaling seems to be distinct for IL-8 release, and it is not shared with the other inflammatory mediators. We conclude that keratinocytes participate in a proinflammatory manner in streptococcal pattern recognition and that expression of the chemoattractant IL-8 by keratinocytes constitutes an important protective mechanism against streptococcal M1 protein. PMID:26416902

  3. Molecular Analysis of Geographic Patterns of Eukaryotic Diversity in Antarctic Soils

    PubMed Central

    Lawley, Blair; Ripley, Sarah; Bridge, Paul; Convey, Peter

    2004-01-01

    We describe the application of molecular biological techniques to estimate eukaryotic diversity (primarily fungi, algae, and protists) in Antarctic soils across a latitudinal and environmental gradient between approximately 60 and 87°S. The data were used to (i) test the hypothesis that diversity would decrease with increasing southerly latitude and environmental severity, as is generally claimed for “higher” faunal and plant groups, and (ii) investigate the level of endemicity displayed in different taxonomic groups. Only limited support was obtained for a systematic decrease in diversity with latitude, and then only at the level of a gross comparison between maritime (Antarctic Peninsula/Scotia Arc) and continental Antarctic sites. While the most southerly continental Antarctic site was three to four times less diverse than all maritime sites, there was no evidence for a trend of decreasing diversity across the entire range of the maritime Antarctic (60 to 72°S). Rather, we found the reverse pattern, with highest diversity at sites on Alexander Island (ca. 72°S), at the southern limit of the maritime Antarctic. The very limited overlap found between the eukaryotic biota of the different study sites, combined with their generally low relatedness to existing sequence databases, indicates a high level of Antarctic site isolation and possibly endemicity, a pattern not consistent with similar studies on other continents. PMID:15466539

  4. Molecular fingerprinting of lacustrian cyanobacterial communities: regional patterns in summer diversity.

    PubMed

    Touzet, Nicolas; McCarthy, David; Fleming, Gerard T A

    2013-12-01

    The assessment of lacustrian water quality is necessary to comply with environmental regulations. At the regional scale, difficulties reside in the selection of representative lakes. Given the risks towards water quality associated with phytoplankton blooms, a mesoscale survey was carried out in Irish lakes to identify patterns in the distribution and diversity of planktonic cyanobacteria. A stratified sampling strategy was carried out via geographic information systems (GIS) analysis of river catchment attributes due to the range of hydrogeomorphological features and the high number of lakes within the study area. 16S rRNA gene denaturing gradient gel electrophoresis analysis showed variation between the cyanobacterial communities sampled, with lower occurrence of cyanobacteria in August concomitant to increased wind and precipitation regimes. Multivariate analysis delineated three ecoregions based on land cover typology and revealed significant patterns in the distribution of cyanobacterial diversity. A majority of filamentous cyanobacteria genotypes occurred in larger lakes contained river catchments with substantial forest cover. In contrast, higher diversity of spherical cyanobacteria genotypes was observed in lakes of lesser trophic state. In the context of aquatic resource management, the combined use of GIS-based sampling strategy and molecular methods offers promising prospects for assessing microbial community structure at varying scales of space and time. PMID:23802655

  5. Molecular dynamics of single-particle impacts predicts phase diagrams for large scale pattern formation.

    PubMed

    Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J

    2011-01-01

    Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation. PMID:21505432

  6. COPD disease severity and innate immune response to pathogen-associated molecular patterns.

    PubMed

    Fan, Vincent S; Gharib, Sina A; Martin, Thomas R; Wurfel, Mark M

    2016-01-01

    The airways of COPD patients are often colonized with bacteria leading to increased airway inflammation. This study sought to determine whether systemic cytokine responses to microbial pathogen-associated molecular patterns (PAMPs) are increased among subjects with severe COPD. In an observational cross-sectional study of COPD subjects, PAMP-induced cytokine responses were measured in whole blood ex vivo. We used PAMPs derived from microbial products recognized by toll-like receptors 1, 2, 4, 5, 6, 7, and 8. Patterns of cytokine response to PAMPs were assessed using hierarchical clustering. One-sided Student's t-tests were used to compare PAMP-induced cytokine levels in blood from patients with and without severe COPD, and for subjects with and without chronic bronchitis. Of 28 male patients, 12 had moderate COPD (FEV1 50%-80%) and 16 severe COPD (FEV1 <50%); 27 participants provided data on self-reported chronic bronchitis, of which 15 endorsed chronic bronchitis symptoms and 12 did not. Cytokine responses to PAMPs in severe COPD were generally lower than in subjects with milder COPD. This finding was particularly strong for PAMP-induced interleukin (IL)-10, granulocyte colony stimulating factor, and IL-1β. Subjects with chronic bronchitis showed higher PAMP-induced IL-1RA responses to most of the PAMPs evaluated. COPD patients with more severe disease demonstrated a diminished cytokine response to PAMPs, suggesting that chronic colonization with bacteria may dampen the systemic innate immune response. PMID:27019597

  7. Pathogen Associated Molecular Pattern (PAMP)-Triggered Immunity Is Compromised under C-Limited Growth

    PubMed Central

    Park, Hyeong Cheol; Lee, Shinyoung; Park, Bokyung; Choi, Wonkyun; Kim, Chanmin; Lee, Sanghun; Chung, Woo Sik; Lee, Sang Yeol; Sabir, Jamal; Bressan, Ray A.; Bohnert, Hans J.; Mengiste, Tesfaye; Yun, Dae-Jin

    2015-01-01

    In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense. PMID:25387755

  8. Molecular insights into the origin of the Hox-TALE patterning system

    PubMed Central

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-01-01

    Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001 PMID:24642410

  9. Molecular characterization and expression patterns of myogenin in compensatory growth of Megalobrama amblycephala.

    PubMed

    Zhu, Kecheng; Chen, Liping; Zhao, Jinkun; Wang, Huijuan; Wang, Weimin; Li, Zhong; Wang, Huanling

    2014-04-01

    Myogenin (myog) is a muscle-specific basic helix-loop-helix (bHLH) transcription factor that plays an essential role in regulating skeletal muscle development and growth. To investigate molecular characterization of myog and the effect of starvation/refeeding on the gene expression, we isolated the myog cDNA sequence and analyzed the expression patterns using quantitative real-time polymerase chain reaction in Megalobrama amblycephala. Sequence analysis indicated that M. amblycephala myog shared an analogous structure with the highly conserved His/Cys-rich, bHLH and C-terminal helix III domains with other vertebrates. Sequence alignment and phylogenetic tree showed that M. amblycephala myog had the highest identity with the homologues of Ctenopharyngodon idella and Cyprinus carpio. Spatio-temporal expression patterns revealed that myog mRNA levels at the segmentation period and 12 h post-hatching (hph) were significantly higher than at other development stages (P<0.05). Furthermore, the highest myog expression level was predominantly observed in white muscle compared with the other types of muscle. Fish body weight continuously decreased during 21-day starvation and then significantly increased after 7days of refeeding and reached the similar level to the control at 21days of refeeding, indicating that the pattern of complete compensatory growth possibly occurred in M. amblycephala; meanwhile, the relative somatic growth rate after refeeding was also dramatically higher than the control group. In addition, the myog expression decreased during 21days of starvation and then exhibited a strong rebound effect after 7days of refeeding and subsequently declined gradually to the control level by 21days of refeeding. PMID:24440962

  10. Phylogenetic Analysis and Molecular Evolution Patterns in the MIR482-MIR1448 Polycistron of Populus L

    PubMed Central

    Zhao, Jia-Ping; Diao, Shu; Zhang, Bing-Yu; Niu, Bao-Qing; Wang, Qing-Ling; Wan, Xian-Chong; Luo, You-Qing

    2012-01-01

    The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the “duplicated MIR482” evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the “frameshift targeted mechanism” to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse. PMID:23094096

  11. Delta-like 1 homolog in Capra hircus: molecular characteristics, expression pattern and phylogeny.

    PubMed

    Hu, Jiangtao; Zhao, Wei; Zhan, Siyuan; Xiao, Ping; Zhou, Jingxuan; Wang, Linjie; Li, Li; Zhang, Hongping; Niu, Lili; Zhong, Tao

    2016-06-01

    To research the molecular characteristics, expression pattern and phylogeny of the Delta-like 1 homolog gene (Dlk1) in goats. Dlk1 transcripts were identified in the Jianyang Da'er goats by reverse-transcription polymerase chain reaction (RT-PCR). Phylogenetic trees were constructed by Bayesian inference and neighbor-joining methods. Quantitative real-time PCR (qPCR), western blotting and in situ hybridization were performed to analyze the expression pattern of Dlk1. Five alternatively transcripts were identified in different tissues and designated as Dlk1-AS1, 2, 3, 4 and 5. Compared with the normal transcript Dlk1-AS1, Dlk1-AS4 and Dlk1-AS5 retained the identical open reading frame (ORF) and encoded proteins with truncated epidermal-growth-factor like repeats of 121 and 83 amino acids, respectively. Using the Bayesian inference method, the consensus phylogenetic tree indicated that caprine Dlk1 had a closer relationship with bovine Dlk1 than with Dlk1 from pigs, humans and mice. qPCR revealed high expression levels of Dlk1 in the kidney (P < 0.01). However, mRNA and protein levels presented an inconsistent correlation, possibly because of post-transcriptional regulation. RNA in situ hybridization indicated that Dlk1 mRNA was localized in the interlobular bile duct and alongside the hepatocyte nuclei, in the epithelial cells of proximal and distal convoluted tubules and in the connective region between the mesothelium and myocardium in the heart. The Dlk1 gene in goats produces alternatively spliced transcripts, with specific expression and cellular localization patterns. These findings would lay the foundation for further study. PMID:27108112

  12. Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis

    PubMed Central

    Ramaswamy, Vijay; Remke, Marc; Bouffet, Eric; Faria, Claudia C.; Perreault, Sebastien; Cho, Yoon-Jae; Shih, David J.; Luu, Betty; Dubuc, Adrian M.; Northcott, Paul A.; Schüller, Ulrich; Gururangan, Sridharan; McLendon, Roger; Bigner, Darell; Fouladi, Maryam; Ligon, Keith L.; Pomeroy, Scott L.; Dunn, Sandra; Triscott, Joanna; Jabado, Nada; Fontebasso, Adam; Jones, David T. W.; Kool, Marcel; Karajannis, Matthias A.; Gardner, Sharon L.; Zagzag, David; Nunes, Sofia; Pimentel, José; Mora, Jaume; Lipp, Eric; Walter, Andrew W.; Ryzhova, Marina; Zheludkova, Olga; Kumirova, Ella; Alshami, Jad; Croul, Sidney E.; Rutka, James T.; Hawkins, Cynthia; Tabori, Uri; Codispoti, Kari-Elise T.; Packer, Roger J.; Pfister, Stefan M.; Korshunov, Andrey; Taylor, Michael D.

    2014-01-01

    Background Recurrent medulloblastoma is a daunting therapeutic challenge as it is almost universally fatal. Recent studies confirmed that medulloblastoma comprises four distinct subgroups. We sought to delineate subgroup specific differences in medulloblastoma recurrence patterns. Methods We retrospectively identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children between 1994-2012, and performed molecular subgrouping on FFPE tissues using a nanoString-based assay. The anatomical site of recurrence (local tumour bed or leptomeningeal metastasis), time to recurrence and survival post-recurrence were determined in a subgroup specific fashion. Subgroup specific recurrence patterns were confirmed in two independent, non-overlapping FFPE validation cohorts. Where possible molecular subgrouping was performed on tissue obtained from both the initial surgery and at recurrence. Results A screening cohort of 30 recurrent medulloblastomas was assembled; nine with local recurrences, and 21 metastatic. When re-analysed in a subgroup specific manner, local recurrences were more frequent in SHH tumours (8/9, 88%) and metastatic recurrences were more common in Group 3 and 4 (17/20 [85%] with one WNT, p=0.0014, local vs metastatic recurrence, SHH vs Group 3 vs Group 4). The subgroup specific location of recurrence was confirmed in a multicenter validation cohort (p=0·0013 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=77), and a second independent validation cohort comprising 96 recurrences (p<0·0001 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=96). Treatment with craniospinal irradiation at diagnosis was not significantly associated with the anatomical pattern of recurrence. Survival post recurrence was significantly longer in Group 4 patients (p=0·013) as confirmed in a multicenter validation cohort (p=0·0075). Strikingly, subgroup affiliation remained stable at recurrence in all 34 cases with available matched primary and recurrent pairs. Conclusions Medulloblastoma does not switch subgroup at the time of recurrence further highlighting the stability of the four principle medulloblastoma subgroups. Significant differences in the location and timing of recurrence across medulloblastoma subgroups were observed which have potential treatment ramifications. Specifically, intensified local (posterior fossa) therapy should be tested in the initial treatment of SHH patients. Refinement of therapy for Groups 3 and 4 should focus on the metastatic compartment, as it is the near universal cause of patient deaths. PMID:24140199

  13. Molecular Characterization and Clinical Implications of Spindle Cells in Nasopharyngeal Carcinoma: A Novel Molecule-Morphology Model of Tumor Progression Proposed

    PubMed Central

    Luo, Weiren; Yao, Kaitai

    2013-01-01

    Up to now, the precise molecular and morphological changes underlying the invasive and metastatic properties of nasopharyngeal carcinoma (NPC) remain largely unresolved. We speculate that neoplastic spindle cells, which are prominently found in the invasive tumor front and the surrounding stroma, might be responsible for the aggressive patterns. Expression profiling of various biomarkers relevant to cancer stem cells (CSCs) and epithelial-mesenchymal transition (EMT) was performed by tissue microarray-based immunohistochemistry in NPC samples. The expression of EBER and LMP1 was detected by in situ hybridization and immunohistochemistry, respectively. We found that overexpression of CSCs-related markers (ALDH1, Nanog and ABCG2) and up-regulation of EMT markers (Fibronectin, MMP-2, Periostin, SPARC, Snail and Slug), together with E- to N-cadherin switching, occurred preferentially in tumors containing a large proportion of spindle-shaped malignant cells. Furthermore, CSCs-like properties were highly present in spindle cells compared with non-spindle cells of tumors, and correlated strongly with EMT features. In addition, EBV-related factors EBER and LMP1 were highly expressed and correlated strongly with CSCs and EMT characteristics in neoplastic spindle cells. Importantly, high proportion of spindle cells (?20%) correlated significantly with various aggressive aspects including lymph node metastasis (P = 0.031) and local recurrence (P = 0.014). Patients with high proportion of spindle cells had poor survival (P = 0.004), though it was not an independent value. In conclusion, we demonstrate that spindle cells could be valuable morphological indicators of tumor progression and unfavorable prognosis of NPC. An integrated molecule-morphology model of NPC firstly constructed may shed significant light on the metastatic cascade and clinical relevance of patients. PMID:24349446

  14. Use of Mo/ller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules

    SciTech Connect

    Dunning, T.H. , Jr.; Peterson, K.A.

    1998-03-01

    The convergence of Mo/ller{endash}Plesset perturbation expansions (MP2{endash}MP4/MP5) for the spectroscopic constants of a selected set of diatomic molecules (BH, CH, HF, N{sub 2}, CO, and F{sub 2}) has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the {ital exact} Mo/ller{endash}Plesset perturbation expansions were investigated using estimates of the {ital complete basis set limits} obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N{sub 2}, CO, and F{sub 2}, the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N{sub 2}, CO, and F{sub 2}, appear to be far from convergence at MP4. In fact, for HF, N{sub 2}, and CO, the errors in the calculated spectroscopic constants for the MP4 method are {ital larger} than those for the MP2 method (the only exception is D{sub e}). The current study, combined with other recent studies, raises serious doubts about the use of Mo/ller{endash}Plesset perturbation theory to describe electron correlation effects in atomic and molecular calculations. {copyright} {ital 1998 American Institute of Physics.}

  15. Molecular profiling of experimental endometriosis identified gene expression patterns in common with human disease

    PubMed Central

    Flores, Idhaliz; Rivera, Elizabeth; Ruiz, Lynnette A.; Santiago, Olga I.; Vernon, Michael W.; Appleyard, Caroline B.

    2007-01-01

    OBJECTIVE To validate a rat model of endometriosis using cDNA microarrays by identifying common gene expression patterns beween experimental and natural disease. DESIGN Autotransplantation rat model. SETTING Medical school department. ANIMALS Female Sprague-Dawley rats. INTERVENTIONS Endometriosis was surgically-induced by suturing uterine horn implants next to the small intestine’s mesentery. Control rats received sutures with no implants. After 60 days, endometriotic implants and uterine horn were obtained. MAIN OUTCOME MEASURES Gene expression levels determined by cDNA microarrays and QRT-PCR. METHODS Cy5-labeled cDNA was synthesized from total RNA obtained from endometriotic implants. Cy3-labeled cDNA was synthesized using uterine RNA from a control rat. Gene expression levels were analyzed after hybridizing experimental and control labeled cDNA to PIQOR™ Toxicology Rat Microarrays (Miltenyi Biotec) containing 1,252 known genes. Cy5/Cy3 ratios were determined and genes with >2-fold higher or <0.5-fold lower expression levels were selected. Microarray results were validated by QRT-PCR. RESULTS We observed differential expression of genes previously shown to be upregulated in patients, including growth factors, inflammatory cytokines/receptors, tumor invasion/metastasis factors, adhesion molecules, and anti-apoptotic factors. CONCLUSIONS This study presents evidence in support of using this rat model to study the natural history of endometriosis and test novel therapeutics for this incurable disease. PMID:17478174

  16. Revealing the molecular structure of single-molecule junctions in different conductance states by fishing-mode tip-enhanced Raman spectroscopy

    PubMed Central

    Liu, Zheng; Ding, Song-Yuan; Chen, Zhao-Bin; Wang, Xiang; Tian, Jing-Hua; Anema, Jason R.; Zhou, Xiao-Shun; Wu, De-Yin; Mao, Bing-Wei; Xu, Xin; Ren, Bin; Tian, Zhong-Qun

    2011-01-01

    The conductance of single-molecule junctions may be governed by the structure of the molecule in the gap or by the way it bonds with the leads, and the information contained in a Raman spectrum is ideal for examining both. Here we demonstrate that molecule-to-surface bonding may be characterized during electron transport by 'fishing-mode' tip-enhanced Raman spectroscopy (FM-TERS). This technique allows mutually verifiable single-molecule conductance and Raman signals with single-molecule contributions to be acquired simultaneously at room temperature. Density functional theory calculations reveal that the most significant spectral change seen for a gold-4,4′-bipyridine-gold junction results from the deformation of the pyridine ring in contact with the drain electrode at high voltage, and these calculations suggest that a stronger bonding interaction between the molecule and the drain may account for the nonlinear dependence of conductance on bias voltage. FM-TERS will lead to a better understanding of electron-transport processes in molecular junctions. PMID:21556059

  17. Patterns of integration of DNA microinjected into cultured mammalian cells: evidence for homologous recombination between injected plasmid DNA molecules.

    PubMed Central

    Folger, K R; Wong, E A; Wahl, G; Capecchi, M R

    1982-01-01

    We examined the fate of DNA microinjected into nuclei of cultured mammalian cells. The sequence composition and the physical form of the vector carrying the selectable gene affected the efficiency of DNA-mediated transformation. Introduction of sequences near the simian virus 40 origin of DNA replication or in the long terminal repeat of avian sarcoma provirus into a recombinant plasmid containing the herpes simplex virus thymidine kinase gene. (pBR322/HSV-tk) enhanced the frequency of transformation of LMtk- and RAT-2tk- cells to the TK+ phenotype 20- to 40-fold. In cells receiving injections of only a few plasmid DNA molecules, the transformation frequency was 40-fold higher after injection of linear molecules than after injection of supercoiled molecules. By controlling the number of gene copies injected into a recipient cell, we could obtain transformants containing a single copy or as many as 50 to 100 copies of the selectable gene. Multiple copies of the transforming gene were not scattered throughout the host genome but were integrated as a concatemer at one or a very few sites in the host chromosome. Independent transformants contained the donated genes in different chromosomes. The orientation of the gene copies within the concatemer was not random; rather, the copies were organized as tandem head-to-tail arrays. By analyzing transformants obtained by coinjecting two vectors which were identical except that in one a portion of the vector was inverted, we were able to conclude that the head-to-tail concatemers were generated predominantly by homologous recombination. Surprisingly, these head-to-tail concatemers were found in transformants obtained by injecting either supercoiled or linear plasmid DNA. Even though we demonstrated that cultured mammalian cells contain the enzymes for ligating two DNA molecules very efficiently irrespective of the sequences or topology at their ends, we found that even linear plasmid DNA was recruited into the concatemer by homologous recombination. Images PMID:6298598

  18. Patterns of integration of DNA microinjected into cultured mammalian cells: Evidence for homologous recombination between injected plasmid DNA molecules

    SciTech Connect

    Folger, K.R.; Wong, E.A.; Wahl, G.; Capecchi, M.R.

    1982-11-01

    The authors examined the fate of DNA microinjected into nuclei of cultured mammalian cells. The sequence composition and the physical form of the vector carrying the selectable gene affected the efficiency of DNA-mediated transformation. Introduction of sequences near the simian virus 40 origin of DNA replication or in the long terminal repeat of avian sarcoma provirus into a recombinant plasmid containing the herpes simplex virus thymidine kinase gene (pBR322/HSV-tk) enhanced the frequency of transformation of LMtk/sup -/ and RAT-2tk/sup -/ cells to the TK/sup +/ phenotype 20- to 40-fold. In cells receiving injections of only a few plasmid DNA molecules, the transformation frequency was 40-fold higher after injection of linear molecules than after injection of supercoiled molecules. By controlling the number of gene copies injected into a recipient cell, we could obtain transformants containing a single copy or as many as 50 to 100 copies of the selectable gene. By analyzing transformants obtained by coinjecting two vectors which were identical except that in one a portion of the vector was inverted, the authors were able to conclude that the head-to-tail concatemers were generated predominantly by homologous recombination. Surprisingly, these head-to-tail concatemers were found in transformants obtained by injecting either supercoiled or linear plasmid DNA.

  19. Biochips - Can molecules compute?

    NASA Astrophysics Data System (ADS)

    Tucker, J. B.

    1984-02-01

    In recent years the possibility has been considered to build 'biochip' computers, in which the silicon transistors of present machines would be replaced by large organic molecules or genetically engineered proteins. Two major advantages of such biochips over current devices would be related to vastly increased densities of computing elements, and entirely new styles of data processing, suited to such high-level tasks as pattern recognition and context-dependent analysis. The limitations of the semiconductor chip with respect to the density of elementary units due to size considerations and heat development could be overcome by making use of molecular switches. Attention is given to soliton switching, soliton logic, bulk molecular devices, analog biochips, 'intelligent' switches based on the employment of enzymes, robot vision, questions of biochip fabrication, protein engineering, and a strategy for the development of biochips.

  20. Methanol and ethanol modulate responses to danger- and microbe-associated molecular patterns

    PubMed Central

    Hann, Claire T.; Bequette, Carlton J.; Dombrowski, James E.; Stratmann, Johannes W.

    2014-01-01

    Methanol is a byproduct of cell wall modification, released through the action of pectin methylesterases (PMEs), which demethylesterify cell wall pectins. Plant PMEs play not only a role in developmental processes but also in responses to herbivory and infection by fungal or bacterial pathogens. Molecular mechanisms that explain how methanol affects plant defenses are poorly understood. Here we show that exogenously supplied methanol alone has weak effects on defense signaling in three dicot species, however, it profoundly alters signaling responses to danger- and microbe-associated molecular patterns (DAMPs, MAMPs) such as the alarm hormone systemin, the bacterial flagellum-derived flg22 peptide, and the fungal cell wall-derived oligosaccharide chitosan. In the presence of methanol the kinetics and amplitudes of DAMP/MAMP-induced MAP kinase (MAPK) activity and oxidative burst are altered in tobacco and tomato suspension-cultured cells, in Arabidopsis seedlings and tomato leaf tissue. As a possible consequence of altered DAMP/MAMP signaling, methanol suppressed the expression of the defense genes PR-1 and PI-1 in tomato. In cell cultures of the grass tall fescue (Festuca arundinacea, Poaceae, Monocots), methanol alone activates MAPKs and increases chitosan-induced MAPK activity, and in the darnel grass Lolium temulentum (Poaceae), it alters wound-induced MAPK signaling. We propose that methanol can be recognized by plants as a sign of the damaged self. In dicots, methanol functions as a DAMP-like alarm signal with little elicitor activity on its own, whereas it appears to function as an elicitor-active DAMP in monocot grasses. Ethanol had been implicated in plant stress responses, although the source of ethanol in plants is not well established. We found that it has a similar effect as methanol on responses to MAMPs and DAMPs. PMID:25360141

  1. Overview of single-molecule methods including high-force, force-fluorescence, and dual-trap studies for probing molecular and cellular machinery

    NASA Astrophysics Data System (ADS)

    Lang, Matthew

    2011-03-01

    High force optical trapping, including double trap geometry and simultaneous visualization with single molecule fluorescence imaging enables a wide range of measurement capabilities applicable for probing molecular and cellular machinery. A series of single molecule measurement methods will be presented. Force-fluorescence microscopy enables visualizing amyloid fibers while physically probing their structures including direct unfolding and rupture of fibers with a high force optical trap. Force spectroscopy is employed to probe the strength of single peptide aptamer bonds. A dual-trap geometry allows for direct tracking of unfolding and translocation machinery of the biological motor ClpXP. Force fluorescence microscopy directly visualizes T-cell activation. Automation and flexibility in our instruments coupled with advances in physical assay design strategies are leveraged to access a broad set of molecular and cellular measurement targets.

  2. Bacterial regulatory networks—from self-organizing molecules to cell shape and patterns in bacterial communities

    PubMed Central

    Hengge, Regine; Sourjik, Victor

    2013-01-01

    The ESF–EMBO Conference on ‘Bacterial Networks' (BacNet13) was held in March 2013, in Pultusk, Poland. It brought together 164 molecular microbiologists, bacterial systems biologists and synthetic biologists to discuss the architecture, function and dynamics of regulatory networks in bacteria. PMID:23846311

  3. Strontium mono-chloride - A new molecule for the determination of chlorine using high-resolution graphite furnace molecular absorption spectrometry and direct solid sample analysis

    NASA Astrophysics Data System (ADS)

    Pereira, Éderson R.; Welz, Bernhard; Lopez, Alfredo H. D.; de Gois, Jefferson S.; Caramori, Giovanni F.; Borges, Daniel L. G.; Carasek, Eduardo; de Andrade, Jailson B.

    2014-12-01

    A new method has been developed for the determination of chlorine in biological reference materials using high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) of the strontium mono-chloride (SrCl) molecule and direct solid sample analysis. The use of the SrCl molecule for high-temperature MAS was not described up to now in the literature. Preliminary time-dependent density functional theory calculations of the SrCl structure were carried out in order to obtain reasonable estimates of the absorption spectrum of the target molecule. The calculations, which were carried out at BHandHLyp/def2-QZVP level of theory, proved a very accurate and inexpensive way to get information about the spectrum of the SrCl molecule, which enabled us to perform the Cl determination with good sensitivity and specificity. The molecular absorption of the SrCl molecule has been measured using the wavelength at 635.862 nm, and zirconium and palladium have been evaluated as the chemical modifiers in order to increase the sensitivity of the gaseous SrCl molecule generated in the graphite furnace. The pyrolysis and vaporization temperatures were 600 °C and 2300 °C, respectively. Accuracy and precision of the method have been evaluated using biological certified reference materials of both animal and plant origins, showing good agreement with the informed and certified values. Limit of detection and characteristic mass were 1.0 and 2.2 ng, respectively. The results found using HR-CS GF MAS were in agreement (95% confidence level) compared to those obtained by electrothermal vaporization-inductively coupled plasma mass spectrometry.

  4. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality. PMID:26863450

  5. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  6. The reactions of the molecular nitrogen doubly charged ion with neutral molecules of relevance to planetary ionospheres

    NASA Astrophysics Data System (ADS)

    Ricketts, Claire Louise

    Diatomic dications (e.g. C02+) have been known to exist for several decades and are believed to be important components of energised media. Molecular dications possess significant internal energy due to the Coulombic repulsion of their two positive charges, meaning that many possible reaction channels are available to dications in a collision with a neutral molecule. Modellers have recently predicted that N22+ is present in the ionosphere of Earth and Titan as well as the dications C>22+ and 02+ in the ionosphere of Earth and CC>22+ in the ionosphere of Mars. These recent predictions, of dications in planetary ionospheres, imply that dications, and processes involving dication-neutral collisions, may have more significance than previously thought in the upper atmospheres of planets. Therefore this thesis describes a study of the reactions between N2 dications and neutrals, potentially of relevance to the ionosphere of Earth and Titan. A position sensitive coincidence (PSCO) time-of flight (TOF) mass spectrometer is used to probe the reactivity, energetics and dynamics of the bimolecular reactions of N22 . Dication-neutrals reactions often result in a pair of singly charged ions. The PSCO experiment is used to collect these pairs of singly-charged ions in coincidence. From the position-sensitive data we extract the velocity vectors of the product ions, and if the reaction of interest involves the formation of a third, undetected, neutral species, its velocity can be determined via conservation of momentum. The electron transfer reactions between dications and neutrals have been well rationalized 2+ previously, so only the electron transfer reactions of N2 with Ne and NO are discussed in this thesis. This thesis concentrates on probing the less well rationalized, bond- forming reactions between dications and neutrals. The bond-forming reactions of N22+ with O2, CO2, H2O, C2H2, CH4, H2 and Ar have been investigated and discussed. Several new bond-forming reactions mechanisms are derived for example, the bond-forming reactions of N22+ with O2 proceed via a 'long' lived complex which dissociates via loss of a neutral and then charge separation, a mechanism which is also operating for one of the bond-forming reactions of N2 with CO2 and N2 with H2O. Additional bond-forming reactions are detected for N22+ with CO2 and H2O, which proceed via shorter lived collision complexes. The reactions of N22+ with C2H2, CH4, H2 and Ar all proceed via a variety of mechanisms involving short-lived collision complexes or H and electron stripping.

  7. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize.

    PubMed

    Hekkala, Evon R; Platt, Steven G; Thorbjarnarson, John B; Rainwater, Thomas R; Tessler, Michael; Cunningham, Seth W; Twomey, Christopher; Amato, George

    2015-09-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062

  8. Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

    PubMed Central

    Condamine, Fabien L.; Clapham, Matthew E.; Kergoat, Gael J.

    2016-01-01

    Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders. PMID:26778170

  9. The Role of Damage-Associated Molecular Patterns (DAMPs) in Human Diseases

    PubMed Central

    Land, Walter G.

    2015-01-01

    This article is the second part of a review that addresses the role of damage-associated molecular patterns (DAMPs) in human diseases by presenting examples of traumatic (systemic inflammatory response syndrome), cardiovascular (myocardial infarction), metabolic (type 2 diabetes mellitus), neurodegenerative (Alzheimer’s disease), malignant and infectious diseases. Various DAMPs are involved in the pathogenesis of all these diseases as they activate innate immune machineries including the unfolded protein response and inflammasomes. These subsequently promote sterile autoinflammation accompanied, at least in part, by subsequent adaptive autoimmune processes. This review article discusses the future role of DAMPs in routine practical medicine by highlighting the possibility of harnessing and deploying DAMPs either as biomarkers for the appropriate diagnosis and prognosis of diseases, as therapeutics in the treatment of tumours or as vaccine adjuncts for the prophylaxis of infections. In addition, this article examines the potential for developing strategies aimed at mitigating DAMPs-mediated hyperinflammatory responses, such as those seen in systemic inflammatory response syndrome associated with multiple organ failure. PMID:26052447

  10. Innate immune memory: Implications for host responses to damage-associated molecular patterns.

    PubMed

    Crișan, Tania O; Netea, Mihai G; Joosten, Leo A B

    2016-04-01

    Cells of the innate immune system build immunological memory via epigenetic reprogramming after stimulations with microbial ligands. This functional readjustment allows for enhanced nonspecific inflammatory responses upon secondary challenges, a process termed "trained immunity." The epigenomic blueprint of trained monocytes has been recently reported, which revealed several important immunologic and metabolic mechanisms that underlie these changes. Interestingly, similar long-term reprogramming of cytokine production has also been described to be induced by endogenous damage-associated molecular patterns (DAMPs). Here, we present an overview of the novel data showing that endogenous alarm signals associated with tissue damage and sterile inflammation can induce trained immunity through epigenetic regulation of transcriptional programs. We describe new and old evidence of persistent effects of DAMPs in driving inflammation and enforce the concept that the influence of tissue-derived signals is critical in adjusting the magnitude and type of immune response built by the host. The better characterization of trained immunity for the persistence of inflammation induced by DAMPs would provide new possibilities for intervention in aging and autoinflammatory disorders. PMID:26970440

  11. Quantitative Analysis of Microbe-Associated Molecular Pattern (MAMP)-Induced Ca(2+) Transients in Plants.

    PubMed

    Trempel, Fabian; Ranf, Stefanie; Scheel, Dierk; Lee, Justin

    2016-01-01

    Ca(2+) is a secondary messenger involved in early signaling events triggered in response to a plethora of biotic and abiotic stimuli. In plants, environmental cues that induce cytosolic Ca(2+) elevation include touch, reactive oxygen species, cold shock, and salt or osmotic stress. Furthermore, Ca(2+) signaling has been implicated in early stages of plant-microbe interactions of both symbiotic and antagonistic nature. A long-standing hypothesis is that there is information encoded in the Ca(2+) signals (so-called Ca(2+) signatures) to enable plants to differentiate between these stimuli and to trigger the appropriate cellular response. Qualitative and quantitative measurements of Ca(2+) signals are therefore needed to dissect the responses of plants to their environment. Luminescence produced by the Ca(2+) probe aequorin upon Ca(2+) binding is a widely used method for the detection of Ca(2+) transients and other changes in Ca(2+) concentrations in cells or organelles of plant cells. In this chapter, using microbe-associated molecular patterns (MAMPs), such as the bacterial-derived flg22 or elf18 peptides as stimuli, a protocol for the quantitative measurements of Ca(2+) fluxes in apoaequorin-expressing seedlings of Arabidopsis thaliana in 96-well format is described. PMID:26867636

  12. Reprogramming cells and tissue patterning via bioelectrical pathways: molecular mechanisms and biomedical opportunities

    PubMed Central

    Levin, Michael

    2013-01-01

    Transformative impact in regenerative medicine requires more than the reprogramming of individual cells: advances in repair strategies for birth defects or injuries, tumor normalization, and the construction of bioengineered organs and tissues all require the ability to control large-scale anatomical shape. Much recent work has focused on the transcriptional and biochemical regulation of cell behaviour and morphogenesis. However, exciting new data reveal that bioelectrical properties of cells and their microenvironment exert a profound influence on cell differentiation, proliferation, and migration. Ion channels and pumps expressed in all cells, not just excitable nerve and muscle, establish resting potentials that vary across tissues and change with significant developmental events. Most importantly, the spatio-temporal gradients of these endogenous transmembrane voltage potentials (Vmem) serve as instructive patterning cues for large-scale anatomy, providing organ identity, positional information, and prepattern template cues for morphogenesis. New genetic and pharmacological techniques for molecular modulation of bioelectric gradients in vivo have revealed the ability to initiate complex organogenesis, change tissue identity, and trigger regeneration of whole vertebrate appendages. A large segment of the spatial information processing that orchestrates individual cells programs towards the anatomical needs of the host organism is electrical; this blurs the line between memory and decision-making in neural networks and morphogenesis in non-neural tissues. Advances in cracking this bioelectric code will enable the rational reprogramming of shape in whole tissues and organs, revolutionizing regenerative medicine, developmental biology, and synthetic bioengineering. PMID:23897652

  13. Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns[W][OA

    PubMed Central

    Millet, Yves A.; Danna, Cristian H.; Clay, Nicole K.; Songnuan, Wisuwat; Simon, Matthew D.; Werck-Reichhart, Danièle; Ausubel, Frederick M.

    2010-01-01

    Despite the fact that roots are the organs most subject to microbial interactions, very little is known about the response of roots to microbe-associated molecular patterns (MAMPs). By monitoring transcriptional activation of β-glucuronidase reporters and MAMP-elicited callose deposition, we show that three MAMPs, the flagellar peptide Flg22, peptidoglycan, and chitin, trigger a strong tissue-specific response in Arabidopsis thaliana roots, either at the elongation zone for Flg22 and peptidoglycan or in the mature parts of the roots for chitin. Ethylene signaling, the 4-methoxy-indole-3-ylmethylglucosinolate biosynthetic pathway, and the PEN2 myrosinase, but not salicylic acid or jasmonic acid signaling, play major roles in this MAMP response. We also show that Flg22 induces the cytochrome P450 CYP71A12-dependent exudation of the phytoalexin camalexin by Arabidopsis roots. The phytotoxin coronatine, an Ile-jasmonic acid mimic produced by Pseudomonas syringae pathovars, suppresses MAMP-activated responses in the roots. This suppression requires the E3 ubiquitin ligase COI1 as well as the transcription factor JIN1/MYC2 but does not rely on salicylic acid–jasmonic acid antagonism. These experiments demonstrate the presence of highly orchestrated and tissue-specific MAMP responses in roots and potential pathogen-encoded mechanisms to block these MAMP-elicited signaling pathways. PMID:20348432

  14. Cellulose binding domains of a Phytophthora cell wall protein are novel pathogen-associated molecular patterns.

    PubMed

    Gaulin, Elodie; Dram, Nani; Lafitte, Claude; Torto-Alalibo, Trudy; Martinez, Yves; Ameline-Torregrosa, Carine; Khatib, Moustafa; Mazarguil, Honor; Villalba-Mateos, Franois; Kamoun, Sophien; Mazars, Christian; Dumas, Bernard; Bottin, Arnaud; Esquerr-Tugay, Marie-Thrse; Rickauer, Martina

    2006-07-01

    The cellulose binding elicitor lectin (CBEL) from Phytophthora parasitica nicotianae contains two cellulose binding domains (CBDs) belonging to the Carbohydrate Binding Module1 family, which is found almost exclusively in fungi. The mechanism by which CBEL is perceived by the host plant remains unknown. The role of CBDs in eliciting activity was investigated using modified versions of the protein produced in Escherichia coli or synthesized in planta through the potato virus X expression system. Recombinant CBEL produced by E. coli elicited necrotic lesions and defense gene expression when injected into tobacco (Nicotiana tabacum) leaves. CBEL production in planta induced necrosis. Site-directed mutagenesis on aromatic amino acid residues located within the CBDs as well as leaf infiltration assays using mutated and truncated recombinant proteins confirmed the importance of intact CBDs to induce defense responses. Tobacco and Arabidopsis thaliana leaf infiltration assays using synthetic peptides showed that the CBDs of CBEL are essential and sufficient to stimulate defense responses. Moreover, CBEL elicits a transient variation of cytosolic calcium levels in tobacco cells but not in protoplasts. These results define CBDs as a novel class of molecular patterns in oomycetes that are targeted by the innate immune system of plants and might act through interaction with the cell wall. PMID:16766692

  15. Changes in holothurian coelomocyte populations following immune stimulation with different molecular patterns

    PubMed Central

    Ramírez-Gómez, Francisco; Aponte-Rivera, Francisco; Méndez-Castaner, Lumen; García-Arrarás, Jose E.

    2010-01-01

    Echinoderms possess a variety of cells populating the coelomic fluid; these cells are responsible for mounting defense against foreign agents. In the sea cucumber Holothuria glaberrima, four different coelomocyte types were readily distinguished using morphological, histochemical and physiological (phagocytic activity) parameters: lymphocytes, phagocytes, spherulocytes and “giant” cells (listed in order of abundance). Monoclonal antibodies generated against sea cucumber tissues and one polyclonal against sea urchin mayor yolk protein (MYP) were also used to characterize these cell populations. The effects of several pathogen-associated molecular patterns (PAMPs): Lipopolysaccharides from E. coli (LPS), heat-killed Staphylococcus aureus (SA) and a synthetic dsRNA were studied on coelomocyte cell populations. PAMPs increased the phagocytic activity of the holothurian coelomocytes, and were able to induce selective immune responses in several of these populations, demonstrating the ability of the sea cucumber to respond to a different variety of immune challenges. Overall, these results show the variety of cells that populate the coelomic fluid of the holothurian and demonstrate their involvement in immune reactions. These animals represent an untapped resource for new findings into the evolution and development of the immune response not only in invertebrates but also in phylogenetically shared reactions with vertebrates. PMID:20412860

  16. Molecular biology of rotaviruses. I. Characterization of basic growth parameters and pattern of macromolecular synthesis.

    PubMed

    McCrae, M A; Faulkner-Valle, G P

    1981-08-01

    The United Kingdom tissue-adapted bovine rotavirus growing in African green monkey kidney (BSC-1) cells was selected as a model system with which to study the detailed molecular virology of rotavirus replication. Study of the kinetics of infectious virus production revealed a fairly rapid replication cycle, with maximum yield of virus after 10 to 12 h at 37 degrees C. Progeny genome synthesis was first detected during the virus latent period at 2 to 3 h postinfection. Study of the kinetics of viral polypeptide synthesis showed that virus rapidly inhibited cellular polypeptide synthesis such that by 4 h postinfection, only virus-induced polypeptides, 15 of which were detected, were being synthesized. No qualitative changes in the pattern of viral polypeptide synthesis were observed during infection, although, based on kinetic synthesis, three quantitative classes of polypeptides were defined. Pulse-chase analysis revealed three post-translational changes in viral proteins, two of which were shown to be due to glycosylation. Tunicamycin inhibition studies were used to identify the putative non-glycosylated precursors of the two glycoproteins. Comparison of the infected-cell polypeptides with those present in purified virions revealed that mot of the virus-induced proteins were incorporated into virions, with only VP9 being a truly nonstructural protein. Some localization of the various polypeptides within the purified virion was achieved by producing viral cores. PMID:6268838

  17. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

    PubMed Central

    Hekkala, Evon R.; Platt, Steven G.; Thorbjarnarson, John B.; Rainwater, Thomas R.; Tessler, Michael; Cunningham, Seth W.; Twomey, Christopher; Amato, George

    2015-01-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet’s crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062

  18. Spectroscopic and Theoretical Study on the Structures and Dynamics of Functional Molecules - Towards AN Understanding of the Molecular Recognition for Encapsulation Complexes

    NASA Astrophysics Data System (ADS)

    Ebata, Takayuki; Kusaka, Ryoji; Inokuchi, Yoshiya; Xantheas, Sotiris S.

    2011-06-01

    Functional molecules, such as crown ethers and calixarenes, can act as hosts for encapsulating guest species through non-covalent interactions. Applications of crown ethers and calixarenes as molecular receptors, metal cation extraction agents, fluoro-ionophores and phase transfer catalytic media have been previously reported in a number of studies in the literature. One of the important aspects of these host/guest molecular assemblies is their selectivity in the encapsulation of guest species. Two important factors that control this selectivity are: (1) the size and the flexibility of the host cavity and (2) the properties of solvent molecules. Molecular complexes formed in supersonic jets provide ideal systems for the selective study of the conformational preference and micro-solvated effects under solvent-controlled conditions. This talk will review our spectroscopic and theoretical studies of the structures of dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6), calix[4]arene (C4A) and their complexes with guest molecules. We apply laser-induced fluorescence (LIF), resonance enhanced two-photon ionization (R2PI) and UV-UV hole-burning (HB) spectroscopy for obtaining electronic spectra and IR-UV doubleresonance and IR photodissociation (IRPD) spectroscopy for the IR spectra. The electronic and IR spectra are compared with the corresponding results obtained by DFT calculations and high-level first principles electronic structure calculations [MP2 and CCSD(T)]. Based on these joint studies we can elucidate the nature of interactions that control the encapsulation of a guest molecular species as well as how the host can adjust its conformation to accommodate a specific guest, leading to the molecular recognition.

  19. Temporal Patterns of Soluble Adhesion Molecules in Cerebrospinal Fluid and Plasma in Patients with the Acute Brain Infraction

    PubMed Central

    Selakovic, Vesna; Raicevic, Ranko; Radenovic, Lidija

    2009-01-01

    The aim of this study was to define concentration changes of soluble adhesion molecules (sICAM-1, sVCAM-1 and sE-Selectin) in cerebrospinal fluid and plasma, as well as, number of peripheral blood leukocytes and the albumin coefficient in the patients with the acute brain infarction. We also, analyzed the correlation between the measured levels, the infarct volume and the degree of neurological and the functional deficit. The study included 50 patients with the acute cerebral infarction and the control group consisted of 16 patients, age and sex matched. Obtained results showed significant increase in number of leukocytes, the albumin coefficient and the level of soluble adhesion molecules within the first seven days in patients. The highest values of measured parameters were noted within the third and the fourth day after the insult, which is the suggested period of maximal intensity of inflammatory reactions. Significant correlation was found between measured parameters and the infarct volume, the degree of neurological and the functional deficit. The results suggest that investigated parameters in CSF and blood represent a dynamic index of inflammatory events as one of the fundametal mechanisms responsible for neuron damage during acute phase of brain infarction. PMID:19407361

  20. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    PubMed Central

    2009-01-01

    Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625

  1. Patterns.

    ERIC Educational Resources Information Center

    McKillip, William D.

    One of a series of experimental units for preschool children, this unit deals with patterns and number concepts. The mathematical background, the organization of the unit, and the objectives are discussed; a list of materials is provided; and directions are given for a sequence of learning activities. For the document reporting the development and…

  2. Electron tunneling through molecule-electrode contacts of single alkane molecular junctions: experimental determination and a practical barrier model.

    PubMed

    Wang, Kun; Xu, Bingqian

    2016-04-14

    An advanced understanding of the molecule-electrode contact interfaces of single-molecule junctions is a necessity for real world application of future single-molecule devices. This study aims to elucidate the change in the contact tunnelling barrier induced by junction extension and how this change affects the resulting junction conductance. The contact barrier of Au-octanedithiol/octanediamine-Au junctions was studied under triangle (TRI) mechanical modulations using the modified scanning tunneling microscopy (STM) break junction technique. The experimental results reveal that as the junction separation extends, the contact barrier of octanedithiol follows a unique trend, a linear increase followed by a plateau in barrier height, which is in contrast to that of octanediamine, a nearly rectangle barrier. We propose a modified contact barrier model for the unique barrier shape of octanedithiol, based on which the calculation agrees well with the experimental data. This study shows unprecedented experimental features of the molecule-electrode contact barrier of single-molecule junctions and provides new insights into the nature of contact effect in determining electron transport through single-molecule junctions. PMID:26988278

  3. In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells.

    PubMed

    Voïtchovsky, Kislon; Ashari-Astani, Negar; Tavernelli, Ivano; Tétreault, Nicolas; Rothlisberger, Ursula; Stellacci, Francesco; Grätzel, Michael; Harms, Hauke A

    2015-05-27

    Amphiphilic sensitizers are central to the function of dye-sensitized solar cells. It is known that the cell's performance depends on the molecular arrangement and the density of the dye on the semiconductor surface, but a molecular-level picture of the cell-electrolyte interface is still lacking. Here, we present subnanometer in situ atomic force microscopy images of the Z907 dye at the surface of TiO2 in a relevant liquid. Our results reveal changes in the conformation and the lateral arrangement of the dye molecules, depending on their average packing density on the surface. Complementary quantitative measurements on the ensemble of the film are obtained by the quartz-crystal microbalance with dissipation technique. An atomistic picture of the dye coverage-dependent packing, the effectiveness of the hydrophobic alkyl chains as blocking layer, and the solvent accessibility is obtained from molecular dynamics simulations. PMID:25936429

  4. Resonance enhanced multiphoton and single-photon ionization of molecules and molecular fragments. Annual technical report, May 1, 1994--April 30, 1995

    SciTech Connect

    McKoy, V.

    1995-12-31

    The overall objective of this work is to carry out quantitative theoretical studies of these laser-driven ionization processes in molecules so as to provide both a robust description of key spectral features of interest in applications and related experiments and needed insight into these spectra. A major focus of this effort is combined theoretical-experimental studies of molecular ion spectra which are being widely studied by the zero-kinetic-energy (ZEKE) technique. This ZEKE technique, which is base3d on pulsed-field ionization (PFI) of very high Rydberg states, makes it possible to obtain ion distributions with sub-wavenumber resolution and is clearly opening up entirely new vistas in studies of molecular ionization. Some highlights of the progress include: (1) The author has extended the theoretical formulation and computational procedures used in these studies of molecular ionization spectra to general polyatomic systems; (2) He has completed combined theoretical-experimental studies of the molecular ion distributions for photoionization of H{sub 2}S, H{sub 2}CO, and CH{sub 3} by coherent VUV radiation; (3) He has carried out the first calculations of the molecular ion rotational distributions for electronically excited states of NO{sup +} (a {sup 3}{Sigma}{sup +}) and CO{sup +} (A {sup 2}{Pi}); (4) he has also completed calculations of the ion rotational distributions for laser ionization of the small prototypical radicals OH, NH, and CH; and (5) Extensions of the studies of molecular photoionization processes of interest here to large polyatomic molecules are computationally quite demanding. These computational demands arise primarily from complexities associated with the quantum mechanical equations which must be solved to obtain the photoelectron wavefunctions required in these studies. To meet these computational needs the author is currently developing strategies for carrying out these calculations on massively parallel computers such as the Intel Paragon and Cray T3D.

  5. Strong-field approximation for ionization of a diatomic molecule by a strong laser field. II. The role of electron rescattering off the molecular centers

    NASA Astrophysics Data System (ADS)

    Busuladžić, M.; Gazibegović-Busuladžić, A.; Milošević, D. B.; Becker, W.

    2008-09-01

    The strong-field approximation for ionization of diatomic molecules by a strong laser field [D. B. Milošević, Phys. Rev. A 74, 063404 (2006)] is generalized to include rescattering of the ionized electron wave packet off the molecular centers (the electron’s parent ion or the second atom). There are four rescattering contributions to the ionization rate, which are responsible for the high-energy plateau in the electron spectra and which interfere in a complicated manner. The spectra are even more complicated due to the different symmetry properties of the atomic orbitals of which a particular molecular orbital consists. Nevertheless, a comparatively simple condition emerges for the destructive interference of all these contributions, which yields a curve in the (Epf,θ) plane. Here θ is the electron emission angle and Epf is the electron kinetic energy. The resulting suppression of the rescattering plateau can be strong and affect a large area of the (Epf,θ) plane, depending on the orientation of the molecule. We illustrate this using the examples of the 3σg molecular orbital of N2 and the 1πg molecular orbital of O2 for various orientations of these molecules with respect to the laser polarization axis. For N2 , for perpendicular orientation and the equilibrium internuclear distance R0 , we find that the minima of the ionization rate form the curve Epfcos2θ=π2/(2R02) in the (Epf,θ) plane. For O2 the rescattering plateau is absent for perpendicular orientation.

  6. Artificial bacterial biomimetic nanoparticles synergize pathogen-associated molecular patterns for vaccine efficacy.

    PubMed

    Siefert, Alyssa L; Caplan, Michael J; Fahmy, Tarek M

    2016-08-01

    Antigen-presenting cells (APCs) sense microorganisms via pathogen-associated molecular patterns (PAMPs) by both extra- and intracellular Toll-like Receptors (TLRs), initiating immune responses against invading pathogens. Bacterial PAMPs include extracellular lipopolysaccharides and intracellular unmethylated CpG-rich oligodeoxynucleotides (CpG). We hypothesized that a biomimetic approach involving antigen-loaded nanoparticles (NP) displaying Monophosphoryl Lipid A (MPLA) and encapsulating CpG may function as an effective "artificial bacterial" biomimetic vaccine platform. This hypothesis was tested in vitro and in vivo using NP assembled from biodegradable poly(lactic-co-glycolic acid) (PLGA) polymer, surface-modified with MPLA, and loaded with CpG and model antigen Ovalbumin (OVA). First, CpG potency, characterized by cytokine profiles, titers, and antigen-specific T cell responses, was enhanced when CpG was encapsulated in NP compared to equivalent concentrations of surface-presented CpG, highlighting the importance of biomimetic presentation of PAMPs. Second, NP synergized surface-bound MPLA with encapsulated CpG in vitro and in vivo, inducing greater pro-inflammatory, antigen-specific T helper 1 (Th1)-skewed cellular and antibody-mediated responses compared to single PAMPs or soluble PAMP combinations. Importantly, NP co-presentation of CpG and MPLA was critical for CD8(+) T cell responses, as vaccination with a mixture of NP presenting either CpG or MPLA failed to induce cellular immunity. This work demonstrates a rational methodology for combining TLR ligands in a context-dependent manner for synergistic nanoparticulate vaccines. PMID:27162077

  7. Functional dissection of a strong and specific microbe-associated molecular pattern-responsive synthetic promoter.

    PubMed

    Lehmeyer, Mona; Kanofsky, Konstantin; Hanko, Erik K R; Ahrendt, Sarah; Wehrs, Maren; Machens, Fabian; Hehl, Reinhard

    2016-01-01

    Synthetic promoters are important for temporal and spatial gene expression in transgenic plants. To identify novel microbe-associated molecular pattern (MAMP)-responsive cis-regulatory sequences for synthetic promoter design, a combination of bioinformatics and experimental approaches was employed. One cis-sequence was identified which confers strong MAMP-responsive reporter gene activity with low background activity. The 35-bp-long cis-sequence was identified in the promoter of the Arabidopsis thaliana DJ1E gene, a homologue of the human oncogene DJ1. In this study, this cis-sequence is shown to be a tripartite cis-regulatory module (CRM). A synthetic promoter with four copies of the CRM linked to a minimal promoter increases MAMP-responsive reporter gene expression compared to the wild-type DJ1E promoter. The CRM consists of two WT-boxes (GGACTTTT and GGACTTTG) and a variant of the GCC-box (GCCACC), all required for MAMP and salicylic acid (SA) responsivity. Yeast one-hybrid screenings using a transcription factor (TF)-only prey library identified two AP2/ERFs, ORA59 and ERF10, interacting antagonistically with the CRM. ORA59 activates reporter gene activity and requires the consensus core sequence GCCNCC for gene expression activation. ERF10 down-regulates MAMP-responsive gene expression. No TFs interacting with the WT-boxes GGACTTTT and GGACTTTG were selected in yeast one-hybrid screenings with the TF-only prey library. In transgenic Arabidopsis, the synthetic promoter confers strong and specific reporter gene activity in response to biotrophs and necrotrophs as well as SA. PMID:25819608

  8. A different molecular pattern of beta-thalassemia mutations in northeast Brazil.

    PubMed

    Araújo, Aderson S; Silva, l Wilson A Júnior; Leão, Silvana A C; Bandeira, Flavia C G M; Petrou, Mary; Modell, Bernadette; Zago, Marco A

    2003-11-01

    The main hereditary hemoglobin (Hb) disorders of clinical significance in Brazil are sickle cell disease and beta-thalassemia (thal). The sickle gene was introduced by the slave trade, whereas beta-thal was introduced later, due to a massive immigration (mostly by Italians) between 1870 and 1953, mainly to the southeast region of Brazil. Molecular studies performed in the southeast of the country showed a marked prevalence of the nonsense mutation at codon 39 (C --> T) (47-54%), leading to severe forms of beta0-thal. However, the northeast region of the country has a different demographic history, characterized by the absence of the massive Italian immigration. Owing to this and since the majority of cases of beta-thal in Pernambuco, a state located in the northeast of the country, have mild or intermediate clinical and laboratory features, we would predict a different spectrum of beta-thal mutations in this region. We examined 60 unrelated patients (86 beta-thal chromosomes) under regular clinical follow-up in Pernambuco: 6 were regularly transfused beta-thal major subjects, 20 had beta-thal intermedia, 20 had Hb S/beta-thal and 14 were beta-thal trait individuals. The following mutations were found: IVS-I-6 (T --> C) 62.8%, IVS-I-1 (G -->A) 15.1%, IVS-I-5 (G --> C) 9.3%, IVS-I-110 (G --> A) 8.2%, codon 39 (C --> T) 3.5%, and codon 30 (AGG --> AGC) 1.1%. These data show different patterns of beta-thal mutations in two regions of Brazil, demonstrating a thus far unrevealed heterogeneity of the disease in the country. PMID:14649311

  9. Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions.

    PubMed

    Bonilla, A; Sarria, A L F; Algar, E; Muñoz Ledesma, F J; Ramos Solano, B; Fernandes, J B; Gutierrez Mañero, F J

    2014-01-01

    Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum. PMID:24296249

  10. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  11. Chemical evolution of the HC3N and N2H+ molecules in dense cores of the Vela C giant molecular cloud complex

    NASA Astrophysics Data System (ADS)

    Ohashi, Satoshi; Tatematsu, Ken'ichi; Fujii, Kosuke; Sanhueza, Patricio; Nguyen Luong, Quang; Choi, Minho; Hirota, Tomoya; Mizuno, Norikazu

    2016-02-01

    We have observed the HC3N(J = 10-9) and N2H+ (J = 1-0) lines toward the Vela C molecular clouds with the Mopra 22 m telescope to study the chemical characteristics of dense cores. The intensity distributions of these molecules are similar to each other at an angular resolution of 53″, corresponding to 0.19 pc, suggesting that these molecules trace the same dense cores. We identified 25 local peaks in the velocity-integrated intensity maps of the HC3N and/or N2H+ emission. Assuming local thermodynamic equilibrium conditions, we calculated the column densities of these molecules and found a tendency for the N2H+/HC3N abundance ratio to be low in starless regions while it seems to be high in star-forming regions, similar to the tendencies in the NH3/CCS, NH3/HC3N, and N2H+/CCS abundance ratios found in previous studies of dark clouds and the Orion A giant molecular cloud (GMC). We suggest that carbon chain molecules, including HC3N, may trace chemically young molecular gas, and that N-bearing molecules, such as N2H+, may trace later stages of chemical evolution in the Vela C molecular clouds. It may be possible that the N2H+/HC3N abundance ratio of ˜1.4 divides the star-forming and starless peaks in Vela C, although it is not as clear as those in NH3/CCS, NH3/HC3N, and N2H+/CCS for the Orion A GMC. This less clear separation may be caused by our lower spatial resolution or the misclassification of star-forming and starless peaks due to the larger distance of Vela C. It might also be possible that the HC3N (J = 10-9) transition is not a good chemical evolution tracer compared with CCS (J = 4-3 and 7-6) transitions.

  12. Origin of spontaneous polarization, tilt, and chiral structure of smectic liquid-crystal phases composed of bent-core molecules: A molecular model

    NASA Astrophysics Data System (ADS)

    Emelyanenko, A. V.; Osipov, M. A.

    2004-08-01

    A simple molecular model is proposed for novel bent-core smectic phases that enables one to explain the origin of the experimentally observed chiral structure of the B2 phase composed of nonchiral banana-shaped molecules. It is shown that in the perfectly ordered smectic phase the distributed dispersion interaction between banana-shaped molecules stabilizes the spontaneous polarization and may be responsible for the tilt of the director. The orientation of the spontaneous polarization with respect to the tilt plane is determined by the balance between the dispersion and electrostatic dipole-dipole intermolecular interactions. In particular, sufficiently strong dipole-dipole interaction promotes the B2 phase where the polarization is normal to the tilt plane. The actual chiral structure of each smectic layer in the B2 phase appears as a result of the symmetry breaking. In the case of small molecular dipoles the nonchiral polar smectic phase is formed where the spontaneous polarization is parallel to the tilt plane. The role of the opening angle and of the axial ratio of banana-shaped molecules is also considered and a phase diagram is presented.

  13. Origin of spontaneous polarization, tilt, and chiral structure of smectic liquid-crystal phases composed of bent-core molecules: a molecular model.

    PubMed

    Emelyanenko, A V; Osipov, M A

    2004-08-01

    A simple molecular model is proposed for novel bent-core smectic phases that enables one to explain the origin of the experimentally observed chiral structure of the B2 phase composed of nonchiral banana-shaped molecules. It is shown that in the perfectly ordered smectic phase the distributed dispersion interaction between banana-shaped molecules stabilizes the spontaneous polarization and may be responsible for the tilt of the director. The orientation of the spontaneous polarization with respect to the tilt plane is determined by the balance between the dispersion and electrostatic dipole-dipole intermolecular interactions. In particular, sufficiently strong dipole-dipole interaction promotes the B2 phase where the polarization is normal to the tilt plane. The actual chiral structure of each smectic layer in the B2 phase appears as a result of the symmetry breaking. In the case of small molecular dipoles the nonchiral polar smectic phase is formed where the spontaneous polarization is parallel to the tilt plane. The role of the opening angle and of the axial ratio of banana-shaped molecules is also considered and a phase diagram is presented. PMID:15447506

  14. Selective catalysts for the hydrogen oxidation and oxygen reduction reactions by patterning of platinum with calix[4]arene molecules.

    SciTech Connect

    Genorio, B.; Strmcnik, D.; Subbaraman, R.; Tripkovic, D.; Karapetrov, G.; Stamenkovic, V. R.; Pejovnik, S.; Markovic, N. M.; Univ. Ljubljana; National Inst. of Chemistry

    2010-12-01

    The design of new catalysts for polymer electrolyte membrane fuel cells must be guided by two equally important fundamental principles: optimization of their catalytic behaviour as well as the long-term stability of the metal catalysts and supports in hostile electrochemical environments. The methods used to improve catalytic activity are diverse, ranging from the alloying and de-alloying of platinum to the synthesis of platinum core-shell catalysts. However, methods to improve the stability of the carbon supports and catalyst nanoparticles are limited, especially during shutdown (when hydrogen is purged from the anode by air) and startup (when air is purged from the anode by hydrogen) conditions when the cathode potential can be pushed up to 1.5 V. Under the latter conditions, stability of the cathode materials is strongly affected (carbon oxidation reaction) by the undesired oxygen reduction reaction (ORR) on the anode side. This emphasizes the importance of designing selective anode catalysts that can efficiently suppress the ORR while fully preserving the Pt-like activity for the hydrogen oxidation reaction. Here, we demonstrate that chemically modified platinum with a self-assembled monolayer of calix[4]arene molecules meets this challenging requirement.

  15. Nuclear Overhauser effect as a probe of molecular structure, dynamics and order of axially reorienting molecules in membranes.

    PubMed

    Davis, James H; Komljenovi?, Ivana

    2016-02-01

    The location, orientation, order and dynamics of cholesterol in model membranes have been well characterized, therefore cholesterol is an ideal molecule for developing new methods for studying structured molecules undergoing rapid axially symmetric reorientation. The use of (13)C filtering via short contact cross polarization transfer to (1)H allows the recovery of the weak cholesterol (1)H magic angle spinning NMR signals from beneath the strong phospholipid background in bicelles composed of chain perdeuterated dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine/[3,4-(13)C]-cholesterol. Measurements of the nuclear Overhauser enhancement for (1)H nuclei located in the first ring of cholesterol are interpreted in terms of a simple two motion model consisting of axial reorientation, with a correlation time ??, and a slower reorientation of the diffusion axis relative to the bilayer normal, with correlation time ??. This approach can be extended to other molecules which undergo rapid axial reorientation such as small membrane associated peptides. PMID:26607012

  16. Theoretical studies of interstellar molecular shocks. I - General formulation and effects of the ion-molecule chemistry

    NASA Astrophysics Data System (ADS)

    Flower, D. R.; Pineau des Forets, G.; Hartquist, T. W.

    1985-10-01

    The authors present a formulation of the problem of magnetohydrodynamic shock propagation through an interstellar cloud in a form which is adapted to the inclusion of the ion-molecule chemistry. Continuous (C-type) shocks are considered and comparison is made with the earlier work of Draine (1980) and of Draine, Roberge and Dalgarno (1983), in which ion-molecule reactions were neglected. The authors find that the inclusion of endothermic ion-molecule reactions, driven by the relative streaming of the ionized and neutral fluids, has a profound effect on the shock structure. In particular, the width of the shock is greatly enhanced and the maximum temperature attained by the neutral gas is much reduced.

  17. Electrical readouts of single and few molecule systems in metal-molecule-metal device structures.

    PubMed

    Mahapatro, Ajit K; Janes, David B

    2007-06-01

    Electrical conduction through molecular junctions are measured in different local environments through two test beds that are ideal for single/few molecule and molecular monolayer systems. A technique has been developed to realize Au films with approximately 1.5 A surface roughness comparable to the best available techniques and suitable for formation of patterned device structures. The technique utilizes room temperature e-beam evaporated Au films over oxidized Si substrates silanized with (3-mercaptopropyl)trimethoxysilane (MPTMS). The lateral (single/few molecule) and vertical (many molecules) device structures are both enabled by the process for realizing ultraflat Au layer. Lateral metal-molecule-metal (M-M-M) device structures are fabricated by forming pairs of Au electrodes with nanometer separation (nano-gap) through an electromigration-induced break-junction (EIBJ) technique at room temperature and conductivity measurements are carried out for dithiol functionalized single molecules. We have used the flat Au layer (using the current technique) as the bottom contact in vertical M-M-M device structures. Here, molecular self-assembly are formed on the Au surface, and patterned (20 x 20 microm2) top Au contacts were successfully transferred on to the device using a stamping technique (where the Au is deposited on a polydimethylsiloxane (PDMS) pad and following a physical contact on the thiolated Au layer). The single molecular property of XYL, a highly conductive molecule and many molecular property of HS-C9-SH, an insulating molecule in its molecular monolayer form are measured. Observation of enhanced conduction following molecular deposition, and comparison of conductance-voltage characteristics to those predicted theoretically, confirms the success of trapping single/few molecules in the nano-gap. The observed approximately 10(2) less conductance through the molecular monolayer of HS-C9-SH compared to the estimation of a linear sum of single molecule conductances over large area indicate that either all the molecules are not in physical contact with the top stamping electrode or electrode-molecule coupling has a less broadening in presence of it own environment or both. PMID:17655006

  18. Altered Expression Patterns of Inflammation-Associated and Trophic Molecules in Substantia Nigra and Striatum Brain Samples from Parkinson's Disease, Incidental Lewy Body Disease and Normal Control Cases

    PubMed Central

    Walker, Douglas G.; Lue, Lih-Fen; Serrano, Geidy; Adler, Charles H.; Caviness, John N.; Sue, Lucia I.; Beach, Thomas G.

    2016-01-01

    Evidence of inflammation has been consistently associated with pathology in Parkinson's disease (PD)-affected brains, and has been suggested as a causative factor. Dopaminergic neurons in the substantia nigra (SN) pars compacta, whose loss results in the clinical symptoms associated with PD, are particularly susceptible to inflammatory damage and oxidative stress. Inflammation in the striatum, where SN dopaminergic neurons project, is also a feature of PD brains. It is not known whether inflammatory changes occur first in striatum or SN. Many animal models of PD have implicated certain inflammatory molecules with dopaminergic cell neuronal loss; however, there have been few studies to validate these findings by measuring the levels of these and other inflammatory factors in human PD brain samples. This study also included samples from incidental Lewy body disease (ILBD) cases, since ILBD is considered a non-symptomatic precursor to PD, with subjects having significant loss of tyrosine hydroxylase-producing neurons. We hypothesized that there may be a progressive change in key inflammatory factors in ILBD samples intermediate between neurologically normal and PD. To address this, we used a quantitative antibody-array platform (Raybiotech-Quantibody arrays) to measure the levels of 160 different inflammation-associated cytokines, chemokines, growth factors, and related molecules in extracts of SN and striatum from clinically and neuropathologically characterized PD, ILBD, and normal control cases. Patterns of changes in inflammation and related molecules were distinctly different between SN and striatum. Our results showed significantly different levels of interleukin (IL)-5, IL-15, monokine induced by gamma interferon, and IL-6 soluble receptor in SN between disease groups. A different panel of 13 proteins with significant changes in striatum, with IL-15 as the common feature, was identified. Although the ability to detect some proteins was limited by sensitivity, patterns of expression indicated involvement of certain T-cell cytokines, vascular changes, and loss of certain growth factors, with disease progression. The results demonstrate the feasibility of profiling inflammatory molecules using diseased human brain samples, and have provided additional targets to validate in relation to PD pathology. PMID:26834537

  19. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation.

    PubMed

    Satoh, Mikiya; Saburi, Hajime; Tanaka, Tomoyuki; Matsuura, Yoshinori; Naitow, Hisashi; Shimozono, Rieko; Yamamoto, Naoyoshi; Inoue, Hideki; Nakamura, Noriko; Yoshizawa, Yoshitaka; Aoki, Takumi; Tanimura, Ryuji; Kunishima, Naoki

    2015-01-01

    Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development. PMID:26199865

  20. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

    PubMed Central

    Satoh, Mikiya; Saburi, Hajime; Tanaka, Tomoyuki; Matsuura, Yoshinori; Naitow, Hisashi; Shimozono, Rieko; Yamamoto, Naoyoshi; Inoue, Hideki; Nakamura, Noriko; Yoshizawa, Yoshitaka; Aoki, Takumi; Tanimura, Ryuji; Kunishima, Naoki

    2015-01-01

    Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development. PMID:26199865

  1. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-09-01

    In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks-Chandler-Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribution in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, referred to as SAFT-γ WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water.

  2. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. III. Molecules with partial charges at bulk phases, confined geometries and interfaces

    SciTech Connect

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-09-07

    In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks–Chandler–Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribution in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, referred to as SAFT-γ WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water.

  3. Generation of structures of molecular crystals with two molecules related by a twofold axis or a plane of symmetry in a primitive unit cell

    SciTech Connect

    Maleev, A. V.

    2006-07-15

    Within the method of discrete modeling of packings, an algorithm of generation of possible structures of molecular crystals with two molecules of known shape in the primitive unit cell, related by a twofold (screw or rotary) axis or a plane of mirror or glide reflection symmetry, is proposed. The algorithm is based on the approximation of molecules by polycubes (geometric figures composed of identical cubes) and calculation of all possible periodic packings of these polycubes with a specified packing factor. On the basis of this algorithm, a software package for personal computers is developed. Examples of approval of this package for several crystal structures, identified previously by X-ray diffraction analysis, are reported.

  4. Identification, molecular characterization, and gene expression analysis of a CD109 molecule in the Hawaiian bobtail squid Euprymna scolopes.

    PubMed

    Yazzie, Natasha; Salazar, Karla A; Castillo, Maria G

    2015-05-01

    All organisms have unique immune systems that help them identify and eliminate invading microorganisms. A group of evolutionary ancient molecules, the thioester-containing proteins (TEP) superfamily, are known to play an important immune role by aiding animal hosts in the recognition, destruction, and elimination of hazardous microorganisms and their products. Our laboratory focuses on studying the role of the immune system in the mutualistic relationship between the sepiolid squid, Euprymna scolopes and its bioluminescent symbiont Vibrio fischeri. In the present study, we report the identification of a novel TEP-like transcript expressed in the light organ of squid. Characterization of the full-length coding sequence showed a molecule of 4218 nucleotides, corresponding to 1406 amino acids. Further sequence analysis revealed it contained structural characteristics of A2M molecules, including the thioester and receptor-binding domains. Analysis using the predicted amino acid sequence suggested this transcript was a homologue of CD109 molecules, thus we named it E. scolopes-CD109 (Es-CD109). In addition to the light organ, we were able to detect and amplify Es-CD109 in 12 out of 14 adult squid tissues tested. Quantification experiments showed that Es-CD109 expression levels were significantly lower in the light organ of symbiotic compared to aposymbiotic juveniles, suggesting a possible down-regulation of the host immune response in the presence of the bacterial symbiont. PMID:25742727

  5. Hydrophilic-Hydrophobic Patterned Molecularly Imprinted Photonic Crystal Sensors for High-Sensitive Colorimetric Detection of Tetracycline.

    PubMed

    Hou, Jue; Zhang, Huacheng; Yang, Qiang; Li, Mingzhu; Jiang, Lei; Song, Yanlin

    2015-06-01

    A hydrophilic-hydrophobic patterned molecularly imprinted (MIP) photonic crystal (PC) sensor is fabricated for highly sensitive tetracycline detection. The relationship between the tetracycline concentration, its corresponding color of the sensor, and the diameter of MIP-PC dot is found using a fan-shaped color card. This work provides a new strategy to design the sensors with tunable detection ranges for practical applications. PMID:25649896

  6. An application of a statistical model for the calculation of the logarithmic mean excitation energy of molecules Molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Kamaratos, E.

    1985-01-01

    A statistical model, the local plasma approximation, is considered for the calculation of the logarithmic mean excitation energy for stopping power of chemically bound particles by taking into consideration chemical bonding. This statistical model is applied to molecular hydrogen and leads to results that suggest a value for the logarithmic mean excitation energy of molecular hydrogen that is larger than the accepted experimental and theoretical values.

  7. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    PubMed Central

    2011-01-01

    Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier. PMID:21639885

  8. Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes

    PubMed Central

    Walter, Vonn; Yin, Xiaoying; Wilkerson, Matthew D.; Cabanski, Christopher R.; Zhao, Ni; Du, Ying; Ang, Mei Kim; Hayward, Michele C.; Salazar, Ashley H.; Hoadley, Katherine A.; Fritchie, Karen; Sailey, Charles G.; Weissler, Mark C.; Shockley, William W.; Zanation, Adam M.; Hackman, Trevor; Thorne, Leigh B.; Funkhouser, William D.; Muldrew, Kenneth L.; Olshan, Andrew F.; Randell, Scott H.; Wright, Fred A.; Shores, Carol G.; Hayes, D. Neil

    2013-01-01

    Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented. PMID:23451093

  9. Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.

    PubMed

    Walter, Vonn; Yin, Xiaoying; Wilkerson, Matthew D; Cabanski, Christopher R; Zhao, Ni; Du, Ying; Ang, Mei Kim; Hayward, Michele C; Salazar, Ashley H; Hoadley, Katherine A; Fritchie, Karen; Sailey, Charles J; Sailey, Charles G; Weissler, Mark C; Shockley, William W; Zanation, Adam M; Hackman, Trevor; Thorne, Leigh B; Funkhouser, William D; Muldrew, Kenneth L; Olshan, Andrew F; Randell, Scott H; Wright, Fred A; Shores, Carol G; Hayes, D Neil

    2013-01-01

    Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented. PMID:23451093

  10. Formation of molecular species of mitochondrial cardiolipin 2. A mathematical model of pattern formation by phospholipid transacylation.

    PubMed

    Schlame, Michael

    2009-04-01

    Formation of the unique molecular species of mitochondrial cardiolipin requires tafazzin, a transacylase that exchanges acyl groups between phospholipid molecular species without strict specificity for acyl groups, head groups, or carbon positions. However, it is not known whether phospholipid transacylations can cause the accumulation of specific fatty acids in cardiolipin. Here, a model is shown in linear algebra representation, in which acyl specificity emerges from the transacylation equilibrium of multiple molecular species, provided that different species have different free energies. The model defines the conditions and energy terms, under which transacylations may generate the characteristic composition of mitochondrial cardiolipin. It is concluded that acyl-specific cardiolipin patterns could arise from phospholipid transacylations in the tafazzin domain, even if tafazzin itself does not have substrate specificity. PMID:19416646

  11. The ejection of triatomic molecular hydrogen ions H3+ produced by the interaction of benzene molecules with ultrafast laser pulses

    NASA Astrophysics Data System (ADS)

    Kaziannis, S.; Liontos, I.; Karras, G.; Corsi, C.; Bellini, M.; Kosmidis, C.

    2009-10-01

    The ejection process of triatomic molecular hydrogen ions produced by the interaction of benzene with ultrafast laser pulses of moderate strong intensity (˜1014 W/cm2) is studied by means of TOF mass spectrometry. The H3+ formation can only take place through the rupture of two C-H bonds and the migration of hydrogen atoms within the molecular structure. The H3+ fragments are released with high kinetic energy (typically 2-8 eV) and at laser intensities ≥1014 W/cm2, well above that required for the double ionization of benzene, suggesting that its formation is taking place within multiply charged parent ions. The relative ejection efficiency of H3+ molecular hydrogen ions with respect to the atomic ones is found to be strongly decreasing as a function of the laser intensity and pulse duration (67-25 fs). It is concluded that the H3+ formation is only feasible within parent molecular precursors of relatively low charged states and before significant elongation of their structure takes place, while the higher multiply charged molecular ions preferentially dissociate into H+ ions. The ejection of H2+ ions is also discussed in comparison to the production of H3+ and H+ ions. Finally, by recording the mass spectra of two deuterium label isotopes of benzene (1,2-C6H4D2, 1,4-C6H4D2) it is verified that the ejection efficiency of some molecular fragments, such as D2H+, DH+, is dependent on the specific position of hydrogen atoms in the molecular skeleton prior dissociation.

  12. The molecular basis for venation patterning of pigmentation and its effect on pollinator attraction in flowers of Antirrhinum.

    PubMed

    Shang, Yongjin; Venail, Julien; Mackay, Steve; Bailey, Paul C; Schwinn, Kathy E; Jameson, Paula E; Martin, Cathie R; Davies, Kevin M

    2011-01-01

    Pigment stripes associated with veins (venation) is a common flower colour pattern. The molecular genetics and function of venation were investigated in the genus Antirrhinum, in which venation is determined by Venosa (encoding an R2R3MYB transcription factor). Pollinator preferences were measured by field tests with Antirrhinum majus. Venosa function was examined using in situ hybridization and transient overexpression. The origin of the venation trait was examined by molecular phylogenetics. Venation and full-red flower colouration provide a comparable level of advantage for pollinator attraction relative to palely pigmented or white lines. Ectopic expression of Venosa confers pigmentation outside the veins. Venosa transcript is produced only in small areas of the corolla between the veins and the adaxial epidermis. Phylogenetic analyses suggest that venation patterning is an ancestral trait in Antirrhinum. Different accessions of three species with full-red pigmentation with or without venation patterning have been found. Epidermal-specific venation is defined through overlapping expression domains of the MYB (myoblastoma) and bHLH (basic Helix-Loop-Helix) co-regulators of anthocyanin biosynthesis, with the bHLH providing epidermal specificity and Venosa vein specificity. Venation may be the ancestral trait, with full-red pigmentation a derived, polyphyletic trait. Venation patterning is probably not fixed once species evolve full-red floral pigmentation. PMID:21039563

  13. Molecular dynamics study of the effects of chain properties on the order formation dynamics of self-assembled monolayers of long-chain molecules.

    PubMed

    Miura, Toshiaki; Mikami, Masuhiro

    2010-02-01

    The order formation dynamics of self-assembled monolayers (SAM) of long-chain molecules were studied using coarse-grained molecular dynamics simulations. The primary kinetic processes of surface order formation from solution are adsorption to the surface and surface diffusion. For long-chain molecules, the degrees of freedom of the chain structure and motion add various complexities to the order formation dynamics. Specifically, the strength of the chain interaction, the chain flexibility and the chain length play a significant role, and this work focused on the effects of these chain properties on the order formation dynamics. The adsorption dynamics of SAM molecules can be explained by the same theoretical framework as the polymer brush. On the other hand, the evolution of highly ordered structure is specific to SAM systems. Simulation results revealed that the development of oriented domains can be grouped into three types, isolated island growth, packing growth, and growth suppression, which depend on temperature and chain flexibility. In packing growth, oriented domains are formed gradually due to the decrease in free volume as the surface density becomes high, while the tilt of the adsorbed chain molecules does not become upright gradually as a whole. Rather, inside the oriented domains, the adsorbed chains adopt "standing" states with tilt angles almost equal to the final values, which contributes to the gradual increase in the total tilt order. The effect of chain length was also studied. In the case of semirigid chain molecules, longer-chain systems showed slightly slower growth in adsorption but faster growth in oriented domains. These simulation results reveal how chain properties influence the dynamics of oriented structure formation on surfaces. PMID:20365584

  14. Joint Measurements of Terahertz Wave Generation and High-Harmonic Generation from Aligned Nitrogen Molecules Reveal Angle-Resolved Molecular Structures.

    PubMed

    Huang, Yindong; Meng, Chao; Wang, Xiaowei; Lü, Zhihui; Zhang, Dongwen; Chen, Wenbo; Zhao, Jing; Yuan, Jianmin; Zhao, Zengxiu

    2015-09-18

    We report the synchronized measurements of terahertz wave generation and high-harmonic generation from aligned nitrogen molecules in dual-color laser fields. Both yields are found to be alignment dependent, showing the importance of molecular structures in the generation processes. By calibrating the angular ionization rates with the terahertz yields, we present a new way of retrieving the angular differential photoionization cross section (PICS) from the harmonic signals which avoids specific model calculations or separate measurements of the alignment-dependent ionization rates. The measured PICS is found to be consistent with theoretical predications, although some discrepancies exist. This all-optical method provides a new alternative for investigating molecular structures. PMID:26430992

  15. Radial dose calculation due to the irradiation of a heavy ion: Role of composite electric field formed from the polarization of molecules and molecular ions

    NASA Astrophysics Data System (ADS)

    Moribayashi, Kengo

    2014-03-01

    This paper discusses the role of composite electric field on radial doses through simulations due to the irradiation of a heavy ion. This composition electric field is formed from molecular ions, the polarization of molecules, and free electrons. Free electrons as well as these molecular ions are produced from the impact ionization of an incident ion or the other free electrons. The motions of the free electrons are simulated using a simulation model shown by Moribayashi, 2011. Phys. Rev. A. 84, 012702-1-012702-7 and Moribayashi, 2013a. Rad. Phys. Chem. 85, 36-41. This simulation model employs an isolated atom model that additionally may be able to treat the advantage of the free electron gas model. Some free electrons are trapped near the track of this incident ion and form plasma. The results obtained here show that this plasma plays a role of bringing about higher radial doses with increasing impact ionization cross sections of incident ions.

  16. Fully numerical soluti ons of molecular Dirac equations for highly charged one-electron homonuclear diatomic molecules

    NASA Astrophysics Data System (ADS)

    Sundholm, Dage

    1994-07-01

    The two-centre four-component Dirac equations for the homonuclear one-electron systems H 2+, Ne 219+, Ca 239+, Zn 259+, Zr 279+, Sn 299+, Nd 2119+, Yb 2139+, Hg 2159+, Th 2179+, and Fm 2199+ are solved numerically by a finite-difference approach. Accurate values for the non-relativistic and relativistic orbital energies are given as benchmarks for these molecules. The assumed bond lengths are 2/ Z au where Z is the nuclear charge. For the lowest ? g orbital of the Th 2179+ molecule, the orbital energy is 14.6 au above the global basis-set result while for the lowest orbital of ? u symmetry the present orbital energy is 19.1 au below the global basis-set results. The relativistic corrections to the quadrupole moment of the ? g orbital are given.

  17. Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region

    SciTech Connect

    Perry, D.S.

    1993-12-01

    Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion o