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Sample records for molecule icam-4 potential

  1. Novel secreted isoform of adhesion molecule ICAM-4: Potential regulator of membrane-associated ICAM-4 interactions

    SciTech Connect

    Lee, Gloria; Spring, Frances A.; Parons, Stephen F.; Mankelow, Tosti J.; Peters, Luanne L.; Koury, Mark J.; Mohandas, Narla; Anstee, David J.; Chasis, Joel Anne

    2003-02-18

    ICAM-4, a newly characterized adhesion molecule, is expressed early in human erythropoiesis and functions as a ligand for binding a4b1 and aV integrin-expressing cells. Within the bone marrow, erythroblasts surround central macrophages forming erythroblastic islands. Evidence suggests that these islands are highly specialized subcompartments where cell adhesion events, in concert with cytokines, play critical roles in regulating erythropoiesis and apoptosis. Since erythroblasts express a4b1 and ICAM-4 and macrophages exhibit aV, ICAM-4 is an attractive candidate for mediating cellular interactions within erythroblastic islands. To determine whether ICAM-4 binding properties are conserved across species, we first cloned and sequenced the murine homologue. The translated amino acid sequence showed 68 percent overall identity with human ICAM-4. Using recombinant murine ICAM-4 extracellular domains, we discovered that hematopoietic a4b1-expressing HEL cells and non-hematopoietic aV-expressing FLY cells adhered to mouse ICAM-4. Cell adhesion studies showed that FLY and HEL cells bound to mouse and human proteins with similar avidity. These data strongly suggest conservation of integrin-binding properties across species. Importantly, we characterized a novel second splice cDNA that would be predicted to encode an ICAM-4 isoform, lacking the membrane-spanning domain. Erythroblasts express both isoforms of ICAM-4. COS-7 cells transfected with GFP constructs of prototypic or novel ICAM-4 cDNA showed different cellular localization patterns. Moreover, analysis of tissue culture medium revealed that the novel ICAM-4 cDNA encodes a secreted protein. We postulate that secretion of this newly described isoform, ICAM-4S, may modulate binding of membrane-associated ICAM-4 and could thus play a critical regulatory role in erythroblast molecular attachments.

  2. Targeted Gene Deletion Demonstrates that Cell Adhesion MoleculeICAM-4 is Critical for Erythroblastic Island Formation

    SciTech Connect

    Lee, Gloria; Lo, Annie; Short, Sarah A.; Mankelow, Tosti J.; Spring, Frances; Parsons, Stephen F.; Mohandas, Narla; Anstee, David J.; Chasis, Joel Anne

    2006-02-15

    Erythroid progenitors differentiate in erythroblastic islands, bone marrow niches composed of erythroblasts surrounding a central macrophage. Evidence suggests that within islands adhesive interactions regulate erythropoiesis and apoptosis. We are exploring whether erythroid intercellular adhesion molecule-4 (ICAM-4), animmunoglobulin superfamily member, participates in island formation. Earlier, we identified alpha V integrins as ICAM-4 counter receptors. Since macrophages express alpha V, ICAM-4 potentially mediates island attachments. To test this, we generated ICAM-4 knockout mice and developed quantitative, live cell techniques for harvesting intact islands and for reforming islands in vitro. We observed a 47 percent decrease in islands reconstituted from ICAM-4 null marrow compared to wild type. We also found a striking decrease in islands formed in vivo in knockout mice. Further, peptides that block ICAM-4 alpha V adhesion produced a 53-57 percent decrease in reconstituted islands, strongly suggesting that ICAM-4 binding to macrophage alpha V functions in island integrity. Importantly, we documented that alpha V integrin is expressed in macrophages isolated from erythro blastic islands. Collectively, these data provide convincing evidence that ICAM-4 is critical in erythroblastic island formation via ICAM-4/alpha V adhesion and also demonstrate that the novel experimental strategies we developed will be valuable in exploring molecular mechanisms of erythroblastic island formation and their functional role in regulating erythropoiesis.

  3. Peptides based on alphaV-binding domains of erythrocyte ICAM-4 inhibit sickle red cell-endothelial interactions and vaso-occlusion in the microcirculation.

    PubMed

    Kaul, Dhananjay K; Liu, Xiao-du; Zhang, Xiaoqin; Mankelow, Tosti; Parsons, Stephen; Spring, Frances; An, Xiuli; Mohandas, Narla; Anstee, David; Chasis, Joel Anne

    2006-11-01

    Growing evidence shows that adhesion molecules on sickle erythrocytes interact with vascular endothelium leading to vaso-occlusion. Erythrocyte intercellular adhesion molecule-4 (ICAM-4) binds alphaV-integrins, including alphaVbeta3 on endothelial cells. To explore the contribution of ICAM-4 to vascular pathology of sickle cell disease, we tested the effects of synthetic peptides, V(16)PFWVRMS (FWV) and T(91)RWATSRI (ATSR), based on alphaV-binding domains of ICAM-4 and capable of inhibiting ICAM-4 and alphaV-binding in vitro. For these studies, we utilized an established ex vivo microvascular model system that enables intravital microscopy and quantitation of adhesion under shear flow. In this model, the use of platelet-activating factor, which causes endothelial oxidant generation and endothelial activation, mimicked physiological states known to occur in sickle cell disease. Infusion of sickle erythrocytes into platelet-activating factor-treated ex vivo rat mesocecum vasculature produced pronounced adhesion of erythrocytes; small-diameter venules were sites of maximal adhesion and frequent blockage. Both FWV and ATSR peptides markedly decreased adhesion, and no vessel blockage was observed with either of the peptides, resulting in improved hemodynamics. ATSR also inhibited adhesion in unactivated microvasculature. Although infused fluoresceinated ATSR colocalized with vascular endothelium, pretreatment with function-blocking antibody to alphaVbeta3-integrin markedly inhibited this interaction. Our data strengthen the thesis that ICAM-4 on sickle erythrocytes binds endothelium via alphaVbeta3 and that this interaction contributes to vaso-occlusion. Thus peptides or small molecule mimetics of ICAM-4 may have therapeutic potential.

  4. Variation in the ICAM1–ICAM4–ICAM5 locus is associated with systemic lupus erythematosus susceptibility in multiple ancestries

    PubMed Central

    Kim, Kwangwoo; Brown, Elizabeth E; Choi, Chan-Bum; Alarcón-Riquelme, Marta E; Kelly, Jennifer A; Glenn, Stuart B; Ojwang, Joshua O; Adler, Adam; Lee, Hye-Soon; Boackle, Susan A; Criswell, Lindsey A; Alarcón, Graciela S; Edberg, Jeffrey C; Stevens, Anne M; Jacob, Chaim O; Gilkeson, Gary S; Kamen, Diane L; Tsao, Betty P; Anaya, Juan-Manuel; Guthridge, Joel M; Nath, Swapan K; Richardson, Bruce; Sawalha, Amr H; Kang, Young Mo; Shim, Seung Cheol; Suh, Chang-Hee; Lee, Soo-Kon; Kim, Chang-sik; Merrill, Joan T; Petri, Michelle; Ramsey-Goldman, Rosalind; Vilá, Luis M; Niewold, Timothy B; Martin, Javier; Pons-Estel, Bernardo A; Vyse, Timothy J; Freedman, Barry I; Moser, Kathy L; Gaffney, Patrick M; Williams, Adrienne; Comeau, Mary; Reveille, John D; James, Judith A; Scofield, R Hal; Langefeld, Carl D; Kaufman, Kenneth M; Harley, John B; Kang, Changwon; Kimberly, Robert P; Bae, Sang-Cheol

    2012-01-01

    Objective Systemic lupus erythematosus (SLE; OMIM 152700) is a chronic autoimmune disease for which the aetiology includes genetic and environmental factors. ITGAM, integrin αΜ (complement component 3 receptor 3 subunit) encoding a ligand for intracellular adhesion molecule (ICAM) proteins, is an established SLE susceptibility locus. This study aimed to evaluate the independent and joint effects of genetic variations in the genes that encode ITGAM and ICAM. Methods The authors examined several markers in the ICAM1–ICAM4–ICAM5 locus on chromosome 19p13 and the single ITGAM polymorphism (rs1143679) using a large-scale case–control study of 17 481 unrelated participants from four ancestry populations. The single marker association and gene–gene interaction were analysed for each ancestry, and a meta-analysis across the four ancestries was performed. Results The A-allele of ICAM1–ICAM4–ICAM5 rs3093030, associated with elevated plasma levels of soluble ICAM1, and the A-allele of ITGAM rs1143679 showed the strongest association with increased SLE susceptibility in each of the ancestry populations and the trans-ancestry meta-analysis (ORmeta=1.16, 95% CI 1.11 to 1.22; p=4.88×10−10 and ORmeta=1.67, 95% CI 1.55 to 1.79; p=3.32×10−46, respectively). The effect of the ICAM single-nucleotide polymorphisms (SNPs) was independent of the effect of the ITGAM SNP rs1143679, and carriers of both ICAM rs3093030-AA and ITGAM rs1143679-AA had an OR of 4.08 compared with those with no risk allele in either SNP (95% CI 2.09 to 7.98; p=3.91×10−5). Conclusion These findings are the first to suggest that an ICAM–integrin-mediated pathway contributes to susceptibility to SLE. PMID:22523428

  5. Fixman compensating potential for general branched molecules

    NASA Astrophysics Data System (ADS)

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-12-01

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

  6. Fixman compensating potential for general branched molecules

    PubMed Central

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-01-01

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules. PMID:24387353

  7. Fixman compensating potential for general branched molecules

    SciTech Connect

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-12-28

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

  8. Potential energy landscapes of tetragonal pyramid molecules

    NASA Astrophysics Data System (ADS)

    Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.

    2016-11-01

    Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.

  9. Adsorbed molecules in external fields: Effect of confining potential

    NASA Astrophysics Data System (ADS)

    Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

    2016-12-01

    We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials.

  10. Adsorbed molecules in external fields: Effect of confining potential.

    PubMed

    Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

    2016-12-05

    We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials.

  11. Optical Stark decelerator for molecules with a traveling potential well

    NASA Astrophysics Data System (ADS)

    Deng, Lianzhong; Hou, Shunyong; Yin, Jianping

    2017-03-01

    We propose a versatile scheme to slow supersonically cooled molecules using a decelerating potential well, obtained by steering a focusing laser beam onto a pair of spinning reflective mirrors under a high-speed brake. The longitudinal motion of molecules in the moving red-detuned light field is analyzed and their corresponding phase-space stability is investigated. Trajectories of C H4 molecules under the influence of the potential well are simulated using the Monte Carlo method. For instance, with a laser beam of power 20 kW focused onto a spot of waist radius 40-100 μm, corresponding to a peak laser intensity on the order of ˜108W /c m2 , a C H4 molecule of ˜250 m /s can be decelerated to ˜10 m /s over a distance of a few centimeters on a time scale of hundreds of microseconds.

  12. General van der Waals potential for common organic molecules.

    PubMed

    Qi, Rui; Wang, Qiantao; Ren, Pengyu

    2016-10-15

    This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman-Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.

  13. NMR studies of electrostatic potential distribution around biologically important molecules.

    PubMed Central

    Likhtenshtein, G I; Adin, I; Novoselsky, A; Shames, A; Vaisbuch, I; Glaser, R

    1999-01-01

    A new experimental approach has been developed to study the distribution of local electrostatic potential around specific protons in biologically important molecules. The approach is the development of a method denoted as "spin label/spin probe," which was proposed by one of us (. Mol. Biol. 6:498-507). The proposed method is based upon the quantitative measurement of the contribution of differently charged nitroxide probes to the spin lattice relaxation rate (1/T1) of protons in the molecule of interest, followed by calculation of local electrostatic potential using the classical Debye equation. In parallel, the theoretical calculation of potential distribution with the use of the MacSpartan Plus 1.0 program has been performed. Application of the method to solutions of simple organic molecules (aliphatic and aromatic alcohols, aliphatic carboxylates (propionate anion), and protonated ethyl amine and imidazole) allowed us to estimate the effective potential around the molecules under investigation. These were found to be in good agreement with theoretically expected values. This technique was then applied to zwitterionic amino acids bearing neutral and charged side chains (glycine, lysine, histidine, and aspartic acid). The reliability of the general approach is proved by the data presented in this paper. Application of this new methodology can afford insight into the biochemical significance of electrostatic effects in biological systems. PMID:10388770

  14. Electronic structure of molecules using relativistic effective core potentials

    SciTech Connect

    Hay, P.J.

    1981-01-01

    Starting with one-component Cowan-Griffin relativistic Hartree-Fock orbitals, which successfully incorporate the mass-velocity and Darwin terms present in more complicated wavefunctions such as Dirac-Hartree-Fock, one can derive relativistic effective core potentials (RECP's) to carry out molecular calculations. These potentials implicitly include the dominant relativistic terms for molecules while allowing one to use the traditional quantum chemical techniques for studying the electronic structure of molecules. The effects of spin-orbit coupling can then be included using orbitals from such calculations using an effective 1-electron, 1-center spin-orbit operator. Applications to molecular systems involving heavy atoms, show good agreement with available spectroscopic data on molecular geometries and excitation energies.

  15. Angle-resolved effective potentials for disk-shaped molecules

    SciTech Connect

    Heinemann, Thomas Klapp, Sabine H. L.; Palczynski, Karol Dzubiella, Joachim

    2014-12-07

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

  16. Angle-resolved effective potentials for disk-shaped molecules.

    PubMed

    Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

    2014-12-07

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

  17. Angle-resolved effective potentials for disk-shaped molecules

    NASA Astrophysics Data System (ADS)

    Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

    2014-12-01

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

  18. A transferable classical potential for the water molecule.

    PubMed

    Baranyai, András; Kiss, Péter T

    2010-10-14

    We developed a new model for the water molecule which contains only three Gaussian charges. Using the gas-phase geometry the dipole moment of the molecule matches, the quadrupole moment closely approximates the experimental values. The negative charge is connected by a harmonic spring to its gas-phase position. The polarized state is identified by the equality of the intermolecular electrostatic force and the spring force acting on the negative charge. In each timestep the instantaneous position of the massless negative charge is determined by iteration. Using the technique of Ewald summation, we derived expressions for the potential energy, the forces, and the pressure for Gaussian charges. The only properties to be fitted are the half-width values of the Gaussian charge distributions and the parameters of the nonelectrostatic repulsion-attraction potential. We determined the properties of gas-phase clusters up to six molecules, the internal energy and density of ambient water and hexagonal ice. We calculated the equilibrium density of ice VII as a function of pressure. As an additional test, we calculated the pair-correlation function, the isotherm compressibility, the heat capacity, and the self-diffusion coefficients for ambient water. As far as we know, this is the first classical model of water which is able to estimate both ends of the phase diagram, the high pressure ice VII, and the gas clusters of water with excellent accuracy.

  19. Chemical potential and dimensions of chain molecules in athermal environments

    NASA Astrophysics Data System (ADS)

    Escobedo, Fernando A.

    A recently developed method for the simulation of chemical potentials of chain molecules (EVALENCH) is applied here to obtain the chemical potential, the mean square end-to-end distance (R2n) and the mean square radius of gyration (R2g) of dilute chains in different athermal media. The environments considered in this work are a frozen network structure, a deformable network matrix and a monomeric solvent at various densities. The properties of all chain lengths smaller than a preset maximum are calculated in a single simulation. A novel method is also presented for locating and computing the fraction of sampling space available to append one segment of an existing chain. This method enhances the range of densities where simulations of chemical potential are feasible. Simulated chemical potentials are compared with the predictions of two theories; good agreement is found in both cases. We find that R2n and R2g are reduced as the density of the medium is increased (network or solvent), while they are increased when the network is frozen and as the monomeric solvent size is made larger than that of the chain sites. At the conditions studied here, no direct evidence of chain collapse is observed.

  20. First-in-class small molecule potentiators of cancer virotherapy

    PubMed Central

    Dornan, Mark H.; Krishnan, Ramya; Macklin, Andrew M.; Selman, Mohammed; El Sayes, Nader; Son, Hwan Hee; Davis, Colin; Chen, Andrew; Keillor, Kerkeslin; Le, Penny J.; Moi, Christina; Ou, Paula; Pardin, Christophe; Canez, Carlos R.; Le Boeuf, Fabrice; Bell, John C.; Smith, Jeffrey C.; Diallo, Jean-Simon; Boddy, Christopher N.

    2016-01-01

    The use of engineered viral strains such as gene therapy vectors and oncolytic viruses (OV) to selectively destroy cancer cells is poised to make a major impact in the clinic and revolutionize cancer therapy. In particular, several studies have shown that OV therapy is safe and well tolerated in humans and can infect a broad range of cancers. Yet in clinical studies OV therapy has highly variable response rates. The heterogeneous nature of tumors is widely accepted to be a major obstacle for OV therapeutics and highlights a need for strategies to improve viral replication efficacy. Here, we describe the development of a new class of small molecules for selectively enhancing OV replication in cancer tissue. Medicinal chemistry studies led to the identification of compounds that enhance multiple OVs and gene therapy vectors. Lead compounds increase OV growth up to 2000-fold in vitro and demonstrate remarkable selectivity for cancer cells over normal tissue ex vivo and in vivo. These small molecules also demonstrate enhanced stability with reduced electrophilicity and are highly tolerated in animals. This pharmacoviral approach expands the scope of OVs to include resistant tumors, further potentiating this transformative therapy. It is easily foreseeable that this approach can be applied to therapeutically enhance other attenuated viral vectors. PMID:27226390

  1. SOCS: potential immune checkpoint molecules for cancer immunotherapy.

    PubMed

    Chikuma, Shunsuke; Kanamori, Mitsuhiro; Mise-Omata, Setsuko; Yoshimura, Akihiko

    2017-02-11

    Inhibition of immune checkpoint molecules, PD-1 and CTLA4, has been shown to be a promising cancer treatment. PD-1 and CTLA4 inhibit TCR and co-stimulatory signals, respectively. The third T cell activation signal represents the signals from the cytokine receptors. The cytokine Interferon-γ (IFNγ) plays an important role in anti-tumor immunity by activating cytotoxic T cells (CTLs). Most cytokines use the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, and the suppressors of cytokine signaling (SOCS) family of proteins are major negative regulators of the JAK/STAT pathway. Among SOCS proteins, CIS, SOCS1, and SOCS3 proteins can be considered the third immunocheckpoint molecules since they regulate cytokine signals that control the polarization of CD4(+) T cells and the maturation of CD8(+) T cells. This review summarizes recent progress on CIS, SOCS1, and SOCS3 in terms of their anti-tumor immunity and potential applications. This article is protected by copyright. All rights reserved.

  2. Carbohydrate-containing molecules as potential biomarkers in colon cancer.

    PubMed

    Joo, Eun Ji; Weyers, Amanda; Li, Guoyun; Gasimli, Leyla; Li, Lingyun; Choi, Won Jun; Lee, Kyung Bok; Linhardt, Robert J

    2014-04-01

    Glycans play a critical role in physiological and pathological processes through interaction with a variety of ligands. Altered expression and dysregulation of these molecules can cause aberrant cellular function such as malignancy. Glycomics provide information of the structure and function of glycans, glycolipids, and glycoproteins such as proteoglycans, and may help to predict cancer development and progression as biomarkers. In this report, we compared the expression of proteoglycans, the content and structure of glycosaminoglycans and glycolipids between patient-matched normal and cancer tissues obtained from colon cancer patients. Tumor-related proteoglycans, glypican-3, and syndecan-1 showed downregulation in cancer tissues compared to normal tissues. In cancer tissue, the total amount of chondroitin sulfate (CS)/dermatan sulfate and heparan sulfate were lower and, interestingly, the level of disaccharide units of both 4S6S (CS-E) and 6S (CS-C) were higher compared to normal tissue. Also, overall lipids including glycolipids, a major glycomics target, were analyzed by hydrophilic interaction liquid chromatography mass spectrometry. Increase of lyso-phosphatidylcholine (phospholipid), sphingomyelin (sphigolipid), and four types of glycolipids (glucosylceramide, lactosylceramide, monosialic acid ganglioside, and globoside 4) in cancer tissue showed the possibility as potential biomarkers in colon cancer. While requiring the need for careful interpretation, this type of broad investigation gives us a better understanding of pathophysiological roles on glycosaminoglycans and glycolipids and might be a powerful tool for colon cancer diagnosis.

  3. Carbohydrate-Containing Molecules as Potential Biomarkers in Colon Cancer

    PubMed Central

    Joo, Eun Ji; Weyers, Amanda; Li, Guoyun; Gasimli, Leyla; Li, Lingyun; Choi, Won Jun

    2014-01-01

    Abstract Glycans play a critical role in physiological and pathological processes through interaction with a variety of ligands. Altered expression and dysregulation of these molecules can cause aberrant cellular function such as malignancy. Glycomics provide information of the structure and function of glycans, glycolipids, and glycoproteins such as proteoglycans, and may help to predict cancer development and progression as biomarkers. In this report, we compared the expression of proteoglycans, the content and structure of glycosaminoglycans and glycolipids between patient-matched normal and cancer tissues obtained from colon cancer patients. Tumor-related proteoglycans, glypican-3, and syndecan-1 showed downregulation in cancer tissues compared to normal tissues. In cancer tissue, the total amount of chondroitin sulfate (CS)/dermatan sulfate and heparan sulfate were lower and, interestingly, the level of disaccharide units of both 4S6S (CS-E) and 6S (CS-C) were higher compared to normal tissue. Also, overall lipids including glycolipids, a major glycomics target, were analyzed by hydrophilic interaction liquid chromatography mass spectrometry. Increase of lyso-phosphatidylcholine (phospholipid), sphingomyelin (sphigolipid), and four types of glycolipids (glucosylceramide, lactosylceramide, monosialic acid ganglioside, and globoside 4) in cancer tissue showed the possibility as potential biomarkers in colon cancer. While requiring the need for careful interpretation, this type of broad investigation gives us a better understanding of pathophysiological roles on glycosaminoglycans and glycolipids and might be a powerful tool for colon cancer diagnosis. PMID:24502776

  4. Up and away in the potential landscape of diatomic molecule potential energy curves

    NASA Astrophysics Data System (ADS)

    Stwalley, William C.

    2016-12-01

    The understanding of the potential curves of a given molecule has expanded in many ways during my last 52 years as an experimental and theoretical molecular chemist/physicist in graduate school in Chemistry at Harvard and in both the Chemistry and Physics Departments at University of Iowa and University of Connecticut. This expansion has been up in energy and vibrational and rotational quantum numbers and away from Re to long range as well. It is clear that Prof. Robert Le Roy, who I have known since the late 1960s, has made many important and greatly appreciated contributions to the landscape I describe below from my personal perspective, especially with regard to long range molecules and solution of the radial Schrödinger equations and related calculations.

  5. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Grimes, David D.; Zhou, Yan; Field, Robert W.; Wong, Bryan M.

    2016-12-01

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r4. We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF+ and HF showing the

  6. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states.

    PubMed

    Coy, Stephen L; Grimes, David D; Zhou, Yan; Field, Robert W; Wong, Bryan M

    2016-12-21

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r(4). We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF(+) and HF showing the

  7. Integrated Computational Solution for Predicting Skin Sensitization Potential of Molecules

    PubMed Central

    Desai, Aarti; Singh, Vivek K.; Jere, Abhay

    2016-01-01

    Introduction Skin sensitization forms a major toxicological endpoint for dermatology and cosmetic products. Recent ban on animal testing for cosmetics demands for alternative methods. We developed an integrated computational solution (SkinSense) that offers a robust solution and addresses the limitations of existing computational tools i.e. high false positive rate and/or limited coverage. Results The key components of our solution include: QSAR models selected from a combinatorial set, similarity information and literature-derived sub-structure patterns of known skin protein reactive groups. Its prediction performance on a challenge set of molecules showed accuracy = 75.32%, CCR = 74.36%, sensitivity = 70.00% and specificity = 78.72%, which is better than several existing tools including VEGA (accuracy = 45.00% and CCR = 54.17% with ‘High’ reliability scoring), DEREK (accuracy = 72.73% and CCR = 71.44%) and TOPKAT (accuracy = 60.00% and CCR = 61.67%). Although, TIMES-SS showed higher predictive power (accuracy = 90.00% and CCR = 92.86%), the coverage was very low (only 10 out of 77 molecules were predicted reliably). Conclusions Owing to improved prediction performance and coverage, our solution can serve as a useful expert system towards Integrated Approaches to Testing and Assessment for skin sensitization. It would be invaluable to cosmetic/ dermatology industry for pre-screening their molecules, and reducing time, cost and animal testing. PMID:27271321

  8. Temperature independent spherical potential which reproduces exactly the second virial coefficient of nonpolar molecules

    SciTech Connect

    Shaw, M.S.; Johnson, J.D.

    1984-10-01

    An expression is derived for a temperature independent spherical potential which reproduces exactly the second virial coefficient for nonpolar molecules given the full anisotropic potential. Comparison is made with the median average over angles and the arithmetic average.

  9. On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules.

    PubMed

    Bhattacharjee, Rituparna; Roy, Ram Kinkar

    2014-10-28

    In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.

  10. Novel small molecules potentiate premature termination codon readthrough by aminoglycosides

    PubMed Central

    Baradaran-Heravi, Alireza; Balgi, Aruna D.; Zimmerman, Carla; Choi, Kunho; Shidmoossavee, Fahimeh S.; Tan, Jason S.; Bergeaud, Célia; Krause, Alexandra; Flibotte, Stéphane; Shimizu, Yoko; Anderson, Hilary J.; Mouly, Vincent; Jan, Eric; Pfeifer, Tom; Jaquith, James B.; Roberge, Michel

    2016-01-01

    Nonsense mutations introduce premature termination codons and underlie 11% of genetic disease cases. High concentrations of aminoglycosides can restore gene function by eliciting premature termination codon readthrough but with low efficiency. Using a high-throughput screen, we identified compounds that potentiate readthrough by aminoglycosides at multiple nonsense alleles in yeast. Chemical optimization generated phthalimide derivative CDX5-1 with activity in human cells. Alone, CDX5-1 did not induce readthrough or increase TP53 mRNA levels in HDQ-P1 cancer cells with a homozygous TP53 nonsense mutation. However, in combination with aminoglycoside G418, it enhanced readthrough up to 180-fold over G418 alone. The combination also increased readthrough at all three nonsense codons in cancer cells with other TP53 nonsense mutations, as well as in cells from rare genetic disease patients with nonsense mutations in the CLN2, SMARCAL1 and DMD genes. These findings open up the possibility of treating patients across a spectrum of genetic diseases caused by nonsense mutations. PMID:27407112

  11. Effect of an improved molecular potential on strong-field tunneling ionization of molecules

    SciTech Connect

    Zhao Songfeng; Jin Cheng; Le, Anh-Thu; Lin, C. D.

    2010-09-15

    We study the effect of one-electron model potentials on the tunneling ionization rates of molecules in strong fields. By including electron correlation using the modified Leeuwen-Baerends (LB {alpha}) model, the binding energies of outer shells of molecules are significantly improved. However, we show that the tunneling ionization rates from the LB {alpha} do not differ much from the earlier calculations [Phys. Rev. A 81, 033423 (2010)], in which the local correlation potential was neglected.

  12. Astrophysical molecules of A1H and CaH - RKR potential and dissociation energies

    NASA Astrophysics Data System (ADS)

    Narasimhamurthy, B.; Rajamanickam, N.

    1983-03-01

    The true potential energy curves for the electronic ground states of astrophysically important AlH and CaH molecules are constructed by the Rydberg-Klein-Rees method. Empirical potential functions, of three-parameters by Lippincott, of five-parameters by Hulburt and Hirschfelder and, of electronegativity by Szöke and Baitz, are examined for the adequacy to represent the true curve. From the best-fitting function, the dissociation energies D00 of AlH and CaH molecules are estimated to be 2.99±0.08 and 2.72±0.06 eV respectively.

  13. The complex susceptibility of a two-potential system of reorientating polar molecules

    NASA Astrophysics Data System (ADS)

    Gaiduk, Vladimir I.; Tseitlin, Boris M.; Gaiduk, Vladimir V.; McConnell, James

    1994-04-01

    The problem of accounting for the finiteness of collision times is elaborated from the viewpoint that the steady state law of motion of a dipolar particle is governed by two potentials. These describe the torque exerted on a given molecule by neighbouring particles. In liquids different classical laws of motion correspond to different potentials. We may consider that in a gaseous state one of the two potential functions U(ϑ) does not depend on the orientational angle of the rotor. In this case the usual quantum (equidistant) rotational spectrum of polar molecules results. Then the other potential, acting when gas particles are close one with another, may be introduced to describe classically the influence of collisions on the above discrete spectrum. The new approach employs fewer parameters of the molecular model than previously in the study of the two-potential state, since the number of particles in either state is expressed through lifetimes τ 1, τ 2 in the two states. Due to the mutual interference of the two potential states there occurs in a classical ensemble of molecules the sharpening of the frequency dependence of the absorption coefficient. The dielectric spectra at lower frequencies also change.

  14. Dynamical Green's function and an exact optical potential for electron-molecule scattering including nuclear dynamics

    NASA Astrophysics Data System (ADS)

    Brand, Joachim; Cederbaum, Lorenz S.; Meyer, Hans-Dieter

    1999-10-01

    We derive a rigorous optical potential for electron-molecule scattering including the effects of nuclear dynamics by extending the common many-body Green's function approach to optical potentials beyond the fixed-nuclei limit for molecular targets. Our formalism treats the projectile electron and the nuclear motion of the target molecule on the same footing whereby the dynamical optical potential rigorously accounts for the complex many-body nature of the scattering target. One central result of the present work is that the common fixed-nuclei optical potential is a valid adiabatic approximation to the dynamical optical potential even when projectile and nuclear motion are (nonadiabatically) coupled as long as the scattering energy is well below the electronic excitation thresholds of the target. For extremely low projectile velocities, however, when the cross sections are most sensitive to the scattering potential, we expect the influences of the nuclear dynamics on the optical potential to become relevant. For these cases, a systematic way to improve the adiabatic approximation to the dynamical optical potential is presented that yields nonlocal operators with respect to the nuclear coordinates.

  15. Non-additivity of molecule-surface van der Waals potentials from force measurements

    PubMed Central

    Wagner, Christian; Fournier, Norman; Ruiz, Victor G.; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F. Stefan

    2014-01-01

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction. PMID:25424490

  16. Therapeutic potential of abalone and status of bioactive molecules: A comprehensive review.

    PubMed

    Suleria, H A R; Masci, P P; Gobe, G C; Osborne, S A

    2017-05-24

    Marine organisms are increasingly being investigated as sources of bioactive molecules with therapeutic applications as nutraceuticals and pharmaceuticals. In particular, nutraceuticals are gaining popularity worldwide owing to their therapeutic potential and incorporation in functional foods and dietary supplements. Abalone, a marine gastropod, contains a variety of bioactive compounds with anti-oxidant, anti-thrombotic, anti-inflammatory, anti-microbial, and anti-cancer activities. For thousands of years different cultures have used abalone as a traditional functional food believing consumption provides health benefits. Abalone meat is one of the most precious commodities in Asian markets where it is considered a culinary delicacy. Recent research has revealed that abalone is composed of many vital moieties like polysaccharides, proteins, and fatty acids that provide health benefits beyond basic nutrition. A review of past and present research is presented with relevance to the therapeutic potential of bioactive molecules from abalone.

  17. Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule

    SciTech Connect

    Párraga, H.; Arranz, F. J. Benito, R. M.; Borondo, F.

    2013-11-21

    An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

  18. A Structure Based Model for the Prediction of Phospholipidosis Induction Potential of Small Molecules

    PubMed Central

    Sun, Hongmao; Shahane, Sampada; Xia, Menghang; Austin, Christopher P.; Huang, Ruili

    2012-01-01

    Drug-induced phospholipidosis (PLD), characterized by an intracellular accumulation of phospholipids and formation of concentric lamellar bodies, has raised concerns in the drug discovery community, due to its potential adverse effects. To evaluate the PLD induction potential, 4,161 non-redundant drug-like molecules from the National Institutes of Health Chemical Genomics Center (NCGC) Pharmaceutical Collection (NPC), the Library of Pharmacologically Active Compounds (LOPAC) and the Tocris Biosciences collection were screened in a quantitative high-throughput screening (qHTS) format. The potential of drug-lipid complex formation can be linked directly to the structures of drug molecules, and many PLD inducing drugs were found to share common structural features. Support vector machine (SVM) models were constructed by using customized atom types or Molecular Operating Environment (MOE) 2D descriptors as structural descriptors. Either the compounds from LOPAC or randomly selected from the entire dataset were used as the training set. The impact of training data with biased structural features and the impact of molecule descriptors emphasizing whole-molecule properties or detailed functional groups at the atom level on model performance were analyzed and discussed. Rebalancing strategies were applied to improve the predictive power of the SVM models. Using the under-sampling method, the consensus model using one third of the compounds randomly selected from the data set as the training set achieved high accuracy of 0.90 in predicting the remaining two thirds of the compounds constituting the test set, as measured by the area under the receiver operator characteristic curve (AUC-ROC). PMID:22725677

  19. Psmir: a database of potential associations between small molecules and miRNAs.

    PubMed

    Meng, Fanlin; Wang, Jing; Dai, Enyu; Yang, Feng; Chen, Xiaowen; Wang, Shuyuan; Yu, Xuexin; Liu, Dianming; Jiang, Wei

    2016-01-13

    miRNAs are key post-transcriptional regulators of many essential biological processes, and their dysregulation has been validated in almost all human cancers. Restoring aberrantly expressed miRNAs might be a novel therapeutics. Recently, many studies have demonstrated that small molecular compounds can affect miRNA expression. Thus, prediction of associations between small molecules and miRNAs is important for investigation of miRNA-targeted drugs. Here, we analyzed 39 miRNA-perturbed gene expression profiles, and then calculated the similarity of transcription responses between miRNA perturbation and drug treatment to predict drug-miRNA associations. At the significance level of 0.05, we obtained 6501 candidate associations between 1295 small molecules and 25 miRNAs, which included 624 FDA approved drugs. Finally, we constructed the Psmir database to store all potential associations and the related materials. In a word, Psmir served as a valuable resource for dissecting the biological significance in small molecules' effects on miRNA expression, which will facilitate developing novel potential therapeutic targets or treatments for human cancers. Psmir is supported by all major browsers, and is freely available at http://www.bio-bigdata.com/Psmir/.

  20. The dispersion interaction between quantum mechanics and effective fragment potential molecules

    SciTech Connect

    Smith, Quentin A.; Ruedenberg, Klaus; Gordon, Mark S.; Slipchenko, Lyudmila

    2012-06-26

    A method for calculating the dispersion energy between molecules modeled with the general effective fragment potential (EFP2) method and those modeled using a full quantum mechanics (QM) method, e.g., Hartree-Fock (HF) or second-order perturbation theory, is presented. C6 dispersion coefficients are calculated for pairs of orbitals using dynamic polarizabilities from the EFP2 portion, and dipole integrals and orbital energies from the QM portion of the system. Dividing by the sixth power of the distance between localized molecular orbital centroids yields the first term in the commonly employed London series expansion. A C8 term is estimated from the C6 term to achieve closer agreement with symmetry adapted perturbation theory values. Two damping functions for the dispersion energy are evaluated. By using terms that are already computed during an ordinary HF or EFP2 calculation, the new method enables accurate and extremely rapid evaluation of the dispersion interaction between EFP2 and QM molecules.

  1. Early-Late Heterobimetallic Complexes Linked by Phosphinoamide Ligands. Tuning Redox Potentials and Small Molecule Activation

    SciTech Connect

    Thomas, Christine M.

    2015-08-01

    Recent attention in the chemical community has been focused on the energy efficient and environmentally benign conversion of abundant small molecules (CO2, H2O, etc.) to useful liquid fuels. This project addresses these goals by examining fundamental aspects of catalyst design to ultimately access small molecule activation processes under mild conditions. Specifically, Thomas and coworkers have targetted heterobimetallic complexes that feature metal centers with vastly different electronic properties, dictated both by their respective positions on the periodic table and their coordination environment. Unlike homobimetallic complexes featuring identical or similar metals, the bonds between metals in early/late heterobimetallics are more polarized, with the more electron-rich late metal center donating electron density to the more electron-deficient early metal center. While metal-metal bonds pose an interesting strategy for storing redox equivalents and stabilizing reactive metal fragments, the polar character of metal-metal bonds in heterobimetallic complexes renders these molecules ideally poised to react with small molecule substrates via cleavage of energy-rich single and double bonds. In addition, metal-metal interactions have been shown to dramatically affect redox potentials and promote multielectron redox activity, suggesting that metal-metal interactions may provide a mechanism to tune redox potentials and access substrate reduction/activation at mild overpotentials. This research project has provided a better fundamental understanding of how interactions between transition metals can be used as a strategy to promote and/or control chemical transformations related to the clean production of fuels. While this project focused on the study of homogeneous systems, it is anticipated that the broad conclusions drawn from these investigations will be applicable to heterogeneous catalysis as well, particularly on heterogeneous processes that occur at interfaces in

  2. Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules.

    PubMed

    White, Alec F; Head-Gordon, Martin; McCurdy, C William

    2017-01-28

    The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. We critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the Πg2 shape resonance of N2(-) which has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.

  3. Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules

    NASA Astrophysics Data System (ADS)

    White, Alec F.; Head-Gordon, Martin; McCurdy, C. William

    2017-01-01

    The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. We critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the Π2g shape resonance of N2- which has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.

  4. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  5. The role of endogenous molecules in modulating pain through transient receptor potential vanilloid 1 (TRPV1).

    PubMed

    Morales-Lázaro, Sara L; Simon, Sidney A; Rosenbaum, Tamara

    2013-07-01

    Pain is a physiological response to a noxious stimulus that decreases the quality of life of those sufferring from it. Research aimed at finding new therapeutic targets for the treatment of several maladies, including pain, has led to the discovery of numerous molecular regulators of ion channels in primary afferent nociceptive neurons. Among these receptors is TRPV1 (transient receptor potential vanilloid 1), a member of the TRP family of ion channels. TRPV1 is a calcium-permeable channel, which is activated or modulated by diverse exogenous noxious stimuli such as high temperatures, changes in pH, and irritant and pungent compounds, and by selected molecules released during tissue damage and inflammatory processes. During the last decade the number of endogenous regulators of TRPV1's activity has increased to include lipids that can negatively regulate TRPV1, as is the case for cholesterol and PIP2 (phosphatidylinositol 4,5-biphosphate) while, in contrast, other lipids produced in response to tissue injury and ischaemic processes are known to positively regulate TRPV1. Among the latter, lysophosphatidic acid activates TRPV1 while amines such as N-acyl-ethanolamines and N-acyl-dopamines can sensitize or directly activate TRPV1. It has also been found that nucleotides such as ATP act as mediators of chemically induced nociception and pain and gases, such as hydrogen sulphide and nitric oxide, lead to TRPV1 activation. Finally, the products of lipoxygenases and omega-3 fatty acids among other molecules, such as divalent cations, have also been shown to endogenously regulate TRPV1 activity. Here we provide a comprehensive review of endogenous small molecules that regulate the function of TRPV1. Acting through mechanisms that lead to sensitization and desensitization of TRPV1, these molecules regulate pathways involved in pain and nociception. Understanding how these compounds modify TRPV1 activity will allow us to comprehend how some pathologies are associated with

  6. Calculation of chemical potentials of chain molecules by the incremental gauge cell method.

    PubMed

    Rasmussen, Christopher J; Vishnyakov, Aleksey; Neimark, Alexander V

    2011-12-07

    The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.

  7. Calculation of chemical potentials of chain molecules by the incremental gauge cell method

    NASA Astrophysics Data System (ADS)

    Rasmussen, Christopher J.; Vishnyakov, Aleksey; Neimark, Alexander V.

    2011-12-01

    The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], 10.1103/PhysRevLett.66.2935, and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.

  8. Psmir: a database of potential associations between small molecules and miRNAs

    PubMed Central

    Meng, Fanlin; Wang, Jing; Dai, Enyu; Yang, Feng; Chen, Xiaowen; Wang, Shuyuan; Yu, Xuexin; Liu, Dianming; Jiang, Wei

    2016-01-01

    miRNAs are key post-transcriptional regulators of many essential biological processes, and their dysregulation has been validated in almost all human cancers. Restoring aberrantly expressed miRNAs might be a novel therapeutics. Recently, many studies have demonstrated that small molecular compounds can affect miRNA expression. Thus, prediction of associations between small molecules and miRNAs is important for investigation of miRNA-targeted drugs. Here, we analyzed 39 miRNA-perturbed gene expression profiles, and then calculated the similarity of transcription responses between miRNA perturbation and drug treatment to predict drug-miRNA associations. At the significance level of 0.05, we obtained 6501 candidate associations between 1295 small molecules and 25 miRNAs, which included 624 FDA approved drugs. Finally, we constructed the Psmir database to store all potential associations and the related materials. In a word, Psmir served as a valuable resource for dissecting the biological significance in small molecules’ effects on miRNA expression, which will facilitate developing novel potential therapeutic targets or treatments for human cancers. Psmir is supported by all major browsers, and is freely available at http://www.bio-bigdata.com/Psmir/. PMID:26759061

  9. Towards a List of Molecules as Potential Biosignature Gases for the Search for Life on Exoplanets

    NASA Astrophysics Data System (ADS)

    Seager, Sara; Bains, William; Petkowski, Janusz

    2015-12-01

    Thousands of exoplanets are known to orbit nearby stars. Plans for the next generation of space-based and ground-based telescopes are fueling the anticipation that a precious few habitable planets can be identified in the coming decade. Even more highly anticipated is the chance to find signs of life on these habitable planets by way of biosignature gases. But which gases should we search for? We expand on the search of possible biosignature gases and go beyond those studied so far, which include O2, O3, N2O, and CH4, as well as secondary metabolites: methanethiol (CH3SH), dimethyl sulfide ((CH3)2S), methyl chloride (CH3Cl), and carbonyl sulfide (CSO).We present the results of a project to map the chemical space of life’s metabolic products. We have constructed a systematic survey of all possible stable volatile molecules (up to N=6 non-H atoms), and identified those made by life on Earth. Some (such as methyl chloride) are made by Earth life in sufficiently substantial quantities to be candidate biosignatures in an Earth-like exoplanet’s atmosphere; some, such as stibine (SbH3), are produced only in trace amounts. Some entire categories of molecules are not made by Earth life (such as the silanes); these and other absences from the list of biogenic volatiles point to functional patterns in biochemical space. Such patterns may be different for different biochemistry, and so we cannot rule out any small, stable molecule as a candidate biosignature gas. Our goal is for the community to use the list to study the chemicals that might be potential biosignature gases on exoplanets with atmospheres and surface environments different from Earth’s.

  10. Multi-Functional Diarylurea Small Molecule Inhibitors of TRPV1 with Therapeutic Potential for Neuroinflammation.

    PubMed

    Feng, Zhiwei; Pearce, Larry V; Zhang, Yu; Xing, Changrui; Herold, Brienna K A; Ma, Shifan; Hu, Ziheng; Turcios, Noe A; Yang, Peng; Tong, Qin; McCall, Anna K; Blumberg, Peter M; Xie, Xiang-Qun

    2016-07-01

    Transient receptor potential vanilloid type 1 (TRPV1), a heat-sensitive calcium channel protein, contributes to inflammation as well as to acute and persistent pain. Since TRPV1 occupies a central position in pathways of neuronal inflammatory signaling, it represents a highly attractive potential therapeutic target for neuroinflammation. In the present work, we have in silico identified a series of diarylurea analogues for hTRPV1, of which 11 compounds showed activity in the nanomolar to micromolar range as validated by in vitro biological assays. Then, we utilized molecular docking to explore the detailed interactions between TRPV1 and the compounds to understand the contributions of the different substituent groups. Tyr511, Leu518, Leu547, Thr550, Asn551, Arg557, and Leu670 were important for the recognition of the small molecules by TRPV1. A hydrophobic group in R2 or a polar/hydrophilic group in R1 contributed significantly to the activities of the antagonists at TRPV1. In addition, the subtle different binding pose of meta-chloro in place of para-fluoro in the R2 group converted antagonism into partial agonism, as was predicted by our short-term molecular dynamics (MD) simulation and validated by bioassay. Importantly, compound 15, one of our best TRPV1 inhibitors, also showed potential binding affinity (1.39 μM) at cannabinoid receptor 2 (CB2), which is another attractive target for immuno-inflammation diseases. Furthermore, compound 1 and its diarylurea analogues were predicted to target the C-X-C chemokine receptor 2 (CXCR2), although bioassay validation of CXCR2 with these compounds still needs to be performed. This prediction from the modeling is of interest, since CXCR2 is also a potential therapeutic target for chronic inflammatory diseases. Our findings provide novel strategies to develop a small molecule inhibitor to simultaneously target two or more inflammation-related proteins for the treatment of a wide range of inflammatory disorders including

  11. Three-body neutral dissociations of a multiply excited water molecule around the double ionization potential

    NASA Astrophysics Data System (ADS)

    Odagiri, Takeshi; Nakano, Motoyoshi; Tanabe, Takehiko; Kumagai, Yoshiaki; Suzuki, Isao H.; Kitajima, Masashi; Kouchi, Noriyuki

    2012-11-01

    The cross sections for emission of two fluorescence photons from a pair of excited fragments in photoexcitation of H2O have been measured as a function of the incident photon energy using the photon-photon coincidence technique. The cross section increased in the range 30-45 eV, i.e. in the vicinity of the double ionization potential of H2O. The increase of the cross section was attributed to three-body neutral dissociations of a water molecule via multiply excited states: H2O** → H(2p) + OH** → H(2p) + H(2p) + O(3P). Some multiply excited states of H2O were also found in the cross section curve around 65 eV.

  12. Clock-Enhancing Small Molecules and Potential Applications in Chronic Diseases and Aging

    PubMed Central

    Gloston, Gabrielle F.; Yoo, Seung-Hee; Chen, Zheng (Jake)

    2017-01-01

    Normal physiological functions require a robust biological timer called the circadian clock. When clocks are dysregulated, misaligned, or dampened, pathological consequences ensue, leading to chronic diseases and accelerated aging. An emerging research area is the development of clock-targeting compounds that may serve as drug candidates to correct dysregulated rhythms and hence mitigate disease symptoms and age-related decline. In this review, we first present a concise view of the circadian oscillator, physiological networks, and regulatory mechanisms of circadian amplitude. Given a close association of circadian amplitude dampening and disease progression, clock-enhancing small molecules (CEMs) are of particular interest as candidate chronotherapeutics. A recent proof-of-principle study illustrated that the natural polymethoxylated flavonoid nobiletin directly targets the circadian oscillator and elicits robust metabolic improvements in mice. We describe mood disorders and aging as potential therapeutic targets of CEMs. Future studies of CEMs will shed important insight into the regulation and disease relevance of circadian clocks. PMID:28360884

  13. Stress-induced molecules MICA as potential target for radioimmunotherapy of cancer

    NASA Astrophysics Data System (ADS)

    Abakushina, E. V.; Anokhin, Yu N.; Abakushin, D. N.; Kaprin, A. D.

    2017-01-01

    Improving the treatment of cancer, increasing their effectiveness and safety is the main objective in the medicine. Molecular nuclear medicine plays an important role in the therapy of cancer. Radioimmunotherapy (RIT) involves the use of antibodies conjugated with therapeutic radionuclides. More often for RIT use the radiolabeled monoclonal antibodies against tumor-associated antigens. Encouraging results have been achieved with this technology in the management of hematologic malignancies. On the contrary, solid tumors have been less responsive. Despite these encouraging results, new potential target for radioimmunodetection and RIT should be found. It was found to increase the level of tumor-associated molecules MICA in the serum of cancer patients. Use of anti-MICA monoclonal antibodies capable a specifically attach to cancer cell via NKG2D ligands and destroy it, is a very promising direction, both therapeutic and diagnostic standpoint.

  14. 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

  15. Uncertainty of the potential curve minimum for diatomic molecules extrapolated from Dunham type coefficients

    NASA Astrophysics Data System (ADS)

    Ilieva, T.; Iliev, I.; Pashov, A.

    2016-12-01

    In the traditional description of electronic states of diatomic molecules by means of molecular constants or Dunham coefficients, one of the important fitting parameters is the value of the zero point energy - the minimum of the potential curve or the energy of the lowest vibrational-rotational level - E00 . Their values are almost always the result of an extrapolation and it may be difficult to estimate their uncertainties, because they are connected not only with the uncertainty of the experimental data, but also with the distribution of experimentally observed energy levels and the particular realization of set of Dunham coefficients. This paper presents a comprehensive analysis based on Monte Carlo simulations, which aims to demonstrate the influence of all these factors on the uncertainty of the extrapolated minimum of the potential energy curve U (Re) and the value of E00 . The very good extrapolation properties of the Dunham coefficients are quantitatively confirmed and it is shown that for a proper estimate of the uncertainties, the ambiguity in the composition of the Dunham coefficients should be taken into account.

  16. Theoretical study of the CsNa molecule: adiabatic and diabatic potential energy and dipole moment.

    PubMed

    Mabrouk, N; Berriche, H

    2014-09-25

    The adiabatic and diabatic potential energy curves of the low-lying electronic states of the NaCs molecule dissociating into Na (3s, 3p) + Cs (6s, 6p, 5d, 7s, 7p, 6d, 8s, 4f) have been investigated. The molecular calculations are performed using an ab initio approach based on nonempirical pseudopotential, parametrized l-dependent polarization potentials and full configuration interaction calculations through the CIPCI quantum chemistry package. The derived spectroscopic constants (Re, De, Te, ωe, ωexe, and Be) of the ground state and lower excited states are compared with the available theoretical and experimental works. Moreover, accurate permanent and transition dipole moment have been determined as a function of the internuclear distance. The adiabatic permanent dipole moment for the first nine (1)Σ(+) electronic states have shown both ionic characters associated with electron transfer related to Cs(+)Na(-) and Cs(-)Na(+) arrangements. By a simple rotation, the diabatic permanent dipole moment is determined and has revealed a linear behavior, particularly at intermediate and large distances. Many peaks around the avoided crossing locations have been observed for the transition dipole moment between neighbor electronic states.

  17. Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee. Timothy J.

    1995-01-01

    The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBRO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

  18. Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.

    1995-01-01

    The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBrO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

  19. Cardioprotective Potentials of Plant-Derived Small Molecules against Doxorubicin Associated Cardiotoxicity

    PubMed Central

    Ojha, Shreesh; Al Taee, Hasan; Goyal, Sameer; Mahajan, Umesh B.; Patil, Chandrgouda R.; Arya, D. S.; Rajesh, Mohanraj

    2016-01-01

    Doxorubicin (DOX) is a potent and widely used anthracycline antibiotic for the treatment of several malignancies. Unfortunately, the clinical utility of DOX is often restricted due to the elicitation of organ toxicity. Particularly, the increased risk for the development of dilated cardiomyopathy by DOX among the cancer survivors warrants major attention from the physicians as well as researchers to develop adjuvant agents to neutralize the noxious effects of DOX on the healthy myocardium. Despite these pitfalls, the use of traditional cytotoxic drugs continues to be the mainstay treatment for several types of cancer. Recently, phytochemicals have gained attention for their anticancer, chemopreventive, and cardioprotective activities. The ideal cardioprotective agents should not compromise the clinical efficacy of DOX and should be devoid of cumulative or irreversible toxicity on the naïve tissues. Furthermore, adjuvants possessing synergistic anticancer activity and quelling of chemoresistance would significantly enhance the clinical utility in combating DOX-induced cardiotoxicity. The present review renders an overview of cardioprotective effects of plant-derived small molecules and their purported mechanisms against DOX-induced cardiotoxicity. Phytochemicals serve as the reservoirs of pharmacophore which can be utilized as templates for developing safe and potential novel cardioprotective agents in combating DOX-induced cardiotoxicity. PMID:27313831

  20. A screen of the NIH Clinical Collection small molecule library identifies potential anti-coronavirus drugs.

    PubMed

    Cao, Jianzhong; Forrest, J Craig; Zhang, Xuming

    2015-02-01

    With the recent emergence of Middle East Respiratory Syndrome coronavirus in humans and the outbreak of devastating porcine epidemic diarrhea coronavirus in swine, therapeutic intervention is urgently needed. However, anti-coronavirus drugs currently are not available. In an effort to assist rapid development of anti-coronavirus drugs, here we screened the NIH Clinical Collection in cell culture using a luciferase reporter-expressing recombinant murine coronavirus. Of the 727 compounds screened, 84 were found to have a significant anti-coronavirus effect. Further experiments revealed that 51 compounds blocked virus entry while 19 others inhibited viral replication. Additional validation studies with the top 3 inhibitors (hexachlorophene, nitazoxanide and homoharringtonine) demonstrated robust anti-coronavirus activities (a reduction of 6 to 8log10 in virus titer) with an IC50 ranging from 11nM to 1.2μM. Furthermore, homoharringtonine and hexachlorophene exhibited broad antiviral activity against diverse species of human and animal coronaviruses. Since the NIH Clinical Collection consists of compounds that have already been through clinical trials, these small molecule inhibitors have a great potential for rapid development as anti-coronavirus drugs.

  1. Small Molecule Modulators of Keap1-Nrf2-ARE Pathway as Potential Preventive and Therapeutic Agents$

    PubMed Central

    Magesh, Sadagopan; Chen, Yu; Hu, Longqin

    2012-01-01

    Keap1-Nrf2-ARE pathway represents one of the most important cellular defense mechanisms against oxidative stress and xenobiotic damage. Activation of Nrf2 signaling induces the transcriptional regulation of ARE-dependent expression of various detoxifying and antioxidant defense enzymes and proteins. Keap1-Nrf2-ARE signaling has become an attractive target for the prevention and treatment of oxidative stress-related diseases and conditions including cancer, neurodegenerative, cardiovascular, metabolic and inflammatory diseases. Over the last few decades, numerous Nrf2 inducers have been developed and some of them are currently undergoing clinical trials. Recently, over-activation of Nrf2 has been implicated in cancer progression as well as in drug resistance to cancer chemotherapy. Thus, Nrf2 inhibitors could potentially be used to improve the effectiveness of cancer therapy. Herein, we review the signaling mechanism of Keap1-Nrf2-ARE pathway, its disease relevance, and currently known classes of small molecule modulators. We also discuss several aspects of Keap1-Nrf2 interaction, Nrf2-based peptide inhibitor design, and the screening assays currently used for the discovery of direct inhibitors of Keap1-Nrf2 interaction. PMID:22549716

  2. A small molecule inhibitior of the NLRP3 inflammasome is a potential therapeutic for inflammatory diseases

    PubMed Central

    Coll, Rebecca C.; Robertson, Avril A. B.; Chae, Jae Jin; Higgins, Sarah C.; Muñoz-Planillo, Raúl; Inserra, Marco C.; Vetter, Irina; Dungan, Lara S.; Monks, Brian G.; Stutz, Andrea; Croker, Daniel E.; Butler, Mark S.; Haneklaus, Moritz; Sutton, Caroline E.; Núñez, Gabriel; Latz, Eicke; Kastner, Daniel L.; Mills, Kingston H. G.; Masters, Seth L.; Schroder, Kate; Cooper, Matthew A.; O’Neill, Luke A. J.

    2015-01-01

    The NLRP3 inflammasome is a component of the inflammatory process and its aberrant activation is pathogenic in inherited disorders such as the cryopyrin associated periodic syndromes (CAPS) and complex diseases such as multiple sclerosis, type 2 diabetes and atherosclerosis. We describe the development of MCC950, a potent, selective, small molecule inhibitor of NLRP3. MCC950 blocks canonical and non-canonical NLRP3 activation at nanomolar concentrations. MCC950 specifically inhibits NLRP3 but not AIM2, NLRC4 or NLRP1 activation. MCC950 reduces Interleukin-1p (IL-1β) production in vivo and attenuates the severity of experimental autoimmune encephalomyelitis (EAE), a disease model of multiple sclerosis. Furthermore, MCC950 treatment rescues neonatal lethality in a mouse model of CAPS and is active in ex vivo samples from individuals with Muckle-Wells syndrome. MCC950 is thus a potential therapeutic for NLRP3-associated syndromes, including autoinflammatory and autoimmune diseases, and a tool for the further study of the NLRP3 inflammasome in human health and disease. PMID:25686105

  3. Ab initio potential energy surface for the carbon dioxide molecule pair and thermophysical properties of dilute carbon dioxide gas

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert

    2014-10-01

    A four-dimensional intermolecular potential energy surface (PES) for two rigid carbon dioxide molecules was determined from quantum-chemical ab initio calculations. Interaction energies for 1229 CO2-CO2 configurations were computed at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. An analytical site-site potential function with seven sites per CO2 molecule was fitted to the interaction energies. The PES was validated by calculating the second virial coefficient as well as viscosity and thermal conductivity in the dilute-gas limit.

  4. Large pi-aromatic molecules as potential sensitizers for highly efficient dye-sensitized solar cells.

    PubMed

    Imahori, Hiroshi; Umeyama, Tomokazu; Ito, Seigo

    2009-11-17

    Recently, dye-sensitized solar cells have attracted much attention relevant to global environmental issues. Thus far, ruthenium(II) bipyridyl complexes have proven to be the most efficient TiO(2) sensitizers in dye-sensitized solar cells. However, a gradual increment in the highest power conversion efficiency has been recognized in the past decade. More importantly, considering that ruthenium is a rare metal, novel dyes without metal or using inexpensive metal are desirable for highly efficient dye-sensitized solar cells. Large pi-aromatic molecules, such as porphyrins, phthalocyanines, and perylenes, are important classes of potential sensitizers for highly efficient dye-sensitized solar cells, owing to their photostability and high light-harvesting capabilities that can allow applications in thinner, low-cost dye-sensitized solar cells. Porphyrins possess an intense Soret band at 400 nm and moderate Q bands at 600 nm. Nevertheless, the poor light-harvesting properties relative to the ruthenium complexes have limited the cell performance of porphyrin-sensitized TiO(2) cells. Elongation of the pi conjugation and loss of symmetry in porphyrins cause broadening and a red shift of the absorption bands together with an increasing intensity of the Q bands relative to that of the Soret band. On the basis of the strategy, the cell performance of porphyrin-sensitized solar cells has been improved intensively by the enhanced light absorption. Actually, some push-pull-type porphyrins have disclosed a remarkably high power conversion efficiency (6-7%) that was close to that of the ruthenium complexes. Phthalocyanines exhibit strong absorption around 300 and 700 nm and redox features that are similar to porphyrins. Moreover, phthalocyanines are transparent over a large region of the visible spectrum, thereby enabling the possibility of using them as "photovoltaic windows". However, the cell performance was poor, owing to strong aggregation and lack of directionality in the

  5. Hybrid MP2/MP4 potential surfaces in VSCF calculations of IR spectra: applications for organic molecules.

    PubMed

    Knaanie, Roie; Šebek, Jiří; Kalinowski, Jaroslaw; Benny Gerber, R

    2014-02-05

    This study introduces an improved hybrid MP2/MP4 ab initio potential for vibrational spectroscopy calculations which is very accurate, yet without high computational demands. The method uses harmonic vibrational calculations with the MP4(SDQ) potential to construct an improved MP2 potential by coordinate scaling. This improved MP2 potential is used for the anharmonic VSCF calculation. The method was tested spectroscopically for four molecules: butane, acetone, ethylene and glycine. Very good agreement with experiment was found. For most of the systems, the more accurate harmonic treatment considerably improved the MP2 anharmonic results.

  6. Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Barclay, V. J.

    "Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations

  7. The bionic retina: a small molecule with big potential for visual restoration.

    PubMed

    Drivas, Theodore G; Bennett, Jean

    2012-07-26

    In this issue of Neuron, Polosukhina et al. (2012) intravitreally deliver the light-activatable molecule acrylamide-azobenzene-quaternary ammonium (AAQ) to the eyes of mice with end-stage retinal degeneration. Results show that, with the appropriate illumination, AAQ restores light sensitivity and visual behavior.

  8. A novel caspase 8 selective small molecule potentiates TRAIL-induced cell death.

    PubMed

    Bucur, Octavian; Gaidos, Gabriel; Yatawara, Achani; Pennarun, Bodvael; Rupasinghe, Chamila; Roux, Jérémie; Andrei, Stefan; Guo, Bingqian; Panaitiu, Alexandra; Pellegrini, Maria; Mierke, Dale F; Khosravi-Far, Roya

    2015-05-11

    Recombinant soluble TRAIL and agonistic antibodies against TRAIL receptors (DR4 and DR5) are currently being created for clinical cancer therapy, due to their selective killing of cancer cells and high safety characteristics. However, resistance to TRAIL and other targeted therapies is an important issue facing current cancer research field. An attractive strategy to sensitize resistant malignancies to TRAIL-induced cell death is the design of small molecules that target and promote caspase 8 activation. For the first time, we describe the discovery and characterization of a small molecule that directly binds caspase 8 and enhances its activation when combined with TRAIL, but not alone. The molecule was identified through an in silico chemical screen for compounds with affinity for the caspase 8 homodimer's interface. The compound was experimentally validated to directly bind caspase 8, and to promote caspase 8 activation and cell death in single living cells or population of cells, upon TRAIL stimulation. Our approach is a proof-of-concept strategy leading to the discovery of a novel small molecule that not only stimulates TRAIL-induced apoptosis in cancer cells, but may also provide insights into the structure-function relationship of caspase 8 homodimers as putative targets in cancer.

  9. A novel caspase 8 selective small molecule potentiates TRAIL-induced cell death

    PubMed Central

    Bucur, Octavian; Gaidos, Gabriel; Yatawara, Achani; Pennarun, Bodvael; Rupasinghe, Chamila; Roux, Jérémie; Andrei, Stefan; Guo, Bingqian; Panaitiu, Alexandra; Pellegrini, Maria; Mierke, Dale F.; Khosravi-Far, Roya

    2015-01-01

    Recombinant soluble TRAIL and agonistic antibodies against TRAIL receptors (DR4 and DR5) are currently being created for clinical cancer therapy, due to their selective killing of cancer cells and high safety characteristics. However, resistance to TRAIL and other targeted therapies is an important issue facing current cancer research field. An attractive strategy to sensitize resistant malignancies to TRAIL-induced cell death is the design of small molecules that target and promote caspase 8 activation. For the first time, we describe the discovery and characterization of a small molecule that directly binds caspase 8 and enhances its activation when combined with TRAIL, but not alone. The molecule was identified through an in silico chemical screen for compounds with affinity for the caspase 8 homodimer’s interface. The compound was experimentally validated to directly bind caspase 8, and to promote caspase 8 activation and cell death in single living cells or population of cells, upon TRAIL stimulation. Our approach is a proof-of-concept strategy leading to the discovery of a novel small molecule that not only stimulates TRAIL-induced apoptosis in cancer cells, but may also provide insights into the structure-function relationship of caspase 8 homodimers as putative targets in cancer. PMID:25962125

  10. Genes and molecules that can potentiate or attenuate psychostimulant dependence: relevance of data from animal models to human addiction.

    PubMed

    Niwa, Minae; Yan, Yijin; Nabeshima, Toshitaka

    2008-10-01

    Recent evidence suggests that a variety of molecule products play critical roles in the transitions from recreational drug use to drug abuse, and then to drug dependence. Elucidation of the roles of specific molecules in the development of drug dependence can come from preclinical animal models and/or from clinical data. Among animal models, behavioral sensitization, conditioned place preference, drug discrimination, drug self-administration, and extensions of these basic procedures have been widely used to identify molecule products that might be involved in psychostimulant dependence. Repeated exposure to psychostimulants causes cellular adaptations in specific neuronal populations that are likely to contribute to dependence in some humans. In animal models, molecules that include shati, piccolo, tumor necrosis factor-alpha, and glial cell line-derived neurotrophic factor can act as antiaddictive factors. In some of these models, other molecules including matrix metalloproteinase and tissue plasminogen activator can act as proaddictive factors. We review evidence that the balance between levels of anti- and proaddictive factors induced by addictive drugs could play important roles in developing drug dependence. We focus on potential risk molecules in animal models for the development of methamphetamine dependence and their relevance to abusers. We propose that dynamic changes in the balance between levels of antiaddictive and proaddictive factors in the brain provide some of the determinants of susceptibility to drug dependence. Exploration of the roles that candidate molecules play in an appropriate repertoire of animal behavioral models, especially drug self-administration and extensions thereof, should thus help us to understand human stimulant dependence.

  11. Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

    NASA Astrophysics Data System (ADS)

    Theis, Riley A.; Fortenberry, Ryan C.

    2016-03-01

    The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

  12. Identification of small molecule Hes1 modulators as potential anticancer chemotherapeutics.

    PubMed

    Sail, Vibhavari; Hadden, M Kyle

    2013-03-01

    Hes1 is a key transcriptional regulator primarily controlled by the Notch signaling pathway, and recent studies have demonstrated both an oncogenic and tumor suppressor role for Hes1, depending on the cell type. Small molecules that activate and inhibit Hes1 activity hold promise as future anticancer chemotherapeutics. We have utilized a cell-based dual luciferase assay to identify modulators of Hes1 expression in a medium-throughput format. A modest screen was performed in HCT-116 colon cancer cell lines, and two small molecules were identified and characterized as Hes1 regulators. Compound 3 induced Hes1 expression and exhibited anticancer effects in pulmonary carcinoid tumor cells, a cell type in which the upregulated Notch/Hes1 signaling plays a tumor suppressive role. Treatment of HCT-116 cells with compound 12 resulted in Hes1 downregulation and antitumor effects.

  13. Ab initio potential curves of the fragments and diatomics-in-molecules potential energy surfaces for the SH⋯Kr complex

    NASA Astrophysics Data System (ADS)

    Nemukhin, A. V.; Grigorenko, B. L.; Granovsky, A. A.

    1999-02-01

    Potential curves of the SH, KrH and KrS molecules needed for the diatomics-in-molecules (DIM) treatment of the ground and excited states of the SH(X,A)⋯Kr complex have been computed at the SOCI/CASSCF level. The ionic and ion-pair states of these diatomic fragments which play an essential role in the DIM model of intermolecular interactions have been considered as well. The new results for the ion-pair states of SH are compared to the corresponding data for OH. The curves for KrS and XeS [M. Yamanishi, K. Hirao, K. Yamashita, J. Chem. Phys. 108 (1998) 1514] are discussed. The main features of the empirical potential surfaces of the SH⋯Kr complex are reproduced by the DIM technique.

  14. Purely-long-range krypton molecules in singly and doubly excited binding potentials

    SciTech Connect

    Smith, Z. S.; Harmon, A.; Banister, J.; Norman, R.; Hoogeboom-Pot, K.; Walhout, M.

    2010-01-15

    Diatomic potentials for krypton are computed and also probed experimentally. For a probe-laser wavelength near 811 nm, several strong dipole-dipole interactions produce purely-long-range potential wells in the singly excited manifold of (s+p) potentials and in the doubly excited manifold of (p+p) and (s+d) potentials. Evidence of resonant photoassociation into bound states of these potential wells is observed in the emission of ions and ultraviolet photons from a magneto-optically trapped krypton cloud.

  15. Numerical Methods for the Preparation of Potential Energy Curves of Diatomic Molecules.

    DTIC Science & Technology

    1983-03-01

    Calculations," Chemical Physics Letters (to be published, 1982). 21. Herzberg, Gerhard . Spectra of Diatomic Molecules. New York: McGraw-Hill Book...1926). 30. Kratzner, K. "Die Gesetamassigkeil der Bandensystema," Ann. Phs.; Leipzig, lxvii: 127 (1922). 31. Kurylo, M. J., et al. "A Study of the...described below. B-20 CARD 15 NAME: NI,NS,IPSIQ,MAXITT,EPSC FORMAT: 414,D10.0 If NI=l, data from each SCHR iteration is printed. If NI=0, the iterations

  16. Investigation of pyridine carboxylic acids in CM2 carbonaceous chondrites: Potential precursor molecules for ancient coenzymes

    NASA Astrophysics Data System (ADS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-07-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We also report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  17. ABCA1-dependent sterol release: sterol molecule specificity and potential membrane domain for HDL biogenesis

    PubMed Central

    Yamauchi, Yoshio; Yokoyama, Shinji; Chang, Ta-Yuan

    2016-01-01

    Mammalian cells synthesize various sterol molecules, including the C30 sterol, lanosterol, as cholesterol precursors in the endoplasmic reticulum. The build-up of precursor sterols, including lanosterol, displays cellular toxicity. Precursor sterols are found in plasma HDL. How these structurally different sterols are released from cells is poorly understood. Here, we show that newly synthesized precursor sterols arriving at the plasma membrane (PM) are removed by extracellular apoA-I in a manner dependent on ABCA1, a key macromolecule for HDL biogenesis. Analysis of sterol molecules by GC-MS and tracing the fate of radiolabeled acetate-derived sterols in normal and mutant Niemann-Pick type C cells reveal that ABCA1 prefers newly synthesized sterols, especially lanosterol, as the substrates before they are internalized from the PM. We also show that ABCA1 resides in a cholesterol-rich membrane domain resistant to the mild detergent, Brij 98. Blocking ACAT activity increases the cholesterol contents of this domain. Newly synthesized C29/C30 sterols are transiently enriched within this domain, but rapidly disappear from this domain with a half-life of less than 1 h. Our work shows that substantial amounts of precursor sterols are transported to a certain PM domain and are removed by the ABCA1-dependent pathway. PMID:26497474

  18. Investigation of Pyridine Carboxylic Acids in CM2 Carbonaceous Chondrites: Potential Precursor Molecules for Ancient Coenzymes

    NASA Technical Reports Server (NTRS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-01-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We also report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  19. Investigation of Pyridine Carboxylic Acids in CM2 Carbonaceous Chondrites: Potential Precursor Molecules for Ancient Coenzymes

    NASA Technical Reports Server (NTRS)

    Smith, Karen E.; Callahan, Michael P.; Gerakines, Perry A.; Dworkin, Jason P.; House, Christopher H.

    2014-01-01

    The distribution and abundances of pyridine carboxylic acids (including nicotinic acid) in eight CM2 carbonaceous chondrites (ALH 85013, DOM 03183, DOM 08003, EET 96016, LAP 02333, LAP 02336, LEW 85311, and WIS 91600) were investigated by liquid chromatography coupled to UV detection and high resolution Orbitrap mass spectrometry. We find that pyridine monocarboxylic acids are prevalent in CM2-type chondrites and their abundance negatively correlates with the degree of pre-terrestrial aqueous alteration that the meteorite parent body experienced. We lso report the first detection of pyridine dicarboxylic acids in carbonaceous chondrites. Additionally, we carried out laboratory studies of proton-irradiated pyridine in carbon dioxide-rich ices (a 1:1 mixture) to serve as a model of the interstellar ice chemistry that may have led to the synthesis of pyridine carboxylic acids. Analysis of the irradiated ice residue shows that a comparable suite of pyridine mono- and dicarboxylic acids was produced, although aqueous alteration may still play a role in the synthesis (and ultimate yield) of these compounds in carbonaceous meteorites. Nicotinic acid is a precursor to nicotinamide adenine dinucleotide, a likely ancient molecule used in cellular metabolism in all of life, and its common occurrence in CM2 chondrites may indicate that meteorites may have been a source of molecules for the emergence of more complex coenzymes on the early Earth.

  20. Small Molecules from Nature Targeting G-Protein Coupled Cannabinoid Receptors: Potential Leads for Drug Discovery and Development

    PubMed Central

    Sharma, Charu; Sadek, Bassem; Goyal, Sameer N.; Sinha, Satyesh; Ojha, Shreesh

    2015-01-01

    The cannabinoid molecules are derived from Cannabis sativa plant which acts on the cannabinoid receptors types 1 and 2 (CB1 and CB2) which have been explored as potential therapeutic targets for drug discovery and development. Currently, there are numerous cannabinoid based synthetic drugs used in clinical practice like the popular ones such as nabilone, dronabinol, and Δ9-tetrahydrocannabinol mediates its action through CB1/CB2 receptors. However, these synthetic based Cannabis derived compounds are known to exert adverse psychiatric effect and have also been exploited for drug abuse. This encourages us to find out an alternative and safe drug with the least psychiatric adverse effects. In recent years, many phytocannabinoids have been isolated from plants other than Cannabis. Several studies have shown that these phytocannabinoids show affinity, potency, selectivity, and efficacy towards cannabinoid receptors and inhibit endocannabinoid metabolizing enzymes, thus reducing hyperactivity of endocannabinoid systems. Also, these naturally derived molecules possess the least adverse effects opposed to the synthetically derived cannabinoids. Therefore, the plant based cannabinoid molecules proved to be promising and emerging therapeutic alternative. The present review provides an overview of therapeutic potential of ligands and plants modulating cannabinoid receptors that may be of interest to pharmaceutical industry in search of new and safer drug discovery and development for future therapeutics. PMID:26664449

  1. Determination of interatomic potentials for diatomic molecules from low resolution spectra

    NASA Astrophysics Data System (ADS)

    Urbanczyk, T.; Koperski, J.; Pashov, A.

    2016-12-01

    Often, experimental spectra with only partially resolved rotational structure are observed. In such cases, determination of potential energy curves for the corresponding electronic states might be not as reliable as in the high resolution studies. In this paper, we estimate the uncertainties of the potential energy curve parameters, obtained from spectra with partially or not resolved rotational structure, where both frequencies and intensities are fitted. As an example, recently reported excitation spectrum of the B31(53P1) ← X10+(51S0) electronic transition in CdAr van der Waals complex is used. Two types of Morse functions are used to model the excited state potential, but method can be readily extended to more complex potential functions. It is shown, that for reliable estimation of the uncertainties of given potential function one should take into account the possible variation of the transition dipole moment function.

  2. Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures

    NASA Astrophysics Data System (ADS)

    Mason, Keith; Patel, Nehal M.; Ledel, Aric; Moallemi, Ciamac C.; Wintner, Edward A.

    2004-01-01

    Previously we demonstrated a method, Quantized Surface Complementarity Diversity (QSCD), of defining molecular diversity by measuring shape and functional complementarity of molecules to a basis set of theoretical target surfaces [Wintner E.A. and Moallemi C.C., J. Med. Chem., 43 (2000) 1993]. In this paper we demonstrate a method of mapping actual protein pockets to the same basis set of theoretical target surfaces, thereby allowing categorization of protein pockets by their properties of shape and functionality. The key step in the mapping is a `dissection' algorithm that breaks any protein pocket into a set of potential small molecule binding volumes. It is these binding volumes that are mapped to the basis set of theoretical target surfaces, thus measuring a protein pocket not as a single surface but as a collection of molecular recognition environments.

  3. Assessment of the potential utility of different regions of Streptococcus uberis adhesion molecule (SUAM) for mastitis subunit vaccine development.

    PubMed

    Perrig, Melina Soledad; Veaute, Carolina; Renna, María Sol; Pujato, Nazarena; Calvinho, Luis; Marcipar, Iván; Barbagelata, María Sol

    2017-03-01

    Streptococcus uberis is one of the most prevalent pathogens causing clinical and subclinical mastitis worldwide. Among bacterial factors involved in intramammary infections caused by this organism, S. uberis adhesion molecule (SUAM) is one of the main virulence factors identified. This molecule is involved in S. uberis internalization to mammary epithelial cells through lactoferrin (Lf) binding. The objective of this study was to evaluate SUAM properties as a potential subunit vaccine component for prevention of S. uberis mastitis. B epitope prediction analysis of SUAM sequence was used to identify potentially immunogenic regions. Since these regions were detected all along the gene, this criterion did not allow selecting a specific region as a potential immunogen. Hence, four fractions of SUAM (-1fr, 2fr, 3fr and 4fr), comprising most of the protein, were cloned and expressed. Every fraction elicited a humoral immune response in mice as predicted by bioinformatics analysis. SUAM-1fr generated antibodies with the highest recognition ability towards SUAM native protein. Moreover, antibodies against SUAM-1fr produced the highest proportion of internalization inhibition of S. uberis to mammary epithelial cells. In conclusion, SUAM immunogenic and functionally relevant regions were identified and allowed to propose SUAM-1fr as a potential candidate for a subunit vaccine for S. uberis mastitis prevention.

  4. Effective Potential Energies and Transport Cross Sections for Atom-Molecule Interactions of Nitrogen and Nitrogen

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Arnold, Jim (Technical Monitor)

    2001-01-01

    The potential energy surfaces for H2-N and N2-N interactions are calculated by accurate ab initio methods and applied to determine transport data. The results confirm that an effective potential energy for accurately determining transport properties can be calculated using a single orientation. A simple method is developed to determine the dispersion coefficients of effective potential energies Effective potential energies required for O2-O collisions are determ=ined. The H2-N, N2-N, O2-H, and O2-O collision integrals are calculated and tabulated for a large range of temperatures. The theoretical values of the N2-N and O2-O diffusion coefficients compare well with measured data available at room temperature.

  5. Positron-electron correlation-polarization potentials for the calculation of positron collisions with atoms and molecules*

    NASA Astrophysics Data System (ADS)

    Franz, Jan

    2017-02-01

    We present correlation-polarization potentials for the calculation of scattering cross sections of positrons with atoms and molecules. The potentials are constructed from a short-range correlation term and a long-range polarization term. For the short-range correlation term we present four different potentials that are derived from multi-component density functionals. For the long-range polarization term we employ a multi-term expansion. Quantum scattering calculations are presented for low energy collisions of positrons with two atomic targets (argon and krypton) and two molecular targets (nitrogen and methane). For collision energies below the threshold for Positronium formation our calculations of scattering cross sections are in good agreement with recent data sets from experiments and theory. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.

  6. RKR1: A computer program implementing the first-order RKR method for determining diatomic molecule potential energy functions

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.

    2017-01-01

    This paper describes computer program RKR1, which implements the first-order semiclassical Rydberg-Klein-Rees procedure for determining the potential energy function for a diatomic molecule from a knowledge of the dependence of the molecular vibrational energies Gv and inertial rotation constants Bv on the vibrational quantum number v. RKR1 allows the vibrational energies and rotational constants to be defined in terms of: (i) conventional Dunham polynomial expansions, (ii) near-dissociation expansions (NDE's), or (iii) the mixed Dunham/NDE "MXR" functions introduced by Tellinghuisen [J Chem Phys 2003; 118: 3532]. Internal convergence tests ascertain and report on the precision of the resulting turning points. For cases in which only vibrational data are available, RKR1 also allows an overall potential to be constructed by combining directly-calculated well widths with inner turning points generated from a Morse function. It can also automatically smooth over irregular or unphysical behavior of the steep inner wall of the potential.

  7. Interatomic potentials of the Hg-Kr Van der Waals molecule

    NASA Astrophysics Data System (ADS)

    Grycuk, T.; Czerwosz, E.

    1981-07-01

    The absorption spectrum of the Hg-Kr Van der Waals quasimolecule has been investigated in the spectral range from 250 to 1000 cm -1 about the center of the Hg 2537 Å line. The results of a careful analysis of this spectrum are presented, including the quasistatic line wings and satellites. Interatomic potentials for Hg-Kr in the ground electronic state 1o + as well as in the excited states 30 + and 31 have been deduced from the data. The ground state potential has been obtained by fitting the Maitland-Smith function to our experimental results and to some other data available in the literature. Its well depth is estimated to be 200 ± 20 cm -1. The potential curve of the 30 + excimer state for a wide range of separations has been obtained by means of the data inversion technique based on the quasistatic theory of line broadening. The well depth of this potential is found to be 430 ± 40 cm -1. A hypothesis concerning the origin of the blue satellites is proposed. The potential curve of the 31 state, determining the structure of the blue wing spectrum is also inferred.

  8. Microbial inhibition of oral epithelial wound recovery: potential role for quorum sensing molecules?

    PubMed

    De Ryck, Tine; Vanlancker, Eline; Grootaert, Charlotte; Roman, Bart I; De Coen, Laurens M; Vandenberghe, Isabel; Stevens, Christian V; Bracke, Marc; Van de Wiele, Tom; Vanhoecke, Barbara

    2015-01-01

    Awareness of the impact of microbiota in both health and disease is growing. Using a new in vitro oral mucosa co-culture model, we recently showed a clear inhibition of epithelial wound healing in the presence of an oral microbial community. In this paper, we have used the same model in combination with specific oral microbial species to obtain a better insight into the role of the oral microbiota in wound healing. Monocultures of Klebsiella oxytoca and Lactobacillus salivarius significantly inhibited wound healing with ~20%, whereas Streptococcus mitis and S. oralis enhanced the healing process with ~15% in 24 h. Yet, neither S. oralis or S. mitis were able to counteract the inhibitory effects from K. oxytoca on wound healing. Other tested microbial species had no effect on wound healing. Apart from this species-dependency, the inhibitory effect on wound healing depended on a microbial threshold concentration. Further mechanistic experiments with K. oxytoca excluded different microbial factors and hypothesized that quorum sensing molecules might play a role in the inter-kingdom signalling during wound healing. These results are important for the development of new strategies for the management of (infected) wounds and ulcerations.

  9. Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

    NASA Astrophysics Data System (ADS)

    Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li

    2015-03-01

    It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.

  10. Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

    NASA Astrophysics Data System (ADS)

    Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li; Allen, Roland E.

    2015-02-01

    It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C=C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Perhaps remarkably, but apparently because of electrostatic repulsion, the direction of rotation is the same for both reactions.

  11. Synchronization modulation of Na/K pump molecules can hyperpolarize the membrane resting potential in intact fibers.

    PubMed

    Chen, Wei; Dando, Robin

    2007-02-01

    Previously, we have theoretically studied the possibility of electrical rhythmic entrainment of carrier-mediated ion transporters, and experimentally realized synchronization and acceleration of the Na/K pumping rate in the cell membrane of skeletal muscle fibers by a specially designed synchronization modulation electric field. In these studies we either used cut fibers under a voltage clamp or intact fibers, but in the presence of ion channels blockers. A question remained as to whether the field-induced activation observed in the pump molecules could effectively increase the intracellular ionic concentration and the membrane potential at physiological conditions. In this paper, we studied the effects of the field on intact fibers without any channel blockers. We monitored the field-induced changes in the ionic concentration gradient across the cell membrane and the membrane potential non-invasively by using a fluorescent probe and confocal microscopic imaging techniques. The results clearly show that the entrainment of the pump molecules by the synchronization modulation electric field can effectively increase the ionic concentration gradient, and hence, hyperpolarize the membrane potential.

  12. The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.

    ERIC Educational Resources Information Center

    Castano, F.; And Others

    1983-01-01

    The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)

  13. Small molecules targeting glycogen synthase kinase 3 as potential drug candidates for the treatment of retinitis pigmentosa.

    PubMed

    Marchena, Miguel; Villarejo-Zori, Beatriz; Zaldivar-Diez, Josefa; Palomo, Valle; Gil, Carmen; Hernández-Sánchez, Catalina; Martínez, Ana; de la Rosa, Enrique J

    2017-12-01

    Retinitis pigmentosa (RP) is an inherited retinal dystrophy that courses with progressive degeneration of retinal tissue and loss of vision. Currently, RP is an unpreventable, incurable condition. We propose glycogen synthase kinase 3 (GSK-3) inhibitors as potential leads for retinal cell neuroprotection, since the retina is also a part of the central nervous system and GSK-3 inhibitors are potent neuroprotectant agents. Using a chemical genetic approach, diverse small molecules with different potency and binding mode to GSK-3 have been used to validate and confirm GSK-3 as a pharmacological target for RP. Moreover, this medicinal chemistry approach has provided new leads for the future disease-modifying treatment of RP.

  14. A Small Molecule Inhibitor of Human RAD51 Potentiates Breast Cancer Cell Killing by Therapeutic Agents in Mouse Xenografts

    PubMed Central

    Huang, Fei; Mazin, Alexander V.

    2014-01-01

    The homologous recombination pathway is responsible for the repair of DNA double strand breaks. RAD51, a key homologous recombination protein, promotes the search for homology and DNA strand exchange between homologous DNA molecules. RAD51 is overexpressed in a variety of cancer cells. Downregulation of RAD51 by siRNA increases radio- or chemo-sensitivity of cancer cells. We recently developed a specific RAD51 small molecule inhibitor, B02, which inhibits DNA strand exchange activity of RAD51 in vitro. In this study, we used human breast cancer cells MDA-MB-231 to investigate the ability of B02 to inhibit RAD51 and to potentiate an anti-cancer effect of chemotherapeutic agents including doxorubicin, etoposide, topotecan, and cisplatin. We found that the combination of B02 with cisplatin has the strongest killing effect on the cancer cells. We then tested the effect of B02 and cisplatin on the MDA-MB-231 cell proliferation in mouse xenografts. Our results showed that B02 significantly enhances the therapeutic effect of cisplatin on tumor cells in vivo. Our current data demonstrate that use of RAD51-specific small molecule inhibitor represents a feasible strategy of a combination anti-cancer therapy. PMID:24971740

  15. Combined single channel and single molecule detection identifies subunit composition of STIM1-activated transient receptor potential canonical (TRPC) channels.

    PubMed

    Asanov, Alexander; Sampieri, Alicia; Moreno, Claudia; Pacheco, Jonathan; Salgado, Alfonso; Sherry, Ryan; Vaca, Luis

    2015-01-01

    Depletion of intracellular calcium ion stores initiates a rapid cascade of events culminating with the activation of the so-called Store-Operated Channels (SOC) at the plasma membrane. Calcium influx via SOC is essential in the initiation of calcium-dependent intracellular signaling and for the refilling of internal calcium stores, ensuring the regeneration of the signaling cascade. In spite of the significance of this evolutionary conserved mechanism, the molecular identity of SOC has been the center of a heated controversy spanning over the last 20 years. Initial studies positioned some members of the transient receptor potential canonical (TRPC) channel superfamily of channels (with the more robust evidence pointing to TRPC1) as a putative SOC. Recent evidence indicates that Stromal Interacting Molecule 1 (STIM1) activates some members from the TRPC family of channels. However, the exact subunit composition of TRPC channels remains undetermined to this date. To identify the subunit composition of STIM1-activated TRPC channels, we developed novel method, which combines single channel electrophysiological measurements based on the patch clamp technique with single molecule fluorescence imaging. We termed this method Single ion Channel Single Molecule Detection technique (SC-SMD). Using SC-SMD method, we have obtained direct evidence of the subunit composition of TRPC channels activated by STIM1. Furthermore, our electrophysiological-imaging SC-SMD method provides evidence at the molecular level of the mechanism by which STIM1 and calmodulin antagonize to modulate TRPC channel activity.

  16. Identification of a potential conformationally disordered mesophase in a small molecule: experimental and computational approaches.

    PubMed

    Chakravarty, Paroma; Bates, Simon; Thomas, Leonard

    2013-08-05

    GNE068, a small organic molecule, was obtained as an amorphous form (GNE068-A) after isolation from ethanol and as a partially disordered form (GNE068-PC) from ethyl acetate. On subsequent characterization, GNE068-PC exhibited a number of properties that were anomalous for a two phase crystalline-amorphous system but consistent with the presence of a solid state phase having intermediate order (mesomorphous). Modulated DSC measurements of GNE068-PC revealed an overlapping endotherm and glass transition in the 135-145 °C range. ΔH of the endotherm showed strong heating rate dependence. Variable temperature XRPD (25-160 °C) revealed structure loss in GNE068-PC, suggesting the endotherm to be an "apparent melt". In addition, gentle grinding of GNE068-PC in a mortar led to a marked decrease in XRPD peak intensities, indicating a "soft" crystalline lattice. Computational analysis of XRPD data revealed the presence of two noncrystalline contributions, one of which was associated with GNE068-A. The second was a variable component that could be modeled as diffuse scattering from local disorder within the associated crystal structure, suggesting a mesomorphous system. Owing to the dominance of the noncrystalline diffuse scattering in GNE068-PC and the observed lattice deformation, the mesomorphous phase exhibited properties consistent with a conformationally disordered mesophase. Because of the intimate association of the residual solvent (ethyl acetate) with the lattice long-range order, loss of solvent on heating through the glass transition temperature of the local disorder caused irrecoverable loss of the long-range order. This precluded the observation of characteristic thermodynamic mesophase behavior above the glass transition temperature.

  17. The (H2)2 potential surface and the interaction between hydrogen molecules at low temperatures

    NASA Astrophysics Data System (ADS)

    Burton, Peter G.; Senff, Ulrich E.

    1982-06-01

    The (H2)2 rigid rotor interaction potential has been calculated for the intermolecular distance range R = 3.0-11.0 a.u. for six relative orientations to estimate both the isotropic and anisotropic components of the full intermolecular potential. A partially optimized basis set limited in size to 78 independent Gaussian functions was used throughout the energy calculations, which required only very small corrections for basis set unsaturation effects. Correlation effects were computed both at the variational (single and) double excitation PNOCI level and using the CEPA2-PNO approximation to estimate higher order excitation effects. While the latter rigid-rotor surface may overestimate the strength of the H2-H2 interaction in the vicinity of the well by a few wave numbers in the rigid-rotor PNOCI surface from the present study, which we regard as an upper bound to the true rigid-rotor surface, is also slightly deeper than almost all previous theoretical and empirical ''fit'' potentials in the well region. Since low energy scattering experiments lack sensitivity to the precise well depth because of the long de Broglie wavelengths appropriate to scattering at energies comparable with the well depth, the significance of the current disagreement on the well depth between the rigid-rotor level of the theory (which puts it at least 27.5 cm-1) and experiment is uncertain. However, coupled with the present uncertainty stemming from the CI formalism of ˜±3 cm-1, is a further uncertainty due to the expected increase in intramolecular zero-point energies due to hindered H2 vibration within the dimer. A zero-point increase within each H2 at Re of 0.1% would effectively raise the rigid-rotor potentials by some 4 cm-1, bringing the well depth into line with experimental estimates. In the low energy part of the repulsive wall of the potential (where the relative importance of these small effects diminishes), which has been probed rather sensitively by recent rotationally

  18. N-acetylation of three aromatic amine hair dye precursor molecules eliminates their genotoxic potential.

    PubMed

    Zeller, Andreas; Pfuhler, Stefan

    2014-01-01

    N-acetylation has been described as a detoxification reaction for aromatic amines; however, there is only limited data available showing that this metabolic conversion step changes their genotoxicity potential. To extend this database, three aromatic amines, all widely used as precursors in oxidative hair dye formulations, were chosen for this study: p-phenylenediamine (PPD), 2,5-diaminotoluene (DAT) and 4-amino-2-hydroxytoluene (AHT). Aiming at a deeper mechanistic understanding of the interplay between activation and detoxification for this chemical class, we compared the genotoxicity profiles of the parent compounds with those of their N-acetylated metabolites. While PPD, DAT and AHT all show genotoxic potential in vitro, their N-acetylated metabolites completely lack genotoxic potential as shown in the Salmonella typhimurium reversion assay, micronucleus test with cultured human lymphocytes (AHT), chromosome aberration assay with V79 cells (DAT) and Comet assay performed with V79 cells. For the bifunctional aromatic amines studied (PPD and DAT), monoacetylation was sufficient to completely abolish their genotoxic potential. Detoxification through N-acetylation was further confirmed by comparing PPD, DAT and AHT in the Comet assay using standard V79 cells (N-acetyltransferase (NAT) deficient) and two NAT-proficient cell lines,V79NAT1*4 and HaCaT (human keratinocytes). Here we observed a clear shift of dose-response curves towards decreased genotoxicity of the parent aromatic amines in the NAT-proficient cells. These findings suggest that genotoxic effects will only be found at concentrations where the N-acetylation (detoxifying) capacity of the cells is overwhelmed, indicating that a 'first-pass' effect in skin could be taken into account for risk assessment of these topically applied aromatic amines. The findings also indicate that the use of liver S-9 preparations, which generally underestimate Phase II reactions, contributes to the generation of irrelevant

  19. Inertial and bias effects in the rotational Brownian motion of rodlike molecules in a uniaxial potential

    NASA Astrophysics Data System (ADS)

    Kalmykov, Yuri P.; Titov, Sergey V.; Coffey, William T.

    2011-01-01

    Inertial effects in the rotational Brownian motion in space of a rigid dipolar rotator (needle) in a uniaxial potential biased by an external field giving rise to asymmetry are treated via the infinite hierarchy of differential-recurrence relations for the statistical moments (orientational correlation functions) obtained by averaging the Euler-Langevin equation over its realizations in phase space. The solutions of this infinite hierarchy for the dipole correlation function and its characteristic times are obtained using matrix continued fractions showing that the model simultaneously predicts both slow overbarrier (or interwell) relaxation at low frequencies accompanied by intermediate frequency Debye relaxation due to fast near-degenerate motion in the wells of the potential (intrawell relaxation) as well as the high frequency resonance (Poley) absorption due to librations of the dipole moments. It is further shown that the escape rate of a Brownian particle from a potential well as extended to the Kramers turnover problem via the depopulation factor yields a close approximation to the longest (overbarrier) relaxation time of the system. For zero and small values of the bias field parameter h, both the dipole moment correlation time and the longest relaxation time have Arrhenius behavior (exponential increase with increasing barrier height). While at values of h in excess of a critical value however far less than that required to achieve nucleation, the Arrhenius behavior of the correlation time disappears.

  20. Properties of a new hydrotrope hydrophobic molecule and its potential applications.

    PubMed

    Schnell, E; Touraud, D; Gick, R; Kunz, W

    2008-10-01

    In the present contribution, the properties of dipropylene glycol isobornyl ether (Pribelance) are discussed, especially in the context of microemulsion and emulsion formulations. Pribelance is a new low-toxic anti-foaming hydrotrope with excellent co-surfactant properties that has some similarities with long-chain alcohols, but in contrast to them, it is liquid at room temperature. In combination with another, more hydrophilic co-surfactant, it allows significant amounts of oil to be solubilized in water. Possible applications such as in cosmetics, as an anti-foaming agent or as additive to cooling lubricants are discussed. Further potential applications are plasticizers, fermentation systems, agrochemicals and waste-water treatments.

  1. Molecules that Mimic Apolipoprotein A-I: Potential Agents for Treating Atherosclerosis

    PubMed Central

    Leman, Luke J.; Maryanoff, Bruce E.; Ghadiri, M. Reza

    2013-01-01

    Certain amphipathic α-helical peptides can functionally mimic many of the properties of full-length apolipoproteins, thereby offering an approach to modulate high-density lipoprotein (HDL) for combating atherosclerosis. In this Perspective, we summarize the key findings and advances over the past 25 years in the development of peptides that mimic apolipoproteins, especially apolipoprotein A-I (apoA-I). This assemblage of information provides a reasonably clear picture of the state of the art in the apolipoprotein mimetic field, an appreciation of the potential for such agents in pharmacotherapy, and a sense of the opportunities for optimizing the functional properties of HDL. PMID:24168751

  2. Parasite annexins--new molecules with potential for drug and vaccine development.

    PubMed

    Hofmann, Andreas; Osman, Asiah; Leow, Chiuan Yee; Driguez, Patrick; McManus, Donald P; Jones, Malcolm K

    2010-11-01

    In the last few years, annexins have been discovered in several nematodes and other parasites, and distinct differences between the parasite annexins and those of the hosts make them potentially attractive targets for anti-parasite therapeutics. Annexins are ubiquitous proteins found in almost all organisms across all kingdoms.Here, we present an overview of novel annexins from parasitic organisms, and summarize their phylogenetic and biochemical properties, with a view to using them as drug or vaccine targets. Building on structural and biological information that has been accumulated for mammalian and plant annexins, we describe a predicted additional secondary structure element found in many parasite annexins that may confer unique functional properties, and present a specific antigenic epitope for use as a vaccine.

  3. Investigations of the potential functions of weakly bound diatomic molecules and laser-assisted excitive Penning ionization

    SciTech Connect

    Goble, J.H. Jr.

    1982-05-01

    Three variations on the Dunham series expansion function of the potential of a diatomic molecule are compared. The differences among these expansions lie in the choice of the expansion variable, lambda. The functional form of these variables are lambda/sub s/ = l-r/sub e//r for the Simon-Parr-Finlan version, lambda/sub T/ - 1-(r/sub e//r)/sup p/ for that of Thakkar, and lambda/sub H/ = 1-exp(-rho(r/r/sub e/-1) for that of Huffaker. A wide selection of molecular systems are examined. It is found that, for potentials in excess of thirty kcal/mole, the Huffaker expansion provides the best description of the three, extrapolating at large internuclear separation to a value within 10% of the true dissociation energy. For potentials that result from the interaction of excited states, all series expansions show poor behavior away from the equilibrium internuclear separation of the molecule. The series representation of the potentials of weakly bound molecules are examined in more detail. The ground states of BeAr/sup +/, HeNe/sup +/, NaAr, and Ar/sub 2/ and the excited states of HeNe+, NaNe, and NaAr are best described by the Thakkar expansion. Finally, the observation of laser-assisted excitive Penning ionization in a flowing afterglow is reported. The reaction Ar(/sup 3/P/sub 2/) + Ca + h nu ..-->.. Ar + Ca/sup +/(5p /sup 2/P/sub J/) + e/sup -/ occurs when the photon energy, h nu, is approximately equal to the energy difference between the metastable argon and one of the fine structure levels of the ion's doublet. By monitoring the cascade fluorescence of the above reaction and comparing it to the flourescence from the field-free process Ar(/sup 3/P/sub 2/) + Ca ..-->.. Ar + Ca/sup +/(4p /sup 2/P/sub J/) + e/sup -/ a surprisingly large cross section of 6.7 x 10/sup 3/ A/sup 2/ is estimated.

  4. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules: A Benchmark of GW Methods

    NASA Astrophysics Data System (ADS)

    Marom, Noa; Knight, Joseph; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, Vincent; Rinke, Patrick; Korzdorfer, Thomas

    The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0) , non-self-consistent G0W0 based on several mean-field starting points, and a ``beyond GW'' second order screened exchange (SOSEX) correction to G0W0. The best performers overall are G0W0 + SOSEX and G0W0 based on an IP-tuned long range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs. delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments.

  5. Staphylococcus epidermidis Biofilms: Functional Molecules, Relation to Virulence, and Vaccine Potential

    NASA Astrophysics Data System (ADS)

    Mack, Dietrich; Davies, Angharad P.; Harris, Llinos G.; Knobloch, Johannes K. M.; Rohde, Holger

    Medical device-associated infections, most frequently caused by Staphylococcus epidermidis and Staphylococcus aureus, are of increasing importance in modern medicine. The formation of adherent, multilayered bacterial biofilms is crucial in the pathogenesis of these infections. Polysaccharide intercellular adhesin (PIA), a homoglycan of β-1,6-linked 2-acetamido-2-deoxy-d-glucopyranosyl residues, of which about 15% are non-N-acetylated, is central to biofilm accumulation in staphylococci. It transpires that polysaccharides - structurally very similar to PIA - are also key to biofilm formation in a number of other organisms including the important human pathogens Escherichia coli, Aggregatibacter (Actinobacillus) actinomycetemcomitans, Yersinia pestis, and Bordetella spp. Apparently, synthesis of PIA and related polysaccharides is a general feature important for biofilm formation in diverse bacterial genera. Current knowledge about the structure and biosynthesis of PIA and related polysaccharides is reviewed. Additionally, information on their role in pathogenesis of biomaterial-related and other type of infections and the potential use of PIA and related compounds for prevention of infection is evaluated.

  6. A Small-Molecule Inhibitor of PIM Kinases as a Potential Treatment for Urothelial Carcinomas12

    PubMed Central

    Foulks, Jason M.; Carpenter, Kent J.; Luo, Bai; Xu, Yong; Senina, Anna; Nix, Rebecca; Chan, Ashley; Clifford, Adrianne; Wilkes, Marcus; Vollmer, David; Brenning, Benjamin; Merx, Shannon; Lai, Shuping; McCullar, Michael V.; Ho, Koc-Kan; Albertson, Daniel J.; Call, Lee T.; Bearss, Jared J.; Tripp, Sheryl; Liu, Ting; Stephens, Bret J.; Mollard, Alexis; Warner, Steven L.; Bearss, David J.; Kanner, Steven B.

    2014-01-01

    The proto-oncogene proviral integration site for moloney murine leukemia virus (PIM) kinases (PIM-1, PIM-2, and PIM-3) are serine/threonine kinases that are involved in a number of signaling pathways important to cancer cells. PIM kinases act in downstream effector functions as inhibitors of apoptosis and as positive regulators of G1-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, and prostate, gastric, and head and neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma and to assess the role PIM function in disease progression and their potential to serve as molecular targets for therapy. One hundred thirty-seven cases of urothelial carcinoma were included in this study of surgical biopsy and resection specimens. High levels of expression of all three PIM family members were observed in both noninvasive and invasive urothelial carcinomas. The second-generation PIM inhibitor, TP-3654, displays submicromolar activity in pharmacodynamic biomarker modulation, cell proliferation studies, and colony formation assays using the UM-UC-3 bladder cancer cell line. TP-3654 displays favorable human ether-à-go-go-related gene and cytochrome P450 inhibition profiles compared with the first-generation PIM inhibitor, SGI-1776, and exhibits oral bioavailability. In vivo xenograft studies using a bladder cancer cell line show that PIM kinase inhibition can reduce tumor growth, suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas. PMID:24953177

  7. Time-dependent density functional study of the electronic potential energy curves and excitation spectrum of the oxygen molecule.

    PubMed

    Guan, Jingang; Wang, Fan; Ziegler, Tom; Cox, Hazel

    2006-07-28

    Orbital energies, ionization potentials, molecular constants, potential energy curves, and the excitation spectrum of O(2) are calculated using time-dependent density functional theory (TDDFT) with Tamm-Dancoff approximation (TDA). The calculated negative highest occupied molecular orbital energy (-epsilon(HOMO)) is compared with the energy difference ionization potential for five exchange correlation functionals consisting of the local density approximation (LDAxc), gradient corrected Becke exchange plus Perdew correlation (B(88X)+P(86C)), gradient regulated asymptotic correction (GRAC), statistical average of orbital potentials (SAOP), and van Leeuwen and Baerends asymptotically correct potential (LB94). The potential energy curves calculated using TDDFT with the TDA at internuclear distances from 1.0 to 1.8 A are divided into three groups according to the electron configurations. The 1pi(u) (4)1pi(g) (2) electron configuration gives rise to the X (3)Sigma(g) (-), a (1)Delta(g), and b (1)Sigma(g) (+) states; the 1pi(u) (3)1pi(g) (3) electron configuration gives rise to the c (1)Sigma(u) (-), C (3)Delta(u), and A (3)Sigma(u) (+) states; and the B (3)Sigma(u) (-), A (1)Delta(u), and f (1)Sigma(u) (+) states are determined by the mixing of two or more electron configurations. The excitation spectrum of the oxygen molecule, calculated with the aforementioned exchange correlation functionals, shows that the results are quite sensitive to the choice of functional. The LDAxc and the B(88X)+P(86C) functionals produce similar spectroscopic patterns with a single strongly absorbing band positioned at 19.82 and 19.72 eV, respectively, while the asymptotically corrected exchange correlation functionals of the SAOP and the LB94 varieties yield similar excitation spectra where the computed strongly absorbing band is located at 16.09 and 16.42 eV, respectively. However, all of the exchange correlation functionals yield only one strongly absorbing band (oscillator strength

  8. Novel macrocyclic molecules based on 12a-N substituted 16-membered azalides and azalactams as potential antifungal agents.

    PubMed

    Wang, Xiaolei; Zhang, Shun; Pang, Yanlong; Yuan, Huihui; Liang, Xiaomei; Zhang, Jianjun; Wang, Daoquan; Wang, Mingan; Dong, Yanhong

    2014-02-12

    Novel macrocyclic molecules comprising sulfonyl and acyl moiety at the position N-12a of 16-membered azalides (6a-n) and azalactams (10a-r) scaffold were synthesized from cyclododecanone 1 as starting material via 5 steps and 4 steps, respectively. The antifungal activity of these compounds against Sclerotinia sclerotiorum, Pyricularia oryzae, Botrytis cinerea, Rhizoctonia solani and Phytophthora capsici were evaluated and found that compounds possessing α-exomethylene (6c, 6d, 6e and 6g) showed antifungal activity comparable to commercial fungicide Chlorothalonil against P. oryzae and compounds possessing p-chlorobenzoyl exhibited enhanced antifungal activity than those with other substituents against S. sclerotiorum, P. oryzae, and B. cinerea. These findings suggested that the α-exomethylene and p-chlorobenzoyl may be two potential pharmacological active groups with antifungal activities.

  9. Effects of Tilt Angle, DNA Concentration, and Surface Potential on Directed Alignment of DNA Molecule for the Application to Nanodevices

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Jin; Hong, Byungyou

    2013-03-01

    This paper reports an efficient approach to control both the density and direction of highly aligned DNA molecules and thus DNA-templated gold nanowires (AuNWs) on Si chips. We utilized tilting method to prepare stretched DNA structures on SiO2/Si substrate and found important parameters in the alignment process that tilt angle, DNA concentration, and surface potential are controlled the density and structure of DNA aligned on the surface. In additional, we also can be directly connected DNA-templated AuNWs between two terminal electrodes on Si chips. This method also describes a simple way to form singled, bundled and networked DNA arrays on Si substrates.

  10. Orthogonal coordinates for the dynamics of four bodies and for the representation of potentials of tetra-atomic molecules

    NASA Astrophysics Data System (ADS)

    Ragni, Mirco; Bitencourt, Ana Carla P.; Aquilanti, Vincenzo

    We discuss systems of orthogonal coordinates for the dynamical treatment of four particles, generated by making extensive use of the concept of kinematic rotations, which act on coordinates of the particles and are represented by matrices only dependent on their masses. The explicit representations of the kinetic rotation matrices are given: this allows us to define alternative particle schemes, such as those based on the Jacobi and Radau-Smith vectors, as well as on mixed types of vectors, of possible interest for specific molecules or aggregates. A list is given of relevant formulas connecting these coordinate sets to the geometrical parameters (internuclear distances, bond and dihedral angles) of use for the representation of the potential energy surface of four atomic systems. Applications are indicated for molecular and cluster physics.0

  11. Nrf2 and HSF-1 Pathway Activation via Hydroquinone-Based Proelectrophilic Small Molecules is Regulated by Electrochemical Oxidation Potential.

    PubMed

    Satoh, Takumi; Stalder, Romain; McKercher, Scott R; Williamson, Robert E; Roth, Gregory P; Lipton, Stuart A

    2015-01-01

    Activation of the Kelch-like ECH-associated protein 1/nuclear factor (erythroid-derived 2)-like 2 and heat-shock protein 90/heat-shock factor-1 signal-transduction pathways plays a central role in combatting cellular oxidative damage and related endoplasmic reticulum stress. Electrophilic compounds have been shown to be activators of these transcription-mediated responses through S-alkylation of specific regulatory proteins. Previously, we reported that a prototype compound (D1, a small molecule representing a proelectrophilic, para-hydroquinone species) exhibited neuroprotective action by activating both of these pathways. We hypothesized that the para-hydroquinone moiety was critical for this activation because it enhanced transcription of these neuroprotective pathways to a greater degree than that of the corresponding ortho-hydroquinone isomer. This notion was based on the differential oxidation potentials of the isomers for the transformation of the hydroquinone to the active, electrophilic quinone species. Here, to further test this hypothesis, we synthesized a pair of para- and ortho-hydroquinone-based proelectrophilic compounds and measured their redox potentials using analytical cyclic voltammetry. The redox potential was then compared with functional biological activity, and the para-hydroquinones demonstrated a superior neuroprotective profile.

  12. Analytic functions for potential energy curves, dipole moments, and transition dipole moments of LiRb molecule

    NASA Astrophysics Data System (ADS)

    You, Yang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang; Wang, Li-Zhi

    2016-01-01

    The analytic potential energy functions (APEFs) of the X1Σ+, 21Σ+, a3Σ+, and 23Σ+ states of the LiRb molecule are obtained using Morse long-range potential energy function with damping function and nonlinear least-squares method. These calculations were based on the potential energy curves (PECs) calculated using the multi-reference configuration interaction (MRCI) method. The reliability of the APEFs is confirmed using the curves of their first and second derivatives. By using the obtained APEFs, the rotational and vibrational energy levels of the states are determined by solving the Schrödinger equation of nuclear movement. The spectroscopic parameters, which are deduced using Dunham expansion, and the obtained rotational and vibrational levels are compared with the reported theoretical and experimental values. The correlation effect of the electrons of the inner shell remarkably improves the results compared with the experimental spectroscopic parameters. For the first time, the APEFs for the dipole moments and transition dipole moments of the states have been determined based on the curves obtained from the MRCI calculations.

  13. Identification of small molecule inhibitors of ERCC1-XPF that inhibit DNA repair and potentiate cisplatin efficacy in cancer cells.

    PubMed

    Arora, Sanjeevani; Heyza, Joshua; Zhang, Hao; Kalman-Maltese, Vivian; Tillison, Kristin; Floyd, Ashley M; Chalfin, Elaine M; Bepler, Gerold; Patrick, Steve M

    2016-11-15

    ERCC1-XPF heterodimer is a 5'-3' structure-specific endonuclease which is essential in multiple DNA repair pathways in mammalian cells. ERCC1-XPF (ERCC1-ERCC4) repairs cisplatin-DNA intrastrand adducts and interstrand crosslinks and its specific inhibition has been shown to enhance cisplatin cytotoxicity in cancer cells. In this study, we describe a high throughput screen (HTS) used to identify small molecules that inhibit the endonuclease activity of ERCC1-XPF. Primary screens identified two compounds that inhibit ERCC1-XPF activity in the nanomolar range. These compounds were validated in secondary screens against two other non-related endonucleases to ensure specificity. Results from these screens were validated using an in vitro gel-based nuclease assay. Electrophoretic mobility shift assays (EMSAs) further show that these compounds do not inhibit the binding of purified ERCC1-XPF to DNA. Next, in lung cancer cells these compounds potentiated cisplatin cytotoxicity and inhibited DNA repair. Structure activity relationship (SAR) studies identified related compounds for one of the original Hits, which also potentiated cisplatin cytotoxicity in cancer cells. Excitingly, dosing with NSC16168 compound potentiated cisplatin antitumor activity in a lung cancer xenograft model. Further development of ERCC1-XPF DNA repair inhibitors is expected to sensitize cancer cells to DNA damage-based chemotherapy.

  14. Analytic functions for potential energy curves, dipole moments, and transition dipole moments of LiRb molecule.

    PubMed

    You, Yang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang; Wang, Li-Zhi

    2016-01-15

    The analytic potential energy functions (APEFs) of the X(1)Σ(+), 2(1)Σ(+), a(3)Σ(+), and 2(3)Σ(+) states of the LiRb molecule are obtained using Morse long-range potential energy function with damping function and nonlinear least-squares method. These calculations were based on the potential energy curves (PECs) calculated using the multi-reference configuration interaction (MRCI) method. The reliability of the APEFs is confirmed using the curves of their first and second derivatives. By using the obtained APEFs, the rotational and vibrational energy levels of the states are determined by solving the Schrödinger equation of nuclear movement. The spectroscopic parameters, which are deduced using Dunham expansion, and the obtained rotational and vibrational levels are compared with the reported theoretical and experimental values. The correlation effect of the electrons of the inner shell remarkably improves the results compared with the experimental spectroscopic parameters. For the first time, the APEFs for the dipole moments and transition dipole moments of the states have been determined based on the curves obtained from the MRCI calculations.

  15. Identification of small molecule inhibitors of ERCC1-XPF that inhibit DNA repair and potentiate cisplatin efficacy in cancer cells

    PubMed Central

    Arora, Sanjeevani; Heyza, Joshua; Zhang, Hao; Kalman-Maltese, Vivian; Tillison, Kristin; Floyd, Ashley M.; Chalfin, Elaine M.; Bepler, Gerold; Patrick, Steve M.

    2016-01-01

    ERCC1-XPF heterodimer is a 5′-3′ structure-specific endonuclease which is essential in multiple DNA repair pathways in mammalian cells. ERCC1-XPF (ERCC1-ERCC4) repairs cisplatin-DNA intrastrand adducts and interstrand crosslinks and its specific inhibition has been shown to enhance cisplatin cytotoxicity in cancer cells. In this study, we describe a high throughput screen (HTS) used to identify small molecules that inhibit the endonuclease activity of ERCC1-XPF. Primary screens identified two compounds that inhibit ERCC1-XPF activity in the nanomolar range. These compounds were validated in secondary screens against two other non-related endonucleases to ensure specificity. Results from these screens were validated using an in vitro gel-based nuclease assay. Electrophoretic mobility shift assays (EMSAs) further show that these compounds do not inhibit the binding of purified ERCC1-XPF to DNA. Next, in lung cancer cells these compounds potentiated cisplatin cytotoxicity and inhibited DNA repair. Structure activity relationship (SAR) studies identified related compounds for one of the original Hits, which also potentiated cisplatin cytotoxicity in cancer cells. Excitingly, dosing with NSC16168 compound potentiated cisplatin antitumor activity in a lung cancer xenograft model. Further development of ERCC1-XPF DNA repair inhibitors is expected to sensitize cancer cells to DNA damage-based chemotherapy. PMID:27650543

  16. dPotFit: A computer program to fit diatomic molecule spectral data to potential energy functions

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.

    2017-01-01

    This paper describes program dPotFit, which performs least-squares fits of diatomic molecule spectroscopic data consisting of any combination of microwave, infrared or electronic vibrational bands, fluorescence series, and tunneling predissociation level widths, involving one or more electronic states and one or more isotopologs, and for appropriate systems, second virial coefficient data, to determine analytic potential energy functions defining the observed levels and other properties of each state. Four families of analytical potential functions are available for fitting in the current version of dPotFit: the Expanded Morse Oscillator (EMO) function, the Morse/Long-Range (MLR) function, the Double-Exponential/Long-Range (DELR) function, and the 'Generalized Potential Energy Function' (GPEF) of Šurkus, which incorporates a variety of polynomial functional forms. In addition, dPotFit allows sets of experimental data to be tested against predictions generated from three other families of analytic functions, namely, the 'Hannover Polynomial' (or "X-expansion") function, and the 'Tang-Toennies' and Scoles-Aziz 'HFD', exponential-plus-van der Waals functions, and from interpolation-smoothed pointwise potential energies, such as those obtained from ab initio or RKR calculations. dPotFit also allows the fits to determine atomic-mass-dependent Born-Oppenheimer breakdown functions, and singlet-state Λ-doubling, or 2Σ splitting radial strength functions for one or more electronic states. dPotFit always reports both the 95% confidence limit uncertainty and the "sensitivity" of each fitted parameter; the latter indicates the number of significant digits that must be retained when rounding fitted parameters, in order to ensure that predictions remain in full agreement with experiment. It will also, if requested, apply a "sequential rounding and refitting" procedure to yield a final parameter set defined by a minimum number of significant digits, while ensuring no

  17. Metronomic Small Molecule Inhibitor of Bcl-2 (TW-37) Is Antiangiogenic and Potentiates the Antitumor Effect of Ionizing Radiation

    SciTech Connect

    Zeitlin, Benjamin D.; Spalding, Aaron C.; Campos, Marcia S.; Ashimori, Naoki; Dong Zhihong; Wang Shaomeng; Lawrence, Theodore S.; Noer, Jacques E.

    2010-11-01

    Purpose: To investigate the effect of a metronomic (low-dose, high-frequency) small-molecule inhibitor of Bcl-2 (TW-37) in combination with radiotherapy on microvascular endothelial cells in vitro and in tumor angiogenesis in vivo. Methods and Materials: Primary human dermal microvascular endothelial cells were exposed to ionizing radiation and/or TW-37 and colony formation, as well as capillary sprouting in three-dimensional collagen matrices, was evaluated. Xenografts vascularized with human blood vessels were engineered by cotransplantation of human squamous cell carcinoma cells (OSCC3) and human dermal microvascular endothelial cells seeded in highly porous biodegradable scaffolds into the subcutaneous space of immunodeficient mice. Mice were treated with metronomic TW-37 and/or radiation, and tumor growth was evaluated. Results: Low-dose TW-37 sensitized primary endothelial cells to radiation-induced inhibition of colony formation. Low-dose TW-37 or radiation partially inhibited endothelial cell sprout formation, and in combination, these therapies abrogated new sprouting. Combination of metronomic TW-37 and low-dose radiation inhibited tumor growth and resulted in significant increase in time to failure compared with controls, whereas single agents did not. Notably, histopathologic analysis revealed that tumors treated with TW-37 (with or without radiation) are more differentiated and showed more cohesive invasive fronts, which is consistent with less aggressive phenotype. Conclusions: These results demonstrate that metronomic TW-37 potentiates the antitumor effects of radiotherapy and suggest that patients with head and neck cancer might benefit from the combination of small molecule inhibitor of Bcl-2 and radiation therapy.

  18. Theoretical investigation of electronic states and spectroscopic properties of tellurium selenide molecule employing relativistic effective core potentials.

    PubMed

    Chattopadhyaya, Surya; Nath, Abhijit; Das, Kalyan Kumar

    2014-04-24

    Ab initio based relativistic configuration interaction calculations have been performed to study the electronic states and spectroscopic properties of tellurium selenide (TeSe) - the heaviest heteronuclear diatomic group 16-16 molecule. Potential energy curves of several spin-excluded (Λ-S) electronic states of TeSe have been constructed and spectroscopic constants of low-lying bound Λ-S states within 3.85 eV are reported in the first stage of calculations. The X(3)Σ(-), a(1)Δ and b(1)Σ(+) are found as the ground, first excited and second excited state, respectively, at the Λ-S level and all these three states are mainly dominated by …π(4)π(*2) configuration. The computed ground state dissociation energy is in very good agreement with the experimental results. In the next stage of calculations, effects of spin-orbit coupling on the potential energy curves and spectroscopic properties of the species are investigated in details and compared with the existing experimental results. After inclusion of spin-orbit coupling the X(3)(1)Σ(-)(0(+)) is found as the ground-state spin component of TeSe. The computed spin-orbit splitting between two components of X(3)Σ(-) state is 1285 cm(-1). Also, significant amount of spin-orbit splitting are found between spin-orbit components (Ω-components) of several other excited states. Transition moments of some important spin-allowed and spin-forbidden transitions are calculated from configuration interaction wave functions. The spin-allowed transition B(3)Σ(-)-X(3)Σ(-) and spin-forbidden transition b(1)Σ(+)(0(+))-X(3)(1)Σ(-)(0(+)) are found to be the strongest in their respective categories. Electric dipole moments of all the bound Λ-S states along with those of the two Ω-components of X(3)Σ(-) are also calculated in the present study.

  19. Systems Based Study of the Therapeutic Potential of Small Charged Molecules for the Inhibition of IL-1 Mediated Cartilage Degradation

    PubMed Central

    Kar, Saptarshi; Smith, David W.; Gardiner, Bruce S.; Grodzinsky, Alan J.

    2016-01-01

    Inflammatory cytokines are key drivers of cartilage degradation in post-traumatic osteoarthritis. Cartilage degradation mediated by these inflammatory cytokines has been extensively investigated using in vitro experimental systems. Based on one such study, we have developed a computational model to quantitatively assess the impact of charged small molecules intended to inhibit IL-1 mediated cartilage degradation. We primarily focus on the simplest possible computational model of small molecular interaction with the IL-1 system—direct binding of the small molecule to the active site on the IL-1 molecule itself. We first use the model to explore the uptake and release kinetics of the small molecule inhibitor by cartilage tissue. Our results show that negatively charged small molecules are excluded from the negatively charged cartilage tissue and have uptake kinetics in the order of hours. In contrast, the positively charged small molecules are drawn into the cartilage with uptake and release timescales ranging from hours to days. Using our calibrated computational model, we subsequently explore the effect of small molecule charge and binding constant on the rate of cartilage degradation. The results from this analysis indicate that the small molecules are most effective in inhibiting cartilage degradation if they are either positively charged and/or bind strongly to IL-1α, or both. Furthermore, our results showed that the cartilage structural homeostasis can be restored by the small molecule if administered within six days following initial tissue exposure to IL-1α. We finally extended the scope of the computational model by simulating the competitive inhibition of cartilage degradation by the small molecule. Results from this model show that small molecules are more efficient in inhibiting cartilage degradation by binding directly to IL-1α rather than binding to IL-1α receptors. The results from this study can be used as a template for the design and

  20. Utilization of photoinduced charge-separated state of donor-acceptor-linked molecules for regulation of cell membrane potential and ion transport.

    PubMed

    Numata, Tomohiro; Murakami, Tatsuya; Kawashima, Fumiaki; Morone, Nobuhiro; Heuser, John E; Takano, Yuta; Ohkubo, Kei; Fukuzumi, Shunichi; Mori, Yasuo; Imahori, Hiroshi

    2012-04-11

    The control of ion transport across cell membranes by light is an attractive strategy that allows targeted, fast control of precisely defined events in the biological membrane. Here we report a novel general strategy for the control of membrane potential and ion transport by using charge-separation molecules and light. Delivery of charge-separation molecules to the plasma membrane of PC12 cells by a membranous nanocarrier and subsequent light irradiation led to depolarization of the membrane potential as well as inhibition of the potassium ion flow across the membrane. Photoregulation of the cell membrane potential and ion transport by using charge-separation molecules is highly promising for control of cell functions.

  1. Double-well potential energy curve of cadmium-krypton molecule in the B1(5(3)P1) excited state.

    PubMed

    Lukomski, M; Koperski, J; Czajkowski, M

    2002-06-01

    The real shape of a double-well B1(5(3)P1)-state potential in CdKr van der Waals molecule was reconstructed applying both the experimental data, using a Birge-Sponer method-based analysis of the B1 <-- X0+(5(1)S0) transition in excitation spectrum, and theoretical result of recent ab initio calculation. An inverse perturbation approach method was used for defining an accurate B1-state potential energy curve.

  2. The Role of Histone Deacetylases in Neurodegenerative Diseases and Small-Molecule Inhibitors as a Potential Therapeutic Approach

    NASA Astrophysics Data System (ADS)

    Bürli, Roland W.; Thomas, Elizabeth; Beaumont, Vahri

    Neurodegenerative disorders are devastating for patients and their social environment. Their etiology is poorly understood and complex. As a result, there is clearly an urgent need for therapeutic agents that slow down disease progress and alleviate symptoms. In this respect, interference with expression and function of multiple gene products at the epigenetic level has offered much promise, and histone deacetylases play a crucial role in these processes. This review presents an overview of the biological pathways in which these enzymes are involved and illustrates the complex network of proteins that governs their activity. An overview of small molecules that interfere with histone deacetylase function is provided.

  3. Kojic acid--a new leading molecule for a preparation of compounds with an anti-neoplastic potential.

    PubMed

    Novotný, L; Rauko, P; Abdel-Hamid, M; Váchalková, A

    1999-01-01

    Kojic acid as a molecule of natural origin may serve as template for the synthesis of new biologically active compounds. The synthetic KA (pyranone) derivatives possess various kinds of biological activities which are related by their similarity to flavonoids. The most important property is the antifungal and antineoplastic activity and capability of chelating metals. It is shown that the antineoplastic activity of kojic acid derivatives is based on various mechanisms of action on different levels of cellular metabolism and functions what makes this compound interesting for future investigation as cytotoxic agent.

  4. Can Femtosecond Transient Absorption Spectroscopy Predict the Potential of Small Molecules as Perspective Donors for Organic Photovoltaics?

    NASA Astrophysics Data System (ADS)

    DiScipio, Regina; Sauve, Genevieve; Crespo-Hernández, Carlos E.

    2015-06-01

    The utility of a perspective donor or acceptor molecule for photoelectric applications is difficult to predict a priori. This hinders productive synthetic exploration and necessitates lengthy device optimization procedures for reasonable estimation of said molecule's applicability. Using femtosecond broadband transient absorption spectroscopy, supported by time-dependent density functional theory computations and steady-state-absorption and emission spectroscopies, we have characterized a family of perspective optoelectronic compounds, in an effort to predict their relative performance in organic photovoltaic devices from information accrued from excited-state dynamics and photophysical properties. A series of tetraphenylazadipyrromethene (ADP) complexes chelated with three different metal centers was investigated. We have determined that the chelating metal has little effect on the ground state properties of this family. However their excited state dynamics are strongly modulated by the metal. Specifically, the zinc-chelated ADP complex remains in the excited state tenfold longer than the cobalt or nickel complexes. We assert that this is key photophysical property that should make the zinc complex outperform the other two complexes in photovoltaic applications. This hypothesis is supported by preliminary power conversion efficiency results in devices.

  5. Laboratory Anion Chemistry: Implications for the DIBs, and a Potential Formation Mechanism for a Known Interstellar Molecule

    NASA Technical Reports Server (NTRS)

    Eichelberger, B.; Barckholtz, C.; Stepanovic, M.; Bierbaum, V.; Snow, T.

    2002-01-01

    Due to recent interest in molecular anions as possible interstellar species, we have carried out several laboratory studies of anion chemistry. The reactions of the series C(sub n)(sup -); and C(sub n)H(sup -) with H and H2 were studied to address the viability of such species in the diffuse interstellar medium and to address their ability to be carriers of the diffuse interstellar bands (DIBs). These same molecules were also reacted with N and O to show possible heteroatomic products. C(sub m)N(sup - was a particularly stable product from the reaction of C(sub n)(sup -) + N. C3N(sup -) was further reacted with H to study chemistry that could produce HC3N, a known interstellar species. The reactions were done in a flowing afterglow selected ion flow tube apparatus (FA-SIFT). The anions were generated in an electron impact or cold cathode discharge source and the anion of interest was then selected by a quadrupole mass filter. The selected ion was then reacted with the atomic or molecular species in the flow tube and products were detected by another quadrupole. While the C(sub n)(sup -) species do not appear to be viable DIB carriers, their possible presence could provide a mechanism for the formation of known heteroatomic neutral molecules detected in the interstellar medium (ISM).

  6. Potential pharmacokinetic interactions of therapeutic cytokines or cytokine modulators on small-molecule drugs: mechanistic understanding via studies using in vitro systems.

    PubMed

    Zhou, Jin; Li, Feng

    2014-01-01

    The potential pharmacokinetic interactions between macromolecules and small-molecule drugs have received more and more attention with the increasing development of macromolecule therapeutics. Studies have shown that cytokines can differentially modulate drug-metabolizing enzymes and transporters, which raises concerns on the potential interactions of therapeutic cytokines and cytokine modulators on the disposition of small-molecule drugs. Although many in vitro studies have been conducted to characterize the effects of cytokines on drug-metabolizing enzymes and transporters, these studies were limited to only a handful of cytokines, such as interleukin-1 (IL-1), IL-6, tumor necrosis factor-α, and interferon. It is also challenging to translate these in vitro results to in vivo. In addition, information on the impact of cytokine modulators on drug-metabolizing enzymes and transporters is rather limited. More research is needed in this area. The present review is to provide a summary of the in vitro findings on the pharmacokinetic interactions of therapeutic cytokines and cytokine modulators on small-molecule drugs. Discussion on current challenges in assessing these interactions is also included.

  7. Dissociation of multiple hydrogen molecules on the non-planar aluminium cluster: stationary points on the Al6 + nH2 potential energy surface

    NASA Astrophysics Data System (ADS)

    Moc, Jerzy

    2013-02-01

    Compared to clusters of transition metal atoms, H-H bond activation by main Group metal clusters is much less known. Here, we have examined a potential new way of obtaining a novel alane Al6H8 through addition of multiple H2 molecules to the aluminium hexamer, i.e., Al6 + nH2 (n=1-4) reactions. To this end, systematic high level quantum chemical modeling calculations using density functional theory (DFT) and coupled-cluster singles-doubles-perturbative triples (CCSD(T)) method in conjunction with the aug-cc-pVTZ basis set were performed to identify the lowest energy barrier paths for the consecutive dissociation of several hydrogen molecules on Al6, the smallest aluminium cluster with a three-dimensional ground-state structure. These computational results are relevant to the issues of hydrogen storage and novel stable alanes.

  8. Toward a List of Molecules as Potential Biosignature Gases for the Search for Life on Exoplanets and Applications to Terrestrial Biochemistry

    NASA Astrophysics Data System (ADS)

    Seager, S.; Bains, W.; Petkowski, J. J.

    2016-06-01

    Thousands of exoplanets are known to orbit nearby stars. Plans for the next generation of space-based and ground-based telescopes are fueling the anticipation that a precious few habitable planets can be identified in the coming decade. Even more highly anticipated is the chance to find signs of life on these habitable planets by way of biosignature gases. But which gases should we search for? Although a few biosignature gases are prominent in Earth's atmospheric spectrum (O2, CH4, N2O), others have been considered as being produced at or able to accumulate to higher levels on exo-Earths (e.g., dimethyl sulfide and CH3Cl). Life on Earth produces thousands of different gases (although most in very small quantities). Some might be produced and/or accumulate in an exo-Earth atmosphere to high levels, depending on the exo-Earth ecology and surface and atmospheric chemistry. To maximize our chances of recognizing biosignature gases, we promote the concept that all stable and potentially volatile molecules should initially be considered as viable biosignature gases. We present a new approach to the subject of biosignature gases by systematically constructing lists of volatile molecules in different categories. An exhaustive list up to six non-H atoms is presented, totaling about 14,000 molecules. About 2500 of these are CNOPSH compounds. An approach for extending the list to larger molecules is described. We further show that about one-fourth of CNOPSH molecules (again, up to N = 6 non-H atoms) are known to be produced by life on Earth. The list can be used to study classes of chemicals that might be potential biosignature gases, considering their accumulation and possible false positives on exoplanets with atmospheres and surface environments different from Earth's. The list can also be used for terrestrial biochemistry applications, some examples of which are provided. We provide an online community usage database to serve as a registry for volatile molecules including

  9. Folate deficiency and aberrant expression of cell adhesion molecule 1 are potential indicators of prognosis in laryngeal squamous cell carcinoma

    PubMed Central

    Chang, Hao; Ma, Min; Ma, Rui; Zhang, Chao; Zeng, Wei; Xing, Lu Qi

    2016-01-01

    The etiology of laryngeal squamous cell carcinoma (LSCC) has not yet been adequately examined. Therefore, the present study aimed to investigate the association between serum folate deficiency and abnormal expression of the cell adhesion molecule 1 (CADM1) protein in the progression of LSCC. Samples were collected from 60 patients with LSCC and 30 healthy people. Radioimmunoassays and immunohistochemical staining were performed to measure serum folate levels and CADM1 protein expression, respectively. The results demonstrated that CADM1 expression in LSCC specimens was significantly lower than in adjacent normal tissues (χ2=28.229, P<0.001), which was associated with histological differentiation and clinical stage (P=0.010 and 0.020, respectively). Levels of serum folate in patients with LSCC were significantly lower than those observed in healthy individuals (P=0.002). Furthermore, TSLCl expression and serum folate levels were positively correlated in LSCC (r=0.642, P=0.001). Thus, the present study determined that decreased CADM1 protein expression and low levels of serum folate were correlated with an increased severity of LSCC. PMID:28105160

  10. Klein-Gordon equation particles in exponential-type molecule potentials and their thermodynamic properties in D dimensions

    NASA Astrophysics Data System (ADS)

    Ikot, A. N.; Lutfuoglu, B. C.; Ngwueke, M. I.; Udoh, M. E.; Zare, S.; Hassanabadi, H.

    2016-12-01

    In this paper we use the Nikiforov-Uvarov method to obtain the approximate solutions for the Klein-Gordon equation with the deformed five-parameter exponential-type potential (DFPEP) model. We also obtain solutions for the Schrödinger equation in the presence of DFPEP in non-relativistic limits. In addition, we calculate in the non-relativistic limits thermodynamics properties, such as vibrational mean energy U, free energy F and the specific heat capacity C. Special cases of the potential are also discussed.

  11. Two-electron R-matrix approach to calculations of potential-energy curves of long-range Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Tarana, Michal; Čurík, Roman

    2016-05-01

    We introduce a computational method developed for study of long-range molecular Rydberg states of such systems that can be approximated by two electrons in a model potential of the atomic cores. The method is based on a two-electron R-matrix approach inside a sphere centered on one of the atoms. The wave function is then connected to a Coulomb region outside the sphere via a multichannel version of the Coulomb Green's function. This approach is applied to a study of Rydberg states of Rb2 for internuclear separations R from 40 to 320 bohrs and energies corresponding to n from 7 to 30. We report bound states associated with the low-lying 3Po resonance and with the virtual state of the rubidium atom that turn into ion-pair-like bound states in the Coulomb potential of the atomic Rydberg core. The results are compared with previous calculations based on single-electron models employing a zero-range contact-potential and short-range modele potential. Czech Science Foundation (Project No. P208/14-15989P).

  12. The Chirped-Pulse Fourier Transform Microwave Cp-Ftmw Spectrum and Potential Energy Calculations for AN Aromatic Claisen Rearrangement Molecule, Allyl Phenyl Ether

    NASA Astrophysics Data System (ADS)

    Grubbs, G. S. Grubbs, Ii; Cooke, S. A.; Novick, Stewart E.

    2012-06-01

    Claisen rearrangement ethers are a fundamental organic, pericyclic rearrangement reaction reagent. In the mechanism of a Claisen rearrangement, a vinyl allyl ether is needed to provide the necessary Lewis acid/base sites on the molecule for the rearrangement and are simply heated. This rearrangement was first discovered by heating up the title molecule, allyl phenyl ether. However, much like the Diels-Alder, Cope, and other pericyclic reactions, conformation and coordination of chemical groups is key to the Claisen mechanism. In this study, the authors present some structural characteristics of allyl phenyl ether from an analysis of the microwave spectra in the 8-14 GHz region using a CP-FTMW spectrometer. This is, to the authors knowledge, the first known microwave region study of the title molecule. Three conformers have been observed and assigned to date and will be discussed. Along with the rotational spectra, geometry calculations and potential energy surfaces performed at the MP2/6-311G++(3d,2p) level will be discussed and compared to the experimental results. Modeling the Claisen aromatic rearrangement mechanism using CP-FTMW spectroscopy will also be discussed. L. Claisen Chemische Berichte 45, 3157, October 1912.

  13. Small and efficient basis sets for the evaluation of accurate interaction energies: aromatic molecule-argon ground-state intermolecular potentials and rovibrational states.

    PubMed

    Cybulski, Hubert; Baranowska-Łączkowska, Angelika; Henriksen, Christian; Fernández, Berta

    2014-11-06

    By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these

  14. A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules

    PubMed Central

    Nagarajan, Balaji; Sankaranarayanan, Nehru Viji; Patel, Bhaumik B.

    2017-01-01

    Glycosaminoglycans (GAGs) are key natural biopolymers that exhibit a range of biological functions including growth and differentiation. Despite this multiplicity of function, natural GAG sequences have not yielded drugs because of problems of heterogeneity and synthesis. Recently, several homogenous non-saccharide glycosaminoglycan mimetics (NSGMs) have been reported as agents displaying major therapeutic promise. Yet, it remains unclear whether sulfated NSGMs structurally mimic sulfated GAGs. To address this, we developed a three-step molecular dynamics (MD)-based algorithm to compare sulfated NSGMs with GAGs. In the first step of this algorithm, parameters related to the range of conformations sampled by the two highly sulfated molecules as free entities in water were compared. The second step compared identity of binding site geometries and the final step evaluated comparable dynamics and interactions in the protein-bound state. Using a test case of interactions with fibroblast growth factor-related proteins, we show that this three-step algorithm effectively predicts the GAG structure mimicking property of NSGMs. Specifically, we show that two unique dimeric NSGMs mimic hexameric GAG sequences in the protein-bound state. In contrast, closely related monomeric and trimeric NSGMs do not mimic GAG in either the free or bound states. These results correspond well with the functional properties of NSGMs. The results show for the first time that appropriately designed sulfated NSGMs can be good structural mimetics of GAGs and the incorporation of a MD-based strategy at the NSGM library screening stage can identify promising mimetics of targeted GAG sequences. PMID:28182755

  15. Electrostatic Potential Determined Magnetic Dynamics Observed in Two Mononuclear β-Diketone Dysprosium(III) Single-Molecule Magnets.

    PubMed

    Cen, Pei-Pei; Zhang, Sheng; Liu, Xiang-Yu; Song, Wei-Ming; Zhang, Yi-Quan; Xie, Gang; Chen, San-Ping

    2017-03-20

    Two β-diketone mononuclear Dy(III) compounds, formulated as Dy(BTFA)3(H2O)2 (1) and Dy(BTFA)3(bpy) (2) (BTFA = 3-benzoyl-1,1,1-trifluoroacetone, bpy = 2,2'-bipyridine), were prepared. Compound 1 can be identified to transform to 2 in the attendance of bpy coligand, when the local geometry symmetry of eight-coordinated Dy(III) ion changes from a dodecahedron (D2d) in 1 to a square antiprism (D4d) in 2. Fine-tuning structure aroused by auxiliary ligand has dramatical impact on magnetic properties of compounds 1 and 2. Magnetic investigations demonstrate that both 1 and 2 display dynamic magnetic relaxation of single-molecule magnets (SMMs) behavior with different effective barriers (ΔE/kB) of 93.09 K for 1 under zero direct-current (DC) field as well as 296.50 K for 1 and 151.01 K for 2 under 1200 Oe DC field, respectively. As noticed, compound 1 possesses higher effective barrier than 2, despite 1 exhibiting a lower geometrical symmetry of the Dy(III) ion. Ab initio studies reveal that the Kramers doublet ground state is predominantly axial with the gz tensors of two compounds matching the Ising-limit factor of 20 anticipated for the pure MJ = ±15/2 state. Electrostatic analysis confirms the uniaxial anisotropy directions, highlighting that the proper electrostatic distribution of the coordination sphere around Ln(III) center is the critical factor to improve the magnetic anisotropy and determine the dynamic behaviors of SMMs.

  16. The significance of interaction potentials of water with other molecules in the EOS of high explosives products

    SciTech Connect

    van Thiel, M.; Ree, F.H.; Haselman, L.C. Jr.

    1993-07-01

    The chemical equilibrium and thermodynamic properties of detonated explosive mixtures at high temperature (T) and pressure (P) depend critically on all interactions between the major products. Improvements in the homomolecular interaction of nitrogen, carbon-dioxide, and condensed carbon have had significant effects on detonation properties of LX-14 (an HMX formulation). Extensive work on O, N, and C products also showed the importance of including high temperature unstable species in determining the potential-constant of the major products of detonation. That work also showed the need to improve the unlike pair interaction constants in our statistical mechanical chemical equilibrium theory (CHEQ). Thirdly, a recent comparison of experimental and theoretical detonation velocities (D) indicated that the original set of interaction potentials used contains canceling errors that limit the overall effectiveness of the code as a predictor of high P and T properties of reactive mixtures. This study proceeds from explosives with simple product mixtures, RX-23-AB, HNB, and PETN, to HMX-like mixtures. The present set of potential constants is compared to the experimental EOS used for a number of experimental systems that use LX-14.

  17. An Improved Empirical Potential for the Highly Multi-Reference Sextuply Bonded Transition Metal Benchamrk Molecule Cr_2

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.; Tomza, Michal; Li Manni, Giovanni

    2016-06-01

    The ground electronic state of the chromium dimer dissociates into Cr (^7S) + Cr (^7S) and therefore the fragments are highly open shell systems with a total of 12 singly occupied orbitals among its constituent atoms. It is considered one of the most difficult homonuclear diatomics for ab initio methods because of its highly multi-reference character. Therefore, every new multi-reference method must be tested against this benchmark system. However, the best empirical potential to compare with, has its own weaknesses. The photoelectron measurements of v=0-9 were fitted to a Morse potential (an old function which has only one parameter controlling the shape from r_e to D_e), and also inverted using a semi-classical theory into a potential after combining these data with measurements from what were hypothesized to be v=24-43. This bridging of a ˜2000 cm-1 gap in data back in 1993 was a valiant spectroscopic analysis. However since 1993, there have been enormous improvements in the field of potentiology. In 2011 a Morse/long-range (MLR) function successfully bridged a gap of more than 5000 cm-1 in experimental data^a, and in 2013 an experiment with ±0.000 02 cm-1 resolution confirmed that the 2011 MLR predicted the energy levels in the very center of this gap correctly within ˜ 1 cm-1,^b. While ab initio methods have very recently been able to predict differences in energy levels correctly to within 1 cm-1 for Li_2 ^c and to a lesser extent for BeH^d, ab initio methods have still not had this level of success for predicting binding energies. The MLR function not only has more flexibility than the original Morse function, but it also converges mathematically to the correct long-range limit expected by the state-of-the-art theory. Fitting the data to an MLR potential function in the Schrödinger equation allows for a fully quantum mechanical treatment over the entire range of data. By avoiding a semi-classical treatment, and using this more flexible, more

  18. The extracellular matrix molecule tenascin-R and its HNK-1 carbohydrate modulate perisomatic inhibition and long-term potentiation in the CA1 region of the hippocampus.

    PubMed

    Saghatelyan, A K; Gorissen, S; Albert, M; Hertlein, B; Schachner, M; Dityatev, A

    2000-09-01

    Perisomatic inhibition of pyramidal cells regulates efferent signalling from the hippocampus. The striking presence of HNK-1, a carbohydrate expressed by neural adhesion molecules, on perisomatic interneurons and around somata of CA1 pyramidal neurons led us to apply monoclonal HNK-1 antibodies to acute murine hippocampal slices. Injection of these antibodies decreased GABAA receptor-mediated perisomatic inhibitory postsynaptic currents (pIPSCs) but did not affect dendritic IPSCs or excitatory postsynaptic currents. The decrease in the mean amplitude of evoked pIPSCs by HNK-1 antibodies was accompanied by an increase in the coefficient of variation of pIPSC amplitude, number of failures and changes in frequency but not amplitude of miniature IPSCs, suggesting that HNK-1 antibodies reduced efficacy of evoked GABA release. HNK-1 antibodies did not affect pIPSCs in knock-out mice deficient in the extracellular matrix molecule tenascin-R which carries the HNK-1 carbohydrate as analysed by immunoblotting in synaptosomal fractions prepared from the CA1 region of the hippocampus. For control, HNK-1 antibody was applied to acute sections of mice deficient in the neural cell adhesion molecule NCAM, another potential carrier of HNK-1, and resulted in decrease of pIPSCs as observed in wild-type mice. Reduction in perisomatic inhibition is expected to promote induction of long-term potentiation (LTP) by increasing the level of depolarization during theta-burst stimulation. Indeed, LTP was increased by HNK-1 antibody applied before stimulation. Moreover, LTP was reduced by an HNK-1 peptide mimic, but not control peptide. These results provide first evidence that tenascin-R and its associated HNK-1 carbohydrate modulate perisomatic inhibition and synaptic plasticity in the hippocampus.

  19. Second-harmonic generation of biological interfaces: probing the membrane protein bacteriorhodopsin and imaging membrane potential around GFP molecules at specific sites in neuronal cells of C. elegans

    NASA Astrophysics Data System (ADS)

    Lewis, Aaron; Khatchatouriants, Artium; Treinin, Millet; Chen, Zhongping; Peleg, Gadi; Friedman, Noga; Bouevitch, Oleg; Rothman, Zvi; Loew, Leslie; Sheres, Mordechai

    1999-07-01

    Second-harmonic generation (SHG) is applied to problems of probing membrane proteins and functionally imaging around selective sites and at single molecules in biological membranes. The membrane protein bacteriorhodopsin (bR) has been shown to have large second-harmonic (SH) intensities that are modulated by protein/retinylidene chromophore interactions. The nonlinear optical properties of model compounds, which simulate these protein chromophore interactions in retinal proteins, are studied in this work by surface SHG and by hyper-Rayleigh scattering. Our results indicate that non-conjugated charges and hydrogen bonding effects have a large effect on the molecular hyperpolarizability of the retinal chromophore. However, mbR, the model system studies suggest that polarizable amino acids strongly affect the vertically excited state of the retinylidene chromophore and appear to play the major role in the observed protein enhancement (>50%) of the retinylidene chromophore molecular hyperpolarizability and associated induced dipole. Furthermore, the data provide insights on emulating these interactions for the design of organic nonlinear optical materials. Our studies have also led to the development of dyes with large SH intensities that can be embedded in cell membranes and can functionally image membrane potential. Single molecules of such dyes in selected single molecular regions of a cell membrane have been detected. SHG from green fluorescent protein (GFP) selectively expressed in concert with a specific protein in neuronal cells in a transgenic form of the worm C. elegans is also reported. The membrane potential around the GFP molecules expressed in these cells has been imaged with SHG in live animals.

  20. Angle-Dependent Ionization of Small Molecules by Time-Dependent Configuration Interaction and an Absorbing Potential.

    PubMed

    Krause, Pascal; Schlegel, H Bernhard

    2015-06-04

    The angle-dependence of strong field ionization of O2, N2, CO2, and CH2O has been studied theoretically using a time-dependent configuration interaction approach with a complex absorbing potential (TDCIS-CAP). Calculation of the ionization yields as a function of the direction of polarization of the laser pulse produces three-dimensional surfaces of the angle-dependent ionization probability. These three-dimensional shapes and their variation with laser intensity can be interpreted in terms of ionization from the highest occupied molecular orbital (HOMO) and lower lying orbitals, and the Dyson orbitals for the ground and excited states of the cations.

  1. Small-molecule inhibitors of proteins involved in base excision repair potentiate the anti-tumorigenic effect of existing chemotherapeutics and irradiation

    PubMed Central

    Reed, April M; Fishel, Melissa L; Kelley, Mark R

    2009-01-01

    There has been a recent upsurge in the development of small-molecule inhibitors specific to DNA repair proteins or proteins peripherally involved in base excision repair and the DNA damage response. These specific, nominally toxic inhibitors are able to potentiate the effect of existing cancer cell treatments in a wide array of cancers. One of the largest obstacles to overcome in the treatment of cancer is incomplete killing with initial cancer treatments, leading to resistant cancer. The progression of our understanding of cancer and normal cell responses to DNA damage has allowed us to develop biomarkers that we can use to help us predict responses of cancers, more specifically target cancer cells and overcome resistance. Initial successes using these small-molecule DNA repair inhibitors in target-validation experiments and in the early stages of clinical trials indicate an important role for these inhibitors, and allow for the possibility of a future in which cancers are potentially treated in a highly specific, individual manner. PMID:19519210

  2. Fragrances and other materials in deodorants: search for potentially sensitizing molecules using combined GC-MS and structure activity relationship (SAR) analysis.

    PubMed

    Rastogi, S C; Lepoittevin, J P; Johansen, J D; Frosch, P J; Menné, T; Bruze, M; Dreier, B; Andersen, K E; White, I R

    1998-12-01

    Deodorants are one of the most frequently-used types of cosmetics and are a source of allergic contact dermatitis. Therefore, a gas chromatography - mass spectrometric analysis of 71 deodorants was performed for identification of fragrance and non-fragrance materials present in marketed deodorants. Futhermore, the sensitizing potential of these molecules was evaluated using structure activity relationships (SARs) analysis. This was based on the presence of 1 or more chemically reactive site(s), in the chemical structure, associated with sensitizing potential. Among the many different substances used to formulate cosmetic products (over 3500), 226 chemicals were identified in a sample of 71 deodorants. 84 molecules were found to contain at least 1 structural alert, and 70 to belong to, or be susceptible to being metabolized into, the chemical group of aldehydes, ketones and alpha,beta-unsaturated aldehydes, ketone or esters. The combination of GC-MS and SARs analysis could be helpful in the selection of substances for supplementary investigations regarding sensitizing properties. Thus, it may be a valuable tool in the management of contact allergy to deodorants and for producing new deodorants with decreased propensity to cause contact allergy.

  3. Rotation and vibration of diatomic molecule in the spatially-dependent mass Schrödinger equation with generalized q-deformed Morse potential

    NASA Astrophysics Data System (ADS)

    Ikhdair, Sameer M.

    2009-06-01

    The analytic solutions of the spatially-dependent mass Schrödinger equation of diatomic molecules with the centrifugal term l(l+1)/r2 for the generalized q-deformed Morse potential are obtained approximately by means of a parametric generalization of the Nikiforov-Uvarov (NU) method combined with the Pekeris approximation scheme. The energy eigenvalues and the corresponding normalized radial wave functions are calculated in closed form with a physically motivated choice of a reciprocal Morse-like mass function, m(r)=m0/(1-δe)2,0⩽δ<1, where a and re are the range of the potential and the equilibrium position of the nuclei. The constant mass case when δ→0 is also studied. The energy states for H 2, LiH, HCl and CO diatomic molecules are calculated and compared favourably well with those obtained by using other approximation methods for arbitrary vibrational n and rotational l quantum numbers.

  4. Vasorelaxant activity of extracts obtained from Apium graveolens: Possible source for vasorelaxant molecules isolation with potential antihypertensive effect

    PubMed Central

    Jorge, Vergara-Galicia; Ángel, Jimenez-Ramirez Luis; Adrián, Tun-Suarez; Francisco, Aguirre-Crespo; Anuar, Salazar-Gómez; Samuel, Estrada-Soto; Ángel, Sierra-Ovando; Emmanuel, Hernandez-Nuñez

    2013-01-01

    Objective To investigate vasorelaxant effect of organic extracts from Apium graveolens (A. graveolens) which is a part of a group of plants subjected to pharmacological and phytochemical study with the purpose of offering it as an ideal source for obtaining lead compounds for designing new therapeutic agents with potential vasorelaxant and antihypertensive effects. Methods An ex vivo method was employed to assess the vasorelaxant activity. This consisted of using rat aortic rings with and without endothelium precontracted with norepinephrine. Results All extracts caused concentration-dependent relaxation in precontracted aortic rings with and without endothelium; the most active extracts were Dichloromethane and Ethyl Acetate extracts from A. graveolens. These results suggested that secondary metabolites responsible for the vasorelaxant activity belong to a group of compounds of medium polarity. Also, our evidence showed that effect induced by dichloromethane and ethyl acetate extracts from A. graveolens is mediated probably by calcium antagonism. Conclusions A. graveolens represents an ideal source for obtaining lead compounds for designing new therapeutic agents with potential vasorelaxant and antihypertensive effects. PMID:24075341

  5. Modeling of Human Prokineticin Receptors: Interactions with Novel Small-Molecule Binders and Potential Off-Target Drugs

    PubMed Central

    Levit, Anat; Yarnitzky, Talia; Wiener, Ayana; Meidan, Rina; Niv, Masha Y.

    2011-01-01

    Background and Motivation The Prokineticin receptor (PKR) 1 and 2 subtypes are novel members of family A GPCRs, which exhibit an unusually high degree of sequence similarity. Prokineticins (PKs), their cognate ligands, are small secreted proteins of ∼80 amino acids; however, non-peptidic low-molecular weight antagonists have also been identified. PKs and their receptors play important roles under various physiological conditions such as maintaining circadian rhythm and pain perception, as well as regulating angiogenesis and modulating immunity. Identifying binding sites for known antagonists and for additional potential binders will facilitate studying and regulating these novel receptors. Blocking PKRs may serve as a therapeutic tool for various diseases, including acute pain, inflammation and cancer. Methods and Results Ligand-based pharmacophore models were derived from known antagonists, and virtual screening performed on the DrugBank dataset identified potential human PKR (hPKR) ligands with novel scaffolds. Interestingly, these included several HIV protease inhibitors for which endothelial cell dysfunction is a documented side effect. Our results suggest that the side effects might be due to inhibition of the PKR signaling pathway. Docking of known binders to a 3D homology model of hPKR1 is in agreement with the well-established canonical TM-bundle binding site of family A GPCRs. Furthermore, the docking results highlight residues that may form specific contacts with the ligands. These contacts provide structural explanation for the importance of several chemical features that were obtained from the structure-activity analysis of known binders. With the exception of a single loop residue that might be perused in the future for obtaining subtype-specific regulation, the results suggest an identical TM-bundle binding site for hPKR1 and hPKR2. In addition, analysis of the intracellular regions highlights variable regions that may provide subtype specificity

  6. Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. III. Discontinuous potentials.

    PubMed

    Uline, Mark J; Corti, David S

    2008-07-07

    Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.

  7. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  8. Theoretical study on the ground state of the polar alkali-metal-barium molecules: Potential energy curve and permanent dipole moment

    SciTech Connect

    Gou, Dezhi; Kuang, Xiaoyu Gao, Yufeng; Huo, Dongming

    2015-01-21

    In this paper, we systematically investigate the electronic structure for the {sup 2}Σ{sup +} ground state of the polar alkali-metal-alkaline-earth-metal molecules BaAlk (Alk = Li, Na, K, Rb, and Cs). Potential energy curves and permanent dipole moments (PDMs) are determined using power quantum chemistry complete active space self-consistent field and multi-reference configuration interaction methods. Basic spectroscopic constants are derived from ro-vibrational bound state calculation. From the calculations, it is shown that BaK, BaRb, and BaCs molecules have moderate values of PDM at the equilibrium bond distance (BaK:1.62 D, BaRb:3.32 D, and BaCs:4.02 D). Besides, the equilibrium bond length (4.93 Å and 5.19 Å) and dissociation energy (0.1825 eV and 0.1817 eV) for the BaRb and BaCs are also obtained.

  9. Theoretical study on the ground state of the polar alkali-metal-barium molecules: Potential energy curve and permanent dipole moment

    NASA Astrophysics Data System (ADS)

    Gou, Dezhi; Kuang, Xiaoyu; Gao, Yufeng; Huo, Dongming

    2015-01-01

    In this paper, we systematically investigate the electronic structure for the 2Σ+ ground state of the polar alkali-metal-alkaline-earth-metal molecules BaAlk (Alk = Li, Na, K, Rb, and Cs). Potential energy curves and permanent dipole moments (PDMs) are determined using power quantum chemistry complete active space self-consistent field and multi-reference configuration interaction methods. Basic spectroscopic constants are derived from ro-vibrational bound state calculation. From the calculations, it is shown that BaK, BaRb, and BaCs molecules have moderate values of PDM at the equilibrium bond distance (BaK:1.62 D, BaRb:3.32 D, and BaCs:4.02 D). Besides, the equilibrium bond length (4.93 Å and 5.19 Å) and dissociation energy (0.1825 eV and 0.1817 eV) for the BaRb and BaCs are also obtained.

  10. Selective inhibition of MBNL1–CCUG interaction by small molecules toward potential therapeutic agents for myotonic dystrophy type 2 (DM2)†

    PubMed Central

    Wong, Chun-Ho; Fu, Yuan; Ramisetty, Sreenivasa Rao; Baranger, Anne M.; Zimmerman, Steven C.

    2011-01-01

    Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disease caused by expanded CCUG repeats that may exhibit toxicity by sequestering the splicing regulator MBNL1. A series of triaminotriazine- and triaminopyrimidine-based small molecules (ligands 1–3) were designed, synthesized and tested as inhibitors of the MBNL1–CCUG interaction. Despite the structural similarities of the triaminotriazine and triaminopyrimidine units, the triaminopyrimidine-based ligands bind with low micromolar affinity to CCUG repeats (Kd ∼ 0.1–3.6 µM) whereas the triaminotriazine ligands do not bind CCUG repeats. Importantly, these simple and small triaminopyrimidine ligands exhibit both strong inhibition (Ki ∼ 2 µM) of the MBNL1–CCUG interaction and high selectivity for CCUG repeats over other RNA targets. These experiments suggest these compounds are potential lead agents for the treatment of DM2. PMID:21768123

  11. Ab initio ro-vibrational Hamiltonian in irreducible tensor formalism: a method for computing energy levels from potential energy surfaces for symmetric-top molecules

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, Vl. G.

    2010-08-01

    A theoretical approach to study ro-vibrational molecular states from a full nuclear Hamiltonian expressed in terms of normal-mode irreducible tensor operators is presented for the first time. Each term of the Hamiltonian expansion can thus be cast in the tensor form in a systematic way using the formalism of ladder operators. Pyramidal XY3 molecules appear to be good candidates to validate this approach which allows taking advantage of the symmetry properties when doubly degenerate vibrational modes are considered. Examples of applications will be given for PH3 where variational calculations have been carried out from our recent potential energy surface [Nikitin et al., J. Chem. Phys. 130, 244312 (2009)].

  12. Thermodynamics properties study of diatomic molecules with q-deformed modified Poschl-Teller plus Manning Rosen non-central potential in D dimensions using SUSYQM approach

    NASA Astrophysics Data System (ADS)

    Suparmi, A.; Cari, C.; Pratiwi, B. N.

    2016-04-01

    D-dimensional Dirac equation of q-deformed modified Poschl-Teller plus Manning Rosen non-central potential was solved using supersymmetric quantum mechanics (SUSY QM). The relativistic energy spectra were analyzed by using SUSY QM and shape invariant properties from radial part of D dimensional Dirac equation and the angular quantum numbers were obtained from angular part of D dimensional Dirac equation. The SUSY operators was used to generate the D dimensional relativistic wave functions both for radial and angular parts. In the non-relativistic limit, the relativistic energy equation was reduced to the non-relativistic energy. In the classical limit, the partition function of vibrational, the specific heat of vibrational, and the mean energy of vibrational of some diatomic molecules were calculated from the equation of non-relativistic energy with the help of error function and Mat-lab 2011.

  13. Virtual screening of natural inhibitors to the predicted HBx protein structure of Hepatitis B Virus using molecular docking for identification of potential lead molecules for liver cancer

    PubMed Central

    Pathak, Rajesh Kumar; Baunthiyal, Mamta; Taj, Gohar; Kumar, Anil

    2014-01-01

    The HBx protein in Hepatitis B Virus (HBV) is a potential target for anti-liver cancer molecules. Therefore, it is of interest to screen known natural compounds against the HBx protein using molecular docking. However, the structure of HBx is not yet known. Therefore, the predicted structure of HBx using threading in LOMET was used for docking against plant derived natural compounds (curcumin, oleanolic acid, resveratrol, bilobetin, luteoline, ellagic acid, betulinic acid and rutin) by Molegro Virtual Docker. The screening identified rutin with binding energy of -161.65 Kcal/mol. Thus, twenty derivatives of rutin were further designed and screened against HBx. These in silico experiments identified compounds rutin01 (-163.16 Kcal/mol) and rutin08 (- 165.76 Kcal/mol) for further consideration and downstream validation. PMID:25187683

  14. Brain-Penetrant, Orally Bioavailable Microtubule-Stabilizing Small Molecules Are Potential Candidate Therapeutics for Alzheimer’s Disease and Related Tauopathies

    PubMed Central

    2015-01-01

    Microtubule (MT) stabilizing drugs hold promise as potential treatments for Alzheimer’s disease (AD) and related tauopathies. However, thus far epothilone D has been the only brain-penetrant MT-stabilizer to be evaluated in tau transgenic mice and in AD patients. Furthermore, this natural product exhibits potential deficiencies as a drug candidate, including an intravenous route of administration and the inhibition of the P-glycoprotein (Pgp) transporter. Thus, the identification of alternative CNS-active MT-stabilizing agents that lack these potential limitations is of interest. Toward this objective, we have evaluated representative compounds from known classes of non-naturally occurring MT-stabilizing small molecules. This led to the identification of selected triazolopyrimidines and phenylpyrimidines that are orally bioavailable and brain-penetrant without disruption of Pgp function. Pharmacodynamic studies confirmed that representative compounds from these series enhance MT-stabilization in the brains of wild-type mice. Thus, these classes of MT-stabilizers hold promise for the development of orally active, CNS-directed MT-stabilizing therapies. PMID:24992153

  15. Redox potentials of primary electron acceptor quinone molecule (QA)- and conserved energetics of photosystem II in cyanobacteria with chlorophyll a and chlorophyll d.

    PubMed

    Allakhverdiev, Suleyman I; Tsuchiya, Tohru; Watabe, Kazuyuki; Kojima, Akane; Los, Dmitry A; Tomo, Tatsuya; Klimov, Vyacheslav V; Mimuro, Mamoru

    2011-05-10

    In a previous study, we measured the redox potential of the primary electron acceptor pheophytin (Phe) a of photosystem (PS) II in the chlorophyll d-dominated cyanobacterium Acaryochloris marina and a chlorophyll a-containing cyanobacterium, Synechocystis. We obtained the midpoint redox potential (E(m)) values of -478 mV for A. marina and -536 mV for Synechocystis. In this study, we measured the redox potentials of the primary electron acceptor quinone molecule (Q(A)), i.e., E(m)(Q(A)/Q(A)(-)), of PS II and the energy difference between [P680·Phe a(-)·Q(A)] and [P680·Phe a·Q(A)(-)], i.e., ΔG(PhQ). The E(m)(Q(A)/Q(A)(-)) of A. marina was determined to be +64 mV without the Mn cluster and was estimated to be -66 to -86 mV with a Mn-depletion shift (130-150 mV), as observed with other organisms. The E(m)(Phe a/Phe a(-)) in Synechocystis was measured to be -525 mV with the Mn cluster, which is consistent with our previous report. The Mn-depleted downshift of the potential was measured to be approximately -77 mV in Synechocystis, and this value was applied to A. marina (-478 mV); the E(m)(Phe a/Phe a(-)) was estimated to be approximately -401 mV. These values gave rise to a ΔG(PhQ) of -325 mV for A. marina and -383 mV for Synechocystis. In the two cyanobacteria, the energetics in PS II were conserved, even though the potentials of Q(A)(-) and Phe a(-) were relatively shifted depending on the special pair, indicating a common strategy for electron transfer in oxygenic photosynthetic organisms.

  16. Cellular toxicity induced by the photorelease of a caged bioactive molecule: design of a potential dual-action Ru(II) complex.

    PubMed

    Sgambellone, Mark A; David, Amanda; Garner, Robert N; Dunbar, Kim R; Turro, Claudia

    2013-07-31

    The series [Ru(tpy)(CH3CN)3](2+) (1), cis-[Ru(tpy)(CH3CN)2Cl](+) (2), and [Ru(tpy)(5CNU)3](2+) (3), where tpy = 2,2':6',2″-terpyridine and 5CNU = 5-cyanouracil, was synthesized, and their photochemical properties were investigated for use as potential photodynamic therapy (PDT) agents. When irradiated with visible light, 1-3 exhibit efficient exchange of the axial CH3CN or 5CNU ligand with H2O solvent molecules. Complexes 1-3 also exhibit photoinitiated binding to DNA when irradiated with λirr ≥ 395 nm light, and DNA binding can be accessed for 2 with λirr > 645 nm, well within the PDT window. Since 3 binds DNA and simultaneously releases biologically active 5CNU, it has the potential to be a dual-action therapeutic agent. Indeed, 3 is cytotoxic upon irradiation with visible light, whereas 1 is not under similar experimental conditions. The lack of toxicity imparted by 1 is explained by the exchange of only one CH3CN ligand in the complex under the irradiation conditions used for the cellular studies. Strategies are being sought to increase the quantum yields of ligand exchange and the cellular penetration of these compounds.

  17. Full dimensional potential energy surface for the ground state of H{sub 4}{sup +} system based on triatomic-in-molecules formalism

    SciTech Connect

    Sanz-Sanz, Cristina E-mail: cristina.sanz@gmail.com; Roncero, Octavio; Paniagua, Miguel; Aguado, Alfredo

    2013-11-14

    In this work, we present a global potential energy surface for the ground electronic state of the H{sub 4}{sup +} based on ab initio calculations. The final fit is based on triatomics-in-molecules (TRIM) approximation and it includes extra four-body terms for the better description of some discrepancies found on the TRIM model. The TRIM method itself allows a very accurate description of the asymptotic regions. The global fit uses more than 19 000 multireference configuration interaction ab initio points. The global potential energy surface has an overall root mean square error of 0.013 eV for energies up to 2 eV above the global minimum. This work presents an analysis of the stationary points, reactant and product channels, and crossing between the two lowest TRIM adiabatic states. It is as well included a brief description of the two first excited states of the TRIM matrix, concluding that TRIM method is a very good approximation not only for the ground state but also for at least two of the excited states of H{sub 4}{sup +} system.

  18. Fixed-node diffusion Monte Carlo potential energy curve of the fluorine molecule F{sub 2} using selected configuration interaction trial wavefunctions

    SciTech Connect

    Giner, Emmanuel; Scemama, Anthony; Caffarel, Michel

    2015-01-28

    The potential energy curve of the F{sub 2} molecule is calculated with Fixed-Node Diffusion Monte Carlo (FN-DMC) using Configuration Interaction (CI)-type trial wavefunctions. To keep the number of determinants reasonable and thus make FN-DMC calculations feasible in practice, the CI expansion is restricted to those determinants that contribute the most to the total energy. The selection of the determinants is made using the CIPSI approach (Configuration Interaction using a Perturbative Selection made Iteratively). The trial wavefunction used in FN-DMC is directly issued from the deterministic CI program; no Jastrow factor is used and no preliminary multi-parameter stochastic optimization of the trial wavefunction is performed. The nodes of CIPSI wavefunctions are found to reduce significantly the fixed-node error and to be systematically improved upon increasing the number of selected determinants. To reduce the non-parallelism error of the potential energy curve, a scheme based on the use of a R-dependent number of determinants is introduced. Using Dunning’s cc-pVDZ basis set, the FN-DMC energy curve of F{sub 2} is found to be of a quality similar to that obtained with full configuration interaction/cc-pVQZ.

  19. C-type lectin-like molecule-1 (CLL1)-targeted TRAIL augments the tumoricidal activity of granulocytes and potentiates therapeutic antibody-dependent cell-mediated cytotoxicity.

    PubMed

    Wiersma, Valerie R; de Bruyn, Marco; Shi, Ce; Gooden, Marloes J M; Wouters, Maartje C A; Samplonius, Douwe F; Hendriks, Djoke; Nijman, Hans W; Wei, Yunwei; Zhou, Jin; Helfrich, Wijnand; Bremer, Edwin

    2015-01-01

    The therapeutic effect of anti-cancer monoclonal antibodies stems from their capacity to opsonize targeted cancer cells with subsequent phagocytic removal, induction of antibody-dependent cell-mediated cytotoxicity (ADCC) or induction of complement-mediated cytotoxicity (CDC). The major immune effector cells involved in these processes are natural killer (NK) cells and granulocytes. The latter and most prevalent blood cell population contributes to phagocytosis, but is not effective in inducing ADCC. Here, we report that targeted delivery of the tumoricidal protein tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) to granulocyte marker C-type lectin-like molecule-1 (CLL1), using fusion protein CLL1:TRAIL, equips granulocytes with high levels of TRAIL. Upon CLL1-selective binding of this fusion protein, granulocytes acquire additional TRAIL-mediated cytotoxic activity that, importantly, potentiates antibody-mediated cytotoxicity of clinically used therapeutic antibodies (e.g., rituximab, cetuximab). Thus, CLL1:TRAIL could be used as an adjuvant to optimize the clinical potential of anticancer antibody therapy by augmenting tumoricidal activity of granulocytes.

  20. Discovery of small-molecule inhibitors of HCV NS3-4A protease as potential therapeutic agents against HCV infection.

    PubMed

    Chen, Shu-Hui; Tan, Seng-Lai

    2005-01-01

    Chronic infection with hepatitis C virus (HCV) is associated with liver cirrhosis that often leads to hepatic failure and hepatocellular carcinoma (HCC). HCV infection has become a global health threat and the main cause of adult liver transplants in developed nations. Current approved anti-HCV therapies (interferon and pegylated interferon alone or in combination with ribavirin) are not effective in eliminating the viral infection in a significant population of patients (e.g., those infected with HCV genotype 1). Furthermore, these therapies are plagued with many undesirable side effects. Therefore, the HCV epidemic represents a huge unmet medical need that has triggered intensive research efforts towards the development of more effective drugs. Given its essential role in the process of HCV replication, the viral NS3/4A serine protease is arguably the most thoroughly characterized HCV enzyme and the most intensively pursued anti-HCV target for drug development. This is further fueled by the successful use of small-molecule inhibitors of the human immunodeficiency virus (HIV) viral protease, which have had an impressive effect on HIV-related morbidity and mortality, offering hope that analogous drugs might also have a similar impact against HCV. Here, we review the recent progress and development of small-molecule inhibitors of the HCV NS3/4A protease. In particular, we focus on the discovery of VX-950, the latest HCV NS3-4A protease inhibitor to be advanced to clinical studies. While the challenges of designing potent inhibitors of the viral protease have been solved, as highlighted by BILN 2061 and VX-950, it is still too early to determine whether these efforts will eventually yield promising drug candidates. For the emerging small-molecule HCV inhibitors, viral resistance will likely be a big problem. Thus, combination therapy of different drugs with different targets/mechanisms will be necessary to effectively inhibit HCV replication. It is also hoped that a

  1. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  2. Erythroid Adhesion Molecules in Sickle Cell Anaemia Infants: Insights Into Early Pathophysiology.

    PubMed

    Brousse, Valentine; Colin, Yves; Pereira, Catia; Arnaud, Cecile; Odièvre, Marie Helene; Boutemy, Anne; Guitton, Corinne; de Montalembert, Mariane; Lapouméroulie, Claudine; Picot, Julien; Le Van Kim, Caroline; El Nemer, Wassim

    2015-01-01

    Sickle cell anaemia (SCA) results from a single mutation in the β globin gene. It is seldom symptomatic in the first semester of life. We analysed the expression pattern of 9 adhesion molecules on red blood cells, in a cohort of 54 SCA and 17 non-SCA very young infants of comparable age (median 144 days, 81-196). Haemoglobin F (HbF) level was unsurprisingly elevated in SCA infants (41.2% ± 11.2) and 2-4 fold higher than in non-SCA infants, yet SCA infants presented significantly decreased Hb level and increased reticulocytosis. Cytometry analysis evidenced a specific expression profile on reticulocytes of SCA infants, with notably an increased expression of the adhesion molecules Lu/BCAM, ICAM-4 and LFA-3, both in percentage of positive cells and in surface density. No significant difference was found on mature red cells. Our findings demonstrate the very early onset of reticulocyte membrane modifications in SCA asymptomatic infants and allow an insight into the first pathological changes with the release of stress reticulocytes expressing a distinctive profile of adhesion molecules.

  3. Full-Dimensional Potential Energy and Dipole Moment Surfaces of GeH4 Molecule and Accurate First-Principle Rotationally Resolved Intensity Predictions in the Infrared.

    PubMed

    Nikitin, A V; Rey, M; Rodina, A; Krishna, B M; Tyuterev, Vl G

    2016-11-17

    Nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) of the germane molecule are constructed using extended ab initio CCSD(T) calculations at 19 882 points. PES analytical representation is determined as an expansion in nonlinear symmetry adapted products of orthogonal and internal coordinates involving 340 parameters up to eighth order. Minor empirical refinement of the equilibrium geometry and of four quadratic parameters of the PES computed at the CCSD(T)/aug-cc-pVQZ-DK level of the theory yielded the accuracy below 1 cm(-1) for all experimentally known vibrational band centers of five stable isotopologues of (70)GeH4, (72)GeH4, (73)GeH4, (74)GeH4, and (76)GeH4 up to 8300 cm(-1). The optimized equilibrium bond re = 1.517 594 Å is very close to best ab initio values. Rotational energies up to J = 15 are calculated using potential expansion in normal coordinate tensors with maximum errors of 0.004 and 0.0006 cm(-1) for (74)GeH4 and (76)GeH4. The DMS analytical representation is determined through an expansion in symmetry-adapted products of internal nonlinear coordinates involving 967 parameters up to the sixth order. Vibration-rotation line intensities of five stable germane isotopologues were calculated from purely ab initio DMS using nuclear motion variational calculations with a full account of the tetrahedral symmetry of the molecules. For the first time a good overall agreement of main absorption features with experimental rotationally resolved Pacific Northwest National Laboratory spectra was achieved in the entire range of 700-5300 cm(-1). It was found that very accurate description of state-dependent isotopic shifts is mandatory to correctly describe complex patterns of observed spectra at natural isotopic abundance resulting from the superposition of five stable isotopologues. The data obtained in this work will be made available through the TheoReTS information system.

  4. Conformational analysis of bis(methylthio)methane and diethyl sulfide molecules in the liquid phase: reverse Monte Carlo studies using classical interatomic potential functions

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-11-01

    Series of flexible molecule reverse Monte Carlo calculations, using bonding and non-bonding interatomic potential functions (FMP-RMC), were performed starting from previous molecular dynamics results that had applied the OPLS-AA and EncadS force fields. During RMC modeling, the experimental x-ray total scattering structure factor was approached. The discrepancy between experimental and calculated structure factors, in comparison with the molecular dynamics results, decreased substantially in each case. The room temperature liquid structure of bis(methylthio)methane is excellently described by the FMP-RMC simulation that applied the EncadS force field parameters. The main conformer was found to be AG with 55.2%, followed by 37.2% of G+G+ (G-G-) and 7.6% of AA; the stability of the G+G+ (G-G-) conformer is most probably caused by the anomer effect. The liquid structure of diethyl sulfide can be best described by applying the OPLS-AA force field parameters during FMP-RMC simulation, although in this case the force field parameters were found to be not fully compatible with experimental data. Here, the two main conformers are AG (50.6%) and the AA (40%). In addition to findings on the actual real systems, a fairly detailed comparison between traditional and FMP-RMC methodology is provided.

  5. Expectation-maximization of the potential of mean force and diffusion coefficient in Langevin dynamics from single molecule FRET data photon by photon.

    PubMed

    Haas, Kevin R; Yang, Haw; Chu, Jhih-Wei

    2013-12-12

    The dynamics of a protein along a well-defined coordinate can be formally projected onto the form of an overdamped Lagevin equation. Here, we present a comprehensive statistical-learning framework for simultaneously quantifying the deterministic force (the potential of mean force, PMF) and the stochastic force (characterized by the diffusion coefficient, D) from single-molecule Förster-type resonance energy transfer (smFRET) experiments. The likelihood functional of the Langevin parameters, PMF and D, is expressed by a path integral of the latent smFRET distance that follows Langevin dynamics and realized by the donor and the acceptor photon emissions. The solution is made possible by an eigen decomposition of the time-symmetrized form of the corresponding Fokker-Planck equation coupled with photon statistics. To extract the Langevin parameters from photon arrival time data, we advance the expectation-maximization algorithm in statistical learning, originally developed for and mostly used in discrete-state systems, to a general form in the continuous space that allows for a variational calculus on the continuous PMF function. We also introduce the regularization of the solution space in this Bayesian inference based on a maximum trajectory-entropy principle. We use a highly nontrivial example with realistically simulated smFRET data to illustrate the application of this new method.

  6. Strategies for potential age dating of fingerprints through the diffusion of sebum molecules on a nonporous surface analyzed using time-of-flight secondary ion mass spectrometry.

    PubMed

    Muramoto, Shin; Sisco, Edward

    2015-08-18

    Age dating of fingerprints could have a significant impact in forensic science, as it has the potential to facilitate the judicial process by assessing the relevance of a fingerprint found at a crime scene. However, no method currently exists that can reliably predict the age of a latent fingerprint. In this manuscript, time-of-flight secondary ion imaging mass spectrometry (TOF-SIMS) was used to measure the diffusivity of saturated fatty acid molecules from a fingerprint on a silicon wafer. It was found that their diffusion from relatively fresh fingerprints (t ≤ 96 h) could be modeled using an error function, with diffusivities (mm(2)/h) that followed a power function when plotted against molecular weight. The equation x = 0.02t(0.5) was obtained for palmitic acid that could be used to find its position in millimeters (where the concentration is 50% of its initial value or c0/2) as a function of time in hours. The results show that on a clean silicon substrate, the age of a fingerprint (t ≤ 96 h) could reliably be obtained through the extent of diffusion of palmitic acid.

  7. Dynamics of H{sub 2} Eley-Rideal abstraction from W(110): Sensitivity to the representation of the molecule-surface potential

    SciTech Connect

    Pétuya, R. Larrégaray, P.; Crespos, C.; Busnengo, H. F.; Martínez, A. E.

    2014-07-14

    Dynamics of the Eley-Rideal (ER) abstraction of H{sub 2} from W(110) is analyzed by means of quasi-classical trajectory calculations. Simulations are based on two different molecule-surface potential energy surfaces (PES) constructed from Density Functional Theory results. One PES is obtained by fitting, using a Flexible Periodic London-Eyring-Polanyi-Sato (FPLEPS) functional form, and the other by interpolation through the corrugation reducing procedure (CRP). Then, the present study allows us to elucidate the ER dynamics sensitivity on the PES representation. Despite some sizable discrepancies between both H+H/W(110) PESs, the obtained projectile-energy dependence of the total ER cross sections are qualitatively very similar ensuring that the main physical ingredients are captured in both PES models. The obtained distributions of the final energy among the different molecular degrees of freedom barely depend on the PES model, being most likely determined by the reaction exothermicity. Therefore, a reasonably good agreement with the measured final vibrational state distribution is observed in spite of the pressure and material gaps between theoretical and experimental conditions.

  8. Collisions of excited Na atoms with H2 molecules. I. Ab initio potential energy surfaces and qualitative discussion of the quenching process

    NASA Astrophysics Data System (ADS)

    Botschwina, Peter; Meyer, Wilfried; Hertel, Ingolf V.; Reiland, W.

    1981-12-01

    Potential energy surfaces have been calculated for the four lowest electronic states of Na (3 2S, 3 2P)+H2(1Σ+g) by means of the RHF-SCF and PNO-CEPA methods. For the so-called quenching process of Na (3 2P) by H2 at low initial translational energies (E-VRT energy transfer) the energetically most favorable path occurs in C2v symmetry, since—at intermediate Na-H2 separation—the ? 2B2 potential energy surface is attractive. From the CEPA calculations, the crossing point of minimal energy between the ? 2A1 and ? 2B2 surfaces is obtained at Rc = 3.57 a.u. and rc = 2.17 a.u. with an energy difference to the asymptotic limit (R = ∞, r = re) of -0.06 eV. It is thus classically accessible without any initial translational energy, but at low initial translational energies (˜0.1 eV) quenching will be efficient only for arrangements of collision partners close to C2v symmetry. There is little indication of an avoiding crossing with an ionic intermediate correlating asymptotically with Na+ and H2- as was assumed in previous discussions of the quenching process. The dependence of the total quenching cross sections on the initial translational energy is discussed by means of the ''absorbing sphere'' model, taking the initial zero-point vibrational energy of the hydrogen molecule into account. New experimental data of the product channel distribution in H2 for center-of-mass forward scattering are presented. The final vibrational states v' = 3, 2, 1, and 0 of H2 are populated to about 26%, 61%, 13%, and 0%, respectively. The observed distributions in H2 (and D2) may be rationalized by simple dynamic considerations on the basis of the calculated surfaces.

  9. Porous organic molecules

    NASA Astrophysics Data System (ADS)

    Holst, James R.; Trewin, Abbie; Cooper, Andrew I.

    2010-11-01

    Most synthetic materials that show molecular-scale porosity consist of one-, two- or three-dimensional networks. Porous metal-organic frameworks in particular have attracted a lot of recent attention. By contrast, discrete molecules tend to pack efficiently in the solid state, leaving as little empty space as possible, which leads to non-porous materials. This Perspective discusses recent developments with discrete organic molecules that are porous in the solid state. Such molecules, which may be either crystalline or amorphous, can be categorized as either intrinsically porous (containing permanent covalent cavities) or extrinsically porous (inefficiently packed). We focus on the possible advantages of organic molecules over inorganic or hybrid systems in terms of molecular solubility, choice of components and functionalities, and structural mobility and responsiveness in non-covalent extended solids. We also highlight the potential for 'undiscovered' porous systems among the large number of cage-like organic molecules that are already known.

  10. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  11. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  12. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  13. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  14. Spectroscopic (FT-IR, FT-Raman, UV, 1H and 13C NMR) profiling and computational studies on methyl 5-methoxy-1H-indole-2-carboxylate: A potential precursor to biologically active molecules

    NASA Astrophysics Data System (ADS)

    Almutairi, Maha S.; Xavier, S.; Sathish, M.; Ghabbour, Hazem A.; Sebastian, S.; Periandy, S.; Al-Wabli, Reem I.; Attia, Mohamed I.

    2017-04-01

    Methyl 5-methoxy-1H-indole-2-carboxylate (MMIC) was prepared via esterification of commercially available 5-methoxyindole-2-carboxylic acid. The title molecule MMIC was characterised using FT-IR and FT-Raman in the ranges of 4000-500 and 4000-50 cm-1, respectively. The fundamental modes of the vibrations were assigned and the UV-visible spectrum of the MMIC molecule was recorded in the range of 200-400 nm to explore its electronic nature. The HOMO-LUMO energy distribution was calculated and the bonding and anti-bonding structures of the title molecule were studied and analysed using the natural bond orbital (NBO) approach. The reactivity of the MMIC molecule was also investigated and both the positive and negative centres of the molecule were identified using chemical descriptors and molecular electrostatic potential (MEP) analysis. The chemical shifts of the 1H and 13C NMR spectra were noted and the magnetic field environment of the MMIC molecule are discussed. The non-linear optical (NLO) properties of the title molecule were studied based on its calculated values of polarisability and hyperpolarisability. All computations were obtained by DFT methods using the 6-311++G (d,p) basis set.

  15. The Jak2 Small Molecule Inhibitor, G6, Reduces the Tumorigenic Potential of T98G Glioblastoma Cells In Vitro and In Vivo

    PubMed Central

    Keserű, György M.; Bisht, Kirpal S.; Wamsley, Heather L.; Sayeski, Peter P.

    2014-01-01

    Glioblastoma multiforme (GBM) is the most common and the most aggressive form of primary brain tumor. Jak2 is a non-receptor tyrosine kinase that is involved in proliferative signaling through its association with various cell surface receptors. Hyperactive Jak2 signaling has been implicated in numerous hematological disorders as well as in various solid tumors including GBM. Our lab has developed a Jak2 small molecule inhibitor known as G6. It exhibits potent efficacy in vitro and in several in vivo models of Jak2-mediated hematological disease. Here, we hypothesized that G6 would inhibit the pathogenic growth of GBM cells expressing hyperactive Jak2. To test this, we screened several GBM cell lines and found that T98G cells express readily detectable levels of active Jak2. We found that G6 treatment of these cells reduced the phosphorylation of Jak2 and STAT3, in a dose-dependent manner. In addition, G6 treatment reduced the migratory potential, invasive potential, clonogenic growth potential, and overall viability of these cells. The effect of G6 was due to its direct suppression of Jak2 function and not via off-target kinases, as these effects were recapitulated in T98G cells that received Jak2 specific shRNA. G6 also significantly increased the levels of caspase-dependent apoptosis in T98G cells, when compared to cells that were treated with vehicle control. Lastly, when T98G cells were injected into nude mice, G6 treatment significantly reduced tumor volume and this was concomitant with significantly decreased levels of phospho-Jak2 and phospho-STAT3 within the tumors themselves. Furthermore, tumors harvested from mice that received G6 had significantly less vimentin protein levels when compared to tumors from mice that received vehicle control solution. Overall, these combined in vitro and in vivo results indicate that G6 may be a viable therapeutic option against GBM exhibiting hyperactivation of Jak2. PMID:25162558

  16. Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Lou, Zhichao; Zhang, Haiqian; Xu, Bingqian

    2016-03-01

    The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

  17. ZRBA1, a Mixed EGFR/DNA Targeting Molecule, Potentiates Radiation Response Through Delayed DNA Damage Repair Process in a Triple Negative Breast Cancer Model

    SciTech Connect

    Heravi, Mitra; Kumala, Slawomir; Rachid, Zakaria; Jean-Claude, Bertrand J.; Radzioch, Danuta; Muanza, Thierry M.

    2015-06-01

    Purpose: ZRBA1 is a combi-molecule designed to induce DNA alkylating lesions and to block epidermal growth factor receptor (EGFR) TK domain. Inasmuch as ZRBA1 downregulates the EGFR TK-mediated antisurvival signaling and induces DNA damage, we postulated that it might be a radiosensitizer. The aim of this study was to further investigate the potentiating effect of ZRBA1 in combination with radiation and to elucidate the possible mechanisms of interaction between these 2 treatment modalities. Methods and Materials: The triple negative human breast MDA-MB-468 cancer cell line and mouse mammary cancer 4T1 cell line were used in this study. Clonogenic assay, Western blot analysis, and DNA damage analysis were performed at multiple time points after treatment. To confirm our in vitro findings, in vivo tumor growth delay assay was performed. Results: Our results show that a combination of ZRBA1 and radiation increases the radiation sensitivity of both cell lines significantly with a dose enhancement factor of 1.56, induces significant numbers of DNA strand breaks, prolongs higher DNA damage up to 24 hours after treatment, and significantly increases tumor growth delay in a syngeneic mouse model. Conclusions: Our data suggest that the higher efficacy of this combination could be partially due to increased DNA damage and delayed DNA repair process and to the inhibition of EGFR. The encouraging results of this combination demonstrated a significant improvement in treatment efficiency and therefore could be applicable in early clinical trial settings.

  18. An accurate density functional theory for the vapor-liquid interface of associating chain molecules based on the statistical associating fluid theory for potentials of variable range

    NASA Astrophysics Data System (ADS)

    Gloor, Guy J.; Jackson, George; Blas, Felipe J.; del Río, Elvira Martín; de Miguel, Enrique

    2004-12-01

    A Helmholtz free energy density functional is developed to describe the vapor-liquid interface of associating chain molecules. The functional is based on the statistical associating fluid theory with attractive potentials of variable range (SAFT-VR) for the homogenous fluid [A. Gil-Villegas, A. Galindo, P. J. Whitehead, S. J. Mills, G. Jackson, and A. N. Burgess, J. Chem. Phys. 106, 4168 (1997)]. A standard perturbative density functional theory (DFT) is constructed by partitioning the free energy density into a reference term (which incorporates all of the short-range interactions, and is treated locally) and an attractive perturbation (which incorporates the long-range dispersion interactions). In our previous work [F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Mol. Phys. 99, 1851 (2001); G. J. Gloor, F. J. Blas, E. Martı´n del Rı´o, E. de Miguel, and G. Jackson, Fluid Phase Equil. 194, 521 (2002)] we used a mean-field version of the theory (SAFT-HS) in which the pair correlations were neglected in the attractive term. This provides only a qualitative description of the vapor-liquid interface, due to the inadequate mean-field treatment of the vapor-liquid equilibria. Two different approaches are used to include the correlations in the attractive term: in the first, the free energy of the homogeneous fluid is partitioned such that the effect of correlations are incorporated in the local reference term; in the second, a density averaged correlation function is incorporated into the perturbative term in a similar way to that proposed by Toxvaerd [S. Toxvaerd, J. Chem. Phys. 64, 2863 (1976)]. The latter is found to provide the most accurate description of the vapor-liquid surface tension on comparison with new simulation data for a square-well fluid of variable range. The SAFT-VR DFT is used to examine the effect of molecular chain length and association on the surface tension. Different association schemes (dimerization, straight and

  19. Dependences of Q-branch integrated intensity of linear-molecule pendular spectra on electric-field strength and rotational temperature and its potential applications

    PubMed Central

    Deng, Min; Wang, Hailing; Wang, Qin; Yin, Jianping

    2016-01-01

    We calculate the pendular-state spectra of cold linear molecules, and investigated the dependences of “Q-branch” integrated intensity of pendular spectra on both electric-field strength and molecular rotation-temperature. A new multi-peak structure in the “Q-branch” spectrum is appearing when the Stark interaction strength ω = μE/B equal to or larger than the critical value. Our study shows that the above results can be used not only to measure the electric-field vector and its spatial distribution in some electrostatic devices, such as the Stark decelerator, Stark velocity filter and electrostatic trap and so on, but also to survey the orientation degree of cold linear molecules in a strong electrostatic field. PMID:27231057

  20. Dependences of Q-branch integrated intensity of linear-molecule pendular spectra on electric-field strength and rotational temperature and its potential applications

    NASA Astrophysics Data System (ADS)

    Deng, Min; Wang, Hailing; Wang, Qin; Yin, Jianping

    2016-05-01

    We calculate the pendular-state spectra of cold linear molecules, and investigated the dependences of “Q-branch” integrated intensity of pendular spectra on both electric-field strength and molecular rotation-temperature. A new multi-peak structure in the “Q-branch” spectrum is appearing when the Stark interaction strength ω = μE/B equal to or larger than the critical value. Our study shows that the above results can be used not only to measure the electric-field vector and its spatial distribution in some electrostatic devices, such as the Stark decelerator, Stark velocity filter and electrostatic trap and so on, but also to survey the orientation degree of cold linear molecules in a strong electrostatic field.

  1. The Crystal Structure of OprG from Pseudomonas aeruginosa a Potential Channel for Transport of Hydrophobic Molecules across the Outer Membrane

    SciTech Connect

    D Touw; D Patel; b van den Berg

    2011-12-31

    The outer membrane (OM) of Gram-negative bacteria provides a barrier to the passage of hydrophobic and hydrophilic compounds into the cell. The OM has embedded proteins that serve important functions in signal transduction and in the transport of molecules into the periplasm. The OmpW family of OM proteins, of which P. aeruginosa OprG is a member, is widespread in Gram-negative bacteria. The biological functions of OprG and other OmpW family members are still unclear. The outer membrane (OM) of Gram-negative bacteria provides a barrier to the passage of hydrophobic and hydrophilic compounds into the cell. The OM has embedded proteins that serve important functions in signal transduction and in the transport of molecules into the periplasm. The OmpW family of OM proteins, of which P. aeruginosa OprG is a member, is widespread in Gram-negative bacteria. The biological functions of OprG and other OmpW family members are still unclear. The crystal structure, together with recent biochemical data, suggests that OprG and other OmpW family members form channels that mediate the diffusion of small hydrophobic molecules across the OM by a lateral diffusion mechanism similar to that of E. coli FadL.

  2. HMGB1, a pathogenic molecule that induces neurite degeneration via TLR4-MARCKS, is a potential therapeutic target for Alzheimer’s disease

    PubMed Central

    Fujita, Kyota; Motoki, Kazumi; Tagawa, Kazuhiko; Chen, Xigui; Hama, Hiroshi; Nakajima, Kazuyuki; Homma, Hidenori; Tamura, Takuya; Watanabe, Hirohisa; Katsuno, Masahisa; Matsumi, Chiemi; Kajikawa, Masunori; Saito, Takashi; Saido, Takaomi; Sobue, Gen; Miyawaki, Atsushi; Okazawa, Hitoshi

    2016-01-01

    Alzheimer’s disease (AD) is the most common neurodegenerative disease, but it remains an intractable condition. Its pathogenesis is predominantly attributed to the aggregation and transmission of two molecules, Aβ and tau; however, other pathological mechanisms are possible. Here, we reveal that phosphorylation of MARCKS, a submembrane protein that regulates the stability of the actin network, occurs at Ser46 prior to aggregation of Aβ and is sustained throughout the course of AD in human and mouse brains. Furthermore, HMGB1 released from necrotic or hyperexcitatory neurons binds to TLR4, triggers the specific phosphorylation of MARCKS via MAP kinases, and induces neurite degeneration, the classical hallmark of AD pathology. Subcutaneous injection of a newly developed monoclonal antibody against HMGB1 strongly inhibits neurite degeneration even in the presence of Aβ plaques and completely recovers cognitive impairment in a mouse model. HMGB1 and Aβ mutually affect polymerization of the other molecule, and the therapeutic effects of the anti-HMGB1 monoclonal antibody are mediated by Aβ-dependent and Aβ-independent mechanisms. We propose that HMGB1 is a critical pathogenic molecule promoting AD pathology in parallel with Aβ and tau and a new key molecular target of preclinical antibody therapy to delay the onset of AD. PMID:27557632

  3. Spin-orbit configuration interaction study of potential energy curves and transition probabilities of the mercury hydride molecule and tests of relativistic effective core potentials for Hg, Hg + , and Hg2 +

    NASA Astrophysics Data System (ADS)

    Alekseyev, Aleksey B.; Liebermann, Heinz-Peter; Buenker, Robert J.; Hirsch, Gerhard

    1996-03-01

    Ab initio CI calculations have been carried out for the low-energy states of the mercury hydride molecule HgH and its isotopomers. A relativistic effective core potential (RECP) given by Ross et al. [J. Chem. Phys. 93, 6654 (1990)] is employed to describe all but the Hg 5d and 6s valence electrons. Tests for a series of low-lying states of Hg, Hg+, and Hg2+ demonstrate that 0.1 eV accuracy is obtained at the SCF level with a high-quality basis set for this RECP in comparison with all-electron Dirac-Fock results up to 32 eV excitation energy. The DF values are themselves in error by 1-3 eV on the average compared to experiment, but the present CI calculations based on this RECP lead to considerably higher accuracy because of the importance of correlation effects in such determinations. Energy differences (12 cases) between states with the same number of electrons are computed to an accuracy of 0.1-0.2 eV in all cases after the spin-orbit interaction is included. These results compare favorably with those obtained by Häussermann et al. [Mol. Phys. 78, 1211 (1993)] with a ... 5s2 5p6 5d10 6s2 RECP and a corresponding larger AO basis to describe the more tightly bound electrons. Good agreement is found for the spectroscopic constants of the HgH molecule in its lowest four electronic states: X 2Σ+1/2, A1 2Π1/2, A2 2Π3/2, and B 2Σ+1/2 (maximal errors of 1000 cm-1 for Te, 0.03 Å for re and 150 cm-1 for ωe). An RKR curve reported for the A1 state is shown to be in error beyond r=4.0 a0 because of its failure to describe a key avoided crossing with the B state. Radiative lifetimes computed for the A 2Π multiplets are both found to agree with values deduced from experiment to within 40%. The calculations find no difference in the HgH and HgD radiative lifetimes for either the A1 or the A2 states, whereas a large distinction in the measured A1 lifetimes of the two isotopomers is observed, thereby supporting the previous experimental conclusion that strong

  4. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  5. Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures.

    PubMed

    Thompson, Damien; Hermes, Jens P; Quinn, Aidan J; Mayor, Marcel

    2012-04-24

    The formation of true single-molecule complexes between organic ligands and nanoparticles is challenging and requires careful design of molecules with size, shape, and chemical properties tailored for the specific nanoparticle. Here we use computer simulations to describe the atomic-scale structure, dynamics, and energetics of ligand-mediated synthesis and interlinking of 1 nm gold clusters. The models help explain recent experimental results and provide insight into how multidentate thioether dendrimers can be employed for synthesis of true single-ligand-nanoparticle complexes and also nanoparticle-molecule-nanoparticle "dumbbell" nanostructures. Electronic structure calculations reveal the individually weak thioether-gold bonds (325 ± 36 meV), which act collectively through the multivalent (multisite) anchoring to stabilize the ligand-nanoparticle complex (∼7 eV total binding energy) and offset the conformational and solvation penalties involved in this "wrapping" process. Molecular dynamics simulations show that the dendrimer is sufficiently flexible to tolerate the strained conformations and desolvation penalties involved in fully wrapping the particle, quantifying the subtle balance between covalent anchoring and noncovalent wrapping in the assembly of ligand-nanoparticle complexes. The computed preference for binding of a single dendrimer to the cluster reveals the prohibitively high dendrimer desolvation barrier (1.5 ± 0.5 eV) to form the alternative double-dendrimer structure. Finally, the models show formation of an additional electron transfer channel between nitrogen and gold for ligands with a central pyridine unit, which gives a stiff binding orientation and explains the recently measured larger interparticle distances for particles synthesized and interlinked using linear ligands with a central pyridine rather than a benzene moiety. The findings stress the importance of organic-inorganic interactions, the control of which is central to the

  6. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range - the case study of CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2014-04-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission over an extended range of photon energies. The vibrational ratios v=1/v=0 from the C 1s photoelectron spectra, although mostly determined by the bond length change, are shown to be affected also by photoelectron recoil and scattering on the neighboring oxygen atom. Density functional theory is used to encompass all these effect in unified treatment. It is also demonstrated that the DFT calculations can be used as a means to extract dynamic and static molecular geometry values.

  7. Potential energy surfaces for atomic oxygen reactions: Formation of singlet and triplet biradicals as primary reaction products with unsaturated organic molecules

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard L.

    1987-01-01

    The experimental study of the interaction of atomic oxygen with organic polymer films under LEO conditions has been hampered by the inability to conduct detailed experiments in situ. As a result, studies of the mechanism of oxygen atom reactions have relied on laboratory O-atom sources that do not fully reproduce the orbital environment. For example, it is well established that only ground electronic state O atoms are present at LEO, yet most ground-based sources are known to produce singlet O atoms and molecules and ions in addition to O(3P). Engineers should not rely on such facilities unless it can be demonstrated either that these different O species are inert or that they react in the same fashion as ground state atoms. Ab initio quantum chemical calculations have been aimed at elucidating the biradical intermediates formed during the electrophilic addition of ground and excited-state O atoms to carbon-carbon double bonds in small olefins and aromatic molecules. These biradicals are critical intermediates in any possible insertion, addition and elimination reaction mechanisms. Through these calculations, we will be able to comment on the relative importance of these pathways for O(3P) and O(1D) reactions. The reactions of O atoms with ethylene and benzene are used to illustrate the important features of the mechanisms of atomic oxygen reaction with unsaturated organic compounds and polymeric materials.

  8. Effects of molecular potential and geometry on atomic core-level photoemission over an extended energy range: The case study of the CO molecule

    NASA Astrophysics Data System (ADS)

    Kukk, E.; Ayuso, D.; Thomas, T. D.; Decleva, P.; Patanen, M.; Argenti, L.; Plésiat, E.; Palacios, A.; Kooser, K.; Travnikova, O.; Mondal, S.; Kimura, M.; Sakai, K.; Miron, C.; Martín, F.; Ueda, K.

    2013-09-01

    We report an experimental and theoretical study of single-molecule inner-shell photoemission measured over an extended range of photon energies. The vibrational intensity ratios I(ν=1)/I(ν=0) from the C 1s photoelectron spectra of carbon monoxide, although mostly determined by the bond length change upon ionization, are shown to be affected also by photoelectron recoil and by scattering from the neighboring oxygen atom. Static-exchange density functional theory (DFT) is used to encompass all these effects in a unified theoretical treatment. The ab initio calculations show that the vibrational ratio as a function of the photoelectron momentum is sensitive to both the ground-state internuclear distance and its contraction upon photoionization. We present a proof-of-principle application of DFT calculations as a quantitative structural analysis tool for extracting the dynamic and static molecular geometry parameters simultaneously.

  9. The gonadotropin releasing hormone (GnRH)-like molecule in prosobranch Patella caerulea: potential biomarker of endocrine-disrupting compounds in marine environments.

    PubMed

    De Lisa, Emilia; Carella, Francesca; De Vico, Gionata; Di Cosmo, Anna

    2013-02-01

    It has been reported that endocrine disrupter compounds (EDCs) interfere with the endocrine system, mimicking the action of sex steroid hormones in different species of mollusks. Prosobranchs are frequently used as a reliable bioindicator to evaluate EDC exposure. In this article, we evaluate the effects of the xenoestrogen 4-n-nonylphenol (NP) in the prosobranch gastropod Patella caerulea, which exhibits protandrous hermaphroditism as its reproductive strategy. We isolated a partial sequence of a GnRH-like molecule from the gonads of Patella caerulea. The deduced amino acid sequence is highly homologous to that reported for the Lottia gigantea GnRH. Patella caerulea GnRH (pGnRH) mRNA expression is widespread in both male and female germ lines during gametogenesis. We suggest pGnRH as a novel biomarker for the early assessment of presence of EDCs and monitoring short and long-term impacts on Patella caerulea community structure.

  10. Experimental and theoretical investigation of the molecular structure, conformational stability, hyperpolarizability, electrostatic potential, thermodynamic properties and NMR spectra of pharmaceutical important molecule: 4‧-Methylpropiophenone

    NASA Astrophysics Data System (ADS)

    Karunakaran, V.; Balachandran, V.

    2014-07-01

    Combined experimental and theoretical studies have been performed on the structure and vibrational spectra (IR and Raman spectra) of 4‧-methylpropiophenone (MPP). The FT-IR and FT-Raman spectra of 4‧-methylpropiophenone (MPP) have been recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of MPP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The 1H and 13C NMR chemical shifts have been calculated by Gauge-Independent Atomic Orbital (GIAO) method with B3LYP/6-311++G(d,p). The natural bond orbital (NBO), natural hybrid orbital (NHO) analysis and electronic properties, such as HOMO and LUMO energies, were performed by DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0) of the novel molecular system and related properties (βtot, α0 and Δα) of MPP are calculated using DFT/6-311++G(d,p) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The thermodynamic functions of the title compound were also performed at the above method and basis set.

  11. A four-dimensional potential energy surface and predicted infrared spectra for the Ne-D2O van der Waals complex in the ν2 bending region of D2O molecule

    NASA Astrophysics Data System (ADS)

    He, Shanshan; Chen, Dong; Li, Ya; Feng, Eryin; Huang, Wuying

    2016-11-01

    In this paper, a four-dimensional potential energy surface (PES) for the Ne-D2O complex is constructed theoretically. The calculations are carried out at CCSD(T) level with large basis sets augmented with mid-bond functions. The PES includes explicit dependence on the ν2 symmetric bending coordinate Q2 of the D2O molecule. Two vibrationally averaged potentials in the ground and first excited bending states are obtained respectively. Using these two potentials we calculate the bound states of the complexes. The theoretical rovibrational transition frequencies for three bands: П(111,ν2 = 1)←Σ000, Σ(111,ν2 = 1)←Σ000 and n = 1, Σ(000,ν2 = 1)←Σ000 are predicted and generally in good agreement with the experimental observed values.

  12. Rotational excitation of symmetric top molecules by collisions with atoms: Close coupling, coupled states, and effective potential calculations for NH3-He

    NASA Technical Reports Server (NTRS)

    Green, S.

    1976-01-01

    The formalism for describing rotational excitation in collisions between symmetric top rigid rotors and spherical atoms is presented both within the accurate quantum close coupling framework and also the coupled states approximation of McGuire and Kouri and the effective potential approximation of Rabitz. Calculations are reported for thermal energy NH3-He collisions, treating NH3 as a rigid rotor and employing a uniform electron gas (Gordon-Kim) approximation for the intermolecular potential. Coupled states are found to be in nearly quantitative agreement with close coupling results while the effective potential method is found to be at least qualitatively correct. Modifications necessary to treat the inversion motion in NH3 are discussed.

  13. A Novel Small Molecule Inhibitor of Candida albicans Biofilm Formation, Filamentation and Virulence with Low Potential for the Development of Resistance

    PubMed Central

    Pierce, Christopher G.; Chaturvedi, Ashok K.; Lazzell, Anna L.; Powell, Alexander T.; Saville, Stephen. P.; McHardy, Stanton F.; Lopez-Ribot, Jose L.

    2015-01-01

    Background/Objectives Candida albicans is the principal causative agent of candidiasis, the most common fungal infection in humans. Candidiasis represents the third-to-fourth most frequent nosocomial infection worldwide, as this normal commensal of humans causes opportunistic infections in an expanding population of immune- and medically-compromised patients. These infections are frequently associated with biofilm formation, which complicates treatment and contributes to unacceptably high mortality rates. Methods To address the pressing need for new antifungals we have performed a high content screen of 20,000 small molecules in a chemical library (NOVACore™) to identify compounds that inhibit C. albicans biofilm formation, and conducted a series of follow-up studies to examine the in vitro and in vivo activity of the identified compounds. Results The screen identified a novel series of diazaspiro-decane structural analogs which were largely represented among the bioactive compounds. Characterization of the leading compound from this series indicated that it inhibits processes associated with C. albicans virulence, most notably biofilm formation and filamentation, without having an effect on overall growth or eliciting resistance. This compound demonstrated in vivo activity in clinically-relevant murine models of both invasive and oral candidiasis and as such represents a promising lead for antifungal drug development. Furthermore, these results provide proof of concept for the implementation of anti-virulence approaches against C. albicans and other fungal infections that would be less likely to foster the emergence of resistance. PMID:26691764

  14. Accurate determination of pair potentials for a C{sub w}H{sub x}N{sub y}O{sub z} system of molecules: A semiempirical method

    SciTech Connect

    Thiel, M. van; Ree, F.H.; Haselman, L.C.

    1995-03-01

    Statistical mechanical chemical equilibrium calculations of the properties of high-pressure high-temperature reactive C,H,N,O mixtures are made to derive an accurate self-consistent set of inter-molecular potentials for the product molecules. Previous theoretical efforts to predict such properties relied in part on Corresponding States theory and shock wave data of argon. More recent high-pressure Hugoniot measurements on a number of elements and molecules allow more accurate determination of the potentials of these materials, and explicit inclusion of additional dissociation products. The present discussion briefly reviews the previous analysis and the method used to produce a self-consistent set of potentials from shock data on N{sub 2}, O{sub 2}, H{sub 2}, NO, an N{sub 2} + O{sub 2} mixture, carbon, CO{sub 2}, and CO, as well as some simple explosive product mixtures from detonation of hexanitrobenzene, PETN, and a mixture of hydrazine nitrate, hydrazine and water. The results are tested using the data from an HMX explosive formulations. The effect of the non-equilibrium nature of carbon clusters is estimated using data for TNT as a standard to determine a nonequilibrium equation of state for carbon. The resulting parameter set is used in a survey of 27 explosives. For the subset that contains no fluorine or two-phase carbon effects the rms deviation from experimental detonation velocity is 1.2%.

  15. Generation of a pair of photons through the three-body dissociation of a multiply excited water molecule around the double ionization potential

    NASA Astrophysics Data System (ADS)

    Odagiri, Takeshi; Nakano, Motoyoshi; Tanabe, Takehiko; Kumagai, Yoshiaki; Suzuki, Isao H.; Kouchi, Noriyuki

    2009-11-01

    The cross sections for the generation of a photon-pair from excited fragments in photoexcitation of H2O have been measured as a function of incident photon energy. The multiply excited states of H2O have been observed even above the adiabatic double ionization potential.

  16. Excited-state potential-energy surfaces of metal-adsorbed organic molecules from linear expansion Δ-self-consistent field density-functional theory (ΔSCF-DFT)

    NASA Astrophysics Data System (ADS)

    Maurer, Reinhard J.; Reuter, Karsten

    2013-07-01

    Accurate and efficient simulation of excited state properties is an important and much aspired cornerstone in the study of adsorbate dynamics on metal surfaces. To this end, the recently proposed linear expansion Δ-self-consistent field method by Gavnholt et al. [Phys. Rev. B 78, 075441 (2008)], 10.1103/PhysRevB.78.075441 presents an efficient alternative to time consuming quasi-particle calculations. In this method, the standard Kohn-Sham equations of density-functional theory are solved with the constraint of a non-equilibrium occupation in a region of Hilbert-space resembling gas-phase orbitals of the adsorbate. In this work, we discuss the applicability of this method for the excited-state dynamics of metal-surface mounted organic adsorbates, specifically in the context of molecular switching. We present necessary advancements to allow for a consistent quality description of excited-state potential-energy surfaces (PESs), and illustrate the concept with the application to Azobenzene adsorbed on Ag(111) and Au(111) surfaces. We find that the explicit inclusion of substrate electronic states modifies the topologies of intra-molecular excited-state PESs of the molecule due to image charge and hybridization effects. While the molecule in gas phase shows a clear energetic separation of resonances that induce isomerization and backreaction, the surface-adsorbed molecule does not. The concomitant possibly simultaneous induction of both processes would lead to a significantly reduced switching efficiency of such a mechanism.

  17. Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

    NASA Astrophysics Data System (ADS)

    Gunde, R.; Ha, T.-K.; Günthard, H. H.

    1990-08-01

    In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix

  18. Streptococcus pneumoniae Cell-Wall-Localized Phosphoenolpyruvate Protein Phosphotransferase Can Function as an Adhesin: Identification of Its Host Target Molecules and Evaluation of Its Potential as a Vaccine

    PubMed Central

    Mizrachi Nebenzahl, Yaffa; Blau, Karin; Kushnir, Tatyana; Shagan, Marilou; Portnoi, Maxim; Cohen, Aviad; Azriel, Shalhevet; Malka, Itai; Adawi, Asad; Kafka, Daniel; Dotan, Shahar; Guterman, Gali; Troib, Shany; Fishilevich, Tali; Gershoni, Jonathan M; Braiman, Alex; Mitchell, Andrea M; Mitchell, Timothy J; Porat, Nurith; Goliand, Inna; Chalifa Caspi, Vered; Swiatlo, Edwin; Tal, Michael; Ellis, Ronald; Elia, Natalie; Dagan, Ron

    2016-01-01

    In Streptococcus pneumonia, phosphoenolpyruvate protein phosphotransferase (PtsA) is an intracellular protein of the monosaccharide phosphotransferase systems. Biochemical and immunostaining methods were applied to show that PtsA also localizes to the bacterial cell-wall. Thus, it was suspected that PtsA has functions other than its main cytoplasmic enzymatic role. Indeed, recombinant PtsA and anti-rPtsA antiserum were shown to inhibit adhesion of S. pneumoniae to cultured human lung adenocarcinoma A549 cells. Screening of a combinatorial peptide library expressed in a filamentous phage with rPtsA identified epitopes that were capable of inhibiting S. pneumoniae adhesion to A549 cells. The insert peptides in the phages were sequenced, and homologous sequences were found in human BMPER, multimerin1, protocadherin19, integrinβ4, epsin1 and collagen type VIIα1 proteins, all of which can be found in A549 cells except the latter. Six peptides, synthesized according to the homologous sequences in the human proteins, specifically bound rPtsA in the micromolar range and significantly inhibited pneumococcal adhesion in vitro to lung- and tracheal-derived cell lines. In addition, the tested peptides inhibited lung colonization after intranasal inoculation of mice with S. pneumoniae. Immunization with rPtsA protected the mice against a sublethal intranasal and a lethal intravenous pneumococcal challenge. In addition, mouse anti rPtsA antiserum reduced bacterial virulence in the intravenous inoculation mouse model. These findings showed that the surface-localized PtsA functions as an adhesin, PtsA binding peptides derived from its putative target molecules can be considered for future development of therapeutics, and rPtsA should be regarded as a candidate for vaccine development. PMID:26990554

  19. MRD-CI potential surfaces using balanced basis sets. IV. The H/sub 2/ molecule and the H/sub 3/ surface

    SciTech Connect

    Wright, J.S.; Kruus, E.

    1986-12-15

    The utility of midbond functions in molecular calculations was tested in two cases where the correct results are known: the H/sub 2/ potential curve and the collinear H/sub 3/ potential surface. For H/sub 2/, a variety of basis sets both with and without bond functions was compared to the exact nonrelativistic potential curve of Kolos and Wolniewicz (J. Chem. Phys. 43, 2429 (1965)). It was found that optimally balanced basis sets at two levels of quality were the double zeta single polarization plus sp bond function basis (BF1) and the triple zeta double polarization plus two sets of sp bond function basis (BF2). These gave bond dissociation energies D/sub e/ = 4.7341 and 4.7368 eV, respectively (expt. 4.7477 eV). Four basis sets were tested for basis set superposition errors, which were found to be small relative to basis set incompleteness and therefore did not affect any conclusions regarding basis set balance. Basis sets BF1 and BF2 were used to construct potential surfaces for collinear H/sub 3/, along with the corresponding basis sets DZ*P and TZ*PP which contain no bond functions. Barrier heights of 12.52, 10.37, 10.06, and 9.96 kcal/mol were obtained for basis sets DZ*P, TZ*PP, BF1, and BF2, respectively, compared to an estimated limiting value of 9.60 kcal/mol. Difference maps, force constants, and relative rms deviations show that the bond functions improve the surface shape as well as the barrier height.

  20. Dissociative electron attachment to the H2O molecule. II. Nuclear dynamics on coupled electronic surfaces within the local complex potential model

    NASA Astrophysics Data System (ADS)

    Haxton, Daniel J.; Rescigno, T. N.; McCurdy, C. W.

    2007-01-01

    We report the results of a first-principles study of dissociative electron attachment to H2O . The cross sections were obtained from nuclear dynamics calculations carried out in full dimensionality within the local complex potential model by using the multiconfiguration time-dependent Hartree method. The calculations employ our previously obtained global, complex-valued, potential-energy surfaces for the three ( B12 , A12 , and B22 ) electronic Feshbach resonances involved in this process. These three metastable states of H2O- undergo several degeneracies, and we incorporate both the Renner-Teller coupling between the B12 and A12 states as well as the conical intersection between the A12 and B22 states into our treatment. The nuclear dynamics are inherently multidimensional and involve branching between different final product arrangements as well as extensive excitation of the diatomic fragment. Our results successfully mirror the qualitative features of the major fragment channels observed, but are less successful in reproducing the available results for some of the minor channels. We comment on the applicability of the local complex potential model to such a complicated resonant system.

  1. First-principle interaction potentials for metastable He(3S) and Ne(3P) with closed-shell molecules: application to Penning-ionizing systems.

    PubMed

    Hapka, Michał; Chałasiński, Grzegorz; Kłos, Jacek; Zuchowski, Piotr S

    2013-07-07

    We present new interaction potential curves, calculated from first-principles, for the He((3)S, 1s(1)2s(1))···H2 and He((3)S)···Ar systems, relevant in recent Penning ionization experiments of Henson et al. [Science 338, 234 (2012)]. Two different approaches were applied: supermolecular using coupled cluster (CC) theory and perturbational within symmetry-adapted perturbation theory (SAPT). Both methods gave consistent results, and the potentials were used to study the elastic scattering and determine the positions of shape resonances for low kinetic energy (up to 1 meV). We found a good agreement with the experiment. In addition, we investigated two other dimers composed of metastable Ne ((3)P, 2p(5)3s(1)) and ground state He and Ar atoms. For the Ne((3)P)···He system, a good agreement between CC and SAPT approaches was obtained. The Ne((3)P)···Ar dimer was described only with SAPT, as CC gave divergent results. Ne* systems exhibit extremely small electronic orbital angular momentum anisotropy of the potentials. We attribute this effect to screening of an open 2p shell by a singly occupied 3s shell.

  2. Highlight on the indigenous organic molecules detected on Mars by SAM and potential sources of artifacts and backgrounds generated by the sample preparation

    NASA Astrophysics Data System (ADS)

    Buch, A.; Belmahdi, I.; Szopa, C.; Freissinet, C.; Glavin, D. P.; Coll, P. J.; Cabane, M.; Millan, M.; Eigenbrode, J. L.; Navarro-Gonzalez, R.; Stern, J. C.; Pinnick, V. T.; Coscia, D.; Teinturier, S.; Stambouli, M.; Dequaire, T.; Mahaffy, P. R.

    2015-12-01

    and molecules that may constitute organic material precursors sources. References: [1] Mahaffy, P. et al. (2012) Space Sci Rev, 170, 401-478. [2] Glavin, D. et al. (2013), JGR. [3] Leshin L. et al. (2013), Science, [4] Williams, A.J., Eigenbrode, J.L.,m Floyd, M.M., Wilhelm, M.B., and Mahaffy, P.R., (2015), GSA. [5] Eigenbrode, J.L. et al. (2010), LPSC, abst.1460.

  3. An optical conveyor for molecules.

    PubMed

    Weinert, Franz M; Braun, Dieter

    2009-12-01

    Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.

  4. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  5. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions.

    PubMed

    Guerard, Jennifer J; Tentscher, Peter R; Seijo, Marianne; Samuel Arey, J

    2015-06-14

    First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

  6. A selected ion flow tube study of the reactions of NO + and O + 2 ions with some organic molecules: The potential for trace gas analysis of air

    NASA Astrophysics Data System (ADS)

    Španěl, Patrik; Smith, David

    1996-02-01

    A study has been carried out using our selected ion flow tube apparatus of the reactions of NO+ and O+2 ions in their vibronic ground states with ten organic species: the hydrocarbons, benzene, toluene, isoprene, cyclopropane, and n-pentane; the oxygen-containing organics, methanol, ethanol, acetaldehyde, acetone, and diethyl ether. The major objectives of this work are, on the one hand, to fully understand the processes involved in these reactions and, on the other hand, to explore the potential of NO+ and O+2 as chemical ionization agents for the analysis of trace gases in air and on human breath. Amongst the NO+ reactions, charge transfer, hydride-ion transfer, and termolecular association occur, and the measured rate coefficients, k, for the reactions vary from immeasurably small to the maximum value, collisional rate coefficient, kc. The O+2 reactions are all fast, in each case the k being equal to or an appreciable fraction of kc, and charge transfer producing the parent organic ion or dissociative charge transfer resulting in two or three fragments of the parent ion are the reaction processes that occur. We conclude from these studies, and from previous studies, that NO+ ions and O+2 ions can be used to great effect as chemical ionization agents for trace gas analysis, especially in combination with H3O+ ions which we now routinely use for this purpose.

  7. N2 non-thermal atmospheric pressure plasma promotes wound healing in vitro and in vivo: Potential modulation of adhesion molecules and matrix metalloproteinase-9.

    PubMed

    Kang, Sung Un; Choi, Jae Won; Chang, Jae Won; Kim, Kang Il; Kim, Yeon Soo; Park, Ju Kyeong; Kim, Yang Eun; Lee, Yun Sang; Yang, Sang Sik; Kim, Chul-Ho

    2017-02-01

    Advances in physics and biology have made it possible to apply non-thermal atmospheric pressure plasma (NTP) in the biomedical field. Although accumulating evidence suggests that NTP has various medicinal effects, such as facilitating skin wound healing on exposed tissue while minimizing undesirable tissue damage, the underlying molecular mechanisms are not fully understood. In this study, NTP generated from N2 optimized wound healing in the scratch wound healing assay. In addition, matrix metalloproteinase (MMP)-9 expression and enzyme activity increased and the urokinase-type plasminogen activator (uPA) system was activated after NTP treatment. We also showed that NTP treatment increased Slug and TCF8/ZEB1 expression and decreased that of E-cadherin, suggesting induction of the epithelial-to-mesenchymal transition (EMT). The effect of N2 NTP was verified on rat wound model. Taken together, these results suggest that N2 NTP promotes wound healing by inducing the EMT and activating the MMP-9/uPA system. These findings show the therapeutic potential of NTP for skin wound healing.

  8. Electronic structure of donor-spacer-acceptor molecules of potential interest for molecular electronics. IV. Geometry and device properties of P3CNQ and Q3CNQ

    NASA Astrophysics Data System (ADS)

    Broo, Anders; Zerner, Michael C.

    1995-07-01

    Z-β-(1-hexadecyl-4-quinolinium)-α-cyano-4-styryldicyanomethanide (C 16H 33-Q3CNQ) and the pyridinium analogue Z-β-(1-hexadecyl-4-pyridinium)-α-cyano-4-styryldicyanomethanide (C 16H 33-P3NCQ) are two very promising candidates for molecular device design. We obtain the geometry of the ground and excited state of these systems using the PM3 quantum mechanical model. The absorption spectra in vacuum and in solution are calculated using the INDO/Cl model, and compared to experimental spectra. The solvatochromic shift of the absorption spectra was calculated using a self-consistent reaction field approach. The observed bleaching of Langmuir-Blodgett films and solutions of C 16H 33-Q3CNQ and C 16H 33-P3CNQ is explained as resulting from a twisted configuration formed without barrier upon absorption into a twisted intramolecular charge transfer state. The observed rectification is explained from a ground state potential energy surface with two minima, one of which is characterized by a very large dipole moment. The relative energy of these minima is easily shifted by an electric field. The overall electron transport rate is found to be very small due to the small electronic coupling between the mono-layers of the L-B film. Thus, the electron transport through the sample is likely through defects of the L-B film. A way to increase the electronic coupling between the mono-layers is also discussed.

  9. Spectroscopic constants of diatomic molecules computed correcting Hartree-Fock or general-valence-bond potential-energy curves with correlation-energy functionals

    NASA Astrophysics Data System (ADS)

    Pérez-Jordá, José M.; San-Fabián, Emilio; Moscardó, Federico

    1992-04-01

    The Kohn-Sham energy with exact exchange [using the exact Hartree-Fock (HF) exchange but an approximate correlation-energy functional] may be computed very accurately by adding the correlation obtained from the HF density to the total HF energy. Three density functionals are used: local spin density (LSD), LSD with self-interaction correction, and LSD with generalized gradient correction. This scheme has been extended (Lie-Clementi, Colle-Salvetti, and Moscardo-San-Fabian) to be used with general-valence-bond (GVB) energies and wave functions, so that the extra correlation included in the GVB energy is not counted again. The effect of all these approximate correlations on HF or GVB spectroscopic constants (Re,ωe, and De) is studied. Approximate relations showing how correlation affects them are derived, and may be summarized as follows: (1) the effect on Re and ωe depends only on the correlation derivative at Re, and (2) the effect on De depends mainly on the correlation difference between quasidissociated and equilibrium geometries. A consequence is that all the correlation corrections tested here give larger ωe and De and shorter Re than the uncorrected HF or GVB values. This trend is correct for De for both HF and GVB. For Re and ωe, it is correct in most cases for GVB, but it often fails for the HF cases. A comparison is made with Kohn-Sham calculations with both exchange and correlation approximated. As a final conclusion, it is found that, within the present scheme, a qualitatively correct HF or GVB potential-energy curve, together with a correlation-energy approximation with correct dissociation behavior, is crucial for obtaining good estimates of spectroscopic constants.

  10. The roles of BTG3 expression in gastric cancer: a potential marker for carcinogenesis and a target molecule for gene therapy.

    PubMed

    Gou, Wen-feng; Yang, Xue-feng; Shen, Dao-fu; Zhao, Shuang; Liu, Yun-peng; Sun, Hong-zhi; Takano, Yasuo; Su, Rong-jian; Luo, Jun-sheng; Zheng, Hua-chuan

    2015-08-14

    BTG (B-cell translocation gene) can inhibit cell proliferation, metastasis and angiogenesis, cell cycle progression, and induce differentiation in various cells. Here, we found that BTG3 overexpression inhibited proliferation, induced S/G2 arrest, differentiation, autophagy, apoptosis, suppressed migration and invasion in MKN28 and MGC803 cells (p < 0.05). BTG3 transfectants showed a higher mRNA expression of p27, Bax, 14-3-3, Caspase-3, Caspase-9, Beclin 1, NF-κB, IL-1, -2, -4, -10 and -17, but a lower mRNA expression of p21, MMP-9 and VEGF than the control and mock (p < 0.05). At protein level, BTG3 overexpression increased the expression of CDK4, AIF, LC-3B, Beclin 1 and p38 (p < 0.05), but decreased the expression of p21 and β-catenin in both transfectants (p < 0.05). After treated with cisplatin, MG132, paclitaxel and SAHA, both BTG3 transfectants showed lower viability and higher apoptosis than the control in both time- and dose-dependent manners (p < 0.05). BTG3 expression was restored after 5-aza-2'-deoxycytidine or MG132 treatment in gastric cancer cells. BTG3 expression was decreased in gastric cancer in comparison to the adjacent mucosa (p < 0.05), and positively correlated with venous invasion and dedifferentiation of cancer (p < 0.05). It was suggested that BTG3 expression might contribute to gastric carcinogenesis. BTG3 overexpression might reverse the aggressive phenotypes and be employed as a potential target for gene therapy of gastric cancer.

  11. The determination of potential energy curve and dipole moment of the (5)0{sup +} electronic state of {sup 85}Rb{sup 133}Cs molecule by high resolution photoassociation spectroscopy

    SciTech Connect

    Yuan, Jinpeng; Zhao, Yanting Ji, Zhonghua; Li, Zhonghao; Xiao, Liantuan; Jia, Suotang; Kim, Jin-Tae

    2015-12-14

    We present the formation of ultracold {sup 85}Rb{sup 133}Cs molecules in the (5)0{sup +} electronic state by photoassociation and their detection via resonance-enhanced two-photon ionization. Up to v = 47 vibrational levels including the lowest v = 0 vibrational and lowest J = 0 levels are identified with rotationally resolved high resolution photoassociation spectra. Precise Dunham coefficients are determined for the (5)0{sup +} state with high accuracy, then the Rydberg-Klein-Rees potential energy curve is derived. The electric dipole moments with respect to the vibrational numbers of the (5)0{sup +} electronic state of {sup 85}Rb{sup 133}Cs molecule are also measured in the range between 1.9 and 4.8 D. These comprehensive studies on previously unobserved rovibrational levels of the (5)0{sup +} state are helpful to understand the molecular structure and discover suitable transition pathways for transferring ultracold atoms to deeply bound rovibrational levels of the electronic ground state.

  12. AW00179 potentiates TRAIL-mediated death of human lung cancer H1299 cells through ROS-JNK-c-Jun-mediated up-regulation of DR5 and down-regulation of anti-apoptotic molecules.

    PubMed

    Hwang, Mi-Kyung; Ryu, Byung Jun; Kim, Seong Hwan

    2012-10-01

    Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) triggers apoptosis in tumor cells, but when used alone, it is not effective at treating TRAIL-resistant tumors. This resistance is challenging for TRAIL-based anti-cancer therapies. In this study, we found that 1-(4-trifluoromethoxy-phenyl)-3-[4-(5-trifluoromethyl-2,5-dihydro-pyrazol-1-yl)-phenyl]-urea (AW00179) sensitized human lung cancer H1299 cells to TRAIL-mediated apoptosis. Even in the absence of TRAIL, AW00179 strongly induced DR5 expression and decreased the expression of anti-apoptotic proteins, suggesting that the sensitizing effect of AW00179 on TRAIL-mediated apoptosis is due to increased levels of DR5 protein and decreased anti-apoptotic molecules. AW00179 also induced the activation of c-Jun and ERK; however, a pharmacologic inhibition study revealed that JNK-c-Jun signaling is involved in the induction of DR5 expression. In addition, reactive oxygen species (ROS) appear to be involved in AW00179 activity. In conclusion, AW00179 has the potential to sensitize H1299 cells to TRAIL-mediated apoptosis through two distinct mechanisms: ROS-JNK-c-Jun-mediated up-regulation of DR5, and down-regulation of anti-apoptotic molecules.

  13. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  14. Dihydrino molecule identification

    SciTech Connect

    Mills, R.L.; Good, W.R. ); Shaubach, R.M. )

    1994-01-01

    Three sets of heat production and [open quotes]ash[close quotes] identification data are presented. An exothermic reaction is reported wherein the electrons of hydrogen and deuterium atoms are stimulated to relax to quantized potential energy levels below that of the [open quotes]ground state[close quotes] via electrochemical reactants K[sup +] and K[sup +]; Pd[sup 2+] and Li[sup +]; or Pd and O[sub 2] of redox energy resonant with the energy hole that stimulates this transition. Calorimetry of pulsed current and continuous electrolysis of aqueous potassium carbonate (K[sup +]/K[sup +] electrocatalytic couple) at a nickel cathode were performed. The excess output power of 41 W exceeded by a factor >8 the total input power given by the product of the electrolysis voltage and current. The product of the exothermic reaction is atoms having electrons of energy below the ground state, which are predicted to form molecules. The predicted molecules were identified by their lack of reactivity with oxygen, by separation from molecular deuterium by cryofiltration, and by mass spectroscopic analysis. 15 refs., 12 figs., 9 tabs.

  15. Second virial coefficients for chain molecules

    SciTech Connect

    Bokis, C.P.; Donohue, M.D. . Dept. of Chemical Engineering); Hall, C.K. . Dept. of Chemical Engineering)

    1994-01-01

    The importance of having accurate second virial coefficients in phase equilibrium calculations, especially for the calculation of dew points, is discussed. The square-well potentials results in a simple but inaccurate equation for the second virial coefficient for small, spherical molecules such as argon. Here, the authors present a new equation for the second virial coefficient of both spherical molecules and chain molecules which is written in a form similar to that for the square-well potential. This new equation is accurate in comparison to Monte Carlo simulation data on second virial coefficients for square-well chain molecules and with second virial coefficients obtained from experiments on n-alkanes.

  16. [Adhesion molecules and diabetes mellitus].

    PubMed

    Urso, C; Hopps, E; Caimi, G

    2010-01-01

    Adhesion molecules play a significant role in leukocyte migration across the endothelium and are also involved in regulating immune system. It is shown that diabetic patients have an increase of soluble adhesion molecules (sICAM-1, sICAM-2, sVCAM-1, sE-selectin, sL-selectin, sP-selectin) considered an integral part of inflammatory state. This inflammation is responsible for the increased cardiovascular risk of these patients. There is a close link between hyperglycemia, oxidative stress, coagulopathy and inflammation and between these factors and the vascular damage. Various studies have showed the potential role of adhesion molecules in the pathogenesis of diabetic vasculopathy. They promote leukocyte recruitment, which is one of the initial steps in the genesis of atherosclerotic plaque. Adhesion molecules are also involved in the pathogenesis of diabetes mellitus type 1; sICAM-1 would have a particular immunomodulatory role in the process of destroying beta-cells and could be used as a subclinical marker of insulitis. Plasma levels of soluble adhesion molecules correlate with hyperglycemia, insulin resistance, dyslipidemia and obesity; they are associated with the development of nephropathy, retinopathy, myocardial infarction, stroke and obliterant peripheral arterial disease in diabetic type 1 and 2. Given the role of these molecules in endothelial dysfunction genesis and tissue damage associated with diabetes, they could constitute a therapeutic target for the prevention of genesis and progression of chronic complications of diabetic disease.

  17. Electrochromic Graphene Molecules

    DOE PAGES

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  18. Phase structure of soliton molecules

    SciTech Connect

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Boehm, M.; Mitschke, F.

    2007-06-15

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E-fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  19. Redox-gated electron transport in electrically wired ferrocene molecules

    NASA Astrophysics Data System (ADS)

    Xiao, Xiaoyin; Brune, Daniel; He, Jin; Lindsay, Stuart; Gorman, Christopher B.; Tao, Nongjian

    2006-07-01

    We have synthesized cysteamine-terminated ferrocene molecules and determined the dependence of the electron transport properties of the molecules on their redox states by measuring the current through the molecules as a function of the electrode potential. The current fluctuates over a large range, but its average value increases with the potential. We attribute the current fluctuation and its increase with the potential to the switching of the molecules from low-conductance reduced state to high-conductance oxidized state.

  20. Electrical conduction through DNA molecule.

    PubMed

    Abdalla, S

    2011-09-01

    Several disorder parameters, inside the DNA molecule, lead to localization of charge carriers inside potential wells in the lowest unoccupied and highest occupied molecular orbits (LUMO and HOMO) which affects drastically the electrical conduction through the molecule, and demonstrates that the band carriers play an essential role in the conduction mechanism. So, a model is presented to shed light on the role of electrons of the LUMO in the electrical conduction through the DNA molecule. DC-, AC-conductivity and dielectric permittivity experimental data are well fitted with the presented model giving evidence that the free carriers in the LUMO and HOMO are responsible to make the DNA molecule conductor, insulator or semiconductor. The obtained results show that the localized charge carriers in the DNA molecule are characterized by four different types of relaxation phenomena which are thermally activated by corresponding four activation energies at 0.56 eV, 0.33 eV, 0.24 eV, and 0.05 eV respectively. Moreover, the calculations after the model, at room temperature, show that the time of the relaxation times of the current carriers are in the order of 5 × 10(-2)s, 1.74 × 10(-4)s, 5 × 10(-7)s, and 1.6 × 10(-10)s, respectively.

  1. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented.

  2. Electrochromic Graphene Molecules

    SciTech Connect

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  3. Formation of Ultracold Molecules

    SciTech Connect

    Cote, Robin

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  4. Metagenomic small molecule discovery methods

    PubMed Central

    Charlop-Powers, Zachary; Milshteyn, Aleksandr; Brady, Sean F.

    2014-01-01

    Metagenomic approaches to natural product discovery provide the means of harvesting bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence- and functional- based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes. PMID:25000402

  5. Intensity calculations of HCN molecules

    NASA Astrophysics Data System (ADS)

    Yasmin, Kausar

    2006-10-01

    Accurate spectroscopic data of HCN are required for many astronomical calculations and modeling. HCN molecules are present in the atmosphere of carbon stars and in galactic centers. Ro-vibrational energy levels and intensity calculations were carried out using the full coupled cluster model and radau coordinates. Accurate ab initio calculated potential energy surface^1 and dipole moment surface^2 were used for computation. The computed values were compared with Hitran^99.^

  6. [Endothelial cell adhesion molecules].

    PubMed

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  7. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  8. 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)

  9. Dynamics of Activated Molecules

    SciTech Connect

    Mullin, Amy S.

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  10. Nano trap for polar molecules

    NASA Astrophysics Data System (ADS)

    Blümel, R.

    2012-07-01

    A new ac/dc monopole trap for neutral polar particles, introduced and explored by Blümel (2011 Phys. Rev. A 83 045402 and 2011 Eur. Phys. J. D 64 85-101), is significantly advanced in several directions. (1) Previously shown to work only for polar classical particles and polar macro-molecules, the trap is shown to work for polar diatomic molecules. (2) A homogeneous electric field, optionally switched on for improved stability in the angular direction, leads to stable trapping in higher order stability regions of the Mathieu equation. (3) Based on the Floquet formalism, analytical and numerical calculations are presented that show that the trap is quantum mechanically stable. (4) Definition and derivation of a quantum pseudo-potential allow a qualitative understanding of the quantum trapping mechanism. (5) It is shown that the proposed ac/dc trap may be realized experimentally using currently available scanning tunnelling microscopy technology.

  11. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  12. Affibody molecules as engineered protein drugs

    PubMed Central

    Frejd, Fredrik Y; Kim, Kyu-Tae

    2017-01-01

    Affibody molecules can be used as tools for molecular recognition in diagnostic and therapeutic applications. There are several preclinical studies reported on diagnostic and therapeutic use of this molecular class of alternative scaffolds, and early clinical evidence is now beginning to accumulate that suggests the Affibody molecules to be efficacious and safe in man. The small size and ease of engineering make Affibody molecules suitable for use in multispecific constructs where AffiMabs is one such that offers the option to potentiate antibodies for use in complex disease. PMID:28336959

  13. Enhancement of the cytotoxic potential of the mixed EGFR and DNA-targeting 'combi-molecule' ZRBA1 against human solid tumour cells by a bis-quinazoline-based drug design approach.

    PubMed

    Al-Safadi, Sherin; Domarkas, Juozas; Han, YingShan; Brahimi, Fouad; Jean-Claude, Bertrand J

    2012-06-01

    ZRBA1 is a quinazoline-based molecule termed 'combi-molecule' designed to block the epidermal growth factor receptor (EGFR) and further degrade to FD105, an EGFR inhibitor plus a DNA-alkylating agent. To augment the potency of ZRBA1, we designed JDE52, a bistriazene that, following degradation, was 'programmed' to yield higher concentrations of the free inhibitor FD105 and a more cytotoxic bifunctional DNA-damaging species. The results indicated that JDE52 was capable of inducing significant blockade of EGFR phosphorylation, DNA strand breaks and interstrand cross-links in human cells. The fluorescent property of FD105, the secondary inhibitor that both JDE52 and ZRBA1 are capable of releasing, has permitted the analysis of its levels in tumour cells by ultraviolet flow cytometry. It was found that JDE52 was indeed capable of significantly releasing higher levels of fluorescence (P<0.05) in human tumour cells when compared with ZRBA1. Apoptosis was triggered by JDE52 at a faster rate than ZRBA1 and led to higher levels of cell killing. The results in toto suggest that the superior potency of JDE52, when compared with ZRBA1, may be imputed to mechanisms associated with the generation of higher intracellular concentrations of FD105 and to the induction of DNA cross-links. These combined mechanisms (blockade of EGFR-tyrosine kinase and induction of cross-links) contributed to an accelerated rate of apoptosis by JDE52. This study conclusively demonstrated that designing molecules as prodrugs of high levels of quinazoline inhibitors of EGFR and bifunctional DNA cross-linking species is a valid strategy to enhance the potency of mixed EGFR-DNA-targeting combi-molecules.

  14. Positronium ions and molecules

    NASA Technical Reports Server (NTRS)

    Ho, Y. K.

    1990-01-01

    Recent theoretical studies on positronium ions and molecules are discussed. A positronium ion is a three particle system consisting of two electrons in singlet spin state, and a positron. Recent studies include calculations of its binding energy, positron annihilation rate, and investigations of its doubly excited resonant states. A positronium molecule is a four body system consisting of two positrons and two electrons in an overall singlet spin state. The recent calculations of its binding energy against the dissociation into two positronium atoms, and studies of auto-detaching states in positronium molecules are discussed. These auto-dissociating states, which are believed to be part of the Rydberg series as a result of a positron attaching to a negatively charged positronium ion, Ps-, would appear as resonances in Ps-Ps scattering.

  15. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  16. Polarization of deuterium molecules

    SciTech Connect

    J. F. J. van den Brand; H. J. Bulten; M. Ferro-Luzzi; Z.-L. Zhou; Ricardo Alarcon; T. Botto; M. Bouwhuis; Rolf Ent; Peter Heimberg; Douglas W. Higinbotham; Kees de Jager; J. Lang; D. J. de Lange; I. Passchier; H. R. Poolman; J. J. M. Steijger; O. Unal; H. de Vries

    1997-08-01

    For molecular systems, spin relaxation is expected to be suppressed compared to the case of atoms, since the paired electrons in a hydrogen or deuterium molecule are chemically stable, and only weakly interact with the spin of the nucleus. Such systems would be largely insensitive to polarization losses due to spin-exchange collisions, to the interaction of the electron spins with external fields (e.g. the RF-field of a bunched charged-particle beam), and/or to the presence of container walls. Here, we discuss the results of a recent experiment where we obtained evidence that nuclear polarization is maintained, when polarized atoms recombine to molecules on a copper surface (in a magnetic field of 23 mT and at a density of about 10{sup 12} molecules {center_dot} cm{sup -3}).

  17. Torsional and rotational couplings in nonrigid molecules

    NASA Astrophysics Data System (ADS)

    Omiste, Juan J.; Madsen, Lars Bojer

    2017-02-01

    We analyze theoretically the interplay between the torsional and the rotational motion of an aligned biphenyl-like molecule. To do so, we consider a transition between two electronic states with different internal torsional potentials, induced by means of a resonant laser pulse. The change in the internal torsional potential provokes the motion of the torsional wave packet in the excited electronic state, modifying the structure of the molecule, and hence, its inertia tensor. We find that this process has a strong impact on the rotational wave function, displaying different behavior depending on the electronic states involved and their associated torsional potentials. We describe the dynamics of the system by considering the degree of alignment and the expectation values of the angular momentum operators for the overall rotation of the molecule.

  18. Single molecule diffraction.

    PubMed

    Spence, J C H; Doak, R B

    2004-05-14

    For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.

  19. Enzyme molecules as nanomotors.

    PubMed

    Sengupta, Samudra; Dey, Krishna K; Muddana, Hari S; Tabouillot, Tristan; Ibele, Michael E; Butler, Peter J; Sen, Ayusman

    2013-01-30

    Using fluorescence correlation spectroscopy, we show that the diffusive movements of catalase enzyme molecules increase in the presence of the substrate, hydrogen peroxide, in a concentration-dependent manner. Employing a microfluidic device to generate a substrate concentration gradient, we show that both catalase and urease enzyme molecules spread toward areas of higher substrate concentration, a form of chemotaxis at the molecular scale. Using glucose oxidase and glucose to generate a hydrogen peroxide gradient, we induce the migration of catalase toward glucose oxidase, thereby showing that chemically interconnected enzymes can be drawn together.

  20. Controlling polar molecules in optical lattices

    SciTech Connect

    Kotochigova, S.; Tiesinga, E.

    2006-04-15

    We theoretically investigate the interaction of polar molecules with optical lattices and microwave fields. We demonstrate the existence of frequency windows in the optical domain where the complex internal structure of the molecule does not influence the trapping potential of the lattice. In such frequency windows the Franck-Condon factors are so small that near-resonant interaction of vibrational levels of the molecule with the lattice fields have a negligible contribution to the polarizability, and light-induced decoherences are kept to a minimum. In addition, we show that microwave fields can induce a tunable dipole-dipole interaction between ground-state rotationally symmetric (J=0) molecules. A combination of a carefully chosen lattice frequency and microwave-controlled interaction between molecules will enable trapping of polar molecules in a lattice and possibly realize molecular quantum logic gates. Our results are based on ab initio relativistic electronic structure calculations of the polar KRb and RbCs molecules combined with calculations of their rovibrational motion.

  1. Sweeping molecules with light

    NASA Astrophysics Data System (ADS)

    Hutzler, Nicholas R.

    2017-03-01

    Many areas of physics—precision measurements, quantum information, and physical chemistry, to name a few—are starting to benefit from the enormous advantages offered by cold and ultracold polar molecules. Molecules have more states, more interactions, and more chemical properties compared to atoms, which make them exciting to study but difficult to tame. In particular, the powerful techniques of atomic laser cooling cannot be naïvely applied to molecules due to their complicated structure. Developments over the past few years have made directly laser cooled and trapped molecules a reality, and now much effort is focused on making these samples larger, denser, and colder—an important step to realizing many of their exciting applications. A careful experimental and numerical study by Truppe et al (2017 New J. Phys. 19 022001) demonstrates a significant improvement and advance in understanding of one of the most limiting steps in laser cooling and trapping of molecules—slowing them from a molecular beam to a near-standstill, with small enough kinetic energy that they can be loaded into a trap.

  2. Disentangling DNA molecules.

    PubMed

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  3. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  4. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  5. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  6. Single molecules: Thermodynamic limits

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    2012-09-01

    Technologies aimed at single-molecule resolution of non-equilibrium systems increasingly require sophisticated new ways of thinking about thermodynamics. An elegant extension to standard fluctuation theory grants access to the kinetic intermediate states of these systems -- as DNA-pulling experiments now demonstrate.

  7. Disentangling DNA molecules

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  8. Three new 'nonterrestrial' molecules

    NASA Astrophysics Data System (ADS)

    Thaddeus, P.; Guelin, M.; Linke, R. A.

    1981-05-01

    Eight new interstellar lines have been detected from three molecules not previously observed spectroscopically in space or in the laboratory. One is a linear or nearly linear molecule with microwave constants B0 equals 21,337.15 plus or minus 0.06 MHz, D0 equals 21.4 plus or minus 1.5 kHz. This is the thioformyl ion HCS(plus), first identified because B0 and D0 are close to those calculated, and now confirmed by laboratory detection of one of the present lines (Gudeman et al.). The second molecule, also linear or nearly so, has microwave constants B0 equals 10,691,406 plus or minus 0.043 MHz, D0 equals 1.84 plus or minus 0.91 kHz close to those expected for the isoelectronic systems HOCO(plus) and HOCN; a choice between the two cannot be made on the basis of the available astronomical data. The existence of a third molecule is deduced from an unidentified line at 85,338 MHz that has been found in many sources, is fairly intense in several, and may be self-absorbed in Sgr B2.

  9. Dietary choline deficiency and excess induced intestinal inflammation and alteration of intestinal tight junction protein transcription potentially by modulating NF-κB, STAT and p38 MAPK signaling molecules in juvenile Jian carp.

    PubMed

    Wu, Pei; Jiang, Wei-Dan; Jiang, Jun; Zhao, Juan; Liu, Yang; Zhang, Yong-An; Zhou, Xiao-Qiu; Feng, Lin

    2016-11-01

    This study investigated the effects of choline on intestinal mucosal immune and the possible mechanisms in fish by feeding juvenile Jian carp (Cyprinus carpio var. Jian) with graded levels of dietary choline (165-1820 mg/kg diet) for 65 days. The results firstly showed that choline deficiency induced inflammatory infiltration in the proximal intestine (PI), mid intestine (MI) and distal intestine (DI) of fish. Meanwhile, compared with the optimal choline group, choline deficiency decreased the activities of lysozyme and acid phosphatase, contents of complement 3 and IgM in the intestine, downregulated the mRNA levels of antimicrobial peptides (liver-expressed antimicrobial peptide (LEAP) 2A and defensin-3 in the PI and MI, LEAP-2B and hepcidin in the PI, MI and DI), anti-inflammatory cytokines (interleukin (IL) 10 and transforming growth factor β2 in the PI, MI and DI), and signaling molecule IκB in the PI, MI and DI; while upregulated the mRNA levels of pro-inflammatory cytokines (IL-6a and tumor necrosis factor α in the MI and DI, interferon γ2b in the PI and MI, IL-1β and IL-6b in the PI, MI and DI), and signaling molecules (Toll-like receptor 4 in the MI, myeloid differentiation primary response 88 in the PI and MI, Janus kinase 3 and tyrosine kinase 2 in the MI and DI, nuclear factor kappa B (NF-κB), signal transducers and activators of transcription (STAT) 4 and STAT5 in the PI, MI and DI) of juvenile Jian carp, further indicating that choline deficiency caused inflammation and immunity depression in the intestine of fish. But choline deficiency decreased the PI IL-6a mRNA level, and increased the DI LEAP-2A and defensin-3 mRNA levels with unknown reasons. Furthermore, dietary choline deficiency downregulated mRNA levels of tight junction (TJ) proteins (claudin 3c in the PI and MI, claudin 7, claudin 11 and occludin in the PI, MI and DI) and signaling molecule mitogen-activated protein kinases p38 in the PI, MI and DI of juvenile Jian carp, whereas

  10. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-09-17

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  11. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  12. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  13. Molecules in Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Berdyugina, Svetlana

    2015-08-01

    Molecules probe cool matter in the Universe and various astrophysical objects. Their ability to sense magnetic fields provides new insights into magnetic properties of these objects. During the past fifteen years we have carried out a theoretical study of molecular magnetic effects such as the Zeeman, Paschen-Back and Hanle effects and their applications for inferring magnetic structures and spatial inhomogeneities on the Sun, cool stars, brown dwarfs, and exoplanets from molecular spectro-polarimetry (e.g., Berdyugina 2011). Here, we present an overview of this study and compare our theoretical predictions with recent laboratory measurements of magnetic properties of some molecules. We present also a new web-based tool to compute molecular magnetic effects and polarized spectra which is supported by the ERC Advanced Grant HotMol.

  14. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  15. Strange skyrmion molecules

    SciTech Connect

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-20

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  16. Model molecules mimicking asphaltenes.

    PubMed

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe

    2015-04-01

    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed.

  17. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  18. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  19. Evidence of water molecules--a statistical evaluation of water molecules based on electron density.

    PubMed

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias

    2015-04-27

    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

  20. Negative ions of polyatomic molecules.

    PubMed Central

    Christophorou, L G

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744

  1. Negative ions of polyatomic molecules.

    PubMed

    Christophorou, L G

    1980-06-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies.

  2. Addition of nucleophiles on cyanoacetylene N≡CCH=CH-X (X = NH2, OH, SH, …). Synthesis and Physico-chemical Properties of Potential Prebiotic Compounds or Interstellar Molecules.

    NASA Astrophysics Data System (ADS)

    Guillemin, Jean-Claude

    Among the molecules detected to date in the interstellar medium (ISM), cyanopolyynes constitute a rich and important subset. These robust compounds exhibit special properties with respect to their reactivity and kinetic stability, and some have been found in other astrochemical environments, such as comets or in lab simulations of planetary atmospheres.[1] These systems are supposed to be good starting materials for the formation of new, more complex, astrochemical species, or amino acids on primitive Earth. The formal addition of water, hydrogen sulfur or ammonia on cyanoacetylene (H-C≡C-C≡N) gives the corresponding heterosubstitued acrylonitriles. We have extensively investigated the study of such adducts. With water, the formed cyanovinylalcohol (NC-CH=CH-OH) is in a tautomeric equilibrium with the kinetically more stable cyanoacetaldehyde (NC-CH2 CH(=O)). Isolation of these compounds in pure form is challenging but the gas phase infrared spectrum has been recorded. Reaction of ammonia with cyanoacetylene gives aminoacrylonitrile (H2 N-CH=CH-CN), a stable enamine; microwave and infrared spectra were obtained.[2] Similarly the MW spectrum of 3-mercapto-2-propenenitrile (HS-CH=CH-CN) has been recorded.[3] Attempts to detect both species in the ISM have been performed. A combined experimental and theoretical study on the gas-phase basicity and acidity of a series of cyanovinyl derivatives is also presented.[4] We will demonstrate that many particular physicochemical properties are associated to these simple adducts of cyanoacetylene, compounds often proposed as prebiotic molecules or components of the ISM. 1] S. W. Fow, K. Dose, Molecular Evolution and the Origin of Life, Marcel Dekker, Stateplace- New York, metricconverterProductID1977. A1977. A. Coustenis, T. Encrenaz, B. BJzard, B. Bjoraker, G. Graner, G. Dang-Nhu, E. AriJ, Icarus 1993, 102, 240 - 269. [2] Benidar, A. ; Guillemin, J.-C. ; M—, O. ; Y‡-ez, M. J. Phys. Chem. A. 2005, 109, 4705-4712. E

  3. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  4. Molecules in crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Mark A.

    2013-04-01

    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  5. Theoretical spectra of floppy molecules

    NASA Astrophysics Data System (ADS)

    Chen, Hua

    2000-09-01

    Detailed studies of the vibrational dynamics of floppy molecules are presented. Six-D bound-state calculations of the vibrations of rigid water dimer based on several anisotropic site potentials (ASP) are presented. A new sequential diagonalization truncation approach was used to diagonalize the angular part of the Hamiltonian. Symmetrized angular basis and a potential optimized discrete variable representation for intermonomer distance coordinate were used in the calculations. The converged results differ significantly from the results presented by Leforestier et al. [J. Chem. Phys. 106 , 8527 (1997)]. It was demonstrated that ASP-S potential yields more accurate tunneling splittings than other ASP potentials used. Fully coupled 4D quantum mechanical calculations were performed for carbon dioxide dimer using the potential energy surface given by Bukowski et al [J. Chem. Phys., 110, 3785 (1999)]. The intermolecular vibrational frequencies and symmetry adapted force constants were estimated and compared with experiments. The inter-conversion tunneling dynamics was studied using the calculated virtual tunneling splittings. Symmetrized Radau coordinates and the sequential diagonalization truncation approach were formulated for acetylene. A 6D calculation was performed with 5 DVR points for each stretch coordinate, and an angular basis that is capable of converging the angular part of the Hamiltonian to 30 cm-1 for internal energies up to 14000 cm-1. The probability at vinylidene configuration were evaluated. It was found that the eigenstates begin to extend to vinylidene configuration from about 10000 cm-1, and the ra, coordinate is closely related to the vibrational dynamics at high energy. Finally, a direct product DVR was defined for coupled angular momentum operators, and the SDT approach were formulated. They were applied in solving the angular part of the Hamiltonian for carbon dioxide dimer problem. The results show the method is capable of giving very accurate

  6. Heteropentameric Cholera Toxin B Subunit Chimeric Molecules Genetically Fused to a Vaccine Antigen Induce Systemic and Mucosal Immune Responses: a Potential New Strategy To Target Recombinant Vaccine Antigens to Mucosal Immune Systems

    PubMed Central

    Harakuni, Tetsuya; Sugawa, Hideki; Komesu, Ai; Tadano, Masayuki; Arakawa, Takeshi

    2005-01-01

    Noninvasive mucosal vaccines are attractive alternatives to parenteral vaccines. Although the conjugation of vaccine antigens with the B subunit of cholera toxin (CTB) is one of the most promising strategies for vaccine delivery to mucosal immune systems, the molecule cannot tolerate large-protein fusion, as it severely impairs pentamerization and loses affinity for GM1-ganglioside. Here we report a new strategy, in which steric hindrance between CTB-antigen fusion subunits is significantly reduced through the integration of unfused CTB “molecular buffers” into the pentamer unit, making them more efficiently self-assemble into biologically active pentamers. In addition, the chimeric protein took a compact configuration, becoming small enough to be secreted, and one-step affinity-purified proteins, when administered through a mucosal route, induced specific immune responses in mice. Since our results are not dependent on the use of a particular expression system or vaccine antigen, this strategy could be broadly applicable to bacterial enterotoxin-based vaccine design. PMID:16113283

  7. Enhancing single-molecule fluorescence with nanophotonics.

    PubMed

    Acuna, Guillermo; Grohmann, Dina; Tinnefeld, Philip

    2014-10-01

    Single-molecule fluorescence spectroscopy has become an important research tool in the life sciences but a number of limitations hinder the widespread use as a standard technique. The limited dynamic concentration range is one of the major hurdles. Recent developments in the nanophotonic field promise to alleviate these restrictions to an extent that even low affinity biomolecular interactions can be studied. After motivating the need for nanophotonics we introduce the basic concepts of nanophotonic devices such as zero mode waveguides and nanoantennas. We highlight current applications and the future potential of nanophotonic approaches when combined with biological systems and single-molecule spectroscopy.

  8. Small molecule inhibitors of ebola virus infection.

    PubMed

    Picazo, Edwige; Giordanetto, Fabrizio

    2015-02-01

    Ebola viruses are extremely virulent and highly transmissible. They are responsible for sporadic outbreaks of severe hemorrhagic fevers with human mortality rates of up to 90%. No prophylactic or therapeutic treatments in the form of vaccine, biologicals or small molecule, currently exist. Yet, a wealth of antiviral research on ebola virus is being generated and potential inhibitors have been identified in biological screening and medicinal chemistry programs. Here, we detail the state-of-the-art in small molecule inhibitors of ebola virus infection, with >60 examples, including approved drugs, compounds currently in clinical trials, and more exploratory leads, and summarize the associated in vitro and in vivo evidence for their effectiveness.

  9. Cavity sideband cooling of trapped molecules

    SciTech Connect

    Kowalewski, Markus; Vivie-Riedle, Regina de; Morigi, Giovanna; Pinkse, Pepijn W. H.

    2011-09-15

    The efficiency of cavity sideband cooling of trapped molecules is theoretically investigated for the case in which the infrared transition between two rovibrational states is used as a cycling transition. The molecules are assumed to be trapped either by a radiofrequency or optical trapping potential, depending on whether they are charged or neutral, and confined inside a high-finesse optical resonator that enhances radiative emission into the cavity mode. Using realistic experimental parameters and COS as a representative molecular example, we show that in this setup, cooling to the trap ground state is feasible.

  10. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  11. 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.

  12. Deceleration of neutral molecules in macroscopic traveling traps

    SciTech Connect

    Osterwalder, Andreas; Meek, Samuel A.; Hammer, Georg; Haak, Henrik; Meijer, Gerard

    2010-05-15

    A decelerator is presented where polar neutral molecules are guided and decelerated using the principle of traveling electric potential wells, such that molecules are confined in stable three-dimensional traps throughout. We compare this decelerator with that of Scharfenberg et al. [Phys. Rev. A 79, 023410 (2009)] and we show that the current decelerator provides a substantially larger phase-space acceptance, even at higher acceleration. The mode of operation is described and experimentally demonstrated by guiding and decelerating CO molecules.

  13. Molecules Best Paper Award 2013.

    PubMed

    McPhee, Derek J

    2013-02-05

    Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.

  14. Hydrogen sulfide and polysulfides as signaling molecules

    PubMed Central

    KIMURA, Hideo

    2015-01-01

    Hydrogen sulfide (H2S) is a familiar toxic gas that smells of rotten eggs. After the identification of endogenous H2S in the mammalian brain two decades ago, studies of this molecule uncovered physiological roles in processes such as neuromodulation, vascular tone regulation, cytoprotection against oxidative stress, angiogenesis, anti-inflammation, and oxygen sensing. Enzymes that produce H2S, such as cystathionine β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase have been studied intensively and well characterized. Polysulfides, which have a higher number of inner sulfur atoms than that in H2S, were recently identified as potential signaling molecules that can activate ion channels, transcription factors, and tumor suppressors with greater potency than that of H2S. This article focuses on our contribution to the discovery of these molecules and their metabolic pathways and mechanisms of action. PMID:25864468

  15. Small molecule modifiers of circadian clocks.

    PubMed

    Chen, Zheng; Yoo, Seung-Hee; Takahashi, Joseph S

    2013-08-01

    Circadian clocks orchestrate 24-h oscillations of essential physiological and behavioral processes in response to daily environmental changes. These clocks are remarkably precise under constant conditions yet highly responsive to resetting signals. With the molecular composition of the core oscillator largely established, recent research has increasingly focused on clock-modifying mechanisms/molecules. In particular, small molecule modifiers, intrinsic or extrinsic, are emerging as powerful tools for understanding basic clock biology as well as developing putative therapeutic agents for clock-associated diseases. In this review, we will focus on synthetic compounds capable of modifying the period, phase, or amplitude of circadian clocks, with particular emphasis on the mammalian clock. We will discuss the potential of exploiting these small molecule modifiers in both basic and translational research.

  16. 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.

  17. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  18. Fiber-mesh photonic molecule

    NASA Astrophysics Data System (ADS)

    Mishra, Subodha; Satpathy, Sashi

    2008-03-01

    Analogous to the photonic crystal, we introduce the concept of a fiber-mesh photonic molecule made up of optical fibers and study its transmission characteristics. We consider a specific example of a photonic molecule, inspired by the well-known C60 molecule, with the arms of the molecule formed out of single-moded optical fibers. The transmittance consists of sharp peaks determined by the pole structure of the scattering matrix in the complex energy plane. A molecule can be designed to control the positions and the widths of the transmission peaks, opening up the possibility of building new photonic devices such as high quality band-pass filters.

  19. Connexin Channel Permeability to Cytoplasmic Molecules

    PubMed Central

    Harris, Andrew L.

    2007-01-01

    Connexin channels are known to be permeable to a variety of cytoplasmic molecules. The first observation of second messenger junctional permeability, made ∼30 years ago, sparked broad interest in gap junction channels as mediators of intercellular molecular signaling. Since then, much has been learned about the diversity of connexin channels with regard to isoform diversity, tissue and developmental distribution, modes of channel regulation, assembly and expression, biochemical modification and permeability, all of which appear to be dynamically regulated. This information has expanded the potential roles of connexin channels in development, physiology and disease, and made their elucidation much more complex - 30 years ago such an orchestra of junctional dynamics was unanticipated. Only recently, however, have investigators been able to directly address, in this more complex framework, the key issue: What specific biological molecules, second messengers and others, are able to permeate the various types of connexin channels, and how well? An important related issue, given the ever-growing list of connexin-related pathologies, is how these permeabilities are altered by disease-causing connexin mutations. Together, many studies show that a variety of cytoplasmic molecules can permeate the different types of connexin channels. A few studies reveal differences in permeation by different molecules through a particular type of connexin channel, and differences in permeation by a particular molecule through different types of connexin channels. This article describes and evaluates the various methods used to obtain these data, presents an annotated compilation of the results, and discusses the findings in the context of what can be inferred about mechanism of selectivity and potential relevance to signaling. The data strongly suggest that highly specific interactions take place between connexin pores and specific biological molecular permeants, and that those

  20. Spectroscopic probes of vibrationally excited molecules at chemically significant energies

    SciTech Connect

    Rizzo, T.R.

    1993-12-01

    This project involves the application of multiple-resonance spectroscopic techniques for investigating energy transfer and dissociation dynamics of highly vibrationally excited molecules. Two major goals of this work are: (1) to provide information on potential energy surfaces of combustion related molecules at chemically significant energies, and (2) to test theoretical modes of unimolecular dissociation rates critically via quantum-state resolved measurements.

  1. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOEpatents

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  2. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  3. Electron-excited molecule interactions

    SciTech Connect

    Christophorou, L.G. Tennessee Univ., Knoxville, TN . Dept. of Physics)

    1991-01-01

    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10{sup 6} to 10{sup 7} times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs.

  4. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  5. Single molecule tracking

    DOEpatents

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  6. Atmospheric trace molecule spectroscopy

    NASA Technical Reports Server (NTRS)

    Farmer, C. B.

    1982-01-01

    The Spacelab investigation entitled Atmospheric Trace Molecule Spectroscopy (ATMOS) is designed to obtain fundamental information related to the chemistry and physics of the Earth's upper atmosphere using the techniques of infrared absorption spectroscopy. There are two principal objectives to be met. The first is the determination, on a global scale, of the compositional structure of the upper atmosphere and its spatial variability. The establishment of this variability represents the first step toward determining the characteristic residence times for the upper atmospheric constituents; the magnitudes of their sources and sinks; and, ultimately, an understanding of their effects on the stability of the stratosphere. The second objective is to provide the high-resolution, calibrated spectral information which is essential for the detailed design of advanced instrumentation for subsequent global monitoring of specific species found to be critical to atmospheric stability. This information will be disseminated in the form of a three dimensional atlas of solar absorption spectra obtained over a range of latitudes, longitudes, and altitudes.

  7. Theory of Long-Range Ultracold Atom-Molecule Photoassociation.

    PubMed

    Pérez-Ríos, Jesús; Lepers, Maxence; Dulieu, Olivier

    2015-08-14

    The creation of ultracold molecules is currently limited to diatomic species. In this Letter, we present a theoretical description of the photoassociation of ultracold atoms and molecules to create ultracold excited triatomic molecules, thus being a novel example of a light-assisted ultracold chemical reaction. The calculation of the photoassociation rate of an ultracold Cs_{2} molecule in its rovibrational ground state with an ultracold Cs atom at frequencies close to its resonant excitation is reported, based on the solution of the quantum dynamics involving the atom-molecule long-range interactions and assuming a model potential for the short-range physics. The rate for the formation of excited Cs_{3} molecules is predicted to be comparable with currently observed atom-atom photoassociation rates. We formulate an experimental proposal to observe this process relying on the available techniques of optical lattices and standard photoassociation spectroscopy.

  8. Collision integrals for isotopic hydrogen molecules.

    NASA Technical Reports Server (NTRS)

    Brown, N. J.; Munn, R. J.

    1972-01-01

    The study was undertaken to determine the effects of reduced mass and differences in asymmetry on the collision integrals and thermal diffusion factors of isotopic hydrogen systems. Each system selected for study consisted of two diatoms, one in the j = 0 rotation state and the other in the j = 1 state. The molecules interacted with a Lennard-Jones type potential modified to include angular terms. A set of cross sections and collision integrals were obtained for each system.

  9. Micro injector sample delivery system for charged molecules

    DOEpatents

    Davidson, James C.; Balch, Joseph W.

    1999-11-09

    A micro injector sample delivery system for charged molecules. The injector is used for collecting and delivering controlled amounts of charged molecule samples for subsequent analysis. The injector delivery system can be scaled to large numbers (>96) for sample delivery to massively parallel high throughput analysis systems. The essence of the injector system is an electric field controllable loading tip including a section of porous material. By applying the appropriate polarity bias potential to the injector tip, charged molecules will migrate into porous material, and by reversing the polarity bias potential the molecules are ejected or forced away from the tip. The invention has application for uptake of charged biological molecules (e.g. proteins, nucleic acids, polymers, etc.) for delivery to analytical systems, and can be used in automated sample delivery systems.

  10. Vibrational autoionization in polyatomic molecules.

    PubMed

    Pratt, S T

    2005-01-01

    The vibrationally autoionizing Rydberg states of small polyatomic molecules provide a fascinating laboratory in which to study fundamental nonadiabatic processes. In this review, recent results on the vibrational mode dependence of vibrational autoionization are discussed. In general, autoionization rates depend strongly on the character of the normal mode driving the process and on the electronic character of the Rydberg electron. Although quantitative calculations based on multichannel quantum defect theory are available for some polyatomic molecules, including H3, only qualitative information exists for most molecules. This review shows how qualitative information, such as Walsh diagrams along different normal coordinates of the molecule, can provide insight into the vibrational autoionization rates.

  11. Electrical Transport through Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lau, C. N.; Chang, Shun-Chi; Williams, Stan

    2003-03-01

    We investigate electrical transport properties of single organic molecules using electromigration break junctions[1]. A self-assembled monolayer of various organic molecules such as 1,4-di(phenylethynyl-4'-methanethiol)benzene was grown on narrow metal wires, and single or a few molecules were incorporated into the junctions which were created by applying a large voltage and breaking the wires. The transport properties of these molecules were then measured at low temperatures. Latest experimental results will be discussed. [1] Park, J. et al, Nature, 417, 722 (2002); Liang W. et al, Nature, 417, 725 (2002).

  12. Coordination programming of photofunctional molecules.

    PubMed

    Sakamoto, Ryota; Kusaka, Shinpei; Hayashi, Mikihiro; Nishikawa, Michihiro; Nishihara, Hiroshi

    2013-04-05

    Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET) initiated by the metal-to-ligand charge transfer (MLCT) transition of the Cu(I) state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinato)zinc(II) complexes. Conventional homoleptic bis(dipyrrinato)zinc(II) complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynyl)fumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

  13. Collisional Transitions in Interstellar Asymmetric Top Molecules

    NASA Astrophysics Data System (ADS)

    Chandra, Suresh

    2012-07-01

    known interaction potential. As an example, we shall discuss collisional rates for rotational transitions in H_2CS molecule.

  14. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  15. Featured Molecules: Sucrose and Vanillin

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-04-01

    The WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  16. Micro-Kelvin cold molecules.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-10-01

    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  17. Single-molecule techniques for drug discovery.

    PubMed

    Skinner, Gary M; Visscher, Koen

    2004-08-01

    Single-molecule techniques offer a number of key benefits over conventional in vitro assay methods for drug screening, as they use less material and unlock the ability to observe transient states. By observing such states, it should be possible to screen for chemical compounds that isolate these steps. The benefit of this is twofold: (a) inhibitors can be found that target key phases in biochemical processes, e.g., transcription initiation; and (b) the total number of drug targets increases as many biochemical processes consist of many transient steps, e.g., transcription promoter binding, initiation, elongation, and termination. Although single-molecule methods offer exciting opportunities for new ways of discovering drugs, there are a number of obstacles to their adoption for drug screening. The main hurdle is to develop robust apparatus that will allow many thousands of individual single molecule experiments to be performed in parallel. By using recently developed integrated microfluidics technology, this hurdle may be overcome. Here, a number of potential single-molecule approaches to drug screening are presented along with a discussion of the benefits and technical obstacles that must be overcome.

  18. System-wide detection of protein-small molecule complexes suggests extensive metabolite regulation in plants

    PubMed Central

    Veyel, Daniel; Kierszniowska, Sylwia; Kosmacz, Monika; Sokolowska, Ewelina Maria; Michaelis, Aenne; Luzarowski, Marcin; Szlachetko, Jagoda; Willmitzer, Lothar; Skirycz, Aleksandra

    2017-01-01

    Protein small molecule interactions are at the core of cell regulation controlling metabolism and development. We reasoned that due to the lack of system wide approaches only a minority of those regulatory molecules are known. In order to see whether or not this assumption is true we developed an effective approach for the identification of small molecules having potential regulatory role that obviates the need of protein or small molecule baits. At the core of this approach is a simple biochemical co-fractionation taking advantage of size differences between proteins and small molecules. Metabolomics based analysis of small molecules co-fractionating with proteins identified a multitude of small molecules in Arabidopsis suggesting the existence of numerous, small molecules/metabolites bound to proteins representing potential regulatory molecules. The approach presented here uses Arabidopsis cell cultures, but is generic and hence applicable to all biological systems. PMID:28205532

  19. Enzyme molecules in solitary confinement.

    PubMed

    Liebherr, Raphaela B; Gorris, Hans H

    2014-09-12

    Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  20. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  1. Adhesion molecules in vernal keratoconjunctivitis

    PubMed Central

    El-Asrar, A.; Geboes, K.; Al-Kharashi, S.; Tabbara, K.; Missotten, L.; Desmet, V.

    1997-01-01

    AIMS/BACKGROUND—Adhesion molecules play a key role in the selective recruitment of different leucocyte population to inflammatory sites. The purpose of the present study was to investigate the presence and distribution of adhesion molecules in the conjunctiva of patients with vernal keratoconjunctivitis (VKC).
METHODS—The presence and distribution of adhesion molecules were studied in 14 conjunctival biopsy specimens from seven patients with active VKC and in four normal conjunctival biopsy specimens. We used a panel of specific monoclonal antibodies (mAbs) directed against intercellular adhesion molecule-1 (ICAM-1), intercellular adhesion molecule-3 (ICAM-3), lymphocyte function associated antigen-1 (LFA-1), very late activation antigen-4 (VLA-4), vascular cell adhesion molecule-1 (VCAM-1), and endothelial leucocyte adhesion molecule-1 (ELAM-1). In addition, a panel of mAbs were used to characterise the composition of the inflammatory infiltrate.
RESULTS—In the normal conjunctiva, ICAM-1 was expressed on the vascular endothelium only, LFA-1 and ICAM-3 on epithelial and stromal mononuclear cells , and VLA-4 on stromal mononuclear cells. The expression of VCAM-1 and ELAM-1 was absent. The number of cells expressing adhesion molecules was found to be markedly increased in all VKC specimens. This was concurrent with a heavy inflammatory infiltrate. Strong ICAM-1 expression was induced on the basal epithelial cells, and vascular endothelial cells. Furthermore, ICAM-1 was expressed on stromal mononuclear cells. LFA-1 and ICAM-3 were expressed on the majority of epithelial and stromal infiltrating mononuclear cells. VLA-4 expression was noted on stromal mononuclear cells. Compared with controls, VKC specimens showed significantly more ICAM-3+, LFA-1+, and VLA-4+ cells. VCAM-1 and ELAM-1 were induced on the vascular endothelial cells.
CONCLUSIONS—Increased expression of adhesion molecules may play an important role in the pathogenesis of VKC.

 PMID

  2. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  3. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  4. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  5. The X(3872) boson: Molecule or charmonium

    SciTech Connect

    Suzuki, Mahiko

    2005-08-01

    It has been argued that the mystery boson X(3872) is a molecular state consisting of primarily D{sup 0}{bar D}*{sup 0} + {bar D}{sup 0}D*{sup 0}. In contrast, apparent puzzles and potential difficulties have been pointed out for the charmonium assignment of X(3872). They examine several aspects of these alternatives by semi-quantitative methods since quantitatively accurate results are often hard to reach on them. they point out that some of the observed properties of X(3872), in particular, the binding and the production rates are incompatible with the molecule interpretation. Despite puzzles and obstacles, X(3872) may fit more likely to the excited {sup 3}P{sub 1} charmonium than to the molecule after the mixing of c{bar c} with D{bar D}* + {bar D}D* is taken into account.

  6. Targeted Protein Degradation by Small Molecules.

    PubMed

    Bondeson, Daniel P; Crews, Craig M

    2017-01-06

    Protein homeostasis networks are highly regulated systems responsible for maintaining the health and productivity of cells. Whereas therapeutics have been developed to disrupt protein homeostasis, more recently identified techniques have been used to repurpose homeostatic networks to effect degradation of disease-relevant proteins. Here, we review recent advances in the use of small molecules to degrade proteins in a selective manner. First, we highlight all-small-molecule techniques with direct clinical application. Second, we describe techniques that may find broader acceptance in the biomedical research community that require little or no synthetic chemistry. In addition to serving as innovative research tools, these new approaches to control intracellular protein levels offer the potential to develop novel therapeutics targeting proteins that are not currently pharmaceutically vulnerable.

  7. Forskolin: upcoming antiglaucoma molecule.

    PubMed

    Wagh, V D; Patil, P N; Surana, S J; Wagh, K V

    2012-01-01

    Forskolin is the first pharmaceutical drug and product derived from a plant to be approved in India by the DCGI in 2006. Forskolin (7beta-acetoxy-8, 13-epoxy-1a, 6β, 9a-trihydroxy-labd-14-en-11-one) is a diterpenoid isolated from plant Coleus forskohlii (Lamiaceae). It is a lipid-soluble compound that can penetrate cell membranes and stimulates the enzyme adenylate cyclase which, in turn, stimulates ciliary epithelium to activate cyclic adenosine monophosphate, which decreases intraocular pressure (IOP) by reducing aqueous humor inflow. The topical application of forskolin is capable of reducing IOP in rabbits, monkeys, and humans. In its drug interactions, forskolin may act synergistically with epinephrine, ephedrine and pseudoephedrine. Whereas the effects of anti-clotting medications like warfarin, clopidogre, aspirin, anoxaparin, etc., may be enhanced by forskolin. Forskolin is contraindicated in the medications for people with ulcers as forskolin may increase acid level. Forskolin has a very good shelf-life of five years. Recently, its Ophthalmic inserts and in situ gels for sustained and delayed-release drug delivery systems were tested in New Zealand Albino Rabbits for its antiglaucoma efficacy. This drug review explains Forskolin as a drug, its antiglaucoma potential and recent findings of forskolin as an antiglaucoma agent. The literature search method used for this review was different databases and search engines like PubMed, International Pharmaceutical Abstracts, Google, Medicinal and Aromatic Plants (MAPA).

  8. Novel hepatocellular carcinoma molecules with prognostic and therapeutic potentials

    PubMed Central

    Scaggiante, Bruna; Kazemi, Maryam; Pozzato, Gabriele; Dapas, Barbara; Farra, Rosella; Grassi, Mario; Zanconati, Fabrizio; Grassi, Gabriele

    2014-01-01

    Hepatocellular carcinoma (HCC), the predominant form of primary liver cancer, is the sixth most common cancer worldwide and the third leading cause of cancer-related death. The difficulty to diagnose early cancer stages, the aggressive behaviors of HCC, and the poor effectiveness of therapeutic treatments, represent the reasons for the quite similar deaths per year and incidence number. Considering the fact that the diagnosis of HCC typically occurs in the advanced stages of the disease when the therapeutic options have only modest efficacy, the possibility to identify early diagnostic markers could be of significant benefit. So far, a large number of biomarkers have been associated to HCC progression and aggressiveness, but many of them turned out not to be of practical utility. This is the reason why active investigations are ongoing in this field. Given the huge amount of published works aimed at the identification of HCC biomarkers, in this review we mainly focused on the data published in the last year, with particular attention to the role of (1) molecular and biochemical cellular markers; (2) micro-interfering RNAs; (3) epigenetic variations; and (4) tumor stroma. It is worth mentioning that a significant number of the HCC markers described in the present review may be utilized also as targets for novel therapeutic approaches, indicating the tight relation between diagnosis and therapy. In conclusion, we believe that integrated researches among the different lines of investigation indicated above should represent the winning strategies to identify effective HCC markers and therapeutic targets. PMID:24574801

  9. Static Trapping of Polar Molecules in a Traveling Wave Decelerator

    NASA Astrophysics Data System (ADS)

    Quintero-Pérez, Marina; Jansen, Paul; Wall, Thomas E.; van den Berg, Joost E.; Hoekstra, Steven; Bethlem, Hendrick L.

    2013-03-01

    We present experiments on decelerating and trapping ammonia molecules using a combination of a Stark decelerator and a traveling wave decelerator. In the traveling wave decelerator, a moving potential is created by a series of ring-shaped electrodes to which oscillating high voltages (HV) are applied. By lowering the frequency of the applied voltages, the molecules confined in the moving trap are decelerated and brought to a standstill. As the molecules are confined in a true 3D well, this kind of deceleration has practically no losses, resulting in a great improvement on the usual Stark deceleration techniques. The necessary voltages are generated by amplifying the output of an arbitrary wave generator using fast HV amplifiers, giving us great control over the trapped molecules. We illustrate this by experiments in which we adiabatically cool trapped NH3 and ND3 molecules and resonantly excite their motion.

  10. Quantum Transport Through Heterocyclic Molecules

    NASA Astrophysics Data System (ADS)

    Maiti, Santanu K.; Karmakar, S. N.

    We explore electron transport properties in molecular wires made of heterocyclic molecules (pyrrole, furan and thiophene) by using the Green's function technique. Parametric calculations are given based on the tight-binding model to describe the electron transport in these wires. It is observed that the transport properties are significantly influenced by (a) the heteroatoms in the heterocyclic molecules and (b) the molecule-to-electrodes coupling strength. Conductance (g) shows sharp resonance peaks associated with the molecular energy levels in the limit of weak molecular coupling, while they get broadened in the strong molecular coupling limit. These resonances get shifted with the change of the heteroatoms in these heterocyclic molecules. All the essential features of the electron transfer through these molecular wires become much more clearly visible from the study of our current-voltage (I-V) characteristics, and they provide several key information in the study of molecular transport.

  11. Molecule-hugging graphene nanopores

    PubMed Central

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel

    2013-01-01

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule. PMID:23836648

  12. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  13. Moving Molecules and Mothball Madness.

    ERIC Educational Resources Information Center

    Strain, John

    1993-01-01

    Describes concrete demonstrations on the states of matter. In the first demonstration, students represent molecules; and, in the second demonstration, moth balls are heated to produce a change of state. (PR)

  14. Charge transport in nitro substituted oligo(phenylene-ethynylene) molecules

    NASA Astrophysics Data System (ADS)

    Cabassi, Marco Alberto

    2007-12-01

    This thesis presents research aimed at tackling two issues in the field of molecular electronics. The first issue is the large range of molecular conductance values reported by various research groups for identical molecules. This is addressed by studying the same molecule in dissimilar environments. The second issue is experimental uncertainty---whether the observed effects are inherent to the molecule or due to external causes. This is addressed by performing in-situ spectroscopy of the molecule as part of its electrical characterization. Oligo(phenylene-ethynylene)s are a well studied class of molecules in the field of molecular electronics, and this work focuses on charge transport through nitro substituted oligo(phenylene-ethynylene) molecules. The electrical characterization of these molecules was performed utilizing two testbeds. An electromigrated break-junction testbed was used to probe individual molecules, while a nanowire molecular junction testbed was used to probe self-assembled monolayers of the molecule. Experiments performed on individual molecules revealed a temperature dependent transition in the dominant charge transport mechanism. Above 50K, hopping is the dominant charge transport mechanism, while below 50K direct tunneling is the dominant charge transport mechanism. Experiments performed on self-assembled monolayers did not reveal any temperature dependent transitions. The dominant charge transport mechanism appears to be direct tunneling throughout the temperature range investigated. The results also indicate that molecules embedded in a self-assembled monolayer have significantly lower conductance than individual molecules. This is primarily due to a second charge transport mechanism (hopping) that opens up above 50K that is available only to individual molecules, and secondarily due to better potential screening properties of the self-assembled monolayers. Inelastic electron tunneling spectra obtained for the molecules in a self

  15. Evaluation of genotoxicity testing of FDA approved large molecule therapeutics.

    PubMed

    Sawant, Satin G; Fielden, Mark R; Black, Kurt A

    2014-10-01

    Large molecule therapeutics (MW>1000daltons) are not expected to enter the cell and thus have reduced potential to interact directly with DNA or related physiological processes. Genotoxicity studies are therefore not relevant and typically not required for large molecule therapeutic candidates. Regulatory guidance supports this approach; however there are examples of marketed large molecule therapeutics where sponsors have conducted genotoxicity studies. A retrospective analysis was performed on genotoxicity studies of United States FDA approved large molecule therapeutics since 1998 identified through the Drugs@FDA website. This information was used to provide a data-driven rationale for genotoxicity evaluations of large molecule therapeutics. Fifty-three of the 99 therapeutics identified were tested for genotoxic potential. None of the therapeutics tested showed a positive outcome in any study except the peptide glucagon (GlucaGen®) showing equivocal in vitro results, as stated in the product labeling. Scientific rationale and data from this review indicate that testing of a majority of large molecule modalities do not add value to risk assessment and support current regulatory guidance. Similarly, the data do not support testing of peptides containing only natural amino acids. Peptides containing non-natural amino acids and small molecules in conjugated products may need to be tested.

  16. Targeting Mycobacterium tuberculosis topoisomerase I by small-molecule inhibitors.

    PubMed

    Godbole, Adwait Anand; Ahmed, Wareed; Bhat, Rajeshwari Subray; Bradley, Erin K; Ekins, Sean; Nagaraja, Valakunja

    2015-03-01

    We describe inhibition of Mycobacterium tuberculosis topoisomerase I (MttopoI), an essential mycobacterial enzyme, by two related compounds, imipramine and norclomipramine, of which imipramine is clinically used as an antidepressant. These molecules showed growth inhibition of both Mycobacterium smegmatis and M. tuberculosis cells. The mechanism of action of these two molecules was investigated by analyzing the individual steps of the topoisomerase I (topoI) reaction cycle. The compounds stimulated cleavage, thereby perturbing the cleavage-religation equilibrium. Consequently, these molecules inhibited the growth of the cells overexpressing topoI at a low MIC. Docking of the molecules on the MttopoI model suggested that they bind near the metal binding site of the enzyme. The DNA relaxation activity of the metal binding mutants harboring mutations in the DxDxE motif was differentially affected by the molecules, suggesting that the metal coordinating residues contribute to the interaction of the enzyme with the drug. Taken together, the results highlight the potential of these small molecules, which poison the M. tuberculosis and M. smegmatis topoisomerase I, as leads for the development of improved molecules to combat mycobacterial infections. Moreover, targeting metal coordination in topoisomerases might be a general strategy to develop new lead molecules.

  17. Ultrasensitive detection and characterization of molecules with infrared plasmonic metamaterials

    PubMed Central

    Cheng, Fei; Yang, Xiaodong; Gao, Jie

    2015-01-01

    Infrared vibrational spectroscopy is an effective technique which enables the direct probe of molecular fingerprints, and such detection can be further enhanced by the emerging engineered plasmonic metamaterials. Here we experimentally demonstrate ultrasensitive detection and characterization of polymer molecules based on an asymmetric infrared plasmonic metamaterial, and quantitatively analyze the molecule detection sensitivity and molecule-structure interactions. A sharp, non-radiative Fano resonance supported by the plasmonic metamaterial exhibits strongly enhanced near-field, and the resonance frequency is tailored to match the vibrational fingerprint of the target molecule. By utilizing the near-field nature of the plasmonic excitation, significantly enhanced absorption signal of molecules in the infrared spectroscopy are obtained, enabling ultrasensitive detection of only minute quantities of organic molecules. The enhancement of molecular absorption up to 105 fold is obtained, and sensitive detection of molecules at zeptomole levels (corresponding to a few tens of molecules within a unit cell) is achieved with high signal-to-noise ratio in our experiment. The demonstrated infrared plasmonic metamaterial sensing platform offers great potential for improving the specificity and sensitivity of label-free, biochemical detection. PMID:26388404

  18. Photoionization of atoms and molecules. [of hydrogen, helium, and xenon

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.

    1976-01-01

    A literature review on the present state of knowledge in photoionization is presented. Various experimental techniques that have been developed to study photoionization, such as fluorescence and photoelectron spectroscopy, mass spectroscopy, are examined. Various atoms and molecules were chosen to illustrate these techniques, specifically helium and xenon atoms and hydrogen molecules. Specialized photoionization such as in positive and negative ions, excited states, and free radicals is also treated. Absorption cross sections and ionization potentials are also discussed.

  19. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-09

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules.

  20. Signaling Molecules: Hydrogen Sulfide and Polysulfide

    PubMed Central

    2015-01-01

    Abstract Significance: Hydrogen sulfide (H2S) has been recognized as a signaling molecule as well as a cytoprotectant. It modulates neurotransmission, regulates vascular tone, and protects various tissues and organs, including neurons, the heart, and kidneys, from oxidative stress and ischemia-reperfusion injury. H2S is produced from l-cysteine by cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3MST) along with cysteine aminotransferase. Recent Advances: In addition to these enzymes, we recently identified a novel pathway to produce H2S from d-cysteine, which involves d-amino acid oxidase (DAO) along with 3MST. These enzymes are localized in the cytoplasm, mitochondria, and peroxisomes. However, some enzymes translocate to organelles under specific conditions. Moreover, H2S-derived potential signaling molecules such as polysulfides and HSNO have been identified. Critical Issues: The physiological stimulations, which trigger the production of H2S and its derivatives and maintain their local levels, remain unclear. Future Directions: Understanding the regulation of the H2S production and H2S-derived signaling molecules and the specific stimuli that induce their release will provide new insights into the biology of H2S and therapeutic development in diseases involving these substances. Antioxid. Redox Signal. 22, 362–376. PMID:24800864

  1. Single molecule thermodynamics in biological motors.

    PubMed

    Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

    2007-04-01

    Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

  2. New Small Molecule Agonists to the Thyrotropin Receptor

    PubMed Central

    Ali, M. Rejwan; Ma, Risheng; David, Martine; Morshed, Syed A.; Ohlmeyer, Michael; Felsenfeld, Dan P.; Lau, Zerlina; Mezei, Mihaly; Davies, Terry F.

    2015-01-01

    Background Novel small molecular ligands (SMLs) to the thyrotropin receptor (TSHR) have potential as improved molecular probes and as therapeutic agents for the treatment of thyroid dysfunction and thyroid cancer. Methods To identify novel SMLs to the TSHR, we developed a transcription-based luciferase-cAMP high-throughput screening system and we screened 48,224 compounds from a 100K library in duplicate. Results We obtained 62 hits using the cut-off criteria of the mean±three standard deviations above the baseline. Twenty molecules with the greatest activity were rescreened against the parent CHO-luciferase cell for nonspecific activation, and we selected two molecules (MS437 and MS438) with the highest potency for further study. These lead molecules demonstrated no detectible cross-reactivity with homologous receptors when tested against luteinizing hormone (LH)/human chorionic gonadotropin receptor and follicle stimulating hormone receptor–expressing cells. Molecule MS437 had a TSHR-stimulating potency with an EC50 of 13×10−8 M, and molecule MS438 had an EC50 of 5.3×10−8 M. The ability of these small molecule agonists to bind to the transmembrane domain of the receptor and initiate signal transduction was suggested by their activation of a chimeric receptor consisting of an LHR ectodomain and a TSHR transmembrane. Molecular modeling demonstrated that these molecules bound to residues S505 and E506 for MS438 and T501 for MS437 in the intrahelical region of transmembrane helix 3. We also examined the G protein activating ability of these molecules using CHO cells co-expressing TSHRs transfected with luciferase reporter vectors in order to measure Gsα, Gβγ, Gαq, and Gα12 activation quantitatively. The MS437 and MS438 molecules showed potent activation of Gsα, Gαq, and Gα12 similar to TSH, but neither the small molecule agonists nor TSH showed activation of the Gβγ pathway. The small molecules MS437 and MS438 also showed upregulation of

  3. Small molecule fluoride toxicity agonists.

    PubMed

    Nelson, James W; Plummer, Mark S; Blount, Kenneth F; Ames, Tyler D; Breaker, Ronald R

    2015-04-23

    Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride.

  4. Small Molecule Fluoride Toxicity Agonists

    PubMed Central

    Nelson1, James W.; Plummer, Mark S.; Blount, Kenneth F.; Ames, Tyler D.; Breaker, Ronald R.

    2015-01-01

    SUMMARY Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch-reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. PMID:25910244

  5. Small Molecule CXCR3 Antagonists.

    PubMed

    Andrews, Stephen P; Cox, Rhona J

    2016-04-14

    Chemokines and their receptors are known to play important roles in disease. More than 40 chemokine ligands and 20 chemokine receptors have been identified, but, to date, only two small molecule chemokine receptor antagonists have been approved by the FDA. The chemokine receptor CXCR3 was identified in 1996, and nearly 20 years later, new areas of CXCR3 disease biology continue to emerge. Several classes of small molecule CXCR3 antagonists have been developed, and two have shown efficacy in preclinical models of inflammatory disease. However, only one CXCR3 antagonist has been evaluated in clinical trials, and there remain many opportunities to further investigate known classes of CXCR3 antagonists and to identify new chemotypes. This Perspective reviews the known CXCR3 antagonists and considers future opportunities for the development of small molecules for clinical evaluation.

  6. Partial Dynamical Symmetry in Molecules

    NASA Astrophysics Data System (ADS)

    Ping, Jia-Lun; Chen, Jin-Quan

    1997-03-01

    It is shown that any Hamiltonian involving only one- and two-bond interactions for a molecule withnbonds and having a point groupPas its symmetry group may have theSn⊃Ppartial dynamical symmetry, i.e., the Hamiltonian can be solved analytically for a part of the states, called the unique states. For example, theXY6molecule has theS6⊃Ohpartial dynamical symmetry. The model of Iachello and Oss forncoupled anharmonic oscillators is revisited in terms of the partial dynamical symmetry. The energies are obtained analytically for the nine unique levels of theXY6molecule and the structures of the eigenstates are disclosed for the first time, while for non-unique states they are obtained by diagonalizing the Hamiltonian in theS6⊃Ohsymmetry adapted basis with greatly reduced dimension.

  7. Autonomous DNA-Molecule Computing

    NASA Astrophysics Data System (ADS)

    Komiya, Ken; Rose, John A.; Yamamura, Masayuki

    DNA molecules autonomously change their forms from the single strand to the double helix by specific binding between complementary sequences according to the Watson-Crick base pairing rule. This paring rule allows us to control connections among molecules and to construct various structures by sequence design. Further, the motion of constructed structures can also be designed by considering sequential bindings. Recently, the feasibility to utilize the programmed DNA structural change for information processing was studied. In the present paper, we report an efficient synthetic chain reaction based on autonomous binding of DNA to realize a computing system, which enable us to implement computational intelligence in vitro.

  8. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  9. Optimized free energies from bidirectional single-molecule force spectroscopy.

    PubMed

    Minh, David D L; Adib, Artur B

    2008-05-09

    An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy-valid for biasing potentials of arbitrary stiffness-are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

  10. Aptamer-based Nanosensors: Juglone as an Attached-Redox Molecule for Detection of Small Molecules

    PubMed Central

    Saberian, Mehdi; Hamzeiy, Hossein; Aghanejad, Ayuob; Asgari, Davoud

    2011-01-01

    Introduction Among several biosensing approaches, electrochemical-based procedures have been described as one of the most common and useful methods for sensing because of their simplicity, sensitivity, accuracy, and low cost. The electroactive species, which called redox, play a main role in the electrochemical-based approaches. Among several redox molecules used for electrochemical experiments, ferrocene is one of the commonly used redox molecules. However, instability of ferrocenium ion in the chloride containing solutions appeared to be weakness of this redox molecule limiting its utilization. Methods In the current study, Juglone was attached (using EDC/NHS coupling method) to the 3'-amino-modified terminus of the immobilized specific aptamer of codeine, which was successfully used in a cyclic electrochemical voltammetry procedure. Results The cyclic voltammogram peak of aptamer-attached Juglone was observed in the potential range of +0.4 to +0.9 V and the fabricated aptamer-based sensor was used for detection of different concentrations of codeine in the phosphate buffer 0.1 M solution containing 2 M NaCl. Conclusion Based on these findings, it can be suggested that the new aptamer-attached Juglone could be considered as an effective alternative redox molecule in particular with oligonucleotide-based sensing systems. PMID:23678405

  11. Effect of lysosomotropic molecules on cellular homeostasis.

    PubMed

    Kuzu, Omer F; Toprak, Mesut; Noory, M Anwar; Robertson, Gavin P

    2017-03-01

    Weak bases that readily penetrate through the lipid bilayer and accumulate inside the acidic organelles are known as lysosomotropic molecules. Many lysosomotropic compounds exhibit therapeutic activity and are commonly used as antidepressant, antipsychotic, antihistamine, or antimalarial agents. Interestingly, studies also have shown increased sensitivity of cancer cells to certain lysosomotropic agents and suggested their mechanism of action as a promising approach for selective destruction of cancer cells. However, their chemotherapeutic utility may be limited due to various side effects. Hence, understanding the homeostatic alterations mediated by lysosomotropic compounds has significant importance for revealing their true therapeutic potential as well as toxicity. In this review, after briefly introducing the concept of lysosomotropism and classifying the lysosomotropic compounds into two major groups according to their cytotoxicity on cancer cells, we focused on the subcellular alterations mediated by class-II lysosomotropic compounds. Briefly, their effect on intracellular cholesterol homeostasis, autophagy and lysosomal sphingolipid metabolism was discussed. Accordingly, class-II lysosomotropic molecules inhibit intracellular cholesterol transport, leading to the accumulation of cholesterol inside the late endosomal-lysosomal cell compartments. However, the accumulated lysosomal cholesterol is invisible to the cellular homeostatic circuits, hence class-II lysosomotropic molecules also upregulate cholesterol synthesis pathway as a downstream event. Considering the fact that Niemann-Pick disease, a lysosomal cholesterol storage disorder, also triggers similar pathologic abnormalities, this review combines the knowledge obtained from the Niemann-Pick studies and lysosomotropic compounds. Taken together, this review is aimed at allowing readers a better understanding of subcellular alterations mediated by lysosomotropic drugs, as well as their potential

  12. New Experimental Approaches and Theoretical Modeling Methods for Laser Cooling Atoms and Molecules

    DTIC Science & Technology

    2006-07-27

    also working on the theory of Bose - Einstein condensates in double well potentials, using a two-mode model that goes beyond the usual Bose -Hubbard...laser-cooled atoms, for applications to "coherent chemistry," studies of molecule-atom and molecule-molecule interactions, Bose condensates of...range of the data, and the potential curves near the 5S+5P limit, are shown in Fig. 2. Since no spin - orbit functions for Rb2 were available at the

  13. Floppy Molecules with Internal Rotation and Inversion

    NASA Astrophysics Data System (ADS)

    Kreglewski, Marek

    2016-06-01

    There are different ways to analyze rovibrational structure of molecules having several large amplitude motions of different type, like internal rotation and inversion or ring-puckering. In my research group we have developed and used methods starting from potential surfaces for large amplitude motions but also applied purely effective Hamiltonians, where tunneling splittings were key parameters. Whatever is the method the following problems must be solved when addressing a rovibrational problem with large amplitude vibrations: 1) a definition of the permutation-inversion molecular symmetry group, 2) a choice of the internal coordinates and their transformation in the symmetry group, 3) derivation of the Hamiltonian in chosen coordinates, 4) calculation of the Hamiltonian matrix elements in a symmetrized basis set. These points will be discussed. The advantage of methods which start from the geometry and potential surface for large amplitude vibrations give much clearer picture of internal dynamics of molecules but generally the fit to experimental data is much poorer. The fitting procedure is strongly non-linear and the iteration procedure much longer. The effective Hamiltonians the fit is generally much better since almost all optimized parameters are linear but the parameters have no clear physical meaning. This method is very useful in the assignment of experimental spectra. Results of the application of both method to methylamine and hydrazine will be presented.

  14. Spin-crossover molecule based thermoelectric junction

    SciTech Connect

    Ghosh, Dibyajyoti; Parida, Prakash; Pati, Swapan K.

    2015-05-11

    Using ab-initio numerical methods, we explore the spin-dependent transport and thermoelectric properties of a spin-crossover molecule (i.e., iron complex of 2-(1H-pyrazol-1-yl)-6-(1H-tetrazole-5-yl)pyridine) based nano-junction. We demonstrate a large magnetoresistance, efficient conductance-switching, and spin-filter activity in this molecule-based two-terminal device. The spin-crossover process also modulates the thermoelectric entities. It can efficiently switch the magnitude as well as spin-polarization of the thermocurrent. We find that thermocurrent is changed by ∼4 orders of magnitude upon spin-crossover. Moreover, it also substantially affects the thermopower and consequently, the device shows extremely efficient spin-crossover magnetothermopower generation. Furthermore, by tuning the chemical potential of electrodes into a certain range, a pure spin-thermopower can be achieved for the high-spin state. Finally, the reasonably large values of figure-of-merit in the presence and absence of phonon demonstrate a large heat-to-voltage conversion efficiency of the device. We believe that our study will pave an alternative way of tuning the transport and thermoelectric properties through the spin-crossover process and can have potential applications in generation of spin-dependent current, information storage, and processing.

  15. Toroidal nanotraps for cold polar molecules

    DOE PAGES

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, andmore » polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.« less

  16. Toroidal nanotraps for cold polar molecules

    SciTech Connect

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, and polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.

  17. Circulating adhesion molecules in obstructive sleep apnea and cardiovascular disease.

    PubMed

    Pak, Victoria M; Grandner, Michael A; Pack, Allan I

    2014-02-01

    Over 20 years of evidence indicates a strong association between obstructive sleep apnea (OSA) and cardiovascular disease. Although inflammatory processes have been heavily implicated as an important link between the two, the mechanism for this has not been conclusively established. Atherosclerosis may be one of the mechanisms linking OSA to cardiovascular morbidity. This review addresses the role of circulating adhesion molecules in patients with OSA, and how these may be part of the link between cardiovascular disease and OSA. There is evidence for the role of adhesion molecules in cardiovascular disease risk. Some studies, albeit with small sample sizes, also show higher levels of adhesion molecules in patients with OSA compared to controls. There are also studies that show that levels of adhesion molecules diminish with continuous positive airway pressure therapy. Limitations of these studies include small sample sizes, cross-sectional sampling, and inconsistent control for confounding variables known to influence adhesion molecule levels. There are potential novel therapies to reduce circulating adhesion molecules in patients with OSA to diminish cardiovascular disease. Understanding the role of cell adhesion molecules generated in OSA will help elucidate one mechanistic link to cardiovascular disease in patients with OSA.

  18. Field Regulation of Single Molecule Conductivity by a Charged Atom

    NASA Astrophysics Data System (ADS)

    Wolkow, Robert

    2006-03-01

    A new concept for a single molecule transistor is demonstrated [1]. A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [1] Paul G. Piva1,Gino A. DiLabio, Jason L. Pitters, Janik Zikovsky, Moh'd Rezeq, Stanislav Dogel, Werner A. Hofer & Robert A. Wolkow, Field regulation of single-molecule conductivity by a charged surface atom, NATURE 435, 658-661 (2005)

  19. Chemical and structural diversity of siRNA molecules.

    PubMed

    Nawrot, Barbara; Sipa, Katarzyna

    2006-01-01

    Short interfering RNAs (siRNAs) are 21-23 nt long double-stranded oligoribonucleotides which in mammalian cells exhibit a potency for sequence-specific gene silencing via an RNA interference (RNAi) pathway. It has been already proven that exogenous, chemically synthesized siRNA molecules are effective inhibitors of gene expression and are widely applied for analysis of protein function and proteomics-based target identification. Moreover, since their discovery siRNA molecules have been implemented as potential candidates for therapeutic applications. Variously modified siRNA molecules containing sugar modifications (2'-OMe, -F, -O-allyl, -amino, orthoesters and LNA analogues), internucleotide phospodiester bond modifications (phosphorothioates, boranophosphates), base modifications (s(2)U) as well as 3'-terminal cholesterol-conjugated constructs were investigated as potential candidates for effective inhibition of gene expression. This chapter reviews an impact of chemical and structural modifications of siRNA molecules on their serum and thermal stability, cellular and in vivo activity, cellular uptake, biodistribution and cytotoxicity. Functional analysis of chemically modified siRNA molecules allows for better understanding of the mechanism of the RNA interference process as well as demonstrates immense efforts in optimizing in vivo potency of siRNA molecules for RNAi-based drug design.

  20. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  1. Small Molecules Target Carcinogenic Proteins

    NASA Astrophysics Data System (ADS)

    Gradinaru, Claudiu

    2009-03-01

    An ingenious cellular mechanism of effecting protein localization is prenylation: the covalent attachment of a hydrophobic prenyl group to a protein that facilitates protein association with cell membranes. Fluorescence microscopy was used to investigate whether the oncogenic Stat3 protein can undergo artificial prenylation via high-affinity prenylated small-molecule binding agents and thus be rendered inactive by localization at the plasma membrane instead of nucleus. The measurements were performed on a home-built instrument capable of recording simultaneously several optical parameters (lifetime, polarization, color, etc) and with single-molecule sensitivity. A pH-invariant fluorescein derivative with double moiety was designed to bridge a prenyl group and a small peptide that binds Stat3 with high affinity. Confocal fluorescence images show effective localization of the ligand to the membrane of liposomes. Stat3 predominantly localizes at the membrane only in the presence of the prenylated ligand. Single-molecule FRET (fluorescence resonance energy transfer) between donor-labeled prenylated agents and acceptor-labeled, surface tethered Stat3 protein is used to determine the dynamic heterogeneity of the protein-ligand interaction and follow individual binding-unbinding events in real time. The data indicates that molecules can effect protein localization, validating a therapeutic design that influences protein activity via induced localization.

  2. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  3. Eckart frames for planar molecules

    NASA Astrophysics Data System (ADS)

    Wei, Hua

    2003-04-01

    Explicit analytic expressions of Eckart frames for planar molecules in Radau, Jacobi and bond coordinates have been presented. The orientation of the frame axis system with respect to the molecular plane at equilibrium is specified by an angle θ1e.

  4. Equation of State and Two-Body Correlations for Fluids of Non-Spherical Molecules.

    DTIC Science & Technology

    1985-01-01

    This report is concerned with the progress made in obtaining the equation of state for fluid mixtures of non-spherical molecules beyond which is...potentials were obtained in the case of the exp-6. Originator supplied keywords include: Equation of State , Non-spherical Molecules, Non-conformal Potentials, Molecular Mixtures, Mixing Rules, Homonuclear Diatomics.

  5. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    SciTech Connect

    Sazhin, O.

    2009-05-15

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  6. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    NASA Astrophysics Data System (ADS)

    Sazhin, O.

    2009-05-01

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  7. From dipolar to multipolar interactions between ultracold Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

    2016-05-01

    Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er2 Feshbach molecules which were produced recently. The interaction between atomic magnetic dipoles gives rise to the usual R-3 leading term of the multipolar expansion, where R is the intermolecular distance. We show that additional terms scaling as R-5, R-7 and so on also appear, which are strongly anisotropic with respect to the orientation of the molecules. These terms can be seen as effective molecular multipole moments reflecting the spatial extension of the molecules which is non-negligible compared to R. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

  8. Optical microscopy using a single-molecule light source

    PubMed

    Michaelis; Hettich; Mlynek; Sandoghdar

    2000-05-18

    Rapid progress in science on nanoscopic scales has promoted increasing interest in techniques of ultrahigh-resolution optical microscopy. The diffraction limit can be surpassed by illuminating an object in the near field through a sub-wavelength aperture at the end of a sharp metallic probe. Proposed modifications of this technique involve replacing the physical aperture by a nanoscopic active light source. Advances in the spatial and spectral detection of individual fluorescent molecules, using near-field and far-field methods, suggest the possibility of using a single molecule as the illumination source. Here we present optical images taken with a single molecule as a point-like source of illumination, by combining fluorescence excitation spectroscopy with shear-force microscopy. Our single-molecule probe has potential for achieving molecular resolution in optical microscopy; it should also facilitate controlled studies of nanometre-scale phenomena (such as resonant energy transfer) with improved lateral and axial spatial resolution.

  9. Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

    PubMed

    Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

    2013-06-20

    When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls.

  10. Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

    PubMed Central

    Li, Yan; Li, Weiguo; Chen, Xin; Sun, Jiatong; Chen, Huan; Lv, Sali

    2014-01-01

    Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. PMID:25114931

  11. Cell Adhesion Molecules and Ubiquitination—Functions and Significance

    PubMed Central

    Homrich, Mirka; Gotthard, Ingo; Wobst, Hilke; Diestel, Simone

    2015-01-01

    Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous system. All members of the Ig superfamily are intensively posttranslationally modified. However, many aspects of their cellular functions are not yet known. Since a few years ago it is known that some of the Ig superfamily members are modified by ubiquitin. Ubiquitination has classically been described as a proteasomal degradation signal but during the last years it became obvious that it can regulate many other processes including internalization of cell surface molecules and lysosomal sorting. The purpose of this review is to summarize the current knowledge about the ubiquitination of cell adhesion molecules of the Ig superfamily and to discuss its potential physiological roles in tumorigenesis and in the nervous system. PMID:26703751

  12. Anisotropic behavior of organic molecules on prepatterned surfaces

    NASA Astrophysics Data System (ADS)

    Hopp, Stefan Frieder; Heuer, Andreas

    2012-04-01

    The nucleation of organic molecules on surfaces, prepatterned with stripes, is investigated with emphasis on anisotropy effects. Representing the molecules as ellipsoids, the related particle-particle interaction is modeled by means of a generalized Gay-Berne potential for similar biaxial particles. The orientation behavior of these ellipsoidal molecules induced by the stripe pattern is studied for the first monolayer by performing kinetic Monte Carlo simulations. It is shown how the properties of the particle alignment depend on energy scales, temperature, and flux. Based on the fact the particles strictly arrange in rows, it is furthermore instructive to analyze the orientation behavior within the different rows. Finally, the transfer of orientation from a preset row of molecules with fixed orientation to other nucleating particles is examined.

  13. Interactions Between Ground-State Nitrogen Atoms and Molecules

    NASA Technical Reports Server (NTRS)

    Vanderslice, Joseph T.; Mason, Edward A.; Lippincott, Ellis R.

    1959-01-01

    Potential-energy curves for nitrogen atom (N-N) interactions corresponding to the X (1)Sigma(sup +, sub g), A (3)Sigma(sup +, sub u), (5)Sigma(sup +, sub g), (7)Sigma(sup +, sub u), B (3) Pi(sub g), C (3)(Pi(su u)and a (1)Pi(sub g) states of the nitrogen molecule N2 as well as curves for the atom-molecules (N-N2) and molecule-molecule (N2-N2) interactions have been calculated. All calculations have been based as nearly as possible on experimental data, including spectroscopically determined vibrational energy levels, scattering cross sections of atomic beams in gases, and measured vibrational relaxation times. In cases where experimental data were not available, approximate quantum-mechanical calculations have been made. Results obtained by these various methods are remarkably consistent with one another and are believed to have good accuracy.

  14. Quantitative single-molecule imaging by confocal laser scanning microscopy.

    PubMed

    Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

    2008-11-25

    A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

  15. Single-molecule emulsion PCR in microfluidic droplets.

    PubMed

    Zhu, Zhi; Jenkins, Gareth; Zhang, Wenhua; Zhang, Mingxia; Guan, Zhichao; Yang, Chaoyong James

    2012-06-01

    The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.

  16. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    öhlich, A Griesmaier, T Pfau, H Saito, Y Kawaguchi and M Ueda High-energy-resolution molecular beams for cold collision studies L P Parazzoli, N Fitch, D S Lobser and H J Lewandowski Collisional effects in the formation of cold guided beams of polar molecules M Motsch, C Sommer, M Zeppenfeld, L D van Buuren, P W H Pinkse and G Rempe Towards sympathetic cooling of large molecules: cold collisions between benzene and rare gas atoms P Barletta, J Tennyson and P F Barker Efficient formation of ground-state ultracold molecules via STIRAP from the continuum at a Feshbach resonance Elena Kuznetsova, Marko Gacesa, Philippe Pellegrini, Susanne F Yelin and Robin Côté Emergent timescales in entangled quantum dynamics of ultracold molecules in optical lattices M L Wall and L D Carr Rotational state resolved photodissociation spectroscopy of translationally and vibrationally cold MgH+ ions: toward rotational cooling of molecular ions K Højbjerre, A K Hansen, P S Skyt, P F Staanum and M Drewsen Collective transverse cavity cooling of a dense molecular beam Thomas Salzburger and Helmut Ritsch A Stark decelerator on a chip Samuel A Meek, Horst Conrad and Gerard Meijer Deceleration of molecules by dipole force potential: a numerical simulation Susumu Kuma and Takamasa Momose Ultracold molecules: vehicles to scalable quantum information processing Kathy-Anne Brickman Soderberg, Nathan Gemelke and Cheng Chin Magnetic field modification of ultracold molecule-molecule collisions T V Tscherbul, Yu V Suleimanov, V Aquilanti and R V Krems Spectroscopy of 39K85Rb triplet excited states using ultracold a 3Σ+ state molecules formed by photoassociation J T Kim, D Wang, E E Eyler, P L Gould and W C Stwalley Pumping vortex into a Bose-Einstein condensate of heteronuclear molecules Z F Xu, R Q Wang and L You Intense atomic and molecular beams via neon buffer-gas cooling David Patterson, Julia Rasmussen and John M Doyle Dynamical properties of dipolar Fermi gases T Sogo, L He, T Miyakawa, S Yi, H Lu

  17. Designing a small molecule erythropoietin mimetic.

    PubMed

    Guarnieri, Frank

    2015-01-01

    the stem cells into red blood cells. Researchers at Amgen published a co-crystal structure of EPO bound to the EPO receptor, which has a beautiful twofold symmetry-it was argued that this is the active state of the receptor. Activating the EPO receptor with EPO induces an almost instantaneous shutdown mechanism to sharply curtail any proliferative signal transduction, and thus, my hypotheses lead to the conclusion that the Amgen co-crystal is actually the state after receptor downregulation and thus an off-state. To put these hypotheses to the test, my computational method of Simulated Annealing of Chemical Potential was run using the co-crystal created at RWJ, which is the receptor trapped in a partial agonist state. The simulations predicted a previously unknown high affinity binding site at the pivot point where the two halves of the dimeric receptor meet, and detailed analysis of the fragment patterns led to the prediction of a molecule less than 300 MW that is basically twofold symmetric with a chiral center on one side and not the other. Thus, to the degree that computer simulations can be taken seriously, these results support my hypotheses on small molecule receptor activation. When this small molecule was synthesized and tested it indeed induced human hematopoietic stems cells to become red blood cells. When the predicted chiral center of this molecule was removed eliminating its one asymmetric feature, the resulting molecule was an antagonist-it could potently displace hot EPO but could no longer induce stem cell proliferation and differentiation. These results provided strong support for my theories on how to create potent small molecule EPO agonists and were used to launch the new company Locus Pharmaceuticals. These molecules, however, required significant chemical changes in order to make them stable in other in vitro assays and to be in vivo active, but these alterations had to be done in a way that maintained the symmetry-asymmetry considerations that

  18. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  19. Non-adiabatic dynamics of molecules in optical cavities

    NASA Astrophysics Data System (ADS)

    Kowalewski, Markus; Bennett, Kochise; Mukamel, Shaul

    2016-02-01

    Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces thereby opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of classical field, coupling to the vacuum state of a cavity has to be described in terms of dressed photon-matter states (polaritons) which require quantized fields. We present a derivation of the non-adiabatic couplings for single molecules in the strong coupling regime suitable for the calculation of the dressed state dynamics. The formalism allows to use quantities readily accessible from quantum chemistry codes like the adiabatic potential energy surfaces and dipole moments to carry out wave packet simulations in the dressed basis. The implications for photochemistry are demonstrated for a set of model systems representing typical situations found in molecules.

  20. Non-adiabatic dynamics of molecules in optical cavities

    SciTech Connect

    Kowalewski, Markus Bennett, Kochise; Mukamel, Shaul

    2016-02-07

    Strong coupling of molecules to the vacuum field of micro cavities can modify the potential energy surfaces thereby opening new photophysical and photochemical reaction pathways. While the influence of laser fields is usually described in terms of classical field, coupling to the vacuum state of a cavity has to be described in terms of dressed photon-matter states (polaritons) which require quantized fields. We present a derivation of the non-adiabatic couplings for single molecules in the strong coupling regime suitable for the calculation of the dressed state dynamics. The formalism allows to use quantities readily accessible from quantum chemistry codes like the adiabatic potential energy surfaces and dipole moments to carry out wave packet simulations in the dressed basis. The implications for photochemistry are demonstrated for a set of model systems representing typical situations found in molecules.

  1. Optical highlighter molecules in neurobiology.

    PubMed

    Datta, Sandeep Robert; Patterson, George H

    2012-02-01

    The development of advanced optical methods has played a key role in propelling progress in neurobiology. Genetically-encoded fluorescent molecules found in nature have enabled labeling of individual neurons to study their physiology and anatomy. Here we discuss the recent use of both native and synthetic optical highlighter proteins to address key problems in neurobiology, including questions relevant to synaptic function, neuroanatomy, and the organization of neural circuits.

  2. Racemic fluids of hard molecules

    NASA Astrophysics Data System (ADS)

    Vatamanu, J.; Cann, N. M.

    2001-05-01

    The structure in four racemic fluids is explored using two integral equation theories: the reference interaction site method (RISM) [D. Chandler and H. C. Andersen, J. Chem. Phys. 57, 1930 (1972)] and the diagrammatically correct theory of Chandler, Silbey, and Ladanyi (CSL) [D. Chandler, R. Silbey, and B. M. Ladanyi, Mol. Phys. 46, 1335 (1982)]. Discrimination is measured by comparison of site pair distributions for sites on identical molecules with the corresponding distributions for sites on mirror-image molecules. We find that discrimination is largest for distributions between the smallest sites in the molecules. Between racemates, those consisting of more asymmetrical chiral molecules (i.e., with a bigger range of site sizes and bond lengths) show the largest discrimination. The indirect correlation function is shown to be nondiscriminating in racemates. Further, exact relationships between like-like and like-unlike differences in the other pair functions have been obtained. From these, the importance of the bridge functions in discrimination is evident. The CSL theory always satisfies the exact relationships, even with approximate bridge diagrams. RISM theory cannot satisfy these exact limits regardless of density and closure relation. We have found that RISM theory predicts qualitatively incorrect pair distributions at low densities, but that the difference in the distributions is more accurate. All bridge diagrams which contribute to O(ρo) have been enumerated and evaluated. Inclusion of these diagrams into the CSL theory leads to exact results at low density. However, we find that the inclusion of the ρo diagrams has dramatically improved the quality of the CSL theory at all densities.

  3. Electron interactions with polar molecules

    SciTech Connect

    Garrett, W.R.

    1981-01-01

    A description is given of a number of the features of discrete and continuous spectra of electrons interacting with polar molecules. Attention is focused on the extent to which theoretical predictions concerning cross sections, resonances, and bound states are strongly influenced by the various approximations that are so ubiquitous in the treatment of such problems. Similarly, threshold scattering and photodetachment processes are examined for the case of weakly bound dipole states whose higher members overlap the continuum.

  4. Small Molecules-Big Data.

    PubMed

    Császár, Attila G; Furtenbacher, Tibor; Árendás, Péter

    2016-11-17

    Quantum mechanics builds large-scale graphs (networks): the vertices are the discrete energy levels the quantum system possesses, and the edges are the (quantum-mechanically allowed) transitions. Parts of the complete quantum mechanical networks can be probed experimentally via high-resolution, energy-resolved spectroscopic techniques. The complete rovibronic line list information for a given molecule can only be obtained through sophisticated quantum-chemical computations. Experiments as well as computations yield what we call spectroscopic networks (SN). First-principles SNs of even small, three to five atomic molecules can be huge, qualifying for the big data description. Besides helping to interpret high-resolution spectra, the network-theoretical view offers several ideas for improving the accuracy and robustness of the increasingly important information systems containing line-by-line spectroscopic data. For example, the smallest number of measurements necessary to perform to obtain the complete list of energy levels is given by the minimum-weight spanning tree of the SN and network clustering studies may call attention to "weakest links" of a spectroscopic database. A present-day application of spectroscopic networks is within the MARVEL (Measured Active Rotational-Vibrational Energy Levels) approach, whereby the transitions information on a measured SN is turned into experimental energy levels via a weighted linear least-squares refinement. MARVEL has been used successfully for 15 molecules and allowed to validate most of the transitions measured and come up with energy levels with well-defined and realistic uncertainties. Accurate knowledge of the energy levels with computed transition intensities allows the realistic prediction of spectra under many different circumstances, e.g., for widely different temperatures. Detailed knowledge of the energy level structure of a molecule coming from a MARVEL analysis is important for a considerable number of modeling

  5. Quantum simulation with cold molecules

    NASA Astrophysics Data System (ADS)

    Rey, Ana Maria

    2014-03-01

    Recent experimental developments on cooling, trapping, manipulating and loading ultra-cold ground state molecules in an optical lattice have opened the door for the exploration of quantum magnetism and the observation of complex quantum dynamics. In this talk I will discuss recent developments towards the implementation of controllable spin lattice models in polar molecules with the spin degrees of freedom encoded in rotational states. The spin-spin couplings are generated by direct dipolar interactions and can be fully controlled by dc electromagnetic fields and microwaves. The spin models realized in this way are long range, anisotropic and can even feature direction-dependent spin interactions. They can emulate Hamiltonians ranging from the Heisenberg spin model, to Hamiltonians with symmetry protected topological phases to Hamiltonians without solid state counterpart. At JILA we have been able to realize for the first time a lattice spin model with fermionic KRb molecules pinned in a 3D lattice. We observe clear manifestation of dipolar exchange interactions in Ramsey spectroscopy even at substantially less than unit lattice filling. I will describe the new theoretical methods that we developed to model the spin dynamics and show that those reproduce the experimental observations. Even though so far the spin dynamics has been restricted to pinned molecules, in part to prevent chemical reactions, I will finish by presenting theoretical calculations supported by experimental measurement at JILA that demonstrate that the continuous quantum Zeno mechanism can actually suppress loss in this highly reactive system. This finding opens the exciting possibility of observing itinerant quantum magnetism in near term experiments. This work is supported by ARO, ARO-DARPA-OLE, NSF-PFC and NSF-PIF

  6. Observation of ultralong range Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Shaffer, James

    2009-05-01

    In 1934, Enrico Fermi described the scattering of a low energy electron from a neutral atom by using the ideas of scattering length and pseudopotential. Although the long range potential for an electron-atom interaction is always attractive, Fermi realized that the s-wave scattering length that characterizes the low energy collision can be either positive or negative. For a positive scattering length, the wavefunction of the electron is shifted away from the atom, the electron is repelled; whereas for a negative scattering length, the wavefunction of the electron is shifted to the atom, the electron is attracted. Based on Fermi's approach, Greene and co-workers predicted a novel molecular binding mechanism where a low energy Rydberg electron is scattered from a ground state atom in the case of negative scattering length. In this situation, the interaction between the electron and ground state atom is attractive and results in the formation of bound states of the ground state atom and the Rydberg atom. Molecules bound by electron scattering can have an internuclear separation of several thousand Bohr radii and are very different from molecules formed by 2 Rydberg atoms where the binding is the result of multipolar forces between the atoms alone. In this talk, we present experimental data on the observation of these exotic molecular states for Rb Rydberg atoms in S states for principal quantum numbers n between 34 and 40. The spectroscopic results for the vibrational ground and first excited state of the dimer Rb(5S)-Rb(nS) are presented and the s-wave scattering length for electron-Rb(5S) scattering in the low energy regime where the kinetic energy is less than 100 meV. Finally, we discuss and present data on the lifetimes and decay mechanisms of these molecules in a magnetic trap.

  7. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  8. A single-molecule diode.

    PubMed

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B; Mayor, Marcel

    2005-06-21

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic pi -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical pi-systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode.

  9. Simple molecules as complex systems

    PubMed Central

    Furtenbacher, Tibor; Árendás, Péter; Mellau, Georg; Császár, Attila G.

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H216O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an “ultra-small-world” property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  10. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions

    PubMed Central

    Ruiz, Lorena; Delgado, Susana; Ruas-Madiedo, Patricia; Margolles, Abelardo; Sánchez, Borja

    2016-01-01

    Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs. PMID:27536282

  11. Single molecule and single cell epigenomics.

    PubMed

    Hyun, Byung-Ryool; McElwee, John L; Soloway, Paul D

    2015-01-15

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.

  12. Towards ultracold RbCa molecules

    NASA Astrophysics Data System (ADS)

    Kleinert, Michaela

    2011-10-01

    Ultracold heteronuclear molecules have received much attention lately because of their potential applications in high-precision spectroscopy, studies of fundamental symmetries and quantum information processing. So far the focus has been on alkaline/alkaline dimers since their constituent atoms have been studied extensively. Recently, several groups have begun work on more challenging alkaline/alkaline-earth or alkaline/rare-earth combinations. In addition to a permanent electric dipole moment, which makes the alkaline/alkaline dimers such an intriguing system, alkaline/alkaline-earth molecules also possess a permanent magnetic dipole moment, thus allowing the manipulation with electric and magnetic fields. In addition, the molecular ground state of an alkaline/alkaline-earth dimer has a non-vanishing spin. Interesting collision dynamics, for example the suppression of collisions in carefully tailored external fields, have been predicted. At Willamette University, we will trap ultracold gases of rubidium and calcium together to form the molecular dimer RbCa via photoassociation of the constituent atoms. In this talk we will discuss the current state of the experiment and our future plans.[4pt] In collaboration with Hayley Whitson, Garrett Potter, and Kristen Norton, Willamette University.

  13. Metal‐Catalysed Azidation of Organic Molecules

    PubMed Central

    Goswami, Monalisa

    2016-01-01

    The azide moiety is a desirable functionality in organic molecules, useful in a variety of transformations such as olefin aziridination, C–H bond amination, isocyanate synthesis, the Staudinger reaction and the formation of azo compounds. To harness the versatility of the azide functionality fully it is important that these compounds be easy to prepare, in a clean and cost‐effective manner. Conventional (non‐catalysed) methods to synthesise azides generally require quite harsh reaction conditions that are often not tolerant of functional groups. In the last decade, several metal‐catalysed azidations have been developed in attempts to circumvent this problem. These methods are generally faster, cleaner and more functional‐group‐tolerant than conventional methods to prepare azides, and can sometimes even be conveniently combined with one‐pot follow‐up transformations of the installed azide moiety. This review highlights metal‐catalysed approaches to azide synthesis, with a focus on the substrate scopes and mechanisms, as well as on advantages and disadvantages of the methods. Overall, metal‐catalysed azidation reactions provide shorter routes to a variety of potentially useful organic molecules containing the azide moiety. PMID:28344503

  14. Uncovering hierarchical data structure in single molecule transport

    NASA Astrophysics Data System (ADS)

    Wu, Ben H.; Ivie, Jeffrey A.; Johnson, Tyler K.; Monti, Oliver L. A.

    2017-03-01

    Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

  15. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    NASA Astrophysics Data System (ADS)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

    Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

  16. A slow source of molecules for high resolution spectroscopy

    NASA Astrophysics Data System (ADS)

    Quintero-Pérez, Marina; Jansen, Paul; Wall, Thomas; Ubachs, Wim; Bethlem, Hendrick; Atomic Laser Physics Team

    2013-05-01

    We present experiments on decelerating and trapping ammonia molecules using a combination of a Stark decelerator and a traveling wave decelerator. In the traveling wave decelerator a moving potential is created by a series of ring-shaped electrodes to which oscillating high voltages are applied. By lowering the frequency of the applied voltages, the molecules confined in the moving trap are decelerated and brought to a standstill. As the molecules are confined in a true 3D well, this new kind of deceleration has practically no losses, resulting in a great improvement on the usual Stark deceleration techniques. The necessary voltages are generated by amplifying the output of an arbitrary wave generator using fast HV-amplifiers, giving us great control over the trapped molecules. We illustrate this by experiments in which we adiabatically cool trapped NH3 and ND3 molecules and resonantly excite their motion. Our main motivation for this research is the possibility to use the traveling wave decelerator as a source of cold molecules for a molecular fountain. Previous attempts to create a fountain using a Stark decelerator were unsuccessful due to losses at low velocities and a complex lens-system for cooling and collimating the slow beam. A traveling wave decelerator should solve both of these issues.

  17. A Slow Source of Molecules for High Resolution Spectroscopy

    NASA Astrophysics Data System (ADS)

    Quintero-Perez, Marina; Jansen, Paul; Wall, Thomas E.; Ubachs, Wim; Bethlem, Hendrick L.

    2013-06-01

    We present experiments on decelerating and trapping ammonia molecules using a combination of a Stark decelerator and a traveling wave decelerator. In the traveling wave decelerator a moving potential is created by a series of ring-shaped electrodes to which oscillating high voltages are applied. By lowering the frequency of the applied voltages, the molecules confined in the moving trap are decelerated and brought to a standstill. As the molecules are confined in a true 3D well, this new kind of deceleration has practically no losses, resulting in a great improvement on the traditional Stark deceleration techniques. The necessary voltages are generated by amplifying the output of an arbitrary wave generator using fast HV-amplifiers, giving us great control over the trapped molecules. We illustrate this by experiments in which we adiabatically cool trapped NH_3 and ND_3 molecules and resonantly excite their motion. Our main motivation for this research is the possibility to use the traveling wave decelerator as a source of cold molecules for a molecular fountain. Previous attempts to create a fountain using a Stark decelerator were unsuccessful due to losses at low velocities and a complex lens-system for cooling and collimating the slow beam. A traveling wave decelerator should solve both of these issues.

  18. On the dissociation energy of the BN molecule

    NASA Astrophysics Data System (ADS)

    Reddy, R. R.; Reddy, A. S. R.; Rao, T. V. R.

    1985-09-01

    For the electronic ground state, X 3II, of the BN molecule, the true potential energy curve is constructed by the method of Rydberg-Klein-Rees as modified by Vanderslice et al. By curve fitting of the modified form of Lippincott's three-parameter empirical potential function, the dissociation energy is estimated to be 3.36±0.16 eV.

  19. Mechanobiology of Short DNA Molecules: A Single Molecule Perspective

    NASA Astrophysics Data System (ADS)

    Raghunathan, Krishnan

    Mechanical properties of DNA are known to play a significant role in several biological processes like wrapping of DNA around histones and looping. Most of these cellular events occur on a DNA length scale of a few hundred basepairs. Single molecule methods have been highly successful in directly investigating heterogeneity in different biomolecular systems and serve as ideal tools to study the mechanical properties of DNA. However, their use in studying DNA of contour lengths less than a kilobase are fraught with experimental difficulties. The research presented in this thesis explores the behavior of short stretches of DNA (≤ 500bp) using existing and novel single molecule methods. We have quantified the variation in persistence lengths between sequences having different elasticity using a constant force axial optical tweezers. Our experiments have also revealed that this difference in persistence lengths manifests itself as a difference in looping lifetimes of lac repressor, in sequences having the aforementioned constructs as the intervening sequence between the operator sites. We have also developed a system to probe DNA dynamics in vivo. We have found that the active processes in the cell have distinct effects on dynamics of DNA and eliminating the active processes causes a 'phase transition' like behavior in the inside the cell. We are currently extending this technique to understand DNA dynamics inside bacterial systems. Our results provide vital insights into mechanical properties of DNA and the effect of athermal fluctuations on DNA dynamics.

  20. Forces from periodic charging of adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Kocić, N.; Decurtins, S.; Liu, S.-X.; Repp, J.

    2017-03-01

    In a recent publication [Kocić et al., Nano Lett. 15, 4406 (2015)], it was shown that gating of molecular levels in the field of an oscillating tip of an atomic force microscope can enable a periodic charging of individual molecules synchronized to the tip's oscillatory motion. Here we discuss further implications of such measurements, namely, how the force difference associated with the single-electron charging manifests itself in atomic force microscopy images and how it can be detected as a function of tip-sample distance. Moreover, we discuss how the critical voltage for the charge-state transition depends on distance and how that relates to the local contact potential difference. These measurements allow also for an estimate of the absolute tip-sample distance.

  1. Alkaline pH sensor molecules.

    PubMed

    Murayama, Takashi; Maruyama, Ichiro N

    2015-11-01

    Animals can survive only within a narrow pH range. This requires continual monitoring of environmental and body-fluid pH. Although a variety of acidic pH sensor molecules have been reported, alkaline pH sensor function is not well understood. This Review describes neuronal alkaline pH sensors, grouped according to whether they monitor extracellular or intracellular alkaline pH. Extracellular sensors include the receptor-type guanylyl cyclase, the insulin receptor-related receptor, ligand-gated Cl- channels, connexin hemichannels, two-pore-domain K+ channels, and transient receptor potential (TRP) channels. Intracellular sensors include TRP channels and gap junction channels. Identification of molecular mechanisms underlying alkaline pH sensing is crucial for understanding how animals respond to environmental alkaline pH and how body-fluid pH is maintained within a narrow range.

  2. Oligomer Molecules for Efficient Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhan, Xiaowei

    2016-02-16

    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability

  3. Quantum Monte Carlo for vibrating molecules

    SciTech Connect

    Brown, W.R. |

    1996-08-01

    Quantum Monte Carlo (QMC) has successfully computed the total electronic energies of atoms and molecules. The main goal of this work is to use correlation function quantum Monte Carlo (CFQMC) to compute the vibrational state energies of molecules given a potential energy surface (PES). In CFQMC, an ensemble of random walkers simulate the diffusion and branching processes of the imaginary-time time dependent Schroedinger equation in order to evaluate the matrix elements. The program QMCVIB was written to perform multi-state VMC and CFQMC calculations and employed for several calculations of the H{sub 2}O and C{sub 3} vibrational states, using 7 PES`s, 3 trial wavefunction forms, two methods of non-linear basis function parameter optimization, and on both serial and parallel computers. In order to construct accurate trial wavefunctions different wavefunctions forms were required for H{sub 2}O and C{sub 3}. In order to construct accurate trial wavefunctions for C{sub 3}, the non-linear parameters were optimized with respect to the sum of the energies of several low-lying vibrational states. In order to stabilize the statistical error estimates for C{sub 3} the Monte Carlo data was collected into blocks. Accurate vibrational state energies were computed using both serial and parallel QMCVIB programs. Comparison of vibrational state energies computed from the three C{sub 3} PES`s suggested that a non-linear equilibrium geometry PES is the most accurate and that discrete potential representations may be used to conveniently determine vibrational state energies.

  4. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  5. Rotational and rotationless states of weakly bound molecules

    SciTech Connect

    Lemeshko, Mikhail; Friedrich, Bretislav

    2009-05-15

    By making use of the quantization rule of Raab and Friedrich [Phys. Rev. A 78, 022707 (2008)], we derive simple and accurate formulae for the number of rotational states supported by a weakly bound vibrational level of a diatomic molecule and the rotational constants of any such levels up to the threshold, and provide a criterion for determining whether a given weakly bound vibrational level is rotationless. The results depend solely on the long-range part of the molecular potential and are applicable to halo molecules.

  6. Comparison of generic force fields for packing of concave molecules

    NASA Astrophysics Data System (ADS)

    Del Regno, Annalaura; Siperstein, Flor R.

    2014-09-01

    Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.

  7. Dual band metamaterial perfect absorber based on artificial dielectric "molecules".

    PubMed

    Liu, Xiaoming; Lan, Chuwen; Li, Bo; Zhao, Qian; Zhou, Ji

    2016-07-13

    Dual band metamaterial perfect absorbers with two absorption bands are highly desirable because of their potential application areas such as detectors, transceiver system, and spectroscopic imagers. However, most of these dual band metamaterial absorbers proposed were based on resonances of metal patterns. Here, we numerically and experimentally demonstrate a dual band metamaterial perfect absorber composed of artificial dielectric "molecules" with high symmetry. The artificial dielectric "molecule" consists of four "atoms" of two different sizes corresponding to two absorption bands with near unity absorptivity. Numerical and experimental absorptivity verify that the dual-band metamaterial absorber is polarization insensitive and can operate in wide-angle incidence.

  8. Advances in magnetic tweezers for single molecule and cell biophysics.

    PubMed

    Kilinc, Devrim; Lee, Gil U

    2014-01-01

    Magnetic tweezers (MTW) enable highly accurate forces to be transduced to molecules to study mechanotransduction at the molecular or cellular level. We review recent MTW studies in single molecule and cell biophysics that demonstrate the flexibility of this technique. We also discuss technical advances in the method on several fronts, i.e., from novel approaches for the measurement of torque to multiplexed biophysical assays. Finally, we describe multi-component nanorods with enhanced optical and magnetic properties and discuss their potential as future MTW probes.

  9. Lyapunov instability of rigid diatomic molecules in three dimensions

    NASA Astrophysics Data System (ADS)

    Shin, Young-Han; Ihm, Dong-Chul; Lee, Eok-Kyun

    2001-10-01

    We study the Lyapunov instability of a three-dimensional fluid composed of rigid diatomic molecules by molecular dynamics simulation. We use center-of-mass coordinates and angular variables for the configurational space variables. The spectra of Lyapunov exponents are obtained for 32 rigid diatomic molecules interacting through the Weeks-Chandler-Andersen potential for various bond lengths and densities. We show the general trends and characteristic features of the spectra of the Lyapunov exponents, and discuss the different contributions between translational and rotational degrees of freedom depending on the density and the bond length from the calculation of the projection of a certain subspace of the tangent space vectors.

  10. Adhesion Molecule-Modified Biomaterials for Neural Tissue Engineering

    PubMed Central

    Rao, Shreyas S.; Winter, Jessica O.

    2009-01-01

    Adhesion molecules (AMs) represent one class of biomolecules that promote central nervous system regeneration. These tethered molecules provide cues to regenerating neurons that recapitulate the native brain environment. Improving cell adhesive potential of non-adhesive biomaterials is therefore a common goal in neural tissue engineering. This review discusses common AMs used in neural biomaterials and the mechanism of cell attachment to these AMs. Methods to modify materials with AMs are discussed and compared. Additionally, patterning of AMs for achieving specific neuronal responses is explored. PMID:19668707

  11. Relativistic rotation-vibrational energies for the Cs2 molecule

    NASA Astrophysics Data System (ADS)

    Jia, Chun-Sheng; Jia, Yue

    2017-01-01

    We present bound state solutions of the Dirac equation with the improved Rosen-Morse potential energy model. In the non-relativistic limit, the relativistic energy equation becomes the non-relativistic rotation-vibrational energy expression of the diatomic molecule. We find that the relativistic effect of the relative motion of the ions produces an obvious decrease in the vibrational energies for the 33Σg + state of the Cs2 molecule. It is observed that the behavior of the relativistic rotation-vibrational energies in larger rotational quantum numbers remains similar to that of the system with zero rotational quantum number.

  12. Toward Triplet Ground State NaLi Molecules

    NASA Astrophysics Data System (ADS)

    Ebadi, Sepehr; Jamison, Alan; Rvachov, Timur; Jing, Li; Son, Hyungmok; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2016-05-01

    The NaLi molecule is expected to have a long lifetime in the triplet ground-state due to its fermionic nature, large rotational constant, and weak spin-orbit coupling. The triplet state has both electric and magnetic dipole moments, affording unique opportunities in quantum simulation and ultracold chemistry. We have mapped the excited state NaLi triplet potential by means of photoassociation spectroscopy. We report on this and our further progress toward the creation of the triplet ground-state molecules using STIRAP. NSF, ARO-MURI, Samsung, NSERC.

  13. Molecules in Studio v. 1.0

    SciTech Connect

    Walker, La Tonya; Malczynski, Leonard

    2016-04-22

    A Powersim Studio implementation of the system dynamics’ ‘Molecules of Structure’. The original implementation was in Ventana’s Vensim language by James Hines. The molecules are fundamental constructs of the system dynamics simulation methodology.

  14. Characterization of Interstellar Organic Molecules

    NASA Astrophysics Data System (ADS)

    Gençaǧa, Deniz; Carbon, Duane F.; Knuth, Kevin H.

    2008-11-01

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  15. Electronic spectroscopy of diatomic molecules

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

    1994-01-01

    This article provides an overview of the principal computational approaches and their accuracy for the study of electronic spectroscopy of diatomic molecules. We include a number of examples from our work that illustrate the range of application. We show how full configuration interaction benchmark calculations were instrumental in improving the understanding of the computational requirements for obtaining accurate results for diatomic spectroscopy. With this understanding it is now possible to compute radiative lifetimes accurate to within 10% for systems involving first- and second-row atoms. We consider the determination of the infrared vibrational transition probabilities for the ground states of SiO and NO, based on a globally accurate dipole moment function. We show how we were able to assign the a(sup "5)II state of CO as the upper state in the recently observed emission bands of CO in an Ar matrix. We next discuss the assignment of the photoelectron detachment spectra of NO and the alkali oxide negative ions. We then present several examples illustrating the state-of-the-art in determining radiative lifetimes for valence-valence and valence-Rydberg transitions. We next compare the molecular spectroscopy of the valence isoelectronic B2, Al2, and AlB molecules. The final examples consider systems involving transition metal atoms, which illustrate the difficulty in describing states with different numbers of d electrons.

  16. Organic Molecules in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Gibb, Erika; Horne, David; Shenoy, Sachindev; Blake, Daniel; van Brunt, Kari; Brittain, Sean; Rettig, Terrence

    2008-08-01

    We propose to use NIRSPEC to search for organic molecules in circumstellar disks toward nearly edge-on T Tauri stars. The feasibility of this study has been recently illustrated by the NIRSPEC detection of HCN toward two edge-on T Tauri stars, GV Tau (Gibb et al. 2007) and IRS 46 (Lahuis et al. 2006), and Spitzer detections of C_2H_2, HCN, and CO_2 toward IRS 46 (Lahuis et al. 2006) and AA Tau (Carr & Najita 2008). We have selected 10 molecules that are predicted to be abundant based on chemical models, observations of high and low mass star forming regions, and comet comae. We will investigate compositional variations among the T Tauri population and compare that to comets and chemical models of disk chemistry. Through this, we can explore the chemistry occurring in the planet-forming regions of protoplanetary disks and investigate the evolution of organic volatiles, which can help establish the mechanism and timescale for planet formation.

  17. Exotic negative molecules in AMS

    NASA Astrophysics Data System (ADS)

    Golser, Robin; Gnaser, Hubert; Kutschera, Walter; Priller, Alfred; Steier, Peter; Wallner, Anton

    2007-06-01

    "The techniques and equipment developed for AMS studies are well suited for identifying exotic negative ions". With this sentence begins a pioneering paper by Roy Middleton and Jeff Klein (M&K) on small doubly-charged negative carbon clusters [Nucl. Instr. and Meth. B 123 (1997) 532]. M&K were the first to utilize Accelerator Mass Spectrometry to prove the existence of these clusters and a number of other exotic molecules. We review M&K's efforts and show how their work is being continued at other laboratories. The latest developments are: (1) the discovery of long-lived molecular hydrogen anions H2-,D2-and (2) the unambiguous identification of the smallest doubly-charged negative molecule (LiF3)2-. In particular we show new experimental data for D3-, and for (LiF3)2-, and we try to answer the question why M&K's search for this di-anion was unsuccessful.

  18. Characterization of Interstellar Organic Molecules

    SciTech Connect

    Gencaga, Deniz; Knuth, Kevin H.; Carbon, Duane F.

    2008-11-06

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  19. Is JPC = 3-+ molecule possible?

    NASA Astrophysics Data System (ADS)

    Zhu, Wei; Liu, Yan-Rui; Yao, Tao

    2015-02-01

    The confirmation of charged charmonium-like states indicates that heavy quark molecules should exist. Here we discuss the possibility of a molecule state with JPC = 3-+. In a one-boson-exchange model investigation for the S wave C = + D*D¯2* states, one finds that the strongest attraction is in the case J = 3 and I = 0 for both π and σ exchanges. Numerical analysis indicates that this hadronic bound state might exist if a phenomenological cutoff parameter around 2.3 GeV (1.5 GeV) is reasonable with a dipole (monopole) type form factor in the one-pion-exchange model. The cutoff for binding solutions may be reduced to a smaller value once the σ exchange contribution is included. If a state around the D*D¯2* threshold (≈4472 MeV) in the channel J/ψω (P wave) is observed, the heavy quark spin symmetry implies that it is not a cc¯ meson and the JPC are likely to be 3-+. Supported by National Natural Science Foundation of China (11275115), Shandong Province Natural Science Foundation (ZR2010AM023), SRF for ROCS, SEM, and Independent Innovation Foundation of Shandong University

  20. Time scales for molecule formation by ion-molecule reactions

    NASA Technical Reports Server (NTRS)

    Langer, W. D.; Glassgold, A. E.

    1976-01-01

    Analytical solutions are obtained for nonlinear differential equations governing the time-dependence of molecular abundances in interstellar clouds. Three gas-phase reaction schemes are considered separately for the regions where each dominates. The particular case of CO, and closely related members of the Oh and CH families of molecules, is studied for given values of temperature, density, and the radiation field. Nonlinear effects and couplings with particular ions are found to be important. The time scales for CO formation range from 100,000 to a few million years, depending on the chemistry and regime. The time required for essentially complete conversion of C(+) to CO in the region where the H3(+) chemistry dominates is several million years. Because this time is longer than or comparable to dynamical time scales for dense interstellar clouds, steady-state abundances may not be observed in such clouds.

  1. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K.; Hickey, Gregory S.

    1994-01-01

    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  2. Visualization of large elongated DNA molecules.

    PubMed

    Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong

    2015-09-01

    Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

  3. 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.

  4. Recent theoretical results on electron-polyatomic molecule collisions

    SciTech Connect

    McCurdy, C.W.

    1994-03-01

    Until recently, the principal barrier to the accurate theoretical description of electronic collisions with polyatomic molecules was the computational problem of scattering by a nonlocal, arbitrarily asymmetric potential. Effective numerical techniques capable of solving this variety of potential scattering problem for electronic collisions have now matured, and the first applications of methods for treating many-body aspects of collisions of electrons with polyatomic molecules have begun to appear in the literature. The past two years have seen the appearance of a large collection of calculations on electron-polyatomic collisions which compare favorably with experimental determinations. In addition to the dramatic developments in methods which explicitly exploit the methods of quantum chemistry to treat the effects of electron correlation, polarization, etc., parameter-free model potential methods for electronically elastic collisions have also evolved markedly in recent years. Progress in both electronically elastic and inelastic processes is reviewed briefly.

  5. A single-molecule diode

    NASA Astrophysics Data System (ADS)

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-06-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode. Author contributions: F.E., H.B.W., and M.M. designed research; M.E., R.O., M.K., M.F., F.E., H.B.W., and M.M. performed research; M.E., R.O., M.K., M.F., C.v.H., F.W., F.E., H.B.W., and M.M. contributed new reagents/analytic tools; M.E., R.O., M.K., C.v.H., F.E., H.B.W., and M.M. analyzed data; and F.E., H.B.W., and M.M. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: A, acceptor; D, donor; MCB, mechanically controlled break junction.Data deposition: The atomic coordinates have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, United Kingdom (CSD reference no. 241632).

  6. Behavior of atypical amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Ko, John

    1997-08-01

    The physical behavior of several atypical amphiphilic molecules was studied in various environments including micelles, model bilayer membranes, and emulsions. The molecules under investigation were nor-chenodeoxycholic acid (nor-CDCA), ursodeoxycholic acid (UDCA), sphingosine (Sp), sphingosine hydrochloride (SpċHCl), and tetrahydrolipstatin (THL). The bile acids, nor-CDCA and UDCA, were studied using 13C-Nuclear Magnetic Resonance ([13C) -NMR) in micelles of taurocholate and in bilayers of phosphatidylcholine. The pK a values of the bile acids in each environment were determined by [13C) -NMR and are as follows: 6.08 ±.03 for nor-CDCA and 6.27 ±.01 for UDCA in micelles, and 7.04 ± 12 for nor-CDCA and 6.89 ±.05 for UDCA in vesicles. Using line shape analysis, the transbilayer movement rate at 36oC for nor-CDCA and UDCA was calculated to be 580 sec--1 and 409 sec-1, respectively. [13C) -NMR titration of Sp gave pK a values of 9.09 ±.02 in micelles and 9.69 ±.21 in bilayers. Differential scanning calorimetry (DSC) and X-ray diffraction were used to establish the Spċwater and SpċHClċwater phase diagrams. Anhydrous and hydrated samples ranging from 5- 90% water were analyzed. The DSC thermograms traced out the transition temperatures of each molecule while the X- ray diffraction patterns revealed their chain and crystalline lattice packing structures. In general, sphingosine exists as a hydrated crystal with β packing phase below 43oC and melts into an Lα phase. Sphingosine hydrochloride, however, exists as a gel phase (L_beta or /beta/sp') below 42oC that swells to 61% hydration. At low water concentrations (0-64%), a lamellar liquid crystal phase (L_alpha) is formed above the chain melting transition of 42oC. At medium concentration (65%), a Hexagonal I phase is present, and at high water concentrations (66-90%), a micellar phase is present. THL, a specific inhibitor of lipases, was analyzed with [ 13C) -NMR to study its behavior in various environments

  7. Methamphetamine-associated cleavage of the synaptic adhesion molecule intercellular adhesion molecule-5.

    PubMed

    Conant, Katherine; Lonskaya, Irina; Szklarczyk, Arek; Krall, Caroline; Steiner, Joseph; Maguire-Zeiss, Kathleen; Lim, Seung T

    2011-08-01

    Methamphetamine (MA) is a highly addictive psychostimulant that, used in excess, may be neurotoxic. Although the mechanisms that underlie its addictive potential are not completely understood, in animal models matrix metalloproteinase (MMP) inhibitors can reduce behavioral correlates of addiction. In addition, evidence from genome-wide association studies suggests that polymorphisms in synaptic cell-adhesion molecules (CAMs), known MMP substrates, are linked to addictive potential in humans. In the present study, we examined the ability of MA to stimulate cleavage of intercellular adhesion molecule-5 (ICAM-5), a synaptic CAM expressed on dendritic spines in the telencephalon. Previous studies have shown that shedding of ICAM-5 is associated with maturation of dendritic spines, and that MMP-dependent shedding occurs with long term potentiation. Herein, we show that MA stimulates ectodomain cleavage of ICAM-5 in vitro, and that this is abrogated by a broad spectrum MMP inhibitor. We also show that an acute dose of MA, administered in vivo, is associated with cleavage of ICAM-5 in murine hippocampus and striatum. This occurs within 6 h and is accompanied by an increase in MMP-9 protein. In related experiments, we examined the potential consequences of ICAM-5 shedding. We demonstrate that the ICAM-5 ectodomain can interact with β(1) integrins, and that it can stimulate β(1) integrin-dependent phosphorylation of cofilin, an event that has previously been linked to MMP-dependent spine maturation. Together these data support an emerging appreciation of MMPs as effectors of synaptic plasticity and suggest a mechanism by which MA may influence the same.

  8. Force-induced tautomerization in a single molecule

    NASA Astrophysics Data System (ADS)

    Ladenthin, Janina N.; Frederiksen, Thomas; Persson, Mats; Sharp, John C.; Gawinkowski, Sylwester; Waluk, Jacek; Kumagai, Takashi

    2016-10-01

    Heat transfer, electrical potential and light energy are common ways to activate chemical reactions. Applied force is another way, but dedicated studies for such a mechanical activation are limited, and this activation is poorly understood at the single-molecule level. Here, we report force-induced tautomerization in a single porphycene molecule on a Cu(110) surface at 5 K, which is studied by scanning probe microscopy and density functional theory calculations. Force spectroscopy quantifies the force needed to trigger tautomerization with submolecular spatial resolution. The calculations show how the reaction pathway and barrier of tautomerization are modified in the presence of a copper tip and reveal the atomistic origin of the process. Moreover, we demonstrate that a chemically inert tip whose apex is terminated by a xenon atom cannot induce the reaction because of a weak interaction with porphycene and a strong relaxation of xenon on the tip as contact to the molecule is formed.

  9. Infrared spectra of molecules and materials of astrophysical interest

    NASA Technical Reports Server (NTRS)

    Durig, J. R.

    1975-01-01

    The vibrational spectra from 4000 to 33 cm-1 of several modecules which may be present in the atmosphere of the Jovian planets are studied to provide vibrational frequencies which can be used to: (1) determine the composition of the cloud covers of several of the planets; (2) provide structural information under favorable circumstances; (3) provide necessary data from which accurate thermodynamic data can be calculated; and (4) furnish information as to the nature of the potential energy function of the molecules and forces acting within them. Some of the molecules are produced photochemically from methane, ammonia, and hydrogen sulfide which are thought to be constituents of the planets with reducing atmospheres. Some of the compounds polymerize under ultraviolet radiation and drop out of the atmospheres. However, planets with a hot base, like that of Jupiter, may rebuild molecules destroyed photochemically.

  10. Chemical materials and their regulation of the movement of molecules.

    PubMed

    Langer, Robert

    2015-11-01

    Materials chemistry has been fundamental to the enormous field that encompasses the delivery of molecules both to desired sites and/or at desired rates and durations. The field encompasses the delivery of molecules including fertilizers, pesticides, herbicides, food ingredients, fragrances and biopharmaceuticals. A personal perspective is provided on our early work in this field that has enabled the controlled release of ionic substances and macromolecules. Also discussed are new paradigms in creating biomaterials for human use, the non-invasive delivery of molecules through the skin and lungs, the development of intelligent delivery systems and extensions to nanomedicine. With the advent of potentially newer biopharmaceutics such as siRNA, mRNA and gene editing approaches and their use being limited by delivery, future research in this field may be more critical than ever before.

  11. Cosmic ray synthesis of organic molecules in Titan's atmosphere

    SciTech Connect

    Capone, L.A.; Dubach, J.; Whitten, R.C.; Prasad, S.S.; Santhanam, K.

    1980-01-01

    The possible synthesis of organic molecules by the absorption of galactic cosmic rays in an N2-CH4-H2 Titan model atmosphere has been studied. The cosmic-ray-induced ionization results in peak electron densities of 2000/cu cm, with NH(+), C3H9(+), and C4H9(+) being among the important positive ions. Details of the ion and neutral chemistry relevant to the production of organic molecules are discussed. The potential importance of N(2D) reactions with CH4 and H2 is also demonstrated. Although the integrated production rate of organic matter due to the absorption of the cosmic ray cascade is much less than that by solar ultraviolet radiation, the production of nitrogen-bearing organic molecules by cosmic rays may be greater.

  12. Cancer Immunotherapy: Selected Targets and Small-Molecule Modulators.

    PubMed

    Weinmann, Hilmar

    2016-03-04

    There is a significant amount of excitement in the scientific community around cancer immunotherapy, as this approach has renewed hope for many cancer patients owing to some recent successes in the clinic. Currently available immuno-oncology therapeutics under clinical development and on the market are mostly biologics (antibodies, proteins, engineered cells, and oncolytic viruses). However, modulation of the immune system with small molecules offers several advantages that may be complementary and potentially synergistic to the use of large biologicals. Therefore, the discovery and development of novel small-molecule modulators is a rapidly growing research area for medicinal chemists working in cancer immunotherapy. This review provides a brief introduction into recent trends related to selected targets and pathways for cancer immunotherapy and their small-molecule pharmacological modulators.

  13. Proposal for the formation of ultracold paramagnetic polar molecules

    NASA Astrophysics Data System (ADS)

    Dulieu, Olivier; Borsalino, Dimitri; Luc, Eliane; Bouloufa-Maafa, Nadia; Zuchowski, Piotr

    2016-05-01

    Alkali-alkaline-earth dimers, such as RbCa and RbSr, possess (in their ground electronic state) both a permanent magnetic and electric dipole moment in the molecular frame, allowing their manipulation with external fields at ultracold temperatures. Such molecules have been proposed as candidates for quantum simulators. We propose an efficient method combining a photoassociation step and a stimulated Raman process to create ultracold RbSr and RbCa molecules in their absolute ground state, suitable for studying dipolar interactions in quantum gases. Our model is based on new accurate quantum chemistry computations of potential energy surfaces of ground and excited molecular states and of relevant transition dipole moments of these molecules. The results are in good agreement with recent low-resolution spectroscopic data recorded with Helium nanodroplets.

  14. Surface-confined electroactive molecules for multistate charge storage information.

    PubMed

    Mas-Torrent, M; Rovira, C; Veciana, J

    2013-01-18

    Bi-stable molecular systems with potential for applications in binary memory devices are raising great interest for device miniaturization. Particular appealing are those systems that operate with electrical inputs since they are compatible with existing electronic technologies. The processing of higher memory densities in these devices could be accomplished by increasing the number of memory states in each cell, although this strategy has not been much explored yet. Here we highlight the recent advances devoted to the fabrication of charge-storage molecular surface-confined devices exhibiting multiple states. Mainly, this goal has been realized immobilizing a variety (or a combination) of electroactive molecules on a surface, although alternative approaches employing non-electroactive systems have also been described. Undoubtedly, the use of molecules with chemically tunable properties and nanoscale dimensions are raising great hopes for the devices of the future in which molecules can bring new perspectives such as multistability.

  15. On the several molecules and nanostructures of water.

    PubMed

    Whitney, Cynthia Kolb

    2012-01-01

    This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called 'Algebraic Chemistry'. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown's gas, and cold fusion.

  16. The synthesis of complex molecules in interstellar clouds

    NASA Technical Reports Server (NTRS)

    Huntress, W. T., Jr.; Mitchell, G. F.

    1979-01-01

    The abundances of polyatomic molecules that may be formed by CH3(+) radiative association reactions in dense interstellar molecular clouds are reevaluated. The formation of a number of complex interstellar molecules via radiative association reactions involving ionic precursors other than CH3(+) is also investigated; these additional precursors include CH3O(+), CH3CO(+), CH5(+), HCO(+), NO(+), H2CN(+), C2H2(+), and NH3(+). The results indicate that the postulated gas-phase ion-molecule radiative association reactions could potentially explain the synthesis of most of the more complex species observed in dense molecular clouds such as Sgr B2. It is concluded, however, that in order to be conclusive, laboratory data are needed to show whether or not these reactions proceed at the required rates at low temperatures.

  17. Effective Atom-Molecule Conversions Using Radio Frequency Fields.

    PubMed

    Ding, Yijue; Pérez-Ríos, Jesús; Greene, Chris H

    2016-11-18

    The present study is inspired by the Wieman group experiment [Phys. Rev. Lett. 2005, 95, 190404], in which they use a slow modulated magnetic field to effectively transfer rubidium atoms into cold molecules near a Feshbach resonance. We develop a time-dependent collision theory based on two channel model potentials to study the atom-molecule population transfer induced by a single-color radio frequency field in an ultracold (87) Rb gas. Wave-packet dynamical simulations allow an investigation of both bound-bound transitions and free-bound transitions. The effects of temperature, detuning and the RF amplitude on the population transfer are discussed in detail. Some of our simulations suggest that oscillatory atom-molecule conversion could originate from the long coherence time of the wave packet. This coherence time is unusually long in ultracold gases because the collision energy is typically quite well-defined.

  18. On the Several Molecules and Nanostructures of Water

    PubMed Central

    Whitney, Cynthia Kolb

    2012-01-01

    This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion. PMID:22312305

  19. The permeation of methane molecules through silicalite-1 surfaces.

    PubMed

    Thompho, Somphob; Chanajaree, Rungroj; Remsungnen, Tawun; Hannongbua, Supot; Bopp, Philippe A; Fritzsche, Siegfried

    2009-03-12

    The permeation of methane molecules through the silicalite-1 surfaces with and without silanol groups has been studied by nonequilibrium molecular dynamics computer simulations. A newly fitted intermolecular potential between the methane molecules and the silanol is used. A control volume provides a nearly stationary gas phase close to the membrane. The nonequilibrium process of filling the (initially empty) membrane with methane molecules until saturation is considered, and the surface permeability has been evaluated. It turns out to be strongly influenced by the presence of silanol groups. Additionally it was found that for a large part of the loading process the particle stream into the zeolite membrane was nearly independent upon the deviation from equilibrium. This means that far from equilibrium the decay of this deviation does not follow an exponential law.

  20. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules

    PubMed Central

    Kim, Sung-Yon; Cho, Jae Hun; Murray, Evan; Bakh, Naveed; Choi, Heejin; Ohn, Kimberly; Ruelas, Luzdary; Hubbert, Austin; McCue, Meg; Vassallo, Sara L.; Keller, Philipp J.; Chung, Kwanghun

    2015-01-01

    Nondestructive chemical processing of porous samples such as fixed biological tissues typically relies on molecular diffusion. Diffusion into a porous structure is a slow process that significantly delays completion of chemical processing. Here, we present a novel electrokinetic method termed stochastic electrotransport for rapid nondestructive processing of porous samples. This method uses a rotational electric field to selectively disperse highly electromobile molecules throughout a porous sample without displacing the low-electromobility molecules that constitute the sample. Using computational models, we show that stochastic electrotransport can rapidly disperse electromobile molecules in a porous medium. We apply this method to completely clear mouse organs within 1–3 days and to stain them with nuclear dyes, proteins, and antibodies within 1 day. Our results demonstrate the potential of stochastic electrotransport to process large and dense tissue samples that were previously infeasible in time when relying on diffusion. PMID:26578787

  1. Small-molecule arginase inhibitors.

    PubMed

    Ivanenkov, Yan A; Chufarova, Nina V

    2014-01-01

    Arginase is an enzyme that metabolizes L-arginine to L-ornithine and urea. In addition to its fundamental role in the hepatic ornithine cycle, it also influences the immune systems in humans and mice. Arginase participates in many inflammatory disorders by decreasing the synthesis of nitric oxide and inducing fibrosis and tissue regeneration. L-arginine deficiency, which is modulated by myeloid cell arginase, suppresses T-cell immune response. This mechanism plays a fundamental role in inflammation-associated immunosuppression. Pathogens can synthesize their own arginase to elude immune reaction. Small-molecule arginase inhibitors are currently described as promising therapeutics for the treatment of several diseases, including allergic asthma, inflammatory bowel disease, ulcerative colitis, cardiovascular diseases (atherosclerosis and hypertension), diseases associated with pathogens (e.g., Helicobacter pylori, Trypanosoma cruzi, Leishmania, Mycobacterium tuberculosis and Salmonella), cancer and induced or spontaneous immune disorders. This article summarizes recent patents in the area of arginase inhibitors and discusses their properties.

  2. Nonadiabatic calculations on hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Komasa, Jacek; Pachucki, Krzysztof

    Since its infancy quantum mechanics has treated hydrogen molecule as a test bed. Contemporary spectroscopy is able to supply the dissociation energy (D0) of H2 with the accuracy of 3 . 7 .10-4cm-1 , while current theoretical predictions are 10-3cm-1 in error. Both the uncertainties are already smaller than the quantum electrodynamic (QED) effects contributing to D0, which poses a particular challenge to theoreticians. Undoubtedly, in order to increase the predictive power of theory one has to not only account for the multitude of the tiny relativistic and QED effects but, especially, significantly increase precision of the largest component of D0--the nonrelativistic contribution. We approach the problem of solving the Schroedinger equation, equipped with new methodology, with the target precision of D0 set at the level of 10-7cm-1 .

  3. Electrokinetic concentration of charged molecules

    DOEpatents

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  4. Special Issue: "Molecules against Alzheimer".

    PubMed

    Decker, Michael; Muñoz-Torrero, Diego

    2016-12-16

    This Special Issue, entitled "Molecules against Alzheimer", gathers a number of original articles, short communications, and review articles on recent research efforts toward the development of novel drug candidates, diagnostic agents and therapeutic approaches for Alzheimer's disease (AD), the most prevalent neurodegenerative disorder and a leading cause of death worldwide. This Special Issue contains many interesting examples describing the design, synthesis, and pharmacological profiling of novel compounds that hit one or several key biological targets, such as cholinesterases, β-amyloid formation or aggregation, monoamine oxidase B, oxidative stress, biometal dyshomeostasis, mitochondrial dysfunction, serotonin and/or melatonin systems, the Wnt/β-catenin pathway, sigma receptors, nicotinamide phosphoribosyltransferase, or nuclear erythroid 2-related factor. The development of novel AD diagnostic agents based on tau protein imaging and the use of lithium or intranasal insulin for the prevention or the symptomatic treatment of AD is also covered in some articles of the Special Issue.

  5. Laser optogalvanic spectroscopy of molecules

    NASA Technical Reports Server (NTRS)

    Webster, C. R.; Rettner, C. T.

    1983-01-01

    In laser optogalvanic (LOG) spectroscopy, a tunable laser is used to probe the spectral characteristics of atomic or molecular species within an electrical discharge in a low pressure gas. Optogalvanic signals arise when the impedance of the discharge changes in response to the absorption of laser radiation. The technique may, therefore, be referred to as impedance spectroscopy. This change in impedance may be monitored as a change in the voltage across the discharge tube. LOG spectra are recorded by scanning the wavelength of a chopped CW dye laser while monitoring the discharge voltage with a lock-in amplifier. LOG signals are obtained if the laser wavelength matches a transition in a species present in the discharge (or flame), and if the absorption of energy in the laser beam alters the impedance of the discharge. Infrared LOG spectroscopy of molecules has been demonstrated and may prove to be the most productive application in the field of optogalvanic techniques.

  6. Low Energy Ion-Molecule Reactions

    SciTech Connect

    James M. Farrar

    2004-05-01

    This objective of this project is to study the dynamics of the interactions of low energy ions important in combustion with small molecules in the gas phase and with liquid hydrocarbon surfaces. The first of these topics is a long-standing project in our laboratory devoted to probing the key features of potential energy surfaces that control chemical reactivity. The project provides detailed information on the utilization of specific forms of incident energy, the role of preferred reagent geometries, and the disposal of total reaction energy into product degrees of freedom. We employ crossed molecular beam methods under single collision conditions, at collision energies from below one eV to several eV, to probe potential surfaces over a broad range of distances and interaction energies. These studies allow us to test and validate dynamical models describing chemical reactivity. Measurements of energy and angular distributions of the reaction products with vibrational state resolution provide the key data for these studies. We employ the crossed beam low energy mass spectrometry methods that we have developed over the last several years.

  7. KK molecules with momentum-dependent interactions

    SciTech Connect

    Lemmer, R. H.

    2009-10-15

    It is shown that the momentum-dependent kaon-antikaon interactions generated via vector-meson exchange from the standard SU{sub V}(3)xSU{sub A}(3) interaction Lagrangian lead to a nonlocal potential in coordinate space that can be incorporated without approximation into a nonrelativistic version of the Bethe-Salpeter wave equation containing a radial-dependent effective kaon mass appearing in a fully symmetrized kinetic energy operator, in addition to a local potential. Estimates of the mass and decay widths of f{sub 0}(980) and a{sub 0}(980), considered as KK molecules of isospin 0 and 1, as well as for K{sup +}K{sup -} atomic bound states (kaonium) are presented and compared with previous studies of a similar nature. It is argued that without a better knowledge of hadronic form factors it is not possible to distinguish between the molecular versus elementary particle models for the structure of the light scalar mesons.

  8. Water: one molecule, two surfaces, one mistake

    NASA Astrophysics Data System (ADS)

    Vega, Carlos

    2015-05-01

    In order to rigorously evaluate the energy and dipole moment of a certain configuration of molecules, one needs to solve the Schrödinger equation. Repeating this for many different configurations allows one to determine the potential energy surface (PES) and the dipole moment surface (DMS). Since the early days of computer simulation, it has been implicitly accepted that for empirical potentials the charges used to fit the PES should also be used to describe the DMS. This is a mistake. Partial charges are not observable magnitudes. They should be regarded as adjustable fitting parameters. Optimal values used to describe the PES are not necessarily the best to describe the DMS. One could use two fits: one for the PES and the other for the DMS. This is a common practice in the quantum chemistry community, but not used so often by the community performing computer simulations. This idea affects all types of modelling of water (with the exception of ab initio calculations) from coarse-grained to non-polarisable and polarisable models. We anticipate that an area that will benefit dramatically from having both, a good PES and a good DMS, is the modelling of water in the presence of electric fields.

  9. Production and application of translationally cold molecules

    NASA Astrophysics Data System (ADS)

    Bethlem, Hendrick L.; Meijer, Gerard

    Inspired by the spectacular successes in the field of cold atoms, there is currently great interest in cold molecules. Cooling molecules is useful for various fundamental physics studies and gives access to an exotic regime in chemistry where the wave property of the molecules becomes important. Although cooling molecules has turned out to be considerably more difficult than cooling atoms, a number of methods to produce samples of cold molecules have been demonstrated over the last few years. This paper aims to review the application of cold molecules and the methods to produce them. Emphasis is put on the deceleration of polar molecules using time-varying electric fields. The operation principle of the array of electrodes that is used to decelerate polar molecules is described in analogy with, and using terminology from, charged-particle accelerators. It is shown that, by applying an appropriately timed high voltage burst, molecules can be decelerated while the phase-space density, i.e. the number of molecules per position-velocity interval, remains constant. In this way the high density and low temperature in the moving frame of a pulsed molecular beam can be transferred to the laboratory frame. Experiments on metastable CO in states that are either repelled by or attracted to high electric fields are presented. Loading of slow molecules into traps and storage rings is discussed.

  10. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  11. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  12. Polyatomic Candidates for Cooling of Molecules with Lasers from Simple Theoretical Concepts

    NASA Astrophysics Data System (ADS)

    Isaev, Timur A.; Berger, Robert

    2016-02-01

    A rational approach to identify polyatomic molecules that appear to be promising candidates for direct Doppler cooling with lasers is outlined. First-principles calculations for equilibrium structures and Franck-Condon factors of selected representatives with different point-group symmetries (including the chiral nonsymmetric C1) have been performed and a high potential for laser cooling of these molecules is indicated.

  13. Observation of pendular butterfly Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-10-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  14. Deformation of DNA molecules by hydrodynamic focusing

    NASA Astrophysics Data System (ADS)

    Wong, Pak Kin; Lee, Yi-Kuen; Ho, Chih-Ming

    2003-12-01

    The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil stretch transition was observed when the Deborah number (De) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.

  15. Observation of pendular butterfly Rydberg molecules.

    PubMed

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-10-05

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  16. Observation of pendular butterfly Rydberg molecules

    PubMed Central

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-01-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

  17. High-harmonic spectroscopy of aligned molecules

    NASA Astrophysics Data System (ADS)

    Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

    2017-01-01

    High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

  18. Allosteric Small-Molecule Inhibitors of the AKT Kinase

    NASA Astrophysics Data System (ADS)

    Dalafave, D. S.

    This research addresses computational design of small druglike molecules for possible anticancer applications. AKT and SGK are kinases that control important cellular functions. They are highly homologous, having similar activators and targets. Cancers with increased SGK activity may develop resistance to AKT-specific inhibitors. Our goal was to design new molecules that would bind both AKT and SGK, thus preventing the development of drug resistance. Most kinase inhibitors target the kinase ATP-binding site. However, the high similarity in this site among kinases makes it difficult to target specifically. Furthermore, mutations in this site can cause resistance to ATP-competitive kinase inhibitors. We used existing AKT inhibitors as initial templates to design molecules that could potentially bind the allosteric sites of both AKT and SGK. Molecules with no implicit toxicities and optimal drug-like properties were used for docking studies. Binding energies of the stable complexes that the designed molecules formed with AKT and SGK were calculated. Possible applications of the designed putative inhibitors against cancers with overexpressed AKT/SGK is discussed.

  19. Recursive construction of perfect DNA molecules from imperfect oligonucleotides.

    PubMed

    Linshiz, Gregory; Yehezkel, Tuval Ben; Kaplan, Shai; Gronau, Ilan; Ravid, Sivan; Adar, Rivka; Shapiro, Ehud

    2008-01-01

    Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology and synthetic biology. Here, we show for the first time how recursion can be used to address this challenge and demonstrate a recursive procedure that constructs error-free DNA molecules and their libraries from error-prone oligonucleotides. Divide and Conquer (D&C), the quintessential recursive problem-solving technique, is applied in silico to divide the target DNA sequence into overlapping oligonucleotides short enough to be synthesized directly, albeit with errors; error-prone oligonucleotides are recursively combined in vitro, forming error-prone DNA molecules; error-free fragments of these molecules are then identified, extracted and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error-free target molecule is formed. Our recursive construction procedure surpasses existing methods for de novo DNA synthesis in speed, precision, amenability to automation, ease of combining synthetic and natural DNA fragments, and ability to construct designer DNA libraries. It thus provides a novel and robust foundation for the design and construction of synthetic biological molecules and organisms.

  20. Surface functionalization of aluminosilicate nanotubes with organic molecules

    PubMed Central

    Ma, Wei; Yah, Weng On; Otsuka, Hideyuki

    2012-01-01

    Summary The surface functionalization of inorganic nanostructures is an effective approach for enriching the potential applications of existing nanomaterials. Inorganic nanotubes attract great research interest due to their one-dimensional structure and reactive surfaces. In this review paper, recent developments in surface functionalization of an aluminosilicate nanotube, “imogolite”, are introduced. The functionalization processes are based on the robust affinity between phosphate groups of organic molecules and the aluminol (AlOH) surface of imogolite nanotubes. An aqueous modification process employing a water soluble ammonium salt of alkyl phosphate led to chemisorption of molecules on imogolite at the nanotube level. Polymer-chain-grafted imogolite nanotubes were prepared through surface-initiated polymerization. In addition, the assembly of conjugated molecules, 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-yl)ethylphosphonic acid (HT3P) and 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-yl)ethylphosphonic acid 1,1-dioxide (HT3OP), on the imogolite nanotube surface was achieved by introducing a phosphonic acid group to the corresponding molecules. The optical and photophysical properties of these conjugated-molecule-decorated imogolite nanotubes were characterized. Moreover, poly(3-hexylthiophene) (P3HT) chains were further hybridized with HT3P modified imogolite to form a nanofiber hybrid. PMID:22428100

  1. First principles Investigations of the Conductance of Stretched Molecules

    NASA Astrophysics Data System (ADS)

    Speyer, Gil; Akis, Richard; Ferry, David K.; Li, Jun; Sankey, Otto F.

    2004-03-01

    A novel experimental setup developed at Arizona State University examines the molecular conductance across a variety of gap lengths by lowering a gold-plated AFM tip into a monolayer deposited on a gold substrate [1]. Theoretical investigations into these systems have revealed interesting trends in the conductance of these molecules as they are stretched. We investigate this system using a variety of theoretical models, such as DFT and Hartree-Fock calculations of the Hamiltonian (and a variety of basis sets), which is implemented into a Landauer formula based rapid transfer matrix method with charge self-consistency [2]. Here we solve a self-consistent potential, which obviates the need to parameterize the voltage. Conduction across the molecule occurs in multiple channels; gold states couple with varying strengths to the orbitals of the molecule. We will report the effects of strain across the molecule, and distortion of the molecule, on the conductive nature of the coupling. * Work supported by the Office of Naval Research [1] B. Xu and N. J. Tao, Science 301, 1221 (2003). [2] T. Usuki, M. Saito, M. Takatsu, R.A. Kiehl, and N. Yokoyama, Phys. Rev. B 52, 8244 (1995).

  2. Cell adhesion molecules: detection with univalent second antibody

    PubMed Central

    1980-01-01

    Identification of cell surface molecules that play a role in cell-cell adhesion (here called cell adhesion molecules) has been achieved by demonstrating the inhibitory effect of univalent antibodies that bind these molecules in an in vitro assay of cell-cell adhesion. A more convenient reagent, intact (divalent) antibody, has been avoided because it might agglutinate the cells rather than blocking cell-cell adhesion. In this report, we show that intact rabbit immunoglobulin directed against certain cell surface molecules of Dictyostelium discoideum blocks cell-cell adhesion when the in vitro assay is performed in the presence of univalent goat anti-rabbit antibody. Under appropriate experimental conditions, the univalent second antibody blocks agglutination induced by the rabbit antibody without significantly interfering with its effect on cell-cell adhesion. This method promises to be useful for screening monoclonal antibodies raised against potential cell adhesion molecules because: (a) it allows for the screening of large numbers of antibody samples without preparation of univalent fragments; and (b) it requires much less antibody because of the greater affinity of divalent antibodies for antigens. PMID:6970200

  3. Coherent Dynamics Following Strong Field Ionization of Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim; Jackson, James; Levine, Benjamin; Dantus, Marcos

    2015-03-01

    Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon strong field ionization. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a ``bag of atoms'' during field induced ionization. We consider here to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The delay scans show that among positional isomers the variations in relative energies, amounting to only a few hundred meVs, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). Ab initio calculations were performed to predict dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose that single electron ionization occurs within an optical cycle with the electron carrying away essentially all of the energy, leaving behind little internal energy in the cation. Evidence for this observation comes from coherent vibrational motion governed by the potential energy surface of the ground state of the cation. Subsequent fragmentation of the cation takes place as a result of further photon absorption modulated by one- and two-photon resonances, which provide sufficient energy to overcome the dissociation energy.

  4. Ultracold Long-Range Rydberg Molecules with Complex Multichannel Spectra

    NASA Astrophysics Data System (ADS)

    Eiles, Matthew; Greene, Chris

    2016-05-01

    A generalized class of exotic long-range Rydberg molecules consisting of a multichannel Rydberg atom bound to a distant ground state atom by the Rydberg electron is predicted. These molecules are characterized by the rich physics provided by the strongly perturbed multichannel Rydberg spectra of divalent atoms, in contrast to the regular Rydberg series of the alkali atoms used to form Rydberg molecules to date. These multichannel Rydberg molecules exhibit favorable properties for laser excitation, because states exist where the quantum defect varies strongly with the principal quantum number n. In particular, the nd Rydberg state of calcium becomes nearly degenerate with states of high orbital angular momentum over the range 17 < n < 22 , promoting its admixture into the high l deeply bound ``trilobite'' molecule states and thereby circumventing the usual difficulty posed by electric dipole selection rules. Further novel molecular states are predicted to occur in the low- J states of silicon, which are strongly perturbed due to channel interactions between Rydberg series leading to the spin-orbit split ionization thresholds. These interactions manifest themselves in potential curves exhibiting two distinct length scales, providing novel opportunities for quantum manipulation. Supported in part by the National Science Foundation under Grant No. PHY-1306905.

  5. Improved Dye Stability in Single-Molecule Fluorescence Experiments

    NASA Astrophysics Data System (ADS)

    EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

    Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

  6. Methods and applications in single molecule electronics

    NASA Astrophysics Data System (ADS)

    Hihath, Joshua

    In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a

  7. Phase equilibria in a system of 'breathing' molecules

    SciTech Connect

    Wu, Jianzhong; Prausnitz, John

    2001-09-30

    It is now well known that details in the intermolecular potential can significantly affect the qualitative features of a phase diagram where temperature is plotted against density for the coexistence curves among fluid and solid phases. While previous calculations of phase diagrams have assumed a time-invariant potential function, this report concerns the phase diagram for ''breathing'' molecules, i.e., molecules whose strength of intermolecular attraction fluctuates in time. Such fluctuations can occur in biomacromolecules where an active site can switch between ''on'' and ''off'' positions. Phase-equilibrium calculations were performed for molecules that have a periodic (breathing) attractive force in addition to the conventional intermolecular forces. The phase diagram for such molecules is as expected when the ''breathing'' properties are independent of density. However, when (more realistically), the ''breathing'' properties are density dependent, the phase diagram exhibits dramatic changes. These calculations may be useful for interpreting experimental data for protein precipitation, for plaque formation in blood vessels and for scaffold-supported tissue formation.

  8. The information content in single-molecule Raman nanoscopy

    SciTech Connect

    El-Khoury, Patrick Z.; Abellan, Patricia; Chantry, Ruth L.; Gong, Yu; Joly, Alan G.; Novikova, Irina V.; Evans, James E.; Aprà, Edoardo; Hu, Dehong; Ramasse, Quentin M.; Hess, Wayne P.

    2016-01-02

    Nowadays, it is possible to establish the chemical identity of a substance at the ultimate detection limit of a single molecule, i.e. the sensitivity required to probe 1.66 yoctomoles (1/NA), using surface-enhanced Raman scattering (SERS). It is also possible to image within an individual molecule, all while retaining chemical selectivity, using tip-enhanced Raman scattering (TERS). The potential applications of ultrasensitive SERS and TERS in chemical and biological detection and imaging are evident, and have attracted significant attention over the past decade. Rather than focusing on conventional single/few-molecule SERS and TERS experiments, where the objective is ultrasensitive spectroscopy and nanoscale chemical imaging, we consider the reverse problem herein. Namely, we review recent efforts ultimately aimed at probing different aspects of a molecule’s local environment through a detailed analysis of its SERS and TERS signatures. Particular attention is devoted to local electric field imaging using TERS; we describe how the vector components and absolute magnitude of a local electric field may be inferred from molecular Raman spectra and images. We also propose experiments that can potentially be used to cross-check the insights gained from the described SERS and TERS measurements. The ultimate goal of this review is to demonstrate that there is much more to single molecule Raman scattering than mere ultrasensitive chemical nanoscopy.

  9. Towards composite spheres as building blocks for structured molecules

    NASA Astrophysics Data System (ADS)

    Lee, Lloyd L.; Pellicane, Giuseppe

    2016-10-01

    In order to design a flexible molecular model that mimics the chemical moieties of a polyatomic molecule, we propose the ‘composite-sphere’ model that can assemble the essential elements to produce the structure of the target molecule. This is likened to the polymerization process where monomers assemble to form the polymer. The assemblage is built into the pair interaction potentials which can ‘react’ (figuratively) with selective pieces into various bonds. In addition, we preserve the spherical symmetries of the individual pair potentials so that the isotropic Ornstein-Zernike equation (OZ) for multi-component mixtures can be used as a theoretical framework. We first test our approach on generating a dumbbell molecule. An equimolar binary mixture of hard spheres and square-well spheres are allowed to react to form a dimer. As the bond length shrinks to zero, we create a site-site model of a Janus-like molecule with a repulsive moiety and an attractive moiety. We employ the zero-separation (ZSEP) closure to solve the OZ equations. The structure and thermodynamic properties are calculated at three isotherms and at several densities and the results are compared with Monte Carlo simulations. The close agreement achieved demonstrates that the ZSEP closure is a reliable theory for this composite-sphere fluid model. Contribution to the George Stell Memorial Issue.

  10. Computational Design of Druglike Small Molecule Plk1 PBD Inhibitors

    NASA Astrophysics Data System (ADS)

    Vanadia, Sean

    2012-02-01

    Polo-like Kinase 1 (Plk1) participates in regulation of the cell cycle and is often overexpressed in cancers. Inhibition of Plk1 was found to suppress cancer development. Most known kinase inhibitors interact with highly conserved ATP binding sites of the kinases. This makes the design of Plk1-specific inhibitors difficult. However, Plk1 has another active site, the Polo-Box Domain (PBD). PBD is not present in other kinases that were studied here. In this research, the PBD site of Plk1 was used as a target for designing small molecules that could potentially bind Plk1. A previously designed small molecule, Purpurogallin (PPG), was found to bind only the PBD of Plk1 and a highly similar site of LYN kinase, but no other kinases. The PPG structure was used as a template to design new putative Plk1-specific inhibitors. Druglike properties of the new molecules were evaluated with the Osiris Property Explorer program. Interactions of the molecules with Plk1, LYN, and eight other kinases were studied using the Argus Lab docking program. Further search for Plk1-specific inhibitors that could potentially target cancers with overexpressed Plk1 is discussed.

  11. Small Molecule-Mediated Cleavage of RNA in Living Cells

    PubMed Central

    Guan, Lirui

    2013-01-01

    Antisense oligonucleotides and small interfering RNAs (siRNAs) control gene expression by triggering the degradation of a mRNA via recruitment of RNase H or the RNA-induced silencing complex (RISC), respectively.[1] These approaches are hampered, however, by the poor cellular permeability of oligonucleotides. A small molecule approach to cleave RNA targets could obviate uptake issues. Several compounds can induce RNA cleavage in vitro,[2] however, to the best of our knowledge no small molecules have been previously described to cleave RNA in living cells. Herein, we describe the development of a potentially general approach to design small molecules that specifically cleave an RNA in a living cell, affecting biological function. Specifically, a designed, modularly assembled small molecule that binds the RNA that causes myotonic dystrophy type 1 (DM1)[3] was appended with a moiety that generates hydroxyl radicals upon irradiation. Cleavage of the transcript improves DM1-associated defects in cell culture, and compounds are non-toxic at an efficacious dose as determined by a MTT viability assay. This approach may allow for the site-specific cleavage and inactivation of other cellular RNAs.[4] Compounds that bind to and cleave RNA have the potential to serve as chemical genetics probes of function or lead therapeutics with spatial and temporal control. PMID:23280953

  12. Geochemical Origin of Biological Molecules

    NASA Astrophysics Data System (ADS)

    Bassez, Marie-Paule

    2013-04-01

    A model for the geochemical origin of biological molecules is presented. Rocks such as peridotites and basalts, which contain ferromagnesian minerals, evolve in the presence of water. Their hydrolysis is an exothermic reaction which generates heat and a release of H2 and of minerals with modified structures. The hydrogen reacts with the CO2 embedded inside the rock or with the CO2 of the environment to form CO in an hydrothermal process. With the N2 of the environment, and with an activation source arising from cosmic radiation, ferromagnesian rocks might evolve towards the abiotic formation of biological molecules, such as peptide like macromolecules which produce amino acids after acid hydrolysis. The reactions concerned are described. The production of hydrothermal CO is discussed in geological sites containing ferromagnesian silicate minerals and the low intensity of the Earth's magnetic field during Paleoarchaean Era is also discussed. It is concluded that excitation sources arising from cosmic radiation were much more abundant during Paleoarchaean Era and that macromolecular structures of biological relevance might consequently form during Archaean Eon, as a product of the chemical evolution of the rocks and of their mineral contents. This synthesis of abiotically formed biological molecules is consecutively discussed for meteorites and other planets such as Mars. This model for the geochemical origin of biological molecules has first been proposed in 2008 in the context of reactions involving catalysers such as kaolinite [Bassez 2008a] and then presented in conferences and articles [Bassez 2008b, 2009, 2012; Bassez et al. 2009a to 2012b]. BASSEZ M.P. 2008a Synthèse prébiotique dans les conditions hydrothermales, CNRIUT'08, Lyon 29-30/05/2008, Conf. and open access article:http://liris.cnrs.fr/~cnriut08/actes/ 29 mai 11h-12h40. BASSEZ M.P. 2008b Prebiotic synthesis under hydrothermal conditions, ISSOL'08, P2-6, Firenze-Italy, 24-29/08/2008. Poster at the

  13. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  14. Cochleates bridged by drug molecules.

    PubMed

    Syed, Uwais M; Woo, Amy F; Plakogiannis, Fotios; Jin, Tuo; Zhu, Hua

    2008-11-03

    A new type of cochleate, able to microencapsulate water-soluble cationic drugs or peptides into its inter-lipid bi-layer space, was formed through interaction between negatively charged lipids and drugs or peptides acting as the inter-bi-layer bridges instead of multi-cationic metal ions. This new type of cochleate opened up to form large liposomes when treated with EDTA, suggesting that cationic organic molecules can be extracted from these cochleates in a way similar to multivalent metal ions from metal ion-bridged cochleates. Cochleates can be produced in sub-micron size using a method known as "hydrogel isolated cochleation" or simply by increasing the ratio of multivalent cationic peptides over negatively charged liposomes. When nanometer-sized cochleates and liposomes containing the same fluorescent labeled lipid component were incubated with human fibroblasts cells under identical conditions, cells exposed to cochleates showed bright fluorescent cell surfaces, whereas those incubated with liposomes did not. This result suggests that cochleates' edges made them fuse with the cell surfaces as compared to edge free liposomes. This mechanism of cochleates' fusion with cell membrane was supported by a bactericidal activity assay using tobramycin cochleates, which act by inhibiting intracellular ribosomes. Tobramycin bridged cochleates in nanometer size showed improved antibacterial activity than the drug's solution.

  15. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  16. Nanoscale Assemblies of Small Molecules Control the Fate of Cells.

    PubMed

    Shi, Junfeng; Xu, Bing

    2015-10-01

    illustrating these experimental strategies for controlling the formation of nanoscale assemblies of small molecules and for identifying their corresponding protein targets, we aim to highlight that, though not being defined at the genetic level, nanoscale assemblies of small molecules are able to perform many critical biological functions. We envision that nanoscale assemblies of small molecules are a new frontier at the intersection of nanoscience and cell biology and biomedicine. In addition, we discuss the challenges and perspectives of relevant potential biomedical applications of nanoscale assemblies of small molecules.

  17. Development of novel small molecules for imaging and drug release

    NASA Astrophysics Data System (ADS)

    Cao, Yanting

    Small organic molecules, including small molecule based fluorescent probes, small molecule based drugs or prodrugs, and smart multifunctional fluorescent drug delivery systems play important roles in biological research, drug discovery, and clinical practices. Despite the significant progress made in these fields, the development of novel and diverse small molecules is needed to meet various demands for research and clinical applications. My Ph.D study focuses on the development of novel functional molecules for recognition, imaging and drug release. In the first part, a turn-on fluorescent probe is developed for the detection of intracellular adenosine-5'-triphosphate (ATP) levels based on multiplexing recognitions. Considering the unique and complicated structure of ATP molecules, a fluorescent probe has been implemented with improved sensitivity and selectivity due to two synergistic binding recognitions by incorporating of 2, 2'-dipicolylamine (Dpa)-Zn(II) for targeting of phospho anions and phenylboronic acid group for cis-diol moiety. The novel probe is able to detect intracellular ATP levels in SH-SY5Y cells. Meanwhile, the advantages of multiplexing recognition design concept have been demonstrated using two control molecules. In the second part, a prodrug system is developed to deliver multiple drugs within one small molecule entity. The prodrug is designed by using 1-(2-nitrophenyl)ethyl (NPE) as phototrigger, and biphenol biquaternary ammonium as the prodrug. With controlled photo activation, both DNA cross-linking agents mechlorethamine and o-quinone methide are delivered and released at the preferred site, leading to efficient DNA cross-links formation and cell death. The prodrug shows negligible cytotoxicity towards normal skin cells (Hekn cells) with and without UV activation, but displays potent activity towards cancer cells (HeLa cells) upon UV activation. The multiple drug release system may hold a great potential for practical application. In the

  18. Supramolecular helices: chirality transfer from conjugated molecules to structures.

    PubMed

    Yang, Yang; Zhang, Yajie; Wei, Zhixiang

    2013-11-13

    Different scales of chirality endow a material with many excellent properties and potential applications. In this review, using π-conjugated molecules as functional building blocks, recent progress on supramolecular helices inspired by biological helicity is summarized. First, induced chirality on conjugated polymers and small molecules is introduced. Molecular chirality can be amplified to nanostructures, superstructures, and even macroscopic structures by a self-assembly process. Then, the principles for tuning the helicity of supramolecular chirality, as well as formation of helical heterojunctions, are summarized. Finally, the potential applications of chiral structures in chiral sensing and organic electronic devices are critically reviewed. Due to recent progress in chiral structures, an interdisciplinary area called "chiral electronics" is expected to gain wide popularity in the near future.

  19. A comparison of internal energy calculation methods for diatomic molecules

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Shakib, Farzin; Vinokur, Marcel

    1990-01-01

    Various methods of calculating the internal energy of diatomic molecules are studied. An accurate and efficient method for computing the eigenvalues of the vibrational Schroedinger equation for an arbitrary potential is developed. The method is based on a finite-element discretization using the cubic Lobatto element. A combination of spectrum slicing and the Laguerre algorithm is used to solve for the eigenvalues. A simple method to compute the quasi-bound states is presented. For N2 molecules, all vibrational-rotational states of eleven available electronic potentials are computed, and summed to obtain the exact internal energy function with temperature. The total computation required 314 seconds of CPU-time on NASA's Cray 2 computer. Various approximate models are discussed and compared with the exact numerical simulation. It is shown that the splitting of the macroscopic internal energy into separate electronic, rotational, and vibrational energies is not justified at high temperatures.

  20. Photocontrolled adsorption of polyelectrolyte molecules on a silicon substrate.

    PubMed

    Malyar, Ivan V; Gorin, Dmitry A; Santer, Svetlana; Stetsyura, Svetlana V

    2013-12-31

    We report on a change in the properties of monomolecular films of polyelectrolyte molecules, induced by illuminating the silicon substrate on which they adsorb. It was found that under illumination the thickness of the adsorbed layer decreases by at least 27% and at the same time the roughness is significantly reduced in comparison to a layer adsorbed without irradiation. Furthermore, the homogeneity of the film topography and the surface potential is shown to be improved by illumination. The effect is explained by a change in surface charge density under irradiation of n- and p-type silicon wafers. The altered charge density in turn induces conformational changes of the adsorbing polyelectrolyte molecules. Their photocontrolled adsorption opens new possibilities for selective manipulation of adsorbed films. This possibility is of potential importance for many applications such as the production of well-defined coatings in biosensors or microelectronics.

  1. Design and applications of bifunctional small molecules: Why two heads are better than one

    PubMed Central

    Corson, Timothy W.; Aberle, Nicholas; Crews, Craig M.

    2009-01-01

    Induction of protein-protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein molecules together for enhanced or novel biological effect. The first such bifunctional molecules were the rapamycin- and FK506-based “Chemical Inducers of Dimerization”, but the field has since expanded with new molecules and new applications in chemical genetics and cell biology. Examples include coumermycin-mediated gyrase B dimerization, proteolysis targeting chimeric molecules (PROTACS), drug hybrids, and strategies for exploiting multivalency in toxin binding and antibody recruitment. This review discusses these and other advances in the design and use of bifunctional small molecules, and potential strategies for future systems. PMID:19112665

  2. Aggregated Gas Molecules: Toxic to Protein?

    PubMed Central

    Zhang, Meng; Zuo, Guanghong; Chen, Jixiu; Gao, Yi; Fang, Haiping

    2013-01-01

    The biological toxicity of high levels of breathing gases has been known for centuries, but the mechanism remains elusive. Earlier work mainly focused on the influences of dispersed gas molecules dissolved in water on biomolecules. However, recent studies confirmed the existence of aggregated gas molecules at the water-solid interface. In this paper, we have investigated the binding preference of aggregated gas molecules on proteins with molecular dynamics simulations, using nitrogen (N2) gas and the Src-homology 3 (SH3) domain as the model system. Aggregated N2 molecules were strongly bound by the active sites of the SH3 domain, which could impair the activity of the protein. In contrast, dispersed N2 molecules did not specifically interact with the SH3 domain. These observations extend our understanding of the possible toxicity of aggregates of gas molecules in the function of proteins. PMID:23588597

  3. Broadband single-molecule excitation spectroscopy

    PubMed Central

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  4. Ballistic electron spectroscopy of individual buried molecules

    NASA Astrophysics Data System (ADS)

    Kirczenow, George

    2007-01-01

    A theoretical study is presented of the ballistic electron emission spectra (BEES) of individual insulating and conducting organic molecules chemisorbed on a silicon substrate and buried under a thin gold film. It is predicted that ballistic electrons injected into the gold film from a scanning tunneling microscope tip should be transmitted so weakly to the silicon substrate by alkane molecules of moderate length (decane, hexane) and their thiolates that individual buried molecules of this type will be difficult to detect in BEES experiments. However, resonant transmission by molecules containing unsaturated C-C bonds or aromatic rings is predicted to be strong enough for BEES spectra of individual buried molecules of these types to be measured. Calculated BEES spectra of molecules of both types are presented and the effects of some simple interstitial and substitutional gold defects that may occur in molecular films are also briefly discussed.

  5. Ro-vibrational excitation, alignment and orientation distributions of fast non-dissociatively scattered molecules

    NASA Astrophysics Data System (ADS)

    Harder, R.; Snowdon, K. J.

    1997-12-01

    The ro-vibrational distribution of fast diatomic molecules scattered from an uncorrugated surface under strongly dissipative glancing incidence conditions is calculated. The classical trajectory simulation includes potential surface switching associated with hot-electron scattering processes. Both ro-vibrational excitation and strong alignment of the classical angular momentum vector in the surface plane ("cartwheel motion") are observed, independent of the occurrence of potential surface switching. Ro-vibrational excitation is enhanced strongly by transitions between potential surfaces. The resultant larger proportion of molecules in highly rotationally excited states leads to a higher fraction of cartwheel-aligned molecules in the scattered molecule ensemble. The molecules which dissociate in the simulation are characterised by surface normal peaked internuclear axis orientation distributions. This is in agreement with the results of recent experiments [A. Nesbitt et al., Surf. Sci. 331-333 (1995) 321]. We observe, in addition, an enhanced rotational population of "topspin" oriented molecules, which arises from differences in the surface parallel oriented friction forces acting on each atom of the molecule. Glancing incidence scattering from well-prepared close-packed metal surfaces would appear to provide an efficient, general method to obtain a beam of preferentially aligned fast neutral diatomic molecules.

  6. Small-Molecule Carbohydrate-Based Immunostimulants.

    PubMed

    Marzabadi, Cecilia H; Franck, Richard W

    2017-02-03

    In this review, we discuss small-molecule, carbohydrate-based immunostimulants that target Toll-like receptor 4 (TLR-4) and cluster of differentiation 1D (CD1d) receptors. The design and use of these molecules in immunotherapy as well as results from their use in clinical trials are described. How these molecules work and their utilization as vaccine adjuvants are also discussed. Future applications and extensions for the use of these analogues as therapeutic agents will be outlined.

  7. Relativistic electronic structure of the Sr2 molecule.

    PubMed

    Kotochigova, Svetlana

    2008-01-14

    Diatomic Sr2 has been proposed as a good candidate for precision measurement of possible time variation of fundamental constants. Precise knowledge of its vibrational structure and Stark shift of its levels in an optical lattice is required for realization of this proposal. Motivated by these ideas we have performed a numerical calculation of interatomic potentials and transition dipole moments of the Sr2 molecule using an ab initio relativistic configuration interaction valence bond self-consistent-field method.

  8. Variational path integral molecular dynamics study of a water molecule

    NASA Astrophysics Data System (ADS)

    Miura, Shinichi

    2013-08-01

    In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

  9. Double photoionization of hydrocarbons and aromatic molecules

    NASA Astrophysics Data System (ADS)

    Wehlitz, R.

    2016-11-01

    This article reviews the recent progress in the field of double photoionization of hydrocarbons and aromatic molecules using synchrotron radiation. First I will describe the importance of carbon-based molecules, which are all around us and are literally part of our life. They exhibit intriguing properties some of which can be probed via double photoionization, i.e., the simultaneous emission of two electrons. Furthermore, I will discuss the different mechanisms that can lead to a doubly charged organic molecule and will highlight those findings by comparing them with the results for atoms and other (simple) molecules. Finally, I will give an outlook on future directions on this subject.

  10. Conserved water molecules in bacterial serine hydroxymethyltransferases.

    PubMed

    Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

    2015-10-01

    Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments.

  11. Rovibrational cooling of molecules by optical pumping.

    PubMed

    Manai, I; Horchani, R; Lignier, H; Pillet, P; Comparat, D; Fioretti, A; Allegrini, M

    2012-11-02

    We demonstrate rotational and vibrational cooling of cesium dimers by optical pumping techniques. We use two laser sources exciting all the populated rovibrational states, except a target state that thus behaves like a dark state where molecules pile up thanks to absorption-spontaneous emission cycles. We are able to accumulate photoassociated cold Cs(2) molecules in their absolute ground state (v = 0, J = 0) with up to 40% efficiency. Given its simplicity, the method could be extended to other molecules and molecular beams. It also opens up general perspectives in laser cooling the external degrees of freedom of molecules.

  12. Negative refraction in Möbius molecules

    NASA Astrophysics Data System (ADS)

    Fang, Y. N.; Shen, Yao; Ai, Qing; Sun, C. P.

    2016-10-01

    We theoretically show the negative refraction existing in Möbius molecules. The negative refractive index is induced by the nontrivial topology of the molecules. With the Möbius boundary condition, the effective electromagnetic fields felt by the electron in a Möbius ring is spatially inhomogeneous. In this regard, the DN symmetry is broken in Möbius molecules and thus the magnetic response is induced through the effective magnetic field. Our findings provide an alternative architecture for negative refractive index materials based on the nontrivial topology of Möbius molecules.

  13. Production and Trapping of Ultracold Polar Molecules

    SciTech Connect

    David, DeMille

    2015-04-21

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

  14. The Arrangement of Information in DNA Molecules

    PubMed Central

    Thomas, Charles A.

    1966-01-01

    The anatomy of DNA molecules isolated from mature bacteriophage is reviewed. These molecules are linear, duplex DNA consisting mainly of uninterrupted polynucleotide chains. Certain phage (T5 and PB) contain four specifically located interruptions. While the nucleotide sequence of most of these molecules is unique (T5, T3, T7, λ), some are circular permutations of each other (T2, T4, P22). Partial degradation of these DNA molecules by exonuclease III predisposes some of them to form circles upon annealing, but indicating they are terminally redundant. PMID:5967428

  15. Ultracold Molecules: Physics in the Quantum Regime

    SciTech Connect

    Doyle, John

    2014-11-17

    Our research encompasses approaches to the trapping of diatomic molecules at low temperature plus the cooling and detection of polyatomic molecules in the kelvin temperature regime. We have cooled and trapped CaF and/or CaH molecules, loaded directly from a molecular beam. As part of this work, we are continuing to develop an important trapping technique, optical loading from a buffer-gas beam. This method was invented in our lab. We are also studying cold polyatomic molecules and their interactions with cold atoms.

  16. Multivalent Molecules as Modulators of RNA Granule Size and Composition.

    PubMed

    Falkenberg, Cibele Vieira; Carson, John H; Blinov, Michael L

    2017-02-24

    RNA granules are ensembles of specific RNA and protein molecules that mediate localized translation in eukaryotic cells. The mechanisms for formation and selectivity of RNA granules are unknown. Here we present a model for assembly of one type of RNA granule based on experimentally measured binding interactions among three core multivalent molecular components necessary for such assembly: specific RNA molecules that contain a cis-acting sequence called the A2 response element (A2RE), hnRNP A2 proteins that bind specifically (with high affinity) to A2RE sequences or nonspecifically (with lower affinity) to other RNA sequences, and heptavalent protein cytoskeleton-associated protein 5 (CKAP5, an alternative name for TOG protein) that binds both hnRNP A2 molecules and RNA. Non-A2RE RNA molecules (RNA without the A2RE sequence) that may be recruited to the granules through nonspecific interactions are also considered in the model. Modeling multivalent molecular interactions in granules is challenging because of combinatorial complexity in the number of potential molecular complexes among these core components and dynamic changes in granule composition and structure in response to changes in local intracellular environment. We use a hybrid modeling approach (deterministic-stochastic-statistical) that is appropriate when the overall compositions of multimolecular ensembles are of greater importance than the specific interactions among individual molecular components. Modeling studies titrating the concentrations of various granule components and varying effective site pair affinities and RNA valency demonstrate that interactions between multivalent components (TOG and RNA) are modulated by a bivalent adaptor molecule (hnRNP A2). Formation and disruption of granules, as well as RNA selectivity in granule composition are regulated by distinct concentration regimes of A2. Our results suggest that granule assembly is tightly controlled by multivalent molecular interactions

  17. Conductance of a Conjugated Molecule with Carbon Nanotube Contacts

    NASA Astrophysics Data System (ADS)

    Bruque, Nicolas; Ashraf, Khalid; Helander, Thomas; Lake, Roger

    2009-03-01

    Quantitative predictions of the energy levels is a well-known weakness of density functional theory (DFT). To understand the HOMO level alignment of a π-cruciform molecule [1] with the Fermi level of a carbon nanotube (CNT) contact, we have performed quantum chemical calculations of the adiabatic ionization potential (IP) of the central molecule. The adiabatic IP of the molecule is -5.86 eV. The image charge potential, calculated using our fully self-consistent DFT - Recursive Green Function (RGF) approach, is 0.7 eV. Treating the image potential as a self-energy correction to the IP, the HOMO energy level is at -5.16 eV which is comparable to the intrinsic CNT Fermi level at -5 eV. The above considerations of the energy level alignments, combined with the DFT-RGF analysis of the molecular orbitals and transmission spectrum, indicate that the HOMO resonance lies within the 50 meV energy window created by the experimental source-drain bias. This appears to be the most likely scenario that would give rise to the relatively small resistance of 6 Mφ. 1. X. Guo, et. al. Science, 311, 356 (2006).

  18. In Situ Detection of Organic Molecules on the Martian Surface With the Mars Organic Molecule Analyzer (MOMA) on Exomars 2018

    NASA Technical Reports Server (NTRS)

    Li, Xiang; Brinckerhoff, William B.; Pinnick, Veronica T; van Amerom, Friso H. W.; Danell, Ryan M.; Arevalo, Ricardo D., Jr.; Getty, Stephanie; Mahaffy, Paul R.

    2015-01-01

    The Mars Organic Molecule Analyzer (MOMA) investigation on the 2018 ExoMars rover will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. The MOMA instrument is centered around a miniaturized linear ion trap (LIT) that facilitates two modes of operation: i) pyrolysisgas chromatography mass spectrometry (pyrGC-MS); and, ii) laser desorptionionization mass spectrometry (LDI-MS) at ambient Mars pressures. The LIT also enables the structural characterization of complex molecules via complementary analytical capabilities, such as multi-frequency waveforms (i.e., SWIFT) and tandem mass spectrometry (MSMS). When combined with the complement of instruments in the rovers Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds.

  19. Aurora kinase inhibitors as anticancer molecules.

    PubMed

    Katayama, Hiroshi; Sen, Subrata

    2010-01-01

    Aurora kinase family of serine/threonine kinases are important regulators of mitosis that are frequently over expressed in human cancers and have been implicated in oncogenic transformation including development of chromosomal instability in cancer cells. In humans, among the three members of the kinase family, Aurora-A, -B and -C, only Aurora-A and -B are expressed at detectable levels in all somatic cells undergoing mitotic cell division and have been characterized in greater detail for their involvement in cellular pathways relevant to the development of cancer associated phenotypes. Aurora-A and -B are being investigated as potential targets for anticancer therapy. Development of inhibitors against Aurora kinases as anticancer molecules gained attention because of the facts that aberrant expression of these kinases leads to chromosomal instability and derangement of multiple tumor suppressor and oncoprotein regulated pathways. Preclinical studies and early phase I and II clinical trials of multiple Aurora kinase inhibitors as targeted anticancer drugs have provided encouraging results. This article discusses functional involvement of Aurora kinase-A and -B in the regulation of cancer relevant cellular phenotypes together with findings on some of the better characterized Aurora kinase inhibitors in modulating the functional interactions of Aurora kinases. Future possibilities about developing next generation Aurora kinase inhibitors and their clinical utility as anticancer therapeutic drugs are also discussed.

  20. Probing translation using small molecule inhibitors

    PubMed Central

    Blanchard, Scott C.; Cooperman, Barry S.; Wilson, Daniel N.

    2010-01-01

    Summary The translational apparatus of the bacterial cell remains one of the principal targets of antibiotics for the clinical treatment of infection worldwide. Since the introduction of specific translation inhibitors into clinical practise in the late 1940’s, intense efforts have been made to understand their precise mechanisms of action. Such research has often revealed significant and sometimes unexpected insights into many fundamental aspects of the translation mechanism. Central to progress in this area, high-resolution crystal structures of the bacterial ribosome identifying the sites of antibiotic binding are now available, which, together with recent developments in single-molecule and fast-kinetic approaches, provide an integrated view of the dynamic translation process. Assays employing these approaches and focusing on specific steps of the overall translation process are amenable for drug-screening. Such assays, coupled with structural studies, have the potential not only to accelerate the discovery of novel and effective antimicrobial agents, but also to refine our understanding of the translation mechanism, since antibiotics often stabilize specific functional states of the ribosome and allow distinct translation steps to be dissected in molecular detail. PMID:20609413

  1. Aurora Kinase inhibitors as Anticancer Molecules

    PubMed Central

    Katayama, Hiroshi; Sen, Subrata

    2015-01-01

    Aurora kinase family of serine/threonine kinases are important regulators of mitosis that are frequently over expressed in human cancers and have been implicated in oncogenic transformation including development of chromosomal instability in cancer cells. In humans, among the three members of the kinase family, Aurora-A, -B and -C, only Aurora-A and -B are expressed in detectable levels in somatic cells undergoing mitotic cell division and have been characterized in greater detail for their involvement in cellular pathways relevant to the development of cancer associated phenotypes. Aurora-A and -B are being investigated as potential targets for anticancer therapy. Development of inhibitors against Aurora kinases as anticancer molecules gained attention because of the facts that aberrant expression of these kinases lead to chromosomal instability and derangement of multiple tumor suppressor and oncoprotein regulated pathways. Pre-clinical studies and early phase I and II clinical trials of multiple Aurora kinase inhibitors as targeted anticancer drugs have provided encouraging results. This article discusses functional involvement of Aurora kinase-A and -B in the regulation of cancer relevant cellular phenotypes together with findings on some of the better characterized Aurora kinase inhibitors in modulating the functional interactions of Aurora kinases. Future possibilities about developing next generation Aurora kinase inhibitors and their clinical utility as anticancer therapeutic drugs are also discussed. PMID:20863917

  2. The Large Quadrupole of Water Molecules

    SciTech Connect

    Niu, Shuqiang; Tan, Ming-Liang; Ichiye, Toshhiko

    2011-04-07

    Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical/molecular mechanical (QM/MM) calculations at the MP2/aug-cc-pVQZ level on a B3LYP/aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM/MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM/MM multipoles is much closer than that from the site models to the potential from the QM/MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment

  3. Planctomycetes as Novel Source of Bioactive Molecules

    PubMed Central

    Graça, Ana P.; Calisto, Rita; Lage, Olga M.

    2016-01-01

    Marine environments are a fruitful source of bioactive compounds some of which are the newest leading drugs in medicinal therapeutics. Of particular importance are organisms like sponges and macroalgae and their associated microbiome. Planctomycetes, abundant in macroalgae biofilms, are promising producers of bioactive compounds since they share characteristics, like large genomes and complex life cycles, with the most bioactive bacteria, the Actinobacteria. Furthermore, genome mining revealed the presence of secondary metabolite pathway genes or clusters in 13 analyzed Planctomycetes genomes. In order to assess the antimicrobial production of a large and diverse collection of Planctomycetes isolated from macroalgae from the Portuguese coast, molecular, and bioactivity assays were performed in 40 bacteria from several taxa. Two genes commonly associated with the production of bioactive compounds, nonribosomal peptide synthetases (NRPS), and polyketide synthases (PKS) genes were screened. Molecular analysis revealed that 95% of the planctomycetes potentially have one or both secondary bioactive genes; 85% amplified with PKS-I primers and 55% with NRPS primers. Some of the amplified genes were confirmed to be involved in secondary metabolite pathways. Using bioinformatic tools their biosynthetic pathways were predicted. The secondary metabolite genomic potential of strains LF1, UC8, and FC18 was assessed using in silico analysis of their genomes. Aqueous and organic extracts of the Planctomycetes were evaluated for their antimicrobial activity against an environmental Escherichia coli, E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 6633, and a clinical isolate of Candida albicans. The screening assays showed a high number of planctomycetes with bioactive extracts revealing antifungal (43%) and antibacterial (54%) activity against C. albicans and B. subtilis, respectively. Bioactivity was observed in

  4. Planctomycetes as Novel Source of Bioactive Molecules.

    PubMed

    Graça, Ana P; Calisto, Rita; Lage, Olga M

    2016-01-01

    Marine environments are a fruitful source of bioactive compounds some of which are the newest leading drugs in medicinal therapeutics. Of particular importance are organisms like sponges and macroalgae and their associated microbiome. Planctomycetes, abundant in macroalgae biofilms, are promising producers of bioactive compounds since they share characteristics, like large genomes and complex life cycles, with the most bioactive bacteria, the Actinobacteria. Furthermore, genome mining revealed the presence of secondary metabolite pathway genes or clusters in 13 analyzed Planctomycetes genomes. In order to assess the antimicrobial production of a large and diverse collection of Planctomycetes isolated from macroalgae from the Portuguese coast, molecular, and bioactivity assays were performed in 40 bacteria from several taxa. Two genes commonly associated with the production of bioactive compounds, nonribosomal peptide synthetases (NRPS), and polyketide synthases (PKS) genes were screened. Molecular analysis revealed that 95% of the planctomycetes potentially have one or both secondary bioactive genes; 85% amplified with PKS-I primers and 55% with NRPS primers. Some of the amplified genes were confirmed to be involved in secondary metabolite pathways. Using bioinformatic tools their biosynthetic pathways were predicted. The secondary metabolite genomic potential of strains LF1, UC8, and FC18 was assessed using in silico analysis of their genomes. Aqueous and organic extracts of the Planctomycetes were evaluated for their antimicrobial activity against an environmental Escherichia coli, E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 6633, and a clinical isolate of Candida albicans. The screening assays showed a high number of planctomycetes with bioactive extracts revealing antifungal (43%) and antibacterial (54%) activity against C. albicans and B. subtilis, respectively. Bioactivity was observed in

  5. The rheology of chain molecules under shear

    NASA Astrophysics Data System (ADS)

    Moore, Jonathan David

    The rheology of chain molecules is a subject that comprises a wide variety of complex physical phenomena, challenging scientific questions, and fundamentally important practical applications. In this work, nonequilibrium molecular dynamics (NEMD) is employed to study linear and branched alkane chains in the melt state under transient and steady-state shearing conditions. This study focuses on three isomers of C30H62 (n- triacontane, squalane, and 9-n- octyldocosane) as well as a linear short-chain polyethylene (C100H202). A transferable united atom potential is used to model these alkane chains, and the simulations of planar Couette flow are performed using the SLLOD algorithm and a multi- timestep, simulation technique. The strain rates studied in this work (108-10 12 s-1) are extremely difficult to study experimentally yet typical of the severe conditions commonly found in engines and other machinery. NEMD and the united atom model underpredict the kinematic viscosities of n-triacontane and 9- n-octyldocosane but accurately predict the values for squalane (within 15%) at temperatures of 311 and 372 K. The predicted kinematic viscosity index values for both 9- n-octyldocosane and squalane are in quantitative agreement with experiment and represent the first such predictions by molecular simulation. Thus, this same general potential model and computational approach can be used to predict this important lubricant property for potential lubricants prior to their synthesis, offering the possibility of simulation-guided lubricant design. Simulations of C100H202 under steady-state shearing conditions reveal a pronounced minimum in the hydrostatic pressure at an intermediate strain rate that is associated with a minimum in the intermolecular potential energy as well as transitions in the strain-rate-dependent behavior of several other viscous and structural properties of the system. Upon onset of shear, the stress overshoot curves calculated for C100 are in good

  6. Single-molecule chemistry of metal phthalocyanine on noble metal surfaces.

    PubMed

    Li, Zhenyu; Li, Bin; Yang, Jinlong; Hou, Jian Guo

    2010-07-20

    To develop new functional materials and nanoscale electronics, researchers would like to accurately describe and precisely control the quantum state of a single molecule on a surface. Scanning tunneling microscopy (STM), combined with first-principles simulations, provides a powerful technique for acquiring this level of understanding. Traditionally, metal phthalocyanine (MPc) molecules, composed of a metal atom surrounded by a ligand ring, have been used as dyes and pigments. Recently, MPc molecules have shown great promise as components of light-emitting diodes, field-effect transistors, photovoltaic cells, and single-molecule devices. In this Account, we describe recent research on the characterization and control of adsorption and electronic states of a single MPc molecule on noble metal surfaces. In general, the electronic and magnetic properties of a MPc molecule largely depend on the type of metal ion within the phthalocyanine ligand and the type of surface on which the molecule is adsorbed. However, with the STM technique, we can use on-site molecular "surgery" to manipulate the structure and the properties of the molecule. For example, STM can induce a dehydrogenation reaction of the MPc, which allows us to control the Kondo effect, which describes the spin polarization of the molecule and its interaction with the complex environment. A specially designed STM tip can allow researchers to detect certain molecule-surface hybrid states that are not accessible by other techniques. By matching the local orbital symmetry of the STM tip and the molecule, we can generate the negative differential resistance effect in the formed molecular junction. This orbital symmetry based mechanism is extremely robust and does not critically depend on the geometry of the STM tip. In summary, this simple model system, a MPc molecule absorbed on a noble metal surface, demonstrates the power of STM for quantum characterization and manipulation of single molecules, highlighting the

  7. Model independence in two dimensions and polarized cold dipolar molecules.

    PubMed

    Volosniev, A G; Fedorov, D V; Jensen, A S; Zinner, N T

    2011-06-24

    We calculate the energy and wave functions of two particles confined to two spatial dimensions interacting via arbitrary anisotropic potentials with negative or zero net volume. The general rigorous analytic expressions are given in the weak coupling limit where universality or model independence are approached. The monopole part of anisotropic potentials is crucial in the universal limit. We illustrate the universality with a system of two arbitrarily polarized cold dipolar molecules in a bilayer. We discuss the transition to universality as a function of polarization and binding energy and compare analytic and numerical results obtained by the stochastic variational method. The universal limit is essentially reached for experimentally accessible strengths.

  8. Estimation of dissociation energy of NiC molecule

    NASA Astrophysics Data System (ADS)

    Sambasiva Rao, P.; Reddy, R. R.; Potukuchi, D. M.

    2006-03-01

    The experimental potential-energy curve for the electronic ground state of an astrophysically important NiC molecule is constructed by applying the Rydberg Klein Rees method as modified by Vanderslice et al. The ground state dissociation energy is estimated by a curve-fitting technique using the modified Lippincott potential function, and this estimated value of D0=3.454eV is in good agreement with the value of D0⩾3.34eV reported by Brugh and Morse.

  9. Water: a responsive small molecule.

    PubMed

    Shultz, Mary Jane; Vu, Tuan Hoang; Meyer, Bryce; Bisson, Patrick

    2012-01-17

    Unique among small molecules, water forms a nearly tetrahedral yet flexible hydrogen-bond network. In addition to its flexibility, this network is dynamic: bonds are formed or broken on a picosecond time scale. These unique features make probing the local structure of water challenging. Despite the challenges, there is intense interest in developing a picture of the local water structure due to water's fundamental importance in many fields of chemistry. Understanding changes in the local network structure of water near solutes likely holds the key to unlock problems from analyzing parameters that determine the three dimensional structure of proteins to modeling the fate of volatile materials released into the atmosphere. Pictures of the local structure of water are heavily influenced by what is known about the structure of ice. In hexagonal I(h) ice, the most stable form of solid water under ordinary conditions, water has an equal number of donor and acceptor bonds; a kind of symmetry. This symmetric tetrahedral coordination is only approximately preserved in the liquid. The most obvious manifestation of this altered tetrahedral bonding is the greater density in the liquid compared with the solid. Formation of an interface or addition of solutes further modifies the local bonding in water. Because the O-H stretching frequency is sensitive to the environment, vibrational spectroscopy provides an excellent probe for the hydrogen-bond structure in water. In this Account, we examine both local interactions between water and small solutes and longer range interactions at the aqueous surface. Locally, the results suggest that water is not a symmetric donor or acceptor, but rather has a propensity to act as an acceptor. In interactions with hydrocarbons, action is centered at the water oxygen. For soluble inorganic salts, interaction is greater with the cation than the anion. The vibrational spectrum of the surface of salt solutions is altered compared with that of neat

  10. Single Molecule Screening of Disease DNA Without Amplification

    SciTech Connect

    Lee, Ji-Young

    2006-01-01

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  11. Potential therapeutic applications of biosurfactants.

    PubMed

    Gudiña, Eduardo J; Rangarajan, Vivek; Sen, Ramkrishna; Rodrigues, Lígia R

    2013-12-01

    Biosurfactants have recently emerged as promising molecules for their structural novelty, versatility, and diverse properties that are potentially useful for many therapeutic applications. Mainly due to their surface activity, these molecules interact with cell membranes of several organisms and/or with the surrounding environments, and thus can be viewed as potential cancer therapeutics or as constituents of drug delivery systems. Some types of microbial surfactants, such as lipopeptides and glycolipids, have been shown to selectively inhibit the proliferation of cancer cells and to disrupt cell membranes causing their lysis through apoptosis pathways. Moreover, biosurfactants as drug delivery vehicles offer commercially attractive and scientifically novel applications. This review covers the current state-of-the-art in biosurfactant research for therapeutic purposes, providing new directions towards the discovery and development of molecules with novel structures and diverse functions for advanced applications.

  12. Monte Carlo simulation of several biologically relevant molecules and zwitterions in water

    NASA Astrophysics Data System (ADS)

    Patuwo, Michael Y.; Bettens, Ryan P. A.

    2012-02-01

    In this work, we study the hydration free energies of butane, zwitterionic alanine, valine, serine, threonine, and asparagine, and two neuraminidase inhibitors by means of Monte Carlo (MC) simulation. The solute molecule, represented in the form of distributed multipoles and modified 6-12 potential, was varied from a non-interacting 'ghost' molecule to its full potential functions in TIP4P water. Intermediate systems with soft-core solute-solvent interaction potentials are simulated separately and then subjected to Bennett's Acceptance ratio (BAR) for the free energy calculation. Hydration shells surrounding the solute particles were used to assess the quality of potential functions.

  13. Tumor suppressor molecules and methods of use

    DOEpatents

    Welch, Peter J.; Barber, Jack R.

    2004-09-07

    The invention provides substantially pure tumor suppressor nucleic acid molecules and tumor suppressor polypeptides. The invention also provides hairpin ribozymes and antibodies selective for these tumor suppressor molecules. Also provided are methods of detecting a neoplastic cell in a sample using detectable agents specific for the tumor suppressor nucleic acids and polypeptides.

  14. The Distribution of Solubilized Molecules among Micelles.

    ERIC Educational Resources Information Center

    Miller, Dennis J.

    1978-01-01

    Conflicting views have been put forward on the derivation of the distribution of solubilized molecules among micelles. This stems from failure to consider the arrangement of the solubilized molecules in the micelles. In the treatment presented enthalpy effects are ignored as they are not amenable to a simple general theory. (Author/BB)

  15. How organic molecules can control electronic devices.

    PubMed

    Vilan, Ayelet; Cahen, David

    2002-01-01

    This article examines a somewhat counter-intuitive approach to molecular-based electronic devices. Control over the electronic energy levels at the surfaces of conventional semiconductors and metals is achieved by assembling on the solid surfaces, poorly organized, partial monolayers (MLs) of molecules instead of the more commonly used ideal ones. Once those surfaces become interfaces, these layers exert electrostatic rather than electrodynamic control over the resulting devices, based on both electrical monopole and dipole effects of the molecules. Thus electronic transport devices, incorporating molecules, can be constructed without current flow through the molecules. This is illustrated for a gallium arsenide (GaAs) sensor as well as for gold-silicon (Au-Si) and Au-GaAs diodes. Incorporating molecules into solid interfaces becomes possible, using a 'soft' electrical contacting procedure, so as not to damage the molecules. Because there are only a few molecular restrictions, this approach opens up possibilities for the use of more complex (including biologically active) molecules as it circumvents requirements for ideal MLs and for molecules that can tolerate actual electron transport through them.

  16. Decelerating and Trapping Large Polar Molecules.

    PubMed

    Patterson, David

    2016-11-18

    Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.

  17. Near-field single molecule spectroscopy

    SciTech Connect

    Xie, X.S.; Dunn, R.C.

    1995-02-01

    The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.

  18. Small Molecules in the Cone Snail Arsenal.

    PubMed

    Neves, Jorge L B; Lin, Zhenjian; Imperial, Julita S; Antunes, Agostinho; Vasconcelos, Vitor; Olivera, Baldomero M; Schmidt, Eric W

    2015-10-16

    Cone snails are renowned for producing peptide-based venom, containing conopeptides and conotoxins, to capture their prey. A novel small-molecule guanine derivative with unprecedented features, genuanine, was isolated from the venom of two cone snail species. Genuanine causes paralysis in mice, indicating that small molecules and not just polypeptides may contribute to the activity of cone snail venom.

  19. Nanoscience: Single-molecule instant replay

    NASA Astrophysics Data System (ADS)

    Camillone, Nicholas

    2016-11-01

    A nanoscale imaging method that uses ultrashort light pulses to initiate and follow the motion of a single molecule adsorbed on a solid surface opens a window onto the physical and chemical dynamics of molecules on surfaces. See Letter p.263

  20. Laboratory Studies Of Astrophysically-interesting Phosphorus-bearing Molecules

    NASA Astrophysics Data System (ADS)

    Ziurys, Lucy M.; Halfen, D. T.; Sun, M.; Clouthier, D. J.

    2009-05-01

    Over the past year, there has been a renewed interest in the presence of phosphorus-containing molecules in the interstellar medium. Recent observations have increased the number of known interstellar phosphorus-bearing species from two (PN, CP) to six with the identification of HCP, CCP, and PH3 in the carbon-rich circumstellar shell of IRC+10216 and PO in the oxygen-rich envelope of VY Canis Majoris. More species of this type may be present in the ISM, but laboratory rest frequencies, necessary for such detections, are not generally known for many potential molecules. To fill in this gap, we have been conducting measurements of the pure rotational spectra of phosphorus-containing molecules of astrophysical interest, using both millimeter/submm direct absorption and Fourier transform microwave (FTMW) spectroscopy. We have developed a new phosphorus source for this purpose. These methods cover the frequency ranges 65-850 GHz and 4-40 GHz, respectively. Our recent study of the CCP radical (X2Πr) using both of these techniques has resulted in its identification in IRC+10216. Rotational spectra of other molecules such as PCN, HPS, and CH3PH2 have been recorded. We will report on these species and additional new laboratory developments