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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. Genetic variation of the whole ICAM4 gene in Caucasians and African Americans

    PubMed Central

    Srivastava, Kshitij; Almarry, Noorah Salman; Flegel, Willy A.

    2014-01-01

    Background Landsteiner-Wiener (LW) is the human blood group system no. 16, which comprises 2 antithetical antigens, LWa and LWb and the high prevalence antigen LWab. LW is encoded by the Intracellular Adhesion Molecule 4 (ICAM4) gene. The ICAM4 protein is part of the Rhesus complex in the red cell membrane and is involved in cell-cell adhesion. Methods We developed a method to sequence the whole 1.9 kb ICAM4 gene from genomic DNA in 1 amplicon. We determined the nucleotide sequence of exons 1 to 3, the 2 introns and 402 bp 5′-UTR and 347 bp 3′-UTR in 97 Caucasian and 91 African American individuals. Results Seven variant ICAM4 alleles were found, distinct from the wild type ICAM4 allele (GenBank KF712272), known as LW*05 and encoding LWa. An effect of the LWa/LWb amino acid substitution on the protein structure was predicted by 2 of the 3 computational modeling programs used. Conclusions We describe a practical approach for sequencing and determining the ICAM4 alleles using genomic DNA. LW*05 is the ancestral allele, which had also been observed in a Neandertal sample. All 7 variant alleles are immediate derivatives of the prevalent LW*05 and caused by 1 single nucleotide polymorphism (SNP) in each allele. Our data were consistent with the NHLBI GO Exome Sequencing Project (ESP) and the dbSNP databases, as all SNPs had been observed before. Our study has the advantage over the other databases in that it adds haplotype (allele) information for the ICAM4 gene, clinically relevant in the field of transfusion medicine. PMID:24673173

  5. 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

  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. Determination of interionic potentials in molecules

    SciTech Connect

    Conradson, S.D.; Leon, J.M.; Bridges, F.

    1996-04-01

    The rationale underlying materials by design is that properties are determined by structure so that if the relationships between structure and properties are understood, an appropriate material can be designed and fabricated to meet any set of criteria. Since ion-ion potentials determine state transformations and reactivity, they are essential to the entire concept of materials and molecules by design. Virtually all of the important state-to-state processes undergone by molecules (excitation, relaxation, ionization, dissociation, and combination) and the selection among these different pathways are determined by the ion-ion potentials and the resulting degree of overlap between molecular vibrational states for different electronic and atomic configurations. Although the depths of these potentials can be obtained from thermodynamic data and the separations between the vibronic states from spectroscopic measurements, the use of these potentials in the ab initio calculation of state-transformation outcomes is limited by the absence of any direct method for determining their extent and shape. The authors have recently developed a generalization of x-ray absorption fine structure (XAFS) and a related set of experimental and analysis procedures that, in principle, will allow them to obtain such potentials from XAFS data. They have undertaken the analysis of temperature-dependent XAFS data of Cu, Ag, and Au to test the accuracy of existing analytical forms (the Morse potential for metals) in predicting the details of pair distributions and to determine the range of validity of a temperature-independent effective pair-potential approximation. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL).

  8. Neopterin as a potential cytoprotective brain molecule.

    PubMed

    Ghisoni, Karina; Martins, Roberta de Paula; Barbeito, Luis; Latini, Alexandra

    2015-12-01

    Neopterin, a byproduct of the tetrahydrobiopterin de novo pathway, is found in increased levels in cerebrospinal fluid and plasma and significantly increases upon damage, infection or during immune system activation. The production of this compound seems almost restricted to the monocyte/macrophage linage cells, in response to interferon-γ stimulation. However, it is unclear whether and which nervous cells are able to synthesize neopterin, respond to any stressor applied extracellularly, or even the role of the compound in the central nervous system. Here we propose a potential cytoprotective role of neopterin in the brain, and show evidence that cultured rat astrocytes are responsive to the molecule; the pterin elicited increased hemeoxygenase-1 cellular content and decreased oxidative stress induced by mitochondrial dysfunction. Further studies are needed to clarify neopterin's cytoprotective effects in the central nervous system, and its potential role in different neuroinflammatory diseases. PMID:26476490

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

    PubMed

    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. PMID:27387127

  10. Kohn-Sham potentials for fullerenes and spherical molecules

    SciTech Connect

    Pavlyukh, Y.; Berakdar, J.

    2010-04-15

    We present a procedure for the construction of accurate Kohn-Sham potentials of quasispherical molecules starting from the first-principles valence densities. The method is demonstrated for the case of icosahedral C{sub 20}{sup 2+} and C{sub 60} molecules. Provided the density is N representable the Hohenberg-Kohn theorem guarantees the uniqueness of the obtained potentials. The potential is iteratively built following the suggestion of R. van Leeuwen and E. J. Baerends [Phys. Rev. A 49, 2421 (1994)]. The high symmetry of the molecules allows a parametrization of the angular dependence of the densities and the potentials using a small number of symmetry-adapted spherical harmonics. The radial behavior of these quantities is represented on a grid and the density is reconstructed from the approximate potential by numerically solving the coupled-channel Kohn-Sham equations. Subsequently, the potential is updated and the procedure is continued until convergence is achieved.

  11. 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.

  12. 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.

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

    PubMed

    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.

  14. Complex absorbing potentials with Voronoi isosurfaces wrapping perfectly around molecules.

    PubMed

    Sommerfeld, Thomas; Ehara, Masahiro

    2015-10-13

    Complex absorbing potentials (CAPs) are imaginary potentials that are added to a Hamiltonian to change the boundary conditions of the problem from scattering to square-integrable. In other words, with a CAP, standard bound-state methods can be used in problems involving unbound states such as identifying resonance states and predicting their energies and lifetimes. Although in wave packet dynamics, many CAP forms are used, in electronic structure theory, the so-called box-CAP is used almost exclusively, because of the ease of evaluating its integrals in a Gaussian basis set. However, the box-CAP does has certain disadvantages. First, it will, e.g., break the symmetry of Cnv molecules if n is odd and the main axis is placed along the z-axis by the "standard orientation" of the electronic structure code. Second, it provides a CAP starting at the smallest box around the entire molecular system. For larger molecules or clusters, which do not fill the space efficiently, that implies that much "dead space" within the molecule will be left, where there is neither a CAP nor a sufficient description with basis functions. Here, two new CAP forms are introduced and systematically explored: first, a Voronoi-CAP (that is, a CAP defined in each atom's Voronoi cell), and second, a smooth Voronoi-CAP (which is similar to the Voronoi-CAP; however, the noncontinuously differentiable behavior at the surfaces between the Voronoi cells is smoothed out). Both have isosurfaces that are similar to the cavities used in solvation modeling. An obvious disadvantage of these two CAPs is that the integrals cannot be obtained analytically, but must be computed numerically. However, Voronoi-CAPs share the advantage of having the same symmetry as the molecular system, and, more importantly, considerably facilitate the treatment of larger molecules with asymmetric side chains and of molecular clusters. PMID:26574253

  15. Contrastive studies of potential energy functions of some diatomic molecules

    NASA Astrophysics Data System (ADS)

    Abdallah, Hassan H.; Abdullah, Hewa Y.

    2016-03-01

    It was proposed that iron hydride, FeH, would be formed only on grains at the clouds through the reaction of the adsorbed H atoms or H2 molecules with the adsorbed Fe atoms on the grains. The importance of FeH in Astrophysics presents an additional motivation to study its energetic, spectroscopic constants and Potential Energy Curves. The structural optimization for ground state of FeH was calculated by different theoretical methods, namely, Hartree-Fock (HF), the density functional theory (DFT), B3LYP, MP2 method and QCISD(T) methods and compared with available data from the literature. The single ionized forms, cation and anion, were also obtained at the same level of calculations. Charges, dipole moment, geometrical parameters, molecular orbital energies and spectroscopic parameters were calculated and reported. In addition, the molecular ionization potential, electron affinity and dissociation energy were investigated.

  16. 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

  17. Chemisorbed-molecule potential energy surfaces and DIET processes

    NASA Astrophysics Data System (ADS)

    Jennison, D. R.; Stechel, E. B.; Burns, A. R.; Li, Y. S.

    1995-06-01

    We report the use of the local-density approximation, with and without gradient corrections, for the calculation of ground-state potential energy surfaces (PESs) for chemisorbed molecules. We focus on chemisorbed NO and ammonia on Pd(1 1 1) and compare our results with the latest experimental information. We then turn to two aspects of excited-state PESs. First, we compare first-principles calculations of the forces on an ammonia ion as a function of distance from the surface. We find that the image-charge model fails significantly at distances which are the most relevant for dynamics, closer than ˜3 Å, and discuss reasons for the failure. We then summarize a purely electronic adiabatic model of the moleuule-surface bond and use empirical parameters to estimate hot carrier-produced excited states of chemisorbed NO. We find multiple PESs and a novel interpretation of the π ∗ resonance, seen in inverse photoemission.

  18. Rovibrational states of Wigner molecules in spherically symmetric confining potentials

    NASA Astrophysics Data System (ADS)

    Cioslowski, Jerzy

    2016-08-01

    The strong-localization limit of three-dimensional Wigner molecules, in which repulsively interacting particles are confined by a weak spherically symmetric potential, is investigated. An explicit prescription for computation of rovibrational wavefunctions and energies that are asymptotically exact at this limit is presented. The prescription is valid for systems with arbitrary angularly-independent interparticle and confining potentials, including those involving Coulombic and screened (i.e., Yukawa/Debye) interactions. The necessary derivations are greatly simplified by explicit constructions of the Eckart frame and the parity-adapted primitive wavefunctions. The performance of the new formalism is illustrated with the three- and four-electron harmonium atoms at their strong-correlation limits. In particular, the involvement of vibrational modes with the E symmetry is readily pinpointed as the origin of the "anomalous" weak-confinement behavior of the 1S+ state of the four-electron species that is absent in its 1D+ companion of the strong-confinement regime.

  19. Rovibrational states of Wigner molecules in spherically symmetric confining potentials.

    PubMed

    Cioslowski, Jerzy

    2016-08-01

    The strong-localization limit of three-dimensional Wigner molecules, in which repulsively interacting particles are confined by a weak spherically symmetric potential, is investigated. An explicit prescription for computation of rovibrational wavefunctions and energies that are asymptotically exact at this limit is presented. The prescription is valid for systems with arbitrary angularly-independent interparticle and confining potentials, including those involving Coulombic and screened (i.e., Yukawa/Debye) interactions. The necessary derivations are greatly simplified by explicit constructions of the Eckart frame and the parity-adapted primitive wavefunctions. The performance of the new formalism is illustrated with the three- and four-electron harmonium atoms at their strong-correlation limits. In particular, the involvement of vibrational modes with the E symmetry is readily pinpointed as the origin of the "anomalous" weak-confinement behavior of the (1)S+ state of the four-electron species that is absent in its (1)D+ companion of the strong-confinement regime. PMID:27497548

  20. A small-molecule photoactivatable optical sensor of transmembrane potential

    PubMed Central

    Grenier, Vincent; Walker, Alison S.; Miller, Evan W.

    2015-01-01

    This paper discloses the design, synthesis, and imaging applications of the first member of a new class of SPOTs, small-molecule photoactivatable optical sensors of transmembrane potential. SPOT2.1.Cl features an established voltage-sensitive dye, VoltageFluor2.1.Cl—or—VF capped with a dimethoxy-o-nitrobenzyl (DMNB) caging group to effectively eliminate fluorescence of the VF dye prior to uncaging. SPOT2.1.Cl localizes to cell membranes and displays weak fluorescence until photoactivated. Illumination generates the parent VF dye which then optically reports on changes in the membrane voltage. After photoactivation with spatially restricted light, SPOT2.1.Cl-loaded cells display bright, voltage-sensitive fluorescence associated with the plasma membrane, while neighboring cells remain dark. Activated SPOT reports on action potentials in single trials. SPOT can be activated in neuron cell bodies or uncaged in dendrites to enable structural tracing via “backfilling” of the dye to the soma, followed by functional imaging in the labeled cell. The combination of cellular specificity achieved through spatially-defined patterns of illumination, coupled with the fast, sensitive, and non-capacitive voltage sensing characteristics of VF dyes makes SPOT2.1.Cl a useful tool for interrogating both structure and function of neuronal systems. PMID:26247778

  1. Screen for small molecules increasing the mitochondrial membrane potential.

    PubMed

    Montague, Christine R; Fitzmaurice, Aileen; Hover, Bradley M; Salazar, Noe A; Fey, Julien P

    2014-03-01

    The identification of small molecules that positively modulate the mitochondrial respiratory function has broad applications in fundamental research, therapeutic target validation, and drug discovery. We present an approach in which primary screens for mitochondrial function in yeast are used to efficiently identify a subset of high-value compounds that can in turn be rapidly tested against a broad range of mammalian cell lines. The ability of the yeast assay to successfully identify in a high-throughput format hit compounds that increase the mitochondrial membrane potential and adenosine triphosphate (ATP) levels by as little as 15% was demonstrated. In this study, 14 hits were identified from a collection of 13,680 compounds. Secondary testing with myotubes, fibroblasts, and PC-12 and HepG2 cells identified two compounds increasing ATP levels in hepatocytes and two other compounds increasing ATP in fibroblasts. The effect on hepatocytes was further studied using genomic and mitochondrial proteomic tools to characterize the changes induced by the two compounds. Changes in the accumulation of a series of factors involved in early gene response or apoptosis or linked to metabolic functions (i.e., β-Klotho, RORα, PGC-1α, G6PC, IGFBP1, FTL) were discovered.

  2. 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

  3. 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

  4. Signal transduction molecule patterns indicating potential glioblastoma therapy approaches

    PubMed Central

    Cruceru, Maria Linda; Enciu, Ana-Maria; Popa, Adrian Claudiu; Albulescu, Radu; Neagu, Monica; Tanase, Cristiana Pistol; Constantinescu, Stefan N

    2013-01-01

    Purpose The expression of an array of signaling molecules, along with the assessment of real-time cell proliferation, has been performed in U87 glioma cell line and in patients’ glioblastoma established cell cultures in order to provide a better understanding of cellular and molecular events involved in glioblastoma pathogenesis. Experimental therapy was performed using a phosphatidylinositol-3′-kinase (PI3K) inhibitor. Patients and methods xMAP technology was employed to assess expression levels of several signal transduction molecules and real-time xCELLigence platform for cell behavior. Results PI3K inhibition induced the most significant effects on global signaling pathways in patient-derived cell cultures, especially on members of the mitogen-activated protein-kinase family, P70S6 serine-threonine kinase, and cAMP response element-binding protein expression and further prevented tumor cell proliferation. Conclusion The PI3K pathway might be a prime target for glioblastoma treatment. PMID:24348050

  5. Potential energy surfaces and reaction dynamics of polyatomic molecules

    SciTech Connect

    Chang, Yan-Tyng.

    1991-11-01

    A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

  6. Azastilbene Analogs as Tyrosinase Inhibitors: New Molecules with Depigmenting Potential

    PubMed Central

    Lima, Larissa Lavorato; Lima, Rebeca Mól; da Silva, Annelisa Farah; do Carmo, Antônio Márcio Resende; da Silva, Adilson David; Raposo, Nádia Rezende Barbosa

    2013-01-01

    This research has been an effort to develop synthetic resveratrol analogs in order to improve the depigmenting potential of natural resveratrol. Six resveratrol analogs were synthesized and tested for tyrosinase inhibitory activity in vitro, by qualitative and quantitative steps. The results showed the analog C as being the most powerful tyrosinase inhibitor (IA50 = 65.67 ± 0.60 μg/mL), followed by the analogs B, E, F, A, and D, respectively. The analog C presented a tyrosinase inhibition potential better than natural resveratrol (P < 0.001). The best depigmenting activity was provided by the presence of hydroxyl in the orthoposition on the second phenolic ring. PMID:23476126

  7. Non Coding RNA Molecules as Potential Biomarkers in Breast Cancer.

    PubMed

    De Leeneer, Kim; Claes, Kathleen

    2015-01-01

    The pursuit of minimally invasive biomarkers is a challenging but exciting area of research. Clearly, such markers would need to be sensitive and specific enough to aid in the detection of breast cancer at an early stage, would monitor progression of the disease, and could predict the individual patient's response to treatment. Unfortunately, to date, markers with such characteristics have not made it to the clinic for breast cancer. Past years, many studies indicated that the non-coding part of our genome (the so called 'junk' DNA), may be an ideal source for these biomarkers. In this chapter, the potential use of microRNAs and long non-coding RNAs as biomarkers will be discussed. PMID:26530371

  8. 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.

  9. Resonant transmission of a weakly bound molecule incident upon a step potential

    NASA Astrophysics Data System (ADS)

    Shegelski, Mark R. A.; Jones, George

    2016-08-01

    The case of a molecule with a single weakly bound state is considered. The molecule is incident in the bound state upon a step potential with an energy increase of V 0. We calculate the probability of reflection p R and transmission p T in the bound state and its dependence on the energy of the molecule. Three energy ranges are examined. For the highest range, resonant transmission occurs for all energies, a behaviour drastically different than that of a single particle. Other unexpected results are obtained and the physical reasons underlying the results are discussed.

  10. Scattering of a two-soliton molecule by Gaussian potentials in dipolar Bose–Einstein condensates

    NASA Astrophysics Data System (ADS)

    Umarov, B. A.; Aklan, N. A. B.; Baizakov, B. B.; Abdullaev, F. Kh

    2016-06-01

    Two bright solitons in a dipolar Bose–Einstein condensate (BEC) can form stable bound states, known as soliton molecules. In this paper we study the scattering of a two-soliton molecule by external potential, using the simplest and analytically tractable Gaussian potential barriers and wells, in one spatial dimension. Collisions of soliton molecules with single solitons are investigated, the latter playing the role of a localized defect. Due to the long-range character of dipolar forces solitons interact with each other even though their waveforms do not appreciably overlap. This is an essentially different feature of dipolar solitons compared to their counterparts in BECs with contact atomic interactions. The result of scattering significantly depends on the potential’s strength and velocity of collision. For weak potentials and/or low velocity the molecule preserves its coherence, meantime the internal modes are excited. Scattering by strong potentials at moderately high velocity ends up with dissociation of the molecule. The theoretical model is based on the variational approximation for the nonlocal Gross–Pitaevskii equation (GPE). Predictions of the mathematical model are compared with numerical simulations of the nonlocal GPE, and good qualitative agreement between them is demonstrated.

  11. LiYb molecule in traps: potential energies, long-range energies, dipole moments, ...

    NASA Astrophysics Data System (ADS)

    Sadeghpour, H. R.; Zhang, P.; Dalgarno, A.

    2010-03-01

    We employ multireference configurations interaction and coupled cluster techniques to determine the potential energy curves of the ground and low-lying excited states of the LiYb molecule. The scalar relativistic effects have been included by means of the Douglas-Kroll Hamiltonian and effective core potentials, and the spin-orbit couplings have been evaluated by the full microscopic Breit-Pauli operator. The dipole moment, static dipole polarizability, transition dipole moments, van der Waals coefficients, and Franck-Condon spectroscopy of the LiYb molecule have been determined. Perturbations to the vibrational spectrum due to the non-adiabatic interactions are included. Implications for double-MOT trapping of LiYb are discussed and we find that dimer of these molecules should easily form.

  12. Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

    PubMed

    Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

    2015-12-01

    The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

  13. Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

    PubMed

    Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

    2015-12-01

    The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed. PMID:26566183

  14. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions.

    PubMed

    Jiang, Bin; Guo, Hua

    2014-07-21

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  15. Delivery of small molecules for bone regenerative engineering: preclinical studies and potential clinical applications

    PubMed Central

    Laurencin, Cato T.; Ashe, Keshia M.; Henry, Nicole; Kan, Ho Man; Lo, Kevin W-H.

    2014-01-01

    Stimulation of bone regeneration using growth factors is a promising approach for musculoskeletal regenerative engineering. Common limitations with protein growth factors are high manufacturing costs, protein instability, contamination issues, and unwanted immunogenic responses of the host. New strategies for bone regeneration that obviate these problems can have a significant impact on the treatment of skeletal injury and diseases. Over the past decade, a large number of small molecules with the potential of regenerating skeletal tissue have been reported in the literature. Here, we review this literature, paying specific attention to the prospects for small molecule-based bone-regenerative engineering. We also review the preclinical study of small molecules associated with bone regeneration. PMID:24508820

  16. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. III. Molecule-surface interactions

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2014-07-01

    The permutation invariant polynomial-neural network (PIP-NN) method for constructing highly accurate potential energy surfaces (PESs) for gas phase molecules is extended to molecule-surface interaction PESs. The symmetry adaptation in the NN fitting of a PES is achieved by employing as the input symmetry functions that fulfill both the translational symmetry of the surface and permutation symmetry of the molecule. These symmetry functions are low-order PIPs of the primitive symmetry functions containing the surface periodic symmetry. It is stressed that permutationally invariant cross terms are needed to avoid oversymmetrization. The accuracy and efficiency are demonstrated in fitting both a model PES for the H2 + Cu(111) system and density functional theory points for the H2 + Ag(111) system.

  17. Nonlinear optical measurement of membrane potential around single molecules at selected cellular sites

    PubMed Central

    Peleg, Gadi; Lewis, Aaron; Linial, Michal; Loew, Leslie M.

    1999-01-01

    Membrane potential around single molecules has been measured by using the nonlinear optical phenomenon of second harmonic generation. This advance results from the interaction between a highly dipolar molecule with a selectively directed highly polarizable 1-nm gold particle. With this approach, a second harmonic signal, which is enhanced by the nanoparticle, is detected from a volume of nanometric dimensions. This present work clearly shows that functional cellular imaging around single molecules is possible by selectively directing an antibody with a 1-nm gold label to a specific membrane protein. The results of this work open the way for three-dimensional, high resolution functional imaging of membrane electrophysiology in cells and cellular networks. PMID:10359775

  18. Nanoelectrode-Gated Detection of Individual Molecules with Potential for Rapid DNA Sequencing

    SciTech Connect

    Lee, James Weifu

    2007-01-01

    A systematic nanoelectrode-gated electron-tunneling molecular-detection concept with potential for rapid DNA sequencing has recently been invented at Oak Ridge National Laboratory (ORNL). A DNA molecule is a polymer that typically contains four different types of nucleotide bases: adenine (A), thymine (T), guanine (G), and cytosine (C) on its phosphate-deoxyribose chain. According to the nanoelectrode-gated molecular-detection concept, it should be possible to obtain genetic sequence information by probing through a DNA molecule base by base at a nanometer scale, as if looking at a strip of movie film. The nanoscale reading of DNA sequences is envisioned to take place at a nanogap (gate) defined by a pair of nanoelectrode tips as a DNA molecule moves through the gate base by base. The rationale is that sample molecules, such as the four different nucleotide bases, each with a distinct chemical composition and structure, should produce a specific perturbation effect on the tunneling electron beam across the two nanoelectrode tips. A sample molecule could thus be detected when it enters the gate. This nanoscience-based approach could lead to a new DNA sequencing technology that could be thousands of times faster than the current technology (Sanger's 'dideoxy' protocol-based capillary electrophoresis systems). Both computational and experimental studies are underway at ORNL towards demonstrating this nanotechnology concept.

  19. 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

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

    PubMed

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

    2014-11-26

    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.

  1. Effective Ion-In Potentials for Non-Penetrating Rydberg States of Polar Molecules

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    Rydberg states of atoms or molecules for which the inner turning point of the Rydberg electron on the radial plus centrifugal potential lies outside the bulk of the ion core electron density are known as core-non-penetrating states. Interpretation of Rydberg spectroscopic data for polar molecules makes use of effective potentials that include ionic bonding and polarizability in order to represent electric properties of the ion core. We examine the accuracy and convergence properties of single-center polarization potentials and show that the center of charge representation, for which the core dipole moment is zero so that first-order l-mixing can be neglected, is excluded by the convergence sphere for use with l-states that can be treated by an expansion about the center or mass, the center of dipole or a newly-defined center of polarizability. The potential expansion converges only outside a sphere enclosing the charge distribution, and the sphere is much larger when the center of charge is used. For higher l-states of the rotating molecule (turning points defined in center of mass), the sphere required for convergence is much smaller for an origin within the charge distribution, so that lower l states are modeled correctly.

  2. Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

    NASA Astrophysics Data System (ADS)

    Fidiani, Elok

    2016-03-01

    Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H2 and O2. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton's Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

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

    NASA Astrophysics Data System (ADS)

    Tautz, Stefan

    2014-03-01

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Their description as an inherently quantum mechanical phenomenon was developed for single atoms and homogeneous macroscopic bodies by London, Casimir, and Lifshitz. For intermediate-sized objects like organic molecules an atomistic description is required, but explicit first principles calculations are very difficult since correlations between many interacting electrons have to be considered. Hence, semi-empirical correction schemes are often used that simplify the vdW interaction to a sum over atom-pair potentials. A similar gap exists between successful measurements of vdW and Casimir forces for single atoms on the one hand and macroscopic bodies on the other, as comparable experiments for molecules are absent. I will present experiments in which long-range vdW potentials between a series of related molecules and a metal surface have been determined experimentally. The experiments rely on the extremely sensitive force detection of an atomic force microscope in combination with its molecular manipulation capabilities. The results allow us to confirm the asymptotic force law and to quantify the non-additive part of the vdW interaction which is particularly challenging for theory. In the present case, cooperative effects account for 10% of the total interaction. This effect is of general validity in molecules and thus relevant at the intersection of chemistry, physics, biology, and materials science.

  4. Proteolysis of cell adhesion molecules by serine proteases: a role in long term potentiation?

    PubMed

    Hoffman, K B; Martinez, J; Lynch, G

    1998-11-16

    Tissue plasminogen activator (tPA), a serine protease endogenous to hippocampal neurons, is shown to recognize a highly conserved sequence in the extracellular domain of cell adhesion molecules (CAMs). When added to brain homogenates, tPA generated a CAM fragment similar in size to that produced in hippocampal slices by brief periods of NMDA receptor stimulation. The serine protease inhibitor 4-(2-Aminoethyl)-benzenesulfonyl fluoride blocked the effects of tPA with an approximately 50% suppression at 250 microM. The inhibitor at this concentration had no evident effect on synaptic responses but caused long term potentiation to decay back to baseline over a 1 h period. These results suggest that extracellular breakdown of cell adhesion molecules initiated by NMDA receptors and mediated by serine proteases contributes to the formation of stable potentiation.

  5. 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

  6. 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/.

  7. 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

    2016-01-01

    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

  8. Proteasome Activation is a Mechanism for Pyrazolone Small Molecules Displaying Therapeutic Potential in Amyotrophic Lateral Sclerosis

    PubMed Central

    2015-01-01

    Amyotrophic lateral sclerosis (ALS) is a progressive and ultimately fatal neurodegenerative disease. Pyrazolone containing small molecules have shown significant disease attenuating efficacy in cellular and murine models of ALS. Pyrazolone based affinity probes were synthesized to identify high affinity binding partners and ascertain a potential biological mode of action. Probes were confirmed to be neuroprotective in PC12-SOD1G93A cells. PC12-SOD1G93A cell lysates were used for protein pull-down, affinity purification, and subsequent proteomic analysis using LC-MS/MS. Proteomics identified the 26S proteasome regulatory subunit 4 (PSMC1), 26S proteasome regulatory subunit 6B (PSMC4), and T-complex protein 1 (TCP-1) as putative protein targets. Coincubation with appropriate competitors confirmed the authenticity of the proteomics results. Activation of the proteasome by pyrazolones was demonstrated in the absence of exogenous proteasome inhibitor and by restoration of cellular protein degradation of a fluorogenic proteasome substrate in PC12-SOD1G93A cells. Importantly, supplementary studies indicated that these molecules do not induce a heat shock response. We propose that pyrazolones represent a rare class of molecules that enhance proteasomal activation in the absence of a heat shock response and may have therapeutic potential in ALS. PMID:25001311

  9. Structural Bacterial Molecules as Potential Candidates for an Evolution of the Classical Concept of Probiotics12

    PubMed Central

    Caselli, Michele; Vaira, Giuseppina; Calo, Girolamo; Papini, Francesco; Holton, John; Vaira, Dino

    2011-01-01

    A large number of experimental and clinical studies published in recent years have demonstrated the beneficial role of probiotic bacteria in the health of the host. However, because the different receptors of the innate immune system can recognize only specific bacterial molecular patterns, knowledge of the role played by individual probiotic molecular patterns is essential to move from the current confused era of live probiotic bacteria to the era of the pharmacobiotic strategies. This article reviews the current knowledge on the probiotic activities of bacterial structural molecules (nucleic acids and surface molecules), which represent the fundamental basis to set up experimental and clinical studies in this emerging field with very promising and potentially invaluable future prospects. PMID:22332079

  10. A full nine-dimensional potential-energy surface for hydrogen molecule-water collisions.

    PubMed

    Faure, Alexandre; Valiron, Pierre; Wernli, Michael; Wiesenfeld, Laurent; Rist, Claire; Noga, Josef; Tennyson, Jonathan

    2005-06-01

    The hydrogen and water molecules are ubiquitous in the Universe. Their mutual collisions drive water masers and other line emission in various astronomical environments, notably molecular clouds and star-forming regions. We report here a full nine-dimensional interaction potential for H2O-H2 calibrated using high-accuracy, explicitly correlated wave functions. All degrees of freedom are included using a systematic procedure transferable to other small molecules of astrophysical or atmospherical relevance. As a first application, we present rate constants for the vibrational relaxation of the upsilon2 bending mode of H2O obtained from quasiclassical trajectory calculations in the temperature range of 500-4000 K. Our high-temperature (T > or = 1500 K) results are found compatible with the single experimental value at 295 K. Our rates are also significantly larger than those currently used in the astrophysical literature and will lead to a thorough reinterpretation of vibrationally excited water emission spectra from space.

  11. 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

  12. Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-21

    The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

  13. CM2 antigen, a potential novel molecule participating in glucuronide transport on rat hepatocyte canalicular membrane.

    PubMed

    Wang, L; Wang, J; Zhou, X; Li, J; Shi, Y; Han, Z; Wang, X; Li, S; Yang, Z; Wang, R; Fan, D; Han, Y

    2012-06-29

    The polarized molecules predominately distributing at hepatocyte canalicular surface play a vital role in disclosing the process of bile formation and etiopathogenisis of cholestatic live diseases. Therefore, it is important to find novel polarized molecules on hepatocyte canalicular membrane. In the present study, canalicular membrane vesicles (CMVs) isolated from rat hepatocyte by density gradient centrifugation were used as immunogens to produce hybridoma and 46 strains of monoclonal antibodies (mAb) against CMVs were obtained. With a series of morphological assay methods, including immunohistochemistry, immunofluorescence and immuno-electron microscope, the antigens recognized by canalicular mAb1 (CM1) and canalicular mAb2 (CM2) were confirmed to predominately distribute at hepatocyte canalicular membrane. Transport activity assay revealed that CM2 could inhibit ATP-dependent E217βG uptake of rat hepatocyte CMVs. Meanwhile, Western blotting analysis showed that the molecular mass of CM2 antigen was approximately 110kDa, which was much less than Mr 180kDa of multidrug resistance-associated protein 2 (MRP2) involved in glucuronide transport. These data indicated that CM2 antigen might be a potential novel molecule participating in glucuronide transport on the hepatocyte canalicular membrane.

  14. Design, synthesis, and characterization of TPA-thiophene-based amide or imine functionalized molecule for potential optoelectronic devices

    NASA Astrophysics Data System (ADS)

    Sarswat, Prashant K.; Sathyapalan, Amarchand; Zhu, Yakun; Free, Michael L.

    2013-01-01

    New sets of molecules containing tri-phenyl-amine (TPA) core and thiophene unit with amide and imine functional groups are designed, synthesized, characterized, and compared. These are solution processable small molecules with high mobility. The newly designed molecules have better solubility due to the C=N (imine) and CONH2 (amide) moiety as compared to the established molecules with CH=CH (methine) for optoelectronic applications. They have an optimal energy band gap, which indicates their potential utility in a variety of optoelectronic applications. These molecules also show efficient intermolecular charge transfer mechanisms similar to conventional organic semiconducting molecules as evidenced by optical measurements. Density functional theory simulation results show that the localization of the frontier highest occupied molecular orbital is around the TPA core for molecules coupled with imine and amide, and is reasonably stable.

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

    PubMed Central

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

    2013-01-01

    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

  16. 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

  17. 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

  18. Animal models of schizophrenia for molecular and pharmacological intervention and potential candidate molecules.

    PubMed

    Mouri, Akihiro; Nagai, Taku; Ibi, Daisuke; Yamada, Kiyofumi

    2013-05-01

    Schizophrenia is a severe and common psychiatric disease with a lifetime prevalence of 0.5% to 1% globally. Because of limitations of the experimental approach in humans, valid animal models are essential in the effort to identify novel therapeutics for schizophrenia. In most animal models of schizophrenia, second generation antipsychotic drugs are reported to be effective in ameliorating behavioral abnormalities, while clinical evidence indicates that some of the patients are resistant to the antipsychotic drug therapy. Accordingly, animal models of antipsychotic drug-resistant schizophrenia are needed for screening of novel agents that may be more effective than the existing antipsychotic drugs. Furthermore, utilization of appropriate behavioral tasks with reference to human testing is essential to facilitate the development of novel pharmacotherapeutic approaches for the treatment in schizophrenia. Experimental data suggest that there are different types of potential candidate molecules as novel antipsychotic drugs with some therapeutic effects on negative symptoms and cognitive deficits in schizophrenia. It is proposed that to develop novel antipsychotic drugs the efficacy of potential candidate molecules should be evaluated using animal models for treatment-resistant schizophrenia with appropriate behavioral tasks in reference to human testing.

  19. Strongly Correlated 2D Quantum Phases with Cold Polar Molecules: Controlling the Shape of the Interaction Potential

    SciTech Connect

    Buechler, H. P.; Micheli, A.; Pupillo, G.; Zoller, P.; Demler, E.; Lukin, M.; Prokof'ev, N.

    2007-02-09

    We discuss techniques to tune and shape the long-range part of the interaction potentials in quantum gases of bosonic polar molecules by dressing rotational excitations with static and microwave fields. This provides a novel tool towards engineering strongly correlated quantum phases in combination with low-dimensional trapping geometries. As an illustration, we discuss the 2D superfluid-crystal quantum phase transition for polar molecules interacting via an electric-field-induced dipole-dipole potential.

  20. 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

  1. Ground state of the polar alkali-metal-atom-strontium molecules: Potential energy curve and permanent dipole moment

    SciTech Connect

    Guerout, R.; Aymar, M.; Dulieu, O.

    2010-10-15

    In this study, we investigate the structure of the polar alkali-metal-atom-strontium diatomic molecules as possible candidates for the realization of samples of ultracold polar molecular species not yet investigated experimentally. Using a quantum chemistry approach based on effective core potentials and core polarization potentials, we model these systems as effective three-valence-electron systems, allowing for calculation of electronic properties with full configuration interaction. The potential curve and the permanent dipole moment of the {sup 2}{Sigma}{sup +} ground state are determined as functions of the internuclear distance for LiSr, NaSr, KSr, RbSr, and CsSr molecules. These molecules are found to exhibit a significant permanent dipole moment, though smaller than those of the alkali-metal-atom-Rb molecules.

  2. Breit interaction contribution to parity violating potentials in chiral molecules containing light nuclei.

    PubMed

    Berger, Robert

    2008-10-21

    The importance of the Breit interaction for an accurate prediction of parity violating energy differences between enantiomers is studied within electroweak quantum chemical frameworks. Besides two-electron orbit-orbit and spin-spin coupling contributions, the Breit interaction gives rise to the spin-other-orbit coupling term of the Breit-Pauli Hamiltonian. The present numerical study demonstrates that neglect of this latter term leads in hydrogen peroxide (H(2)O(2)) to relative deviations in the parity violating potential (V(pv)) by about 10%, whereas further relativistic corrections accounted for within a four-component Dirac-Hartree-Fock-Coulomb (DHFC) framework remain smaller, below 5%. Thus, the main source of discrepancy between previous one-component based (coupled perturbed) Hartree-Fock (HF) and four-component Dirac-Hartree-Fock results for parity violating potentials in H(2)O(2) is the neglect of the Breit contribution in DHFC. In heavier homologs of hydrogen peroxide the relative contribution of the spin-other-orbit coupling term to V(pv) decreases with increasing nuclear charge, whereas other relativistic effects become increasingly important. As shown for the H(2)X(2) (X = O,S,Se,Te,Po) series of molecules and for CHBrClF, to a good approximation these other relativistic influences on V(pv) can be accounted for in one-component based HF calculations with the help of relativistic enhancement factors proposed earlier in the theory of atomic parity violation.

  3. 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.

  4. 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.

  5. Gramicidin-based fluorescence assay; for determining small molecules potential for modifying lipid bilayer properties.

    PubMed

    Ingólfsson, Helgi I; Sanford, R Lea; Kapoor, Ruchi; Andersen, Olaf S

    2010-10-13

    Many drugs and other small molecules used to modulate biological function are amphiphiles that adsorb at the bilayer/solution interface and thereby alter lipid bilayer properties. This is important because membrane proteins are energetically coupled to their host bilayer by hydrophobic interactions. Changes in bilayer properties thus alter membrane protein function, which provides an indirect way for amphiphiles to modulate protein function and a possible mechanism for "off-target" drug effects. We have previously developed an electrophysiological assay for detecting changes in lipid bilayer properties using linear gramicidin channels as probes. Gramicidin channels are mini-proteins formed by the transbilayer dimerization of two non-conducting subunits. They are sensitive to changes in their membrane environment, which makes them powerful probes for monitoring changes in lipid bilayer properties as sensed by bilayer spanning proteins. We now demonstrate a fluorescence assay for detecting changes in bilayer properties using the same channels as probes. The assay is based on measuring the time-course of fluorescence quenching from fluorophore-loaded large unilamellar vesicles due to the entry of a quencher through the gramicidin channels. We use the fluorescence indicator/quencher pair 8-aminonaphthalene-1,3,6-trisulfonate (ANTS)/Tl(+) that has been successfully used in other fluorescence quenching assays. Tl(+) permeates the lipid bilayer slowly but passes readily through conducting gramicidin channels. The method is scalable and suitable for both mechanistic studies and high-throughput screening of small molecules for bilayer-perturbing, and potential "off-target", effects. We find that results using this method are in good agreement with previous electrophysiological results.

  6. Therapeutic potential of an orally effective small molecule inhibitor of plasminogen activator inhibitor for asthma.

    PubMed

    Liu, Rui-Ming; Eldridge, Stephanie; Watanabe, Nobuo; Deshane, Jessy; Kuo, Hui-Chien; Jiang, Chunsun; Wang, Yong; Liu, Gang; Schwiebert, Lisa; Miyata, Toshio; Thannickal, Victor J

    2016-02-15

    Asthma is one of the most common respiratory diseases. Although progress has been made in our understanding of airway pathology and many drugs are available to relieve asthma symptoms, there is no cure for chronic asthma. Plasminogen activator inhibitor 1 (PAI-1), a primary inhibitor of tissue-type and urokinase-type plasminogen activators, has pleiotropic functions besides suppression of fibrinolysis. In this study, we show that administration of TM5275, an orally effective small-molecule PAI-1 inhibitor, 25 days after ovalbumin (OVA) sensitization-challenge, significantly ameliorated airway hyperresponsiveness in an OVA-induced chronic asthma model. Furthermore, we show that TM5275 administration significantly attenuated OVA-induced infiltration of inflammatory cells (neutrophils, eosinophils, and monocytes), the increase in the levels of OVA-specific IgE and Th2 cytokines (IL-4 and IL-5), the production of mucin in the airways, and airway subepithelial fibrosis. Together, the results suggest that the PAI-1 inhibitor TM5275 may have therapeutic potential for asthma through suppressing eosinophilic allergic response and ameliorating airway remodeling. PMID:26702150

  7. 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

  8. Therapeutic potential of an orally effective small molecule inhibitor of plasminogen activator inhibitor for asthma.

    PubMed

    Liu, Rui-Ming; Eldridge, Stephanie; Watanabe, Nobuo; Deshane, Jessy; Kuo, Hui-Chien; Jiang, Chunsun; Wang, Yong; Liu, Gang; Schwiebert, Lisa; Miyata, Toshio; Thannickal, Victor J

    2016-02-15

    Asthma is one of the most common respiratory diseases. Although progress has been made in our understanding of airway pathology and many drugs are available to relieve asthma symptoms, there is no cure for chronic asthma. Plasminogen activator inhibitor 1 (PAI-1), a primary inhibitor of tissue-type and urokinase-type plasminogen activators, has pleiotropic functions besides suppression of fibrinolysis. In this study, we show that administration of TM5275, an orally effective small-molecule PAI-1 inhibitor, 25 days after ovalbumin (OVA) sensitization-challenge, significantly ameliorated airway hyperresponsiveness in an OVA-induced chronic asthma model. Furthermore, we show that TM5275 administration significantly attenuated OVA-induced infiltration of inflammatory cells (neutrophils, eosinophils, and monocytes), the increase in the levels of OVA-specific IgE and Th2 cytokines (IL-4 and IL-5), the production of mucin in the airways, and airway subepithelial fibrosis. Together, the results suggest that the PAI-1 inhibitor TM5275 may have therapeutic potential for asthma through suppressing eosinophilic allergic response and ameliorating airway remodeling.

  9. Prediction of physicochemical properties of organic molecules using van der Waals surface electrostatic potentials.

    PubMed

    Kim, Chan Kyung; Lee, Kyung A; Hyun, Kwan Hoon; Park, Heung Jin; Kwack, In Young; Kim, Chang Kon; Lee, Hai Whang; Lee, Bon-Su

    2004-12-01

    The generalized interaction properties function (GIPF) methodology developed by Politzer and coworkers, which calculated molecular surface electrostatic potential (MSESP) on a density envelope surface, was modified by calculating the MSESP on a much simpler van der Waals (vdW) surface of a molecule. In this work, vdW molecular surfaces were obtained from the fully optimized structures confirmed by frequency calculations at B3LYP/6-31G(d) level of theory. Multiple linear regressions for normal boiling point, heats of vaporization, heats of sublimation, heats of fusion, liquid density, and solid density were performed using GIPF variables from vdW model surface. Results from our model are compared with those from Politzer and coworkers. The surface-dependent beta (and gamma) values are dependent on the surface models but the surface-independent alpha and regression coefficients (r) are constant when vdW surface and density surface with 0.001 a.u. contour value are compared. This interesting phenomenon is explained by linear dependencies of GIPF variables.

  10. Screening for small molecules' bilayer-modifying potential using a gramicidin-based fluorescence assay.

    PubMed

    Ingólfsson, Helgi I; Andersen, Olaf S

    2010-08-01

    Many drugs and other small molecules used to modulate biological function are amphiphiles that adsorb at the bilayer/solution interface and thereby alter lipid bilayer properties. This is important because membrane proteins are energetically coupled to their host bilayer by hydrophobic interactions. Changes in bilayer properties thus alter membrane protein function, which provides a possible mechanism for "off-target" drug effects. We have previously shown that channels formed by the linear gramicidins are suitable probes for changes in lipid bilayer properties, as experienced by bilayer-spanning proteins. We now report a gramicidin-based fluorescence assay for changes in bilayer properties. The assay is based on measuring the time course of fluorescence quenching in fluorophore-loaded large unilamellar vesicles, due to entry of a gramicidin channel-permeable quencher. The method is scalable and suitable for both mechanistic studies and high-throughput screening for bilayer-perturbing, potential off-target effects, which we illustrate using capsaicin (Cap) and other compounds.

  11. 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

  12. Potential function of the internal rotation of a methacrolein molecule in the ground ( S 0) electronic state

    NASA Astrophysics Data System (ADS)

    Koroleva, L. A.; Krasnoshchekov, S. V.; Matveev, V. K.; Pentin, Yu. A.

    2016-08-01

    The structural parameters of s- trans- and s- cis-isomers of a methacrolein molecule in the ground ( S 0) electronic state are determined by means of MP2 method with the cc-pVTZ basis set. Kinematic factor F(φ) is expanded in a Fourier series. The potential function of internal rotation (PFIR) of methacrolein in this state is built using experimental frequencies of transitions of the torsional vibration of both isomers, obtained from an analysis of the vibrational structure of the high-resolution UV spectrum with allowance for the geometry and difference between the energy (Δ H) of the isomers. It is shown that the V n parameters of the potential function of internal rotation of the molecule, built using the frequencies of the transition of the torsional vibrations of s- trans- and s- cis-isomers of the methacrolein molecule, determined from vibrational structure of the high-resolution UV spectrum and the FTIR spectrum, are close.

  13. 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

  14. Theoretical study of the structure and analytic potential energy function for the ground state of the PO2 molecule

    NASA Astrophysics Data System (ADS)

    Zeng, Hui; Zhao, Jun

    2012-07-01

    In this paper, the energy, equilibrium geometry, and harmonic frequency of the ground electronic state of PO2 are computed using the B3LYP, B3P86, CCSD(T), and QCISD(T) methods in conjunction with the 6-311++G(3df, 3pd) and cc-pVTZ basis sets. A comparison between the computational results and the experimental values indicates that the B3P86/6-311++G(3df, 3pd) method can give better energy calculation results for the PO2 molecule. It is shown that the ground state of the PO2 molecule has C2ν symmetry and its ground electronic state is X2A1. The equilibrium parameters of the structure are RP-O = 0.1465 nm, ∠OPO = 134.96°, and the dissociation energy is Ed = 19.218 eV. The bent vibrational frequency ν1 = 386 cm-1, symmetric stretching frequency ν2 = 1095 cm-1, and asymmetric stretching frequency ν3 = 1333 cm-1 are obtained. On the basis of atomic and molecular reaction statics, a reasonable dissociation limit for the ground state of the PO2 molecule is determined. Then the analytic potential energy function of the PO2 molecule is derived using many-body expansion theory. The potential curves correctly reproduce the configurations and the dissociation energy for the PO2 molecule.

  15. 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

    2014-02-01

    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. PMID:23838574

  16. Small Molecule Restores Itaconate Sensitivity in Salmonella enterica: A Potential New Approach to Treating Bacterial Infections.

    PubMed

    Hammerer, Fabien; Chang, Justin H; Duncan, Dustin; Castañeda Ruiz, Angel; Auclair, Karine

    2016-08-17

    In the context of increasing global antibiotic resistance, the need for alternative therapeutic targets is great. Although new antibiotics and resistance inhibitors provide temporary solutions, they are bound to become obsolete. In this work, we propose a new approach, coined "bacterio-modulation" that aims to restore macrophage potency towards bacterial strains that are able to survive in phagolysosomes. One key defense in the macrophage's arsenal is itaconate, an endogenous molecule with antimicrobial activity. Some intracellular pathogens have evolved to produce itaconate-degrading enzymes, which are required for intracellular proliferation and to promote pathogenicity. We herein present the first molecule able to resensitize Salmonella enterica to itaconate. PMID:27254798

  17. 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

  18. Cellular reprogramming for pancreatic β-cell regeneration: clinical potential of small molecule control.

    PubMed

    Pandian, Ganesh N; Taniguchi, Junichi; Sugiyama, Hiroshi

    2014-03-27

    Recent scientific breakthroughs in stem cell biology suggest that a sustainable treatment approach to cure diabetes mellitus (DM) can be achieved in the near future. However, the transplantation complexities and the difficulty in obtaining the stem cells from adult cells of pancreas, liver, bone morrow and other cells is a major concern. The epoch-making strategy of transcription-factor based cellular reprogramming suggest that these barriers could be overcome, and it is possible to reprogram any cells into functional β cells. Contemporary biological and analytical techniques help us to predict the key transcription factors needed for β-cell regeneration. These β cell-specific transcription factors could be modulated with diverse reprogramming protocols. Among cellular reprogramming strategies, small molecule approach gets proclaimed to have better clinical prospects because it does not involve genetic manipulation. Several small molecules targeting certain epigenetic enzymes and/or signaling pathways have been successful in helping to induce pancreatic β-cell specification. Recently, a synthetic DNA-based small molecule triggered targeted transcriptional activation of pancreas-related genes to suggest the possibility of achieving desired cellular phenotype in a precise mode. Here, we give a brief overview of treating DM by regenerating pancreatic β-cells from various cell sources. Through a comprehensive overview of the available transcription factors, small molecules and reprogramming strategies available for pancreatic β-cell regeneration, this review compiles the current progress made towards the generation of clinically relevant insulin-producing β-cells.

  19. Theoretical demonstration of the potentiality of boron nitride nanotubes to encapsulate anticancer molecule.

    PubMed

    El Khalifi, Mohammed; Duverger, Eric; Gharbi, Tijani; Boulahdour, Hatem; Picaud, Fabien

    2015-11-28

    Anticancer drug transport is now becoming an important scientific challenge since it would allow localizing the drug release near the tumor cell, avoiding secondary medical effects. We present theoretical results, based on density functional theory and molecular dynamics simulations, which demonstrate the stability of functionalized single (10,10) boron nitride nanotubes (BNNTs) filled with anticancer molecule such as carboplatin (CPT). For this functionalized system we determine the dependence of the adsorption energy on the molecule displacement near the inner BNNTs surface, together with their local morphological and electrical changes and compare the values to the adsorption energy obtained on the outer surface. Quantum simulations show that the most stable physisorption state is located inside the nanotube, with no net charge transfer. This demonstrates that chemotherapeutic encapsulation is the most favorable way to transport drug molecules. The solvent effect and dispersion repulsion contributions are then taken into account using molecular dynamics simulations. Our results confirm that carboplatin therapeutic agents are not affected when they are adsorbed inside BNNTs by the surrounding water molecules. PMID:26498990

  20. 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.

  1. 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.

  2. Soluble cell adhesion molecules in hypertriglyceridemia and potential significance on monocyte adhesion.

    PubMed

    Abe, Y; El-Masri, B; Kimball, K T; Pownall, H; Reilly, C F; Osmundsen, K; Smith, C W; Ballantyne, C M

    1998-05-01

    Hypertriglyceridemia may contribute to the development of atherosclerosis by increasing expression of cell adhesion molecules (CAMs). Although the cellular expression of CAMs is difficult to assess clinically, soluble forms of CAMs (sCAMs) are present in the circulation and may serve as markers for CAMs. In this study, we examined the association between sCAMs and other risk factors occurring with hypertriglyceridemia, the effect of triglyceride reduction on sCAM levels, and the role of soluble vascular cell adhesion molecule-1 (sVCAM-1) in monocyte adhesion in vitro. Compared with normal control subjects (n=20), patients with hypertriglyceridemia and low HDL (n=39) had significantly increased levels of soluble intercellular adhesion molecule-1 (sICAM-1) (316+/-28.8 versus 225+/-16.6 ng/mL), sVCAM-1 (743+/-52.2 versus 522+/-43.6 ng/mL), and soluble E-selectin (83+/-5.9 versus 49+/-3.6 ng/mL). ANCOVA showed that the higher sCAM levels in patients occurred independently of diabetes mellitus and other risk factors. In 27 patients who received purified n-3 fatty acid (Omacor) 4 g/d for > or =7 months, triglyceride level was reduced by 47+/-4.6%, sICAM-1 level was reduced by 9+/-3.4% (P=.02), and soluble E-selectin level was reduced by 16+/-3.2% (P<.0001), with the greatest reduction in diabetic patients. These results support previous in vitro data showing that disorders in triglyceride and HDL metabolism influence CAM expression and treatment with fish oils may alter vascular cell activation. In a parallel-plate flow chamber, recombinant sVCAM-1 at the concentration seen in patients significantly inhibited adhesion of monocytes to interleukin-1-stimulated cultured endothelial cells under conditions of flow by 27.5+/-7.2%. Thus, elevated sCAMs may negatively regulate monocyte adhesion.

  3. Identification of small molecule inhibitors of Tau aggregation by targeting monomeric Tau as a potential therapeutic approach for Tauopathies

    PubMed Central

    Pickhardt, Marcus; Neumann, Thomas; Schwizer, Daniel; Callaway, Kari; Vendruscolo, Michele; Schenk, Dale; George-Hyslop, Peter; Mandelkow, Eva M.; Dobson, Christopher M.; McConlogue, Lisa; Mandelkow, Eckhard; Tóth, Gergely

    2016-01-01

    A potential strategy to alleviate the aggregation of intrinsically disordered proteins (IDPs) is to maintain the native functional state of the protein by small molecule binding. However, the targeting of the native state of IDPs by small molecules has been challenging due to their heterogeneous conformational ensembles. To tackle this challenge, we applied a high-throughput chemical microarray surface plasmon resonance imaging screen to detect the binding between small molecules and monomeric full-length Tau, a protein linked with the onset of a range of Tauopathies. The screen identified a novel set of drug-like fragment and lead-like compounds that bound to Tau. We verified that the majority of these hit compounds reduced the aggregation of different Tau constructs in vitro and in N2a cells. These results demonstrate that Tau is a viable receptor of drug-like small molecules. The drug discovery approach that we present can be applied to other IDPs linked to other misfolding diseases such as Alzheimer’s and Parkinson’s diseases. PMID:26510979

  4. Identification of Small Molecule Inhibitors of Tau Aggregation by Targeting Monomeric Tau As a Potential Therapeutic Approach for Tauopathies

    PubMed Central

    Pickhardt, Marcus; Neumann, Thomas; Schwizer, Daniel; Callaway, Kari; Vendruscolo, Michele; Schenk, Dale; St. George-Hyslop, Peter; Mandelkow, Eva M.; Dobson, Christopher M.; McConlogue, Lisa; Mandelkow, Eckhard; Tóth, Gergely

    2015-01-01

    A potential strategy to alleviate the aggregation of intrinsically disordered proteins (IDPs) is to maintain the native functional state of the protein by small molecule binding. However, the targeting of the native state of IDPs by small molecules has been challenging due to their heterogeneous conformational ensembles. To tackle this challenge, we applied a high-throughput chemical microarray surface plasmon resonance imaging screen to detect the binding between small molecules and monomeric full-length Tau, a protein linked with the onset of a range of Tauopathies. The screen identified a novel set of drug-like fragment and lead-like compounds that bound to Tau. We verified that the majority of these hit compounds reduced the aggregation of different Tau constructs in vitro and in N2a cells. These results demonstrate that Tau is a viable receptor of drug-like small molecules. The drug discovery approach that we present can be applied to other IDPs linked to other misfolding diseases such as Alzheimer’s and Parkinson’s diseases.

  5. 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.

  6. 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.

  7. 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.

  8. Scattering of slow electrons by polar molecules: Application of effective-range potential theory to HC1

    SciTech Connect

    Vanroose, Wim; McCurdy, C.W.; Rescigno, T.N.

    2003-06-19

    We present a non-empirical potential model for studying threshold vibrational excitation of polar molecules by electron impact. This work builds on the zero-range potential virtual state model of Gauyacq and Herzenberg (J.P. Gauyacq and A. Herzenberg, Phys. Rev. A 25, 2959 (1982)), using known analytic properties of the S-matrix for a dipole potential to predict the analytic continuation of the negative ion potential curve into the continuum. We derive an equation that determines the nuclear dynamics which can be solved without the need for an expansion in target vibrational states. The model is applied to e{sup -} - HCl and is found to capture the essential features of the observed excitation cross sections, including both the threshold peaks as well as oscillatory structures at energies above threshold.

  9. 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

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

    PubMed

    Sharma, Charu; Sadek, Bassem; Goyal, Sameer N; Sinha, Satyesh; Kamal, Mohammad Amjad; 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 Δ(9)-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

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

    PubMed

    Sharma, Charu; Sadek, Bassem; Goyal, Sameer N; Sinha, Satyesh; Kamal, Mohammad Amjad; 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 Δ(9)-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.

  12. Fusion Molecules of Heat Shock Protein HSPX with Other Antigens of Mycobacterium tuberculosis Show High Potential in Serodiagnosis of Tuberculosis

    PubMed Central

    Khalid, Ruqyya; Afzal, Madeeha; Khurshid, Sana; Paracha, Rehan Zafar; Khan, Imran H.

    2016-01-01

    Variable individual response against the antigens of Mycobacterium tuberculosis necessitates detection of multiple antibodies for enhancing reliability of serodiagnosis of tuberculosis. Fusion molecules consisting of two or more antigens showing high sensitivity would be helpful in achieving this objective. Antigens of M. tuberculosis HSPX and PE35 were expressed in a soluble form whereas tnPstS1 and FbpC1 were expressed as inclusion bodies at 37°C. Heat shock protein HSPX when attached to the N-termini of the antigens PE35, tnPstS1 and FbpC1, all the fusion molecules were expressed at high levels in E. coli in a soluble form. ELISA analysis of the plasma samples of TB patients against HSPX-tnPstS1 showed 57.7% sensitivity which is nearly the same as the expected combined value obtained after deducting the number of plasma samples (32) containing the antibodies against both the individual antigens. Likewise, the 54.4% sensitivity of HSPX-PE35 was nearly the same as that expected from the combined values of the contributing antigens. Structural analysis of all the fusion molecules by CD spectroscopy showed that α-helical and β-sheet contents were found close to those obtained through molecular modeling. Molecular modeling studies of HSPX-tnPstS1 and HSPX-PE35 support the analytical results as most of the epitopes of the contributing antigens were found to be available for binding to the corresponding antibodies. Using these fusion molecules in combination with other antigenic molecules should reduce the number of antigenic proteins required for a more reliable and economical serodiagnosis of tuberculosis. Also, HSPX seems to have potential application in soluble expression of heterologous proteins in E. coli. PMID:27654048

  13. Umbrella motion of the methyl cation, radical, and anion molecules. I. Potentials, energy levels and partition functions

    NASA Astrophysics Data System (ADS)

    Ragni, Mirco; Bitencourt, Ana Carla P.; Prudente, Frederico V.; Barreto, Patricia R. P.; Posati, Tamara

    2016-03-01

    A study of the umbrella motion of the methyl cation, radical, and anion molecules is presented. This is the floppiest mode of vibration of all three species and its characterization is of fundamental importance for understanding their reactivity. Minimum Energy Paths of the umbrella motions according to the hyperspherical treatment were obtained, by single point calculations, at the CCSD(T)/aug-cc-pVQT level of theory in the Born-Oppenheimer approximation. These energy profiles permit us to calculate the vibrational levels through the Hyperquantization algorithm, which is shown appropriated for the description of the umbrella motion of these three molecules. The adiabatic electron affinity and ionization potentials were estimated to good accuracy. Partition functions are also calculated in order to obtain information on the reaction rates involving these groups.

  14. Fucoidan and Cancer: A Multifunctional Molecule with Anti-Tumor Potential

    PubMed Central

    Atashrazm, Farzaneh; Lowenthal, Ray M.; Woods, Gregory M.; Holloway, Adele F.; Dickinson, Joanne L.

    2015-01-01

    There is a wide variety of cancer types yet, all share some common cellular and molecular behaviors. Most of the chemotherapeutic agents used in cancer treatment are designed to target common deregulated mechanisms within cancer cells. Many healthy tissues are also affected by the cytotoxic effects of these chemical agents. Fucoidan, a natural component of brown seaweed, has anti-cancer activity against various cancer types by targeting key apoptotic molecules. It also has beneficial effects as it can protect against toxicity associated with chemotherapeutic agents and radiation. Thus the synergistic effect of fucoidan with current anti-cancer agents is of considerable interest. This review discusses the mechanisms by which fucoidan retards tumor development, eradicates tumor cells and synergizes with anti-cancer chemotherapeutic agents. Challenges to the development of fucoidan as an anti-cancer agent will also be discussed. PMID:25874926

  15. 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.

  16. Potential and matrix elements of the hamiltonian of internal rotation in molecules in the basis set of Mathieu functions

    NASA Astrophysics Data System (ADS)

    Turovtsev, V. V.; Orlov, Yu. D.; Tsirulev, A. N.

    2015-08-01

    The advantages of the orthonormal basis set of 2π-periodic Mathieu functions compared to the trigonometric basis set in calculations of torsional states of molecules are substantiated. Explicit expressions are derived for calculating the Hamiltonian matrix elements of a one-dimensional torsional Schrödinger equation with a periodic potential of the general form in the basis set of Mathieu functions. It is shown that variation of a parameter of Mathieu functions allows the rotation potential and the structural function to be approximated with a good accuracy by a small number of series terms. The conditions for the best choice of this parameter are specified, and approximations are obtained for torsional potentials of n-butane upon rotation about the central C-C bond and of its univalent radical n-butyl C2H5C·H2 upon rotation of the C·H2 group. All algorithms are implemented in the Maple package.

  17. Identification of arginine and its "Downstream" molecules as potential markers of breast cancer.

    PubMed

    Hu, Lu; Gao, Yu; Cao, Yunfeng; Zhang, Yinxu; Xu, Minghao; Wang, Yuanyuan; Jing, Yu; Guo, Shengnan; Jing, Fangyu; Hu, Xiaodan; Zhu, Zhitu

    2016-10-01

    Breast cancer (BC) is the most commonly diagnosed cancer in women worldwide. Arginine is a semiessential amino acid in humans and is essential for several biological pathways in malignant and normal cells, such as ornithine and N1, N12-diacetylspermine (DiAcSpm). This study aimed to determine the role of arginine and these downstream molecules in BC. Plasma arginine, ornithine, and arginine-to-ornithine ratio (AOR) were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Urine samples were measured by the colloid gold aggregation to test determination of urinary diAcSpm. A principal component analysis was performed to evaluate the results observed between breast tumor and control characteristics. Differences in individual metabolite concentrations between BC patients and controls were tested by receiver operating characteristics (ROC) analyses. Student's t tests were used to detect the differences between two groups of normally distributed variables, and Wilcoxon sign rank tests were performed for asymmetrically distributed variables. As we analyzed, BC patients had lower plasma arginine and arginine/ornithine level, and higher plasma ornithine and urinary DiAcSpm concentrations as compared with control patients (P = 0.028, 0.020, 0.002, and 0.011, respectively). And the ROC curve was drawn and the area under the curve of the metabolites was calculated to be 0.659 (P = 0.028), 0.645 (P = 0.045), 0.7233 (P = 0.002), 0.683 (P = 0.011), respectively. In addition, our analysis showed that arginine concentrations and AOR had a positive correlation with ER status, while ornithine had a negative correlation with T stage (P = 0.042, 0.023, respectively).In conclusion, arginine and these downstream molecules were biomarkers for BC. More studies are needed to highlight the theoretical strengths. © 2016 IUBMB Life, 68(10):817-822, 2016. PMID:27641058

  18. Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts.

    PubMed

    Zhang, Xue-Xian; Ritchie, Stephen R; Rainey, Paul B

    2014-02-01

    Host recognition is the crucial first step in infectious disease pathogenesis. Recognition allows pathogenic bacteria to identify suitable niches and deploy appropriate phenotypes for successful colonization and immune evasion. However, the mechanisms underlying host recognition remain largely unknown. Mounting evidence suggests that urocanate-an intermediate of the histidine degradation pathway-accumulates in tissues, such as skin, and acts as a molecule that promotes bacterial infection via molecular interaction with the bacterial regulatory protein HutC. In Gram-negative bacteria, HutC has long been known as a transcriptional repressor of hut genes for the utilization of histidine (and urocanate) as sources of carbon and nitrogen. Recent work on the opportunistic human pathogen Pseudomonas aeruginosa and zoonotic pathogen Brucella abortus shows that urocanate, in conjunction with HutC, plays a significant role in the global control of cellular metabolism, cell motility, and expression of virulence factors. We suggest that in addition to being a valuable source of carbon and nitrogen, urocanate may be central to the elicitation of bacterial pathogenesis.

  19. Dissociation of diatomic molecules and the exact-exchange Kohn-Sham potential: The case of LiF

    SciTech Connect

    Makmal, Adi; Kronik, Leeor; Kuemmel, Stephan

    2011-06-15

    We examine the role of the exact-exchange (EXX) Kohn-Sham potential in curing the problem of fractional molecular dissociation. This is achieved by performing EXX calculations for the illustrative case of the LiF molecule. We show that by choosing the lowest-energy electronic configuration for each interatomic distance, a qualitatively correct binding energy curve, reflecting integer dissociation, is obtained. Surprisingly, for LiF this comes at the cost of violating the Aufbau principle, a phenomenon we discuss at length. Furthermore, we numerically confirm that in the EXX potential of the diatomic molecule, one of the atomic potentials is shifted by a constant while the other one is not, depending on where the highest occupied molecular orbital is localized. This changes the relative positions of the energies of each atom and enforces the integer configuration by preventing spurious charge transfer. The size of the constant shift becomes increasingly unstable numerically the larger the interatomic separation is, reflecting the increasing absence of coupling between the atoms.

  20. 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.

  1. Relativistic and nonrelativistic solutions for diatomic molecules in the presence of double ring-shaped Kratzer potential.

    PubMed

    Durmus, Aysen; Yasuk, Fevziye

    2007-02-21

    The authors investigate solutions of the three dimensional Klein-Gordon and Schrodinger equations in the presence of a new exactly solvable potential of V(r,theta)=-2De(re/r-(1/2)(re2/r2))+b/r2 sin2 theta+a/r2 cos2 theta type, the so-called double ring-shaped Kratzer potential. For a diatomic molecule system in double ring-shaped Kratzer potential, the exact bound state energy eigenvalues and corresponding wave functions have been determined within the framework of the asymptotic iteration method. Bound state eigenfunction solutions used in applications related to molecular spectroscopy are obtained in terms of confluent hypergeometric function and Jacobi polynomial. This new formulation is tested by calculating the energies of rovibrational states of a number of diatomic molecules. Also, the author-prove that in the nonrelativistic limit c-->infinity, where c is the speed of light, solutions of the Klein-Gordon system converge to those of the Schrodinger system.

  2. 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.

  3. Synthesis and photophysical characterization of conjugated molecules for potential solar cell uses

    NASA Astrophysics Data System (ADS)

    Chudomel, John Matthew

    Three new strategies were successfully pursued for the synthesis of defined length oligomers of p-phenylene-vinylene. These strategies are interchangeable and allow the fast and efficient synthesis of a wide variety of oligomers with a number of different substituents. An assortment of new molecules and oligomers were synthesized and characterized during this study to prove the effectiveness of each strategy. The new strategies were compared to previous methodology for making similar oligomers. A large, nonplanar, conjugated chromophore 9BrH was synthesized based on an adaptation of previous work. 9BrH and its synthetic precursor, pre9BrH, were characterized using X-Ray crystallography. The experimentally determined conformation and bond lengths of 9BrH were compared to previous theoretical studies and confirmed much of what was predicted. The 9BrH chromophore was stockpiled for use in additional studies. Three highly twisted triarylamines were synthesized and investigated for internal charge transfer behavior. Using a large chromophore as one aryl group forced the triarylamines into twisted, propeller-like conformations. The chromophore anthracene was utilized to induce the twist in the triarylamines 9DAAA and 910BAA. The previously synthesized 9BrH was utilized to induce a twisted conformation for the triarylamine 9DAAH. Theoretical predictions indicated that electron density should be delocalized in the ground state and localized on the large chromophore in the excited state, behavior consistent with molecular internal charge transfer. 9DAAA and 910BAA were characterized by X-Ray crystallography which confirmed the desired twisted conformation of the triarylamines in the solid state. UV-Vis absorption spectra for all three triarylamines had long wavelength, broad absorption peaks characteristic of internal charge transfer. Solution fluorescence of each triarylamine demonstrated a large dependence on the surrounding environment; when solvent polarity was

  4. Investigation of potential molecular biomarkers and small molecule drugs for hepatocellular carcinoma transformed from cirrhosis

    PubMed Central

    XIE, FENG; ZHU, FANG; LU, ZAIMING; LIU, ZHENGRONG; WANG, HONGYAN

    2016-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China and the third leading cause of cancer-associated morality. The aim of the present study was to investigate and analyze differentially-expressed genes (DEGs) between cirrhosis and HCC, in order to screen the key genes involved in the transformation from cirrhosis to HCC and provide novel targets for the diagnosis and treatment of HCC in patients with cirrhosis. The gene expression profile, GSE17548, was obtained from Gene Expression Omnibus database and the DEGs were identified by LIMMA package in R language. Kyoto Encyclopedia of Genes and Genomes and gene ontology biology process analysis were performed for the DEGs. Differential co-expression network (DEN) analysis was conducted and the network was visualized using Cytoscape. Small molecule drugs were also screened from the Comparative Toxicogenomics Database for higher degree DEGs. A total of 95 DEGs were obtained, including 46 upregulated and 49 downregulated genes. The upregulated DEGs were primarily involved in biological processes and pathways associated with the cell cycle, while the downregulated DEGs were primarily involved in immune-associated biological processes. A total of 22 key DEGs were identified by DEN analysis, which distinguished HCC from cirrhosis samples. Furthermore, estradiol, benzo(a)pyrene, acetaminophen, copper sulfate and bisphenol A were identified as the five most associated chemicals to these 22 DEGs. In conclusion, the hub genes and chemicals identified by the present study may provide a theoretical basis for additional research on diagnosis and treatment of HCC transformed from cirrhosis. PMID:27347171

  5. Two-dimensional deformation potential model of mobility in small molecule organic semiconductors

    NASA Astrophysics Data System (ADS)

    Northrup, J. E.

    2011-08-01

    An acoustic deformation potential model appropriate for transport in two dimensions is employed to estimate upper limits on the intrinsic hole mobility of DNTT-C10 [2,9-dialkyl-dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene] and BTBT-C12 [2,7-dialkyl[1]benzo-thieno[3,2-b][1]benzothiophene]. First-principles calculations are employed to determine the values of effective masses, deformation potentials, and elastic constants entering the model. The analysis suggests that the upper limit on room temperature mobility within a single crystalline region in DNTT-C10 or BTBT-C12 may be some tens of cm2/Vs. The width of the π-bonded molecular core in the direction perpendicular to the transport plane is identified as a structural feature affecting mobility in two-dimensional organic semiconductors.

  6. Ion/molecule reactions of arsenic and phosphorus cluster ions: Ionization potentials and novel reaction pathways

    SciTech Connect

    Zimmerman, J.A.; Bach, S.B.H.; Watson, C.H.; Eyler, J.R. )

    1991-01-10

    Ionization potentials (IP's) for arsenic and phosphorus clusters (As{sub n}, n = 1-5; P{sub n}, n = 1-4) have been determined by gas-phase charge-transfer reactions. Arsenic and phosphorus cluster ions were generated by pulsed CO{sub 2} laser desorption from GaAs and InP substrates, mass-selected, thermalized, and allowed to react with compounds of known ionization potential in a Fourier transform ion cyclotron resonance mass spectrometer. The IP's for As{sub 3} and As{sub 5} previously unreported, as well as more accurate IP values for several of the other clusters, have been determined. Products and rate coefficients of some interesting reactions of the cluster ions with the charge-transfer agents are also reported.

  7. 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

  8. Analytical potential energy function for the Van der Waals molecule He 2Ne +

    NASA Astrophysics Data System (ADS)

    Huang, Z.; Zhu, Z. H.

    1998-01-01

    A potential energy function has been derived for the two linear isomer structures He 2Ne +(X 2Σ +) using ab initio calculations with the {QCISD(T)}/{6-31++ G(d,p)} method. Because we use the reasonable dissociation limit (3) instead of the unacceptable one (1), our potential energy function represents considerable topographical features in detail, including the linear [HeNe +He] structure ( R HeNe = 1.4694 Å, R He'Ne = 2.0069 Å ∠HeNeHe = 180°) with two symmetric linear saddles ( R HeNe = R He'Ne = 1.80 Å, ∠HeNeHe = 180° and R HeNe = 1.5 Å, R He'Ne = 3.2 A°, ∠HeNeHe = 180°), and the topographical minimum of the [HeHeNe +] structure ( R HeHe = 2.2217 Å, R HeNe = 1.4426 Å, ∠HeHeNe = 180°), with a linear saddle ( R HeHe' = 3.0 Å, R HeNe = 1.8 Å, ∠HeHeNe = 180°).

  9. Small-molecule PARP modulators--current status and future therapeutic potential.

    PubMed

    Penning, Thomas D

    2010-09-01

    PARP-1 inhibitors have emerged as a promising therapeutic class of compounds, and numerous PARP inhibitors, including iniparib (BiPar Sciences Inc/sanofi-aventis), olaparib (AstraZeneca plc), veliparib (Abbott Laboratories), PF-1367338 (Pfizer Inc), MK-4827 (Merck & Co Inc) and CEP-9722 (Cephalon Inc), have advanced into clinical trials. Several additional inhibitors are expected to enter clinical trials within the next year. Early investigations with PARP-1 inhibitors involved non-oncological indications, but development has since progressed to focus primarily on oncology, for use both as single chemotherapeutic agents in specific patient populations (eg, BRCA-deficient) and as combination therapies with various chemotherapeutics. This review focuses on new developments in lead clinical PARP inhibitors, recent disclosures of new inhibitors and the potential use of PARP-1 inhibitors in new disease settings.

  10. Molecular Dynamics simulations of Inhibitor of Apoptosis Proteins and identification of potential small molecule inhibitors.

    PubMed

    Jayakumar, Jayanthi; Anishetty, Sharmila

    2014-05-01

    Chemotherapeutic resistance due to over expression of Inhibitor of Apoptosis Proteins (IAPs) XIAP, survivin and livin has been observed in various cancers. In the current study, Molecular Dynamics (MD) simulations were carried out for all three IAPs and a common ligand binding scaffold was identified. Further, a novel sequence based motif specific to these IAPs was designed. SMAC is an endogenous inhibitor of IAPs. Screening of ChemBank for compounds similar to lead SMAC-non-peptidomimetics yielded a cemadotin related compound NCIMech_000654. Cemadotin is a derivative of natural anti-tumor peptide dolastatin-15; hence these compounds were docked against all three IAPs. Based on our analysis, we propose that NCIMech_000654/dolastatin-15/cemadotin derivatives may be investigated for their potential in inhibiting XIAP, survivin and livin.

  11. 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.

  12. 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.

  13. Hybrid molecules of carvacrol and benzoyl urea/thiourea with potential applications in agriculture and medicine.

    PubMed

    Pete, Umesh D; Zade, Chetan M; Bhosale, Jitendra D; Tupe, Santosh G; Chaudhary, Preeti M; Dikundwar, Amol G; Bendre, Ratnamala S

    2012-09-01

    Benzoyl phenyl urea, a class of insect growth regulator's acts by inhibiting chitin synthesis. Carvacrol, a naturally occurring monoterpenoid is an effective antifungal agent. We have structurally modified carvacrol (2-methyl-5-[1-methylethyl] phenol) by introducing benzoylphenyl urea linkage. Two series of benzoylcarvacryl thiourea (BCTU, 4a-f) and benzoylcarvacryl urea (BCU, 5a-f) derivatives were prepared and characterized by elemental analysis, IR, (1)H and (13)C NMR and Mass spectroscopy. Derivatives 4b, 4d, 4e, 4f and 5d, 5f showed comparable insecticidal activity with the standard BPU lufenuron against Dysdercus koenigii. BCTU derivatives 4c, 4e and BCU 5c showed good antifungal activity against phytopathogenic fungi viz. Magnaporthe grisae, Fusarium oxysporum, Dreschlera oryzae; food spoilage yeasts viz. Debaromyces hansenii, Pichia membranifaciens; and human pathogens viz. Candida albicans and Cryptococcus neoformans. Compounds 5d, 5e and 5f showed potent activity against human pathogens. Moderate and selective activity was observed for other compounds. All the synthesized compounds were non-haemolytic. These compounds have potential application in agriculture and medicine. PMID:22850211

  14. Idalopirdine - a small molecule antagonist of 5-HT6 with therapeutic potential against obesity.

    PubMed

    Dudek, Magdalena; Marcinkowska, Monika; Bucki, Adam; Olczyk, Adrian; Kołaczkowski, Marcin

    2015-12-01

    5HT6 receptor antagonists offer the potential for safe and effective drugs against obesity, because they can reduce weight without causing serious side effects in the cardiovascular system. Also, their anorexic effect is associated with reduced food intake via an enhancement of satiety. In the present study we investigated the anorexic effect of idalopirdine (LuAE58054) in a model of obesity induced by high-fat diet. To induce obesity in rats, the animals were treated with feed with a fat content of 40 %. Body weight was controlled and the amount of food and water consumed was determined. The influence of the test compound on the lipid profile and glucose level was measured, as well as locomotor activity in home cages on the 20th day of the treatment. LuAE58054, at 5 mg kg(-1)/day i.p., was significantly anorectic in this model of obesity. Animals treated with LuAE58054 weighed 8 and 9.2 % less than the control obese animals on the 12th and 21st days, respectively. It significantly reduced food intake and the amount of peritoneal fat in animals, and reduced the level of triglycerides in plasma. LuAE58054 did not have a statistically significant effect on the spontaneous activity of diet-induced obese rats. The present study clearly demonstrates the effectiveness of LuAE58054 in reducing body weight. This compound is in phase III of clinical trials for the treatment of cognitive deficits associated with Alzheimer's disease and schizophrenia. It is a 5HT6 receptor antagonist and is, therefore, free of those unacceptable side effects that preclude chronic use of anti-obesity drugs with other mechanisms of action. The search for an effective and safe anti-obesity drug is essential for an increasingly obese population; therefore, the anorectic action of LuAE58054 is important and there is a need for more research in this direction. PMID:26419385

  15. Idalopirdine - a small molecule antagonist of 5-HT6 with therapeutic potential against obesity.

    PubMed

    Dudek, Magdalena; Marcinkowska, Monika; Bucki, Adam; Olczyk, Adrian; Kołaczkowski, Marcin

    2015-12-01

    5HT6 receptor antagonists offer the potential for safe and effective drugs against obesity, because they can reduce weight without causing serious side effects in the cardiovascular system. Also, their anorexic effect is associated with reduced food intake via an enhancement of satiety. In the present study we investigated the anorexic effect of idalopirdine (LuAE58054) in a model of obesity induced by high-fat diet. To induce obesity in rats, the animals were treated with feed with a fat content of 40 %. Body weight was controlled and the amount of food and water consumed was determined. The influence of the test compound on the lipid profile and glucose level was measured, as well as locomotor activity in home cages on the 20th day of the treatment. LuAE58054, at 5 mg kg(-1)/day i.p., was significantly anorectic in this model of obesity. Animals treated with LuAE58054 weighed 8 and 9.2 % less than the control obese animals on the 12th and 21st days, respectively. It significantly reduced food intake and the amount of peritoneal fat in animals, and reduced the level of triglycerides in plasma. LuAE58054 did not have a statistically significant effect on the spontaneous activity of diet-induced obese rats. The present study clearly demonstrates the effectiveness of LuAE58054 in reducing body weight. This compound is in phase III of clinical trials for the treatment of cognitive deficits associated with Alzheimer's disease and schizophrenia. It is a 5HT6 receptor antagonist and is, therefore, free of those unacceptable side effects that preclude chronic use of anti-obesity drugs with other mechanisms of action. The search for an effective and safe anti-obesity drug is essential for an increasingly obese population; therefore, the anorectic action of LuAE58054 is important and there is a need for more research in this direction.

  16. Potential siRNA Molecules for Nucleoprotein and M2/L Overlapping Region of Respiratory Syncytial Virus: In Silico Design

    PubMed Central

    Shatizadeh Malekshahi, Somayeh; Arefian, Ehsan; Salimi, Vahid; Mokhtari Azad, Talat; Yavarian, Jila

    2016-01-01

    Background Human respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in the pediatric population, elderly and in immunosuppressed individuals. Respiratory syncytial virus is also responsible for bronchiolitis, pneumonia, and chronic obstructive pulmonary infections in all age groups. With this high disease burden and the lack of an effective RSV treatment and vaccine, there is a clear need for discovery and development of novel, effective and safe drugs to prevent and treat RSV disease. The most innovative approach is the use of small interfering RNAs (siRNAs) which represent a revolutionary new concept in human therapeutics. The nucleoprotein gene of RSV which is known as the most conserved gene and the M2/L mRNA, which encompass sixty-eight overlapping nucleotides, were selected as suitable targets for siRNA design. Objectives The present study is aimed to design potential siRNAs for silencing nucleoprotein and an overlapping region of M2-L coding mRNAs by computational analysis. Materials and Methods Various computational methods (target alignment, similarity search, secondary structure prediction, and RNA interaction calculation) have been used for siRNA designing against different strains of RSV. Results In this study, seven siRNA molecules were rationally designed against the nucleoprotein gene and validated using various computational methods for silencing different strains of RSV. Additionally, three effective siRNA molecules targeting the overlapping region of M2/L mRNA were designed. Conclusions This approach provides insight and a validated strategy for chemical synthesis of an antiviral RNA molecule which meets many sequence features for efficient silencing and treatment at the genomic level. PMID:27303618

  17. 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. PMID:24469079

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

    PubMed Central

    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. PMID:26243592

  19. 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.

  20. A brief update on potential molecular mechanisms underlying antimicrobial and wound-healing potency of snake venom molecules.

    PubMed

    Samy, Ramar Perumal; Sethi, Gautam; Lim, Lina H K

    2016-09-01

    Infectious diseases remain a significant cause of morbidity and mortality worldwide. A wide range of diverse, novel classes of natural antibiotics have been isolated from different snake species in the recent past. Snake venoms contain diverse groups of proteins with potent antibacterial activity against a wide range of human pathogens. Some snake venom molecules are pharmacologically attractive, as they possess promising broad-spectrum antibacterial activities. Furthermore, snake venom proteins (SVPs)/peptides also bind to integrins with high affinity, thereby inhibiting cell adhesion and accelerating wound healing in animal models. Thus, SVPs are a potential alternative to chemical antibiotics. The mode of action for many antibacterial peptides involves pore formation and disruption of the plasma membrane. This activity often includes modulation of nuclear factor kappa B (NF-κB) activation during skin wound healing. The NF-κB pathway negatively regulates the transforming growth factor (TGF)-β1/Smad pathway by inducing the expression of Smad7 and eventually reducing in vivo collagen production at the wound sites. In this context, SVPs that regulate the NF-κB signaling pathway may serve as potential targets for drug development. PMID:26975619

  1. Non-adiabatic effects within a single thermally averaged potential energy surface: thermal expansion and reaction rates of small molecules.

    PubMed

    Alonso, J L; Castro, A; Clemente-Gallardo, J; Echenique, P; Mazo, J J; Polo, V; Rubio, A; Zueco, D

    2012-12-14

    At non-zero temperature and when a system has low-lying excited electronic states, the ground-state Born-Oppenheimer approximation breaks down and the low-lying electronic states are involved in any chemical process. In this work, we use a temperature-dependent effective potential for the nuclei which can accommodate the influence of an arbitrary number of electronic states in a simple way, while at the same time producing the correct Boltzmann equilibrium distribution for the electronic part. With the help of this effective potential, we show that thermally activated low-lying electronic states can have a significant effect in molecular properties for which electronic excitations are oftentimes ignored. We study the thermal expansion of the Manganese dimer, Mn(2), where we find that the average bond length experiences a change larger than the present experimental accuracy upon the inclusion of the excited states into the picture. We also show that, when these states are taken into account, reaction-rate constants are modified. In particular, we study the opening of the ozone molecule, O(3), and show that in this case the rate is modified as much as a 20% with respect to the ground-state Born-Oppenheimer prediction.

  2. Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1

    PubMed Central

    Ferguson, Paul P.; Holloway, W. Blake; Setzer, William N.; McFeeters, Hana; McFeeters, Robert L.

    2016-01-01

    Peptidyl-tRNA hydrolases (Pths) play ancillary yet essential roles in protein biosynthesis by recycling peptidyl-tRNA. In E. coli, inhibition of bacterial Pth1 leads to accumulation of peptidyl-tRNA, depletion of aminoacyl-tRNA, and cell death. Eukaryotes have multiple Pths and Pth1 knock out was shown to have no effect on viability in yeast. Thereby, bacterial Pth1 is a promising target for novel antibiotic development. With the abundance of Pth1 structural data, molecular docking was used for virtual screening of existing, commercially available antibiotics to map potential interactions with Pth enzymes. Overall, 83 compounds were docked to eight different bacterial Pth1 and three different Pth2 structures. A variety of compounds demonstrated favorable docking with Pths. Whereas, some compounds interacted favorably with all Pths (potential broad spectrum inhibition), more selective interactions were observed for Pth1 or Pth2 and even specificity for individual Pth1s. While the correlation between computational docking and experimentation still remains unknown, these findings support broad spectrum inhibition, but also point to the possibility of narrow spectrum Pth1 inhibition. Also suggested is that Pth1 can be distinguished from Pth2 by small molecule inhibitors. The findings support continued development of Pth1 as an antibiotic target. PMID:27171117

  3. Basic Fibroblast Growth Factor (bFGF, FGF-2) Potentiates Leukocyte Recruitment to Inflammation by Enhancing Endothelial Adhesion Molecule Expression

    PubMed Central

    Zittermann, Sandra I.; Issekutz, Andrew C.

    2006-01-01

    Basic fibroblast growth factor (bFGF, FGF-2) is a potent angiogenic factor and endothelial cell mitogen. Although bFGF levels are increased in chronically inflamed tissue, its role in inflammation is unclear. We investigated the effect of bFGF on acute dermal inflammation and the recruitment of monocytes, T cells, and neutrophils. Leukocyte recruitment to inflamed sites was quantified with radiolabeled leukocytes. Intradermal injection of bFGF in rats did not induce leukocyte recruitment or inflammation. However, the recruitment of leukocytes to inflammation induced by tumor necrosis factor-α, interferon-γ, C5a, or a delayed hypersensitivity reaction was enhanced by bFGF by 55 to 132% (P < 0.05). Either acute or prolonged bFGF treatment of dermal sites had this effect. The potentiating effect of bFGF on leukocyte recruitment was also seen in joints. There was no associated modulation of vascular permeability, blood flow, or angiogenesis in the sites by bFGF. However, the expression of the endothelial cell adhesion molecules (CAMs) for leukocytes, P-selectin, E-selectin, and ICAM-1, was significantly up-regulated in the inflamed tissue by bFGF, as quantified by radiolabeled anti-CAM antibody binding in vivo. Thus, although not directly proinflammatory, bFGF synergistically potentiates inflammatory mediator-induced leukocyte recruitment, at least in part, by enhancing CAM up-regulation on endothelium. PMID:16507899

  4. Antitumor potential of a synthetic interferon-alpha/PLGF-2 positive charge peptide hybrid molecule in pancreatic cancer cells

    PubMed Central

    Yin, Hongmei; Chen, Naifei; Guo, Rui; Wang, Hong; Li, Wei; Wang, Guanjun; Cui, Jiuwei; Jin, Haofan; Hu, Ji-Fan

    2015-01-01

    Pancreatic cancer is the most aggressive malignant disease, ranking as the fourth leading cause of cancer-related death among men and women in the United States. Interferon alpha (IFNα) has been used to treat pancreatic cancer, but its clinical application has been significantly hindered due to the low antitumor activity. We used a “cDNA in-frame fragment library” screening approach to identify short peptides that potentiate the antitumor activity of interferons. A short positively charged peptide derived from the C-terminus of placental growth factor-2 (PLGF-2) was selected to enhance the activity of IFNα. For this, we constructed a synthetic interferon hybrid molecule (SIFα) by fusing the positively charged PLGF-2 peptide to the C-terminus of the human IFNα. Using human pancreatic cell lines (ASPC and CFPAC1) as a model system, we found that SIFα exhibited a significantly higher activity than did the wild-type IFNα in inhibiting the tumor cell growth. The enhanced activity of the synthetic SIFα was associated with the activation of interferon pathway target genes and the increased binding of cell membrane receptor. This study demonstrates the potential of a synthetic SIFα as a novel antitumor agent. PMID:26584517

  5. 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.

  6. Calculation of rotation-vibration energy levels of the ammonia molecule based on an ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Polyansky, Oleg L.; Ovsyannikov, Roman I.; Kyuberis, Aleksandra A.; Lodi, Lorenzo; Tennyson, Jonathan; Yachmenev, Andrey; Yurchenko, Sergei N.; Zobov, Nikolai F.

    2016-09-01

    An ab initio potential energy surface (PES) for gas-phase ammonia NH3 has been computed using the methodology pioneered for water (Polyansky et al., 2013). Multireference configuration interaction calculations are performed at about 50 000 points using the aug-cc-pCVQZ and aug-cc-pCV5Z basis sets and basis set extrapolation. Relativistic and adiabatic surfaces are also computed. The points are fitted to a suitable analytical form, producing the most accurate ab initio PES for this molecule available. The rotation-vibration energy levels are computed using nuclear motion program TROVE in both linearised and curvilinear coordinates. Better convergence is obtained using curvilinear coordinates. Our results are used to assign the visible spectrum of 14NH3 recorded by Coy and Lehmann (1986). Rotation-vibration energy levels for the isotopologues NH2D, NHD2, ND3 and 15NH3 are also given. An ab initio value for the dissociation energy D0 of 14NH3 is also presented.

  7. Neurotrophic signaling molecules associated with cholinergic damage in young and aged rats: environmental enrichment as potential therapeutic agent.

    PubMed

    Paban, Véronique; Chambon, Caroline; Manrique, Christine; Touzet, Claude; Alescio-Lautier, Béatrice

    2011-03-01

    The aim of this study was to determine the neurobiological bases of behavioral deficits associated with cholinergic damage and the potential of long-term environmental enrichment as a therapeutic agent. Rats were submitted to intra-structures injection of 192 IgG-saporin and then behaviorally tested 1 month and 1 year post-lesion in a nonmatching-to-position task. The gene expression changes were assessed by cDNA macroarray technology using the GE array Q series designed to profile the expression of neurotrophic signaling molecules. Results showed that (1) cholinergic injury modulated the expression of genes such as brain-derived neurotrophin factor but also genes associated with inflammatory response, neuron apoptosis, regulation of angiogenesis, and synaptic plasticity, (2) aging is associated with regulation of glial proliferation and apoptosis, and (3) long-term enriched environment housing enhanced behavioral performance in lesioned and non-lesioned rats and upregulated gene expression. This therapeutic role of the enriched environment seemed to be associated with a suppression of expression of genes involved in apoptosis, glial cell differentiation, and cell cycle, but also with an enhanced expression of a subset of genes involved in signal transduction. PMID:19398249

  8. N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP): Potential target molecule in research of heart, kidney and brain.

    PubMed

    Hrenak, Jaroslav; Paulis, Ludovit; Simko, Fedor

    2015-01-01

    N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) is a ubiquitous molecule generated in all mammalian tissues from the N-terminal sequence of thymosin β4 (Tβ4) by the action of propyl oligopeptidase. Ac-SDKP is an alternative substrate for angiotensin converting enzyme (ACE). There are several indications that Ac-SDKP may be protective in the cardiovascular system. First, the level of Ac- SDKP in plasma and tissues is reduced in some cardiovascular pathologies such as hypertension. Second, an administration of Ac-SDKP to rodents attenuates inflammation, cell differentiation, proliferation, and migration resulting in a reduction of fibrosis in the heart, vessels and kidneys in conditions of their disorders. Third, the treatment with ACE-inhibitors is associated with a reduced degradation and hence increased levels of Ac-SDKP, while a simultaneous treatment with monoclonal antibodies against Ac- SDKP partly counteracts the benefit of ACE-inhibition. Since Ac-SDKP fails to reduce blood pressure and left ventricular hypertrophy (LVH), its potential structural benefit is obviously mediated by direct action on tissue in preventing or reversing excessive fibrosis. The protection by ACE-inhibition seems to be partly mediated by increased availability of Ac-SDKP. Thus, it is to suppose that harvesting the knowledge on the role of Ac-SDKP in cardiovascular physiology and pathology could deepen our insight into the mechanisms of action of the renin-angiotensin system (RAS) as well as agents interfering with this system. The exciting protective potential of Ac-SDKP suggests that this compound could be a focused drug target not only in animal experiments but also in the clinical cardio-pharmacologic research in the near future.

  9. Formal redox potentials of organic molecules in ionic liquids on the basis of quaternary nitrogen cations as adiabatic electron affinities.

    PubMed

    Seto, Kunimasa; Nakayama, Tatsushi; Uno, Bunji

    2013-09-19

    Formal redox potentials E°' involving neutral species R and radical anions R(•-) in ionic liquids (ILs) composed of ammonium, pyridinium, and imidazolium cations are discussed from the point of view of the adiabatic electron affinity as a molecular property. The dependence of the 1,4-benzoquinone (BQ)/BQ(•-) redox process in CH2Cl2 and CH3CN is primarily investigated over a wide concentration range of ILs as the supporting electrolyte. A logarithmic relationship involving a positive shift of E°' with increasing concentration is obtained when the concentration is changed from 0.01 to 1.0 M. The relationship of E°' at IL concentrations greater than 1.0 M gradually reaches a plateau and remains there even for the neat ILs. It is found that the E°' values in the neat ILs are not influenced by the measurement conditions, and that they remain considerably dependent on the nature and concentration of the electrolyte when measured using the traditional method involving molecular solvents combined with a supporting electrolyte (0.1-0.5 M). The difference in the E°' values observed in the ammonium and pyridinium ILs is only several millivolts. In addition, ESR and self-consistent isodensity polarized continuum model calculation results reveal that the potential shift toward positive values upon the transition from molecular solvents containing ILs to neat ILs is adequately accounted for by changes in the electrostatic interaction of R(•-) taken into the cavity composed of the solvent and IL. On the other hand, the first reduction waves of quinones, electron-accepting molecules, and polynuclear aromatic hydrocarbons are reversibly or quasi-reversibly observed in the ILs. The electrochemical stability of the ILs is exploited in the facile measurement of these quasi-reversible waves at quite negative potentials, such as for the naphthalene (NP)/NP(•-) couple. Notably, the E°' values obtained in the ammonium ILs correlate well with the calculated standard redox

  10. Formal redox potentials of organic molecules in ionic liquids on the basis of quaternary nitrogen cations as adiabatic electron affinities.

    PubMed

    Seto, Kunimasa; Nakayama, Tatsushi; Uno, Bunji

    2013-09-19

    Formal redox potentials E°' involving neutral species R and radical anions R(•-) in ionic liquids (ILs) composed of ammonium, pyridinium, and imidazolium cations are discussed from the point of view of the adiabatic electron affinity as a molecular property. The dependence of the 1,4-benzoquinone (BQ)/BQ(•-) redox process in CH2Cl2 and CH3CN is primarily investigated over a wide concentration range of ILs as the supporting electrolyte. A logarithmic relationship involving a positive shift of E°' with increasing concentration is obtained when the concentration is changed from 0.01 to 1.0 M. The relationship of E°' at IL concentrations greater than 1.0 M gradually reaches a plateau and remains there even for the neat ILs. It is found that the E°' values in the neat ILs are not influenced by the measurement conditions, and that they remain considerably dependent on the nature and concentration of the electrolyte when measured using the traditional method involving molecular solvents combined with a supporting electrolyte (0.1-0.5 M). The difference in the E°' values observed in the ammonium and pyridinium ILs is only several millivolts. In addition, ESR and self-consistent isodensity polarized continuum model calculation results reveal that the potential shift toward positive values upon the transition from molecular solvents containing ILs to neat ILs is adequately accounted for by changes in the electrostatic interaction of R(•-) taken into the cavity composed of the solvent and IL. On the other hand, the first reduction waves of quinones, electron-accepting molecules, and polynuclear aromatic hydrocarbons are reversibly or quasi-reversibly observed in the ILs. The electrochemical stability of the ILs is exploited in the facile measurement of these quasi-reversible waves at quite negative potentials, such as for the naphthalene (NP)/NP(•-) couple. Notably, the E°' values obtained in the ammonium ILs correlate well with the calculated standard redox

  11. Rotational spectrum of 4-methylcyanoallene (CH3CH=C=CH-CN), a chiral molecule of potential astrochemical interest

    NASA Astrophysics Data System (ADS)

    Carles, S.; Møllendal, H.; Trolez, Y.; Guillemin, J.-C.

    2014-04-01

    Context. A successful identification of an interstellar compound requires that its spectrum has first been assigned in the laboratory. New and sensitive radiotelescopes, such as ALMA, will make it possible to detect interstellar molecules in much smaller concentrations than before. Cyanoallene (CH2=C=CH-CN) has recently been observed in the dense molecular cloud TMC-1 by means of its rotational spectrum. Its methyl congener, 4-methylcyanoallene (CH3CH=C=CH-CN), may also be present in the interstellar medium (ISM). This chiral compound exists in two forms, which are mirror images. Chirality is an essential feature of life. So far, no chiral compounds have been detected in the ISM. Aims: The synthesis and assignment of the rotational spectrum of CH3CH=C=CH-CN, will facilitate the potential detection of this compound in the ISM. Methods: The spectrum of 4-methylcyanoallene has been recorded between 13 and 116 GHz using the microwave spectrometer at the University of Oslo. The spectroscopic study has been augmented with high-level quantum chemical calculations at the B3LYP/cc-pVTZ and CCSD/cc-pVTZ levels of theory. Results: The rotational spectra of CH3CH=C=CH-CN in the ground vibrational state and in the first vibrationally excited state are reported for the first time and accurate spectroscopic constants have been obtained from a large number of transitions. Full Tables 3 and 4 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/564/A82

  12. Adhesion molecule expression in Graves' thyroid glands; potential relevance of granule membrane protein (GMP-140) and intercellular adhesion molecule-1 (ICAM-1) in the homing and antigen presentation processes.

    PubMed Central

    Miyazaki, A; Mirakian, R; Bottazzo, G F

    1992-01-01

    To assess the potential role of adhesion molecules in the pathogenesis of Graves' disease, we examined the expression of several of these adhesion molecules, including intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule (VCAM-1) and granule membrane protein-140 (GMP-140), in sections of Graves' thyroid glands and control thyroids, using immunohistochemical techniques. Up-regulated expression of GMP-140 was frequently observed on endothelial cells (EC) of post-capilliary venules in all Graves' thyroids examined, compared with an occasional weak staining on EC control glands. Some capillary EC around thyroid follicles (perifollicular EC) were strongly positive for GMP-140 in the Graves' thyroids in contrast to a negative staining on the same structures in the control glands. In addition, there was a correlation between the reactivity and frequency of GMP-140 expression on EC and the severity of mononuclear cell (MNC) infiltration in the Graves' thyroids. The expression of ICAM-1 was up-regulated on perifollicular EC and EC of small venules in some thyroids of both Graves' and control groups. Conversely, no significant expression was observed on any type of EC for both endothelial-leucocyte adhesion molecule-1 (ELAM-1) and VCAM-1. However, dendritic-like cells, present within lymphocytic infiltrates, were positive for VCAM-1 in most of the Graves' thyroids examined, especially in those with a severe lymphocytic infiltration. Thyrocytes were constantly negative for the expression of all four adhesion molecules investigated. These data suggest that GMP-140, as well as ICAM-1, could play an important role in the initiation of MNC infiltration in Graves' disease. ELAM-1 and VCAM-1 appear not to be relevant for the migration of MNC from the blood vessels into the target gland, although VCAM-1 expression on dendritic-like cells might play an additively tissue-selective role in autoantigen presentation and subsequent elicitation of autoimmune

  13. 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.

  14. ATOMIC AND MOLECULAR PHYSICS: High order correlation-polarization potential for vibrational excitation scattering of diatomic molecules by low-energy electrons

    NASA Astrophysics Data System (ADS)

    Feng, Hao; Sun, Wei-Guo; Zeng, Yang-Yang

    2009-11-01

    This paper introduces a correlation-polarization potential with high order terms for vibrational excitation in electron-molecule scattering. The new polarization potential generalizes the two-term approximation so that it can better reflect the dependence of correlation and polarization effects on the position coordinate of the scattering electron. It applies the new potential on the vibrational excitation scattering from N2 in an energy range which includes the 2Πg shape resonance. The good agreement of theoretical resonant peaks with experiments shows that polarization potentials with high order terms are important and should be included in vibrational excitation scattering.

  15. Reactions of oxygen-containing molecules on transition metal carbides: Surface science insight into potential applications in catalysis and electrocatalysis

    NASA Astrophysics Data System (ADS)

    Stottlemyer, Alan L.; Kelly, Thomas G.; Meng, Qinghe; Chen, Jingguang G.

    2012-09-01

    Historically the interest in the catalytic properties of transition metal carbides (TMC) has been inspired by their "Pt-like" properties in the transformation reactions of hydrocarbon molecules. Recent studies, however, have revealed that the reaction pathways of oxygen-containing molecules are significantly different between TMCs and Pt-group metals. Nonetheless, TMCs demonstrate intriguing catalytic properties toward oxygen-containing molecules, either as the catalyst or as the catalytically active substrate to support metal catalysts, in several important catalytic and electrocatalytic applications, including water electrolysis, alcohol electrooxidation, biomass conversion, and water gas shift reactions. In the current review we provide a summary of theoretical and experimental studies of the interaction of TMC surfaces with oxygen-containing molecules, including both inorganic (O2, H2O, CO and CO2) and organic (alcohols, aldehydes, acids and esters) molecules. We will discuss the general trends in the reaction pathways, as well as future research opportunities in surface science studies that would facilitate the utilization of TMCs as catalysts and electrocatalysts.

  16. Reactions of oxygen-containing molecules on transition metal carbides: Surface science insight into potential applications in catalysis and electrocatalysis

    NASA Astrophysics Data System (ADS)

    Stottlemyer, Alan L.; Kelly, Thomas G.; Meng, Qinghe; Chen, Jingguang G.

    2012-09-01

    Historically the interest in the catalytic properties of transition metal carbides (TMC) has been inspired by their “Pt-like” properties in the transformation reactions of hydrocarbon molecules. Recent studies, however, have revealed that the reaction pathways of oxygen-containing molecules are significantly different between TMCs and Pt-group metals. Nonetheless, TMCs demonstrate intriguing catalytic properties toward oxygen-containing molecules, either as the catalyst or as the catalytically active substrate to support metal catalysts, in several important catalytic and electrocatalytic applications, including water electrolysis, alcohol electrooxidation, biomass conversion, and water gas shift reactions. In the current review we provide a summary of theoretical and experimental studies of the interaction of TMC surfaces with oxygen-containing molecules, including both inorganic (O2, H2O, CO and CO2) and organic (alcohols, aldehydes, acids and esters) molecules. We will discuss the general trends in the reaction pathways, as well as future research opportunities in surface science studies that would facilitate the utilization of TMCs as catalysts and electrocatalysts.

  17. Slags in a Large Variation Range of Oxygen Potential Based on the Ion and Molecule Coexistence Theory

    NASA Astrophysics Data System (ADS)

    Yang, Xue-Min; Li, Jin-Yan; Zhang, Meng; Chai, Guo-Min; Zhang, Jian

    2014-12-01

    A thermodynamic model for predicting sulfide capacity of CaO-FeO-Fe2O3-Al2O3-P2O5 slags in a large variation range of oxygen potential corresponding to mass percentage of FetO from 1.88 to 55.50 pct, i.e., IMCT- model, has been developed by coupling with the deduced desulfurization mechanism of the slags based on the ion and molecule coexistence theory (IMCT). The developed IMCT- model has been verified through comparing the determined sulfide capacity after Ban-ya et al.[20] with the calculated by the developed IMCT- model and the calculated by the reported sulfide capacity models such as the KTH model. Mass percentage of FetO as 6.75 pct corresponding to the mass action concentration of FetO as 0.0637 or oxygen partial as 2.27 × 10-6 Pa is the criterion for distinguishing reducing and oxidizing zones for the slags. Sulfide capacity of the slags in reducing zone is controlled by reaction ability of CaO regardless of slag oxidization ability. However, sulfide capacity of the slags in oxidizing zone shows an obvious increase tendency with the increasing of slag oxidization ability. Sulfide capacity of the slags in reducing zone keeps almost constant with variation of the simplified complex basicity (pct CaO)/((pct Al2O3) + (pct P2O5)), or optical basicity, or the mass action concentration ratios of N FeO/ N CaO, , , and . Sulfide capacity of the slags in oxidizing zone shows an obvious increase with the increasing of the simplified complex basicity (pct CaO)/((pct Al2O3) + (pct P2O5)) or optical basicity, or the aforementioned mass action concentration ratios. Thus, the aforementioned mass action concentration ratios and the corresponding mass percentage ratios of various iron oxides to basic oxide CaO are recommended to represent the comprehensive effect of various iron oxides and basic oxide CaO on sulfide capacity of the slags.

  18. Cell-based high-throughput screening identifies galactocerebrosidase enhancers as potential small-molecule therapies for Krabbe's disease.

    PubMed

    Jang, Dae Song; Ye, Wenjuan; Guimei, Tian; Solomon, Melani; Southall, Noel; Hu, Xin; Marugan, Juan; Ferrer, Marc; Maegawa, Gustavo H B

    2016-11-01

    Krabbe's disease, also known as globoid cell leukodystrophy (GLD), is a lysosomal storage disease caused by the deficiency of the lysosomal enzyme β-galactocerebrosidase (GALC), resulting in severe neurological manifestations related to demyelination secondary to elevated galactosylsphingosine (psychosine) with its subsequent cytotoxicity. The only available treatment is hematopoietic stem cell transplantation, which delays disease onset but does not prevent long-term neurological manifestations. This article describes the identification of small molecules that enhance mutant GALC activity, identified by quantitative cell-based high-throughput screening (qHTS). Using a specific neurologically relevant murine cell line (145M-Twi) modified to express common human hGALC-G270D mutant, we were able to detect GALC activity in a 1,536-well microplate format. The qHTS of approximately 46,000 compounds identified three small molecules that showed significant enhancements of residual mutant GALC activity in primary cell lines from GLD patients. These compounds were shown to increase the levels of GALC-G270D mutant in the lysosomal compartment. In kinetic assessments, these small molecules failed to disturb the GALC kinetic profile under acidic conditions, which is highly desirable for folding-assisting molecules operating in the endoplasmic reticulum and not affecting GALC catalytic properties in the lysosomal compartment. In addition, these small molecules rescued the decreased GALC activity at neutral pH and partially stabilized GALC under heat-denaturating conditions. These drug-like compounds can be used as the starting point to develop novel small-molecule agents to treat the progressive neurodegenerative course of GLD. © 2016 Wiley Periodicals, Inc. PMID:27638606

  19. Far-infrared spectra and ring-puckering potential energy functions of two oxygen-containing ring molecules with unusual bonding interactions

    NASA Astrophysics Data System (ADS)

    Choo, J.; Cortez, E.; Laane, Jaan; Majors, R.; Verastegui, R.; Villareal, Genaro R.

    1994-01-01

    Over the past quarter century we have carried out a large number of studies of the ring- puckering vibrations of small ring-molecules. The far-infrared and Raman spectra of these large amplitude motions have been used to determine the molecular conformation and 1-D potential energy functions. The forces which are usually the principal contributors to the potential functions are the ring-angle strain and torsional forces, which often result when CH2 groups are next to each other. In the present study we have examined the far-infrared and Raman spectra of two oxygen-containing molecules which have turned out to have unusual potential energy functions. 1,3-dioxole and 4H-pyran.

  20. Interactions of Hydrogen Molecules with Halogen-Containing Diatomics from Ab Initio Calculations: Spherical-Harmonics Representation and Characterization of the Intermolecular Potentials.

    PubMed

    Albernaz, Alessandra F; Aquilanti, Vincenzo; Barreto, Patricia R P; Caglioti, Concetta; Cruz, Ana Claudia P S; Grossi, Gaia; Lombardi, Andrea; Palazzetti, Federico

    2016-07-14

    For the prototypical diatomic-molecule-diatomic-molecule interactions H2-HX and H2-X2, where X = F, Cl, Br, quantum-chemical ab initio calculations are carried out on grids of the configuration space, which permit a spherical-harmonics representation of the potential energy surfaces (PESs). Dimer geometries are considered for sets of representative leading configurations, and the PESs are analyzed in terms of isotropic and anisotropic contributions. The leading configurations are individuated by selecting a minimal set of mutual orientations of molecules needed to build the spherical-harmonic expansion on geometrical and symmetry grounds. The terms of the PESs corresponding to repulsive and bonding dimer geometries and the averaged isotropic term, for each pair of interacting molecules, are compared with representations in terms of a potential function proposed by Pirani et al. (see Chem. Phys. Lett. 2004, 394, 37-44 and references therein). Connections of the involved parameters with molecular properties provide insight into the nature of the interactions.

  1. The Yeast Three-Hybrid System as an Experimental Platform to Identify Proteins Interacting with Small Signaling Molecules in Plant Cells: Potential and Limitations

    PubMed Central

    Cottier, Stéphanie; Mönig, Timon; Wang, Zheming; Svoboda, Jiří; Boland, Wilhelm; Kaiser, Markus; Kombrink, Erich

    2011-01-01

    Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time-consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H) technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx). In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA-binding domain (encoded in the yeast strain), and the bioactive molecule part binding to its potential protein target fused to a DNA-activating domain (encoded on a cDNA expression vector). During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discuss the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules. PMID:22639623

  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. 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).

  4. Spectroscopic investigation of the binding interactions of a membrane potential molecule in various supramolecular confined environments: contrasting behavior of surfactant molecules in relocation or release of the probe between nanocarriers and DNA surface.

    PubMed

    Ghosh, Surajit; Banik, Debasis; Roy, Arpita; Kundu, Niloy; Kuchlyan, Jagannath; Sarkar, Nilmoni

    2014-12-01

    The fluorescence and optical properties of membrane potential probes are widely used to measure cellular transmembrane potentials. Hemicyanine dyes are also able to bind to membranes. The spectral properties of these molecules depend upon the charge shift from the donor moiety to the acceptor moiety. Changes in their spectral properties, i.e. absorption and emission maxima or intensities, are helpful in characterizing model membranes, microheterogeneous media, etc. In this article, we have demonstrated the binding interaction of a membrane potential probe, 1-ethyl-2-(4-(p-dimethylaminophenyl)-1,3-butadienyl)-pyridinium perchlorate (LDS 698), with various supramolecular confined environments. The larger dipole moment in the ground state compared to the excited state is a unique feature of hemicyanine dyes. Due to this unique feature, red shifts in the absorption maxima are observed in hydrophobic environments, compared with bulk solvent. On addition of surfactants and CT DNA to an aqueous solution containing LDS 698, significant increase in the emission intensity along with the quantum yield and lifetime indicate partition of the probe molecules into organized assemblies. In the case of the sodium dodecyl sulfate (SDS)-water system, due to interactions between the cationic LDS 698 and the anionic dodecyl sulfate moiety, the fluorescence intensity at ∼666 nm decreases and an additional peak at ∼590 nm appears at premicellar concentration (∼0.20 mM-4.50 mM). But at ∼5.50 mM SDS concentration, the absorbance in the higher wavelength region increases again, indicating encapsulation of the probe in micellar aggregates. This observation indicates that the premicellar aggregation behavior of SDS can also be judged by observing the changes in the UV-vis and fluorescence spectral patterns. The temperature dependent study also indicates that non-radiative deactivation of the dye molecules is highly restricted in the DNA micro-environment, compared with micelles

  5. The determination of potential energy curve and dipole moment of the (5)0+ electronic state of 85Rb133Cs molecule by high resolution photoassociation spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    We present the formation of ultracold 85Rb133Cs molecules in the (5)0+ 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+ 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+ electronic state of 85Rb133Cs 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+ 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.

  6. Qualitative and Quantitative Study of the Potential of Lipid Nanocapsules of One Hundred Twenty Nanometers for the Topical Administration of Hydrophobic Molecules.

    PubMed

    Nguyen, Hoang Truc Phuong; Munnier, Emilie; Perse, Xavier; Vial, Francis; Yvergnaux, Florent; Perrier, Thomas; Soucé, Martin; Chourpa, Igor

    2016-10-01

    In this study, we evaluated the potential of lipid nanocapsules (LNC) of 120 nm as drug nanocarriers to treat skin diseases. As a model molecule, we encapsulated the fluorescent dye curcumin, which also is an antioxidant. Curcumin-loaded LNC showed interesting antioxidant properties and a low toxicity on human skin cells. The penetration of curcumin in the skin was determined by 2 complementary methods: high performance liquid chromatography was used to measure total curcumin accumulation in the skin, whereas fluorescence confocal spectral imaging of skin sections showed that curcumin preferentially accumulates in the stratum corneum and the viable epidermis. These results confirm that LNC of a size above 100 nm can vectorize hydrophobic compounds to the keratinocytes without transdermal delivery. They also demonstrate the interest of combining 2 analytical methods when studying the skin penetration of nanovectorized molecules.

  7. The pharmacology and therapeutic potential of small molecule inhibitors of acid-sensing ion channels in stroke intervention

    PubMed Central

    Leng, Tian-dong; Xiong, Zhi-gang

    2013-01-01

    In the nervous system, a decrease in extracellular pH is a common feature of various physiological and pathological processes, including synaptic transmission, cerebral ischemia, epilepsy, brain trauma, and tissue inflammation. Acid-sensing ion channels (ASICs) are proton-gated cation channels that are distributed throughout the central and peripheral nervous systems. Following the recent identification of ASICs as critical acid-sensing extracellular proton receptors, growing evidence has suggested that the activation of ASICs plays important roles in physiological processes such as nociception, mechanosensation, synaptic plasticity, learning and memory. However, the over-activation of ASICs is also linked to adverse outcomes for certain pathological processes, such as brain ischemia and multiple sclerosis. Based on the well-demonstrated role of ASIC1a activation in acidosis-mediated brain injury, small molecule inhibitors of ASIC1a may represent novel therapeutic agents for the treatment of neurological disorders, such as stroke. PMID:22820909

  8. The hydrogen peroxide-rare gas systems: quantum chemical calculations and hyperspherical harmonic representation of the potential energy surface for atom-floppy molecule interactions.

    PubMed

    Barreto, Patricia R P; Vilela, Alessandra F A; Lombardi, Andrea; Maciel, Glauciete S; Palazzetti, Federico; Aquilanti, Vincenzo

    2007-12-13

    A quantum chemical exploration is reported on the interaction potentials of H2O2 with the rare gases, He, Ne, Ar, Kr, and Xe. Hydrogen peroxide (the simplest example of chiral molecule in its equilibrium geometry) is modeled as rigid except for the torsional mode around the O-O bond. However, on the basis of previous work (Maciel, G. S.; et al. Chem. Phys. Lett. 2006 432, 383), the internal mode description is based, rather than on the vectors of the usual valence picture, on the orthogonal local representation, which was demonstrated useful for molecular dynamics simulations, because the torsion around the vector joining the center-of-mass of the two OH radicals mimics accurately the adiabatic reaction path for chirality changing isomerization, following the torsional potential energy profile from equilibrium through the barriers for the trans and cis geometries. The basic motivation of this work is the determination of potential energy surfaces for the interactions to be used in classical and quantum simulations of molecular collisions, specifically those leading to chirality changes of possible relevance in the modeling of prebiotic phenomena. Particular attention is devoted to the definition of coordinates and expansion formulas for the potentials, allowing for a faithful representation of geometrical and symmetry properties of these systems, prototypical of the interaction of an atom with a floppy molecule.

  9. 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

  10. Electrostatic potential and Born energy of charged molecules interacting with phospholipid membranes: calculation via 3-D numerical solution of the full Poisson equation.

    PubMed

    Schnitzer, J E; Lambrakis, K C

    1991-09-21

    Understanding the physicochemical basis of the interaction of molecules with lipid bilayers is fundamental to membrane biology. In this study, a new, three-dimensional numerical solution of the full Poisson equation including local dielectric variation is developed using finite difference techniques in order to model electrostatic interactions of charged molecules with a non-uniform dielectric. This solution is used to describe the electric field and electrostatic potential profile of a charged molecule interacting with a phospholipid bilayer in a manner consistent with the known composition and structure of the membrane. Furthermore, the Born interaction energy is then calculated by appropriate integration of the electric field over whole space. Numerical computations indicate that the electrostatic potential profile surrounding a charge molecule and its resultant Born interaction energy are a function of molecular position within the membrane and change most significantly within the polar region of the bilayer. The maximum interaction energy is observed when the charge is placed at the center of the hydrophobic core of the membrane and is strongly dependent on the size of the charge and on the thickness of the hydrocarbon core of the bilayer. The numerical results of this continuum model are compared with various analytical approximations for the Born energy including models established for discontinuous slab dielectrics. The calculated energies agree with the well-known Born analytical expression only when the charge is located near the center of a hydrocarbon core of greater than 60 A in thickness. The Born-image model shows excellent agreement with the numerical results only when modified to include an appropriate effective thickness of the low dielectric region. In addition, a newly derived approximation which considers the local mean dielectric provides a simple and continuous solution that also agrees well with the numerical results.

  11. Small molecule activators of the insulin receptor: potential new therapeutic agents for the treatment of diabetes mellitus.

    PubMed

    Laborde, Edgardo; Manchem, Vara Prasad

    2002-12-01

    Diabetes mellitus refers to a spectrum of syndromes characterized by abnormally high levels of glucose in blood. These syndromes are associated with an absolute (Type 1 diabetes) or relative (Type 2 diabetes) deficiency of insulin, coupled with varying degrees of peripheral resistance to the actions of insulin. Clinical studies have shown that controlling hyperglycemia significantly reduces the appearance and progression of the vascular complications associated with diabetes. Insulin's regulation of glucose homeostasis is mediated by a cascade of signaling events that take place upon insulin binding to its cell surface receptor. Autophosphorylation of the receptor and activation of its intrinsic tyrosine kinase are critical processes for transmitting these intracellular signals. Type 1 diabetes patients depend on exogenous insulin to achieve these effects, whereas Type 2 diabetes patients can accomplish a similar response through oral medications that increase the production of endogenous insulin or enhance its actions on the target tissues. Current biochemical and clinical evidence suggests that defects within the insulin receptor itself may be a cause of insulin resistance leading to Type 2 diabetes. This review focuses on the insulin receptor as a target for therapeutic intervention, and describes the recent discovery of small molecules that act on the receptor and either enhance or directly emulate the actions of insulin both in vitro and in vivo.

  12. 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).

  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

    2014-11-01

    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. 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

  15. 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.

  16. Zinc Chelation by a Small-Molecule Adjuvant Potentiates Meropenem Activity in Vivo against NDM-1-Producing Klebsiella pneumoniae.

    PubMed

    Falconer, Shannon B; Reid-Yu, Sarah A; King, Andrew M; Gehrke, Sebastian S; Wang, Wenliang; Britten, James F; Coombes, Brian K; Wright, Gerard D; Brown, Eric D

    2015-11-13

    The widespread emergence of antibiotic drug resistance has resulted in a worldwide healthcare crisis. In particular, the extensive use of β-lactams, a highly effective class of antibiotics, has been a driver for pervasive β-lactam resistance. Among the most important resistance determinants are the metallo-β-lactamases (MBL), which are zinc-requiring enzymes that inactivate nearly all classes of β-lactams, including the last-resort carbapenem antibiotics. The urgent need for new compounds targeting MBL resistance mechanisms has been widely acknowledged; however, the development of certain types of compounds-namely metal chelators-is actively avoided due to host toxicity concerns. The work herein reports the identification of a series of zinc-selective spiro-indoline-thiadiazole analogues that, in vitro, potentiate β-lactam antibiotics against an MBL-carrying pathogen by withholding zinc availability. This study demonstrates the ability of one such analogue to inhibit NDM-1 in vitro and, using a mouse model of infection, shows that combination treatment of the respective analogue with meropenem results in a significant decrease in bacterial burden in contrast to animals that received antibiotic treatment alone. These results support the therapeutic potential of these chelators in overcoming antibiotic resistance. PMID:27623408

  17. Classical and Mexican hat-type potential energy curve for the hydrogen molecule from a confined Kratzer oscillator

    NASA Astrophysics Data System (ADS)

    van Hooydonk, G.

    2016-03-01

    We review harmonic oscillator theory for closed, stable quantum systems. The H2 potential energy curve (PEC) of Mexican hat-type, calculated with a confined Kratzer oscillator, is better than the Rydberg-Klein-Rees (RKR) H2 PEC. Compared with QM, the theory of chemical bonding is simplified, since a confined Kratzer oscillator can also lead to the long sought for universal function, once called the Holy Grail of Molecular Spectroscopy. This is validated by reducing PECs for different bonds H2, HF, I2, N2 and O2 to a single one. The equal probability for H2, originating either from HA + HB or HB + HA, is quantified with a Gauss probability density function. At the Bohr scale, a confined harmonic oscillator behaves properly at the extremes of bound two-nucleon quantum systems.

  18. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  19. Progress Towards the Accurate Calculation of Anharmonic Vibrational States of Fluxional Molecules and Clusters Without a Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Petit, Andrew S.; McCoy, Anne B.

    2011-06-01

    The accurate calculation of anharmonic vibrational states of highly fluxional systems is complicated by the need to first obtain the full-dimensional potential energy surface(PES). Although commonly exploited as a way around this problem, grid-based methodologies scale exponentially with system size while reduced dimensional approaches are highly system dependent, both in terms of the details of their application and in terms of their suitability. Moreover, the achievement of converged variational calculations of highly anharmonic systems is complicated by the necessity of using a very large basis and hence the construction and diagonalization of enormous Hamiltonian matrices. We report here our recent efforts to develop an algorithm capable of accurately calculating anharmonic vibrational energies, even for very floppy systems, without first obtaining a PES and using only a handful of basis functions per degree of freedom. More specifically, the potential energy and G-matrix elements are calculated on a set of points obtained from a Monte Carlo sampling of the most important regions of configuration space, allowing for a significant reduction in the number of required sampling points. The Hamiltonian matrix is then constructed using an evolving basis which, with each iteration, captures the effect of building H from an ever-expanding basis despite the fact that the actual dimensionality of H is fixed throughout the calculation. This latter property of the algorithm also greatly reduces the size of basis needed for the calculation relative to more traditional variational approaches. The results obtained from the application of our method to several test systems, including ion water complexes, will be reported along with its observed convergence properties.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Calculation of Rotation-Vibration Energy Levels of the Water Molecule with Near-Experimental Accuracy Based on an ab Initio Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Polyansky, Oleg L.; Ovsyannikov, Roman I.; Kyuberis, Aleksandra A.; Lodi, Lorenzo; Tennyson, Jonathan; Zobov, Nikolai F.

    2013-10-01

    A recently computed, high-accuracy ab initio Born-Oppenheimer (BO) potential energy surface (PES) for the water molecule is combined with relativistic, adiabatic, quantum electrodynamics, and, crucially, nonadiabatic corrections. Calculations of ro-vibrational levels are presented for several water isotopologues and shown to have unprecedented accuracy. A purely ab initio calculation reproduces some 200 known band origins associated with seven isotopologues of water with a standard deviation (σ) of about 0.35 cm-1. Introducing three semiempirical scaling parameters, two affecting the BO PES and one controlling nonadiabatic effects, reduces σ below 0.1 cm-1. Introducing one further rotational nonadiabatic parameter gives σ better than 0.1 cm-1 for all observed ro-vibrational energy levels up to J = 25. We conjecture that the energy levels of closed-shell molecules with roughly the same number of electrons as water, such as NH3, CH4, and H3O+, could be calculated to this accuracy using an analogous procedure. This means that near-ab initio calculations are capable of predicting transition frequencies with an accuracy only about a factor of 5 worse than high resolution experiments.

  5. Pulling-spring modulation as a method for improving the potential-of-mean-force reconstruction in single-molecule manipulation experiments.

    PubMed

    Perišić, Ognjen

    2013-01-01

    The free-energy calculation is usually limited to close to equilibrium perturbation regimes because faster perturbations introduce a bias into the estimate. The Jarzynski equality offers a solution to this problem by directly connecting the free-energy difference and the external work, regardless how far from equilibrium that work may be. However, a limited sampling coupled to the fast perturbation introduces a slowly converging bias into the Jarzynski free-energy estimate also. In this paper we present two perturbation protocols devised with the intention to overcome the convergence issues of the Jarzynski-based potential of mean force estimation in the single-molecule, constant velocity manipulation experiments. The protocols are designed to improve the convergence issues by increasing the variation of the external work through the modulation of the spring used to pull a molecule. Of the two methods, the one which continuously changes the amplitude of the spring stiffness offers an excellent reconstruction and requires less than one tenth of the samples required by the normal, constant spring pulling to produce the same quality of the reconstruction.

  6. 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

    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

  7. 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.

  8. Characterization of a Novel Small Molecule That Potentiates β-Lactam Activity against Gram-Positive and Gram-Negative Pathogens

    PubMed Central

    Nair, Dhanalakshmi R.; Monteiro, João M.; Memmi, Guido; Thanassi, Jane; Pucci, Michael; Schwartzman, Joseph; Pinho, Mariana G.

    2015-01-01

    In a loss-of-viability screen using small molecules against methicillin-resistant Staphylococcus aureus (MRSA) strain USA300 with a sub-MIC of a β-lactam, we found a small molecule, designated DNAC-1, which potentiated the effect of oxacillin (i.e., the MIC of oxacillin decreased from 64 to 0.25 μg/ml). Fluorescence microscopy indicated a disruption in the membrane structures within 15 min of exposure to DNAC-1 at 2× MIC. This permeabilization was accompanied by a rapid loss of membrane potential, as monitored by use of the DiOC2 (3,3′-diethyloxacarbocyanine iodide) dye. Macromolecular analysis showed the inhibition of staphylococcal cell wall synthesis by DNAC-1. Transmission electron microscopy of treated MRSA USA300 cells revealed a slightly thicker cell wall, together with mesosome-like projections into the cytosol. The exposure of USA300 cells to DNAC-1 was associated with the mislocalization of FtsZ accompanied by the localization of penicillin-binding protein 2 (PBP2) and PBP4 away from the septum, as well as mild activation of the vraRS-mediated cell wall stress response. However, DNAC-1 does not have any generalized toxicity toward mammalian host cells. DNAC-1 in combination with ceftriaxone is also effective against an assortment of Gram-negative pathogens. Using a murine subcutaneous coinjection model with 108 CFU of USA300 as a challenge inoculum, DNAC-1 alone or DNAC-1 with a sub-MIC of oxacillin resulted in a 6-log reduction in bacterial load and decreased abscess formation compared to the untreated control. We propose that DNAC-1, by exerting a bimodal effect on the cell membrane and cell wall, is a viable candidate in the development of combination therapy against many common bacterial pathogens. PMID:25583731

  9. Characterization of a novel small molecule that potentiates β-lactam activity against gram-positive and gram-negative pathogens.

    PubMed

    Nair, Dhanalakshmi R; Monteiro, João M; Memmi, Guido; Thanassi, Jane; Pucci, Michael; Schwartzman, Joseph; Pinho, Mariana G; Cheung, Ambrose L

    2015-04-01

    In a loss-of-viability screen using small molecules against methicillin-resistant Staphylococcus aureus (MRSA) strain USA300 with a sub-MIC of a β-lactam, we found a small molecule, designated DNAC-1, which potentiated the effect of oxacillin (i.e., the MIC of oxacillin decreased from 64 to 0.25 μg/ml). Fluorescence microscopy indicated a disruption in the membrane structures within 15 min of exposure to DNAC-1 at 2× MIC. This permeabilization was accompanied by a rapid loss of membrane potential, as monitored by use of the DiOC2 (3,3'-diethyloxacarbocyanine iodide) dye. Macromolecular analysis showed the inhibition of staphylococcal cell wall synthesis by DNAC-1. Transmission electron microscopy of treated MRSA USA300 cells revealed a slightly thicker cell wall, together with mesosome-like projections into the cytosol. The exposure of USA300 cells to DNAC-1 was associated with the mislocalization of FtsZ accompanied by the localization of penicillin-binding protein 2 (PBP2) and PBP4 away from the septum, as well as mild activation of the vraRS-mediated cell wall stress response. However, DNAC-1 does not have any generalized toxicity toward mammalian host cells. DNAC-1 in combination with ceftriaxone is also effective against an assortment of Gram-negative pathogens. Using a murine subcutaneous coinjection model with 10(8) CFU of USA300 as a challenge inoculum, DNAC-1 alone or DNAC-1 with a sub-MIC of oxacillin resulted in a 6-log reduction in bacterial load and decreased abscess formation compared to the untreated control. We propose that DNAC-1, by exerting a bimodal effect on the cell membrane and cell wall, is a viable candidate in the development of combination therapy against many common bacterial pathogens.

  10. High-order expansion of T2×t2 Jahn-Teller potential-energy surfaces in tetrahedral molecules

    NASA Astrophysics Data System (ADS)

    Opalka, Daniel; Domcke, Wolfgang

    2010-04-01

    Methods from Jahn-Teller theory and invariant theory have been combined for the construction of analytic diabatic potential-energy surfaces of triply degenerate states in tetrahedral molecules. The potentials of a threefold degenerate electronic state of T2 symmetry, subject to the T2×t2 or T2×(t2+t2) Jahn-Teller effect in a three-dimensional or six-dimensional space of nuclear coordinates, respectively, are considered. The permutation symmetry of four identical nuclei is taken into account in the polynomial expansion of the diabatic surfaces. Symmetry adapted polynomials up to high orders are explicitly given and a simple combinatorial scheme was developed to express terms of arbitrary order as products of a small number of polynomials which are invariant under the permutation of identical nuclei. The method is applied to the methane cation in its triply degenerate ground state. The parameters of the analytic surfaces have been fitted to accurate ab initio data calculated at the full-valence CASSCF/MRCI/cc-pVTZ level. A three-sheeted six-dimensional analytic potential-energy surface of the T22 ground state of CH4+ is reported, which involves terms up to eighth order in the degenerate stretching coordinate, up to 12th order in the degenerate bending coordinate, and up to fourth order in the stretch-bend coupling.

  11. Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches.

    PubMed

    Isegawa, Miho; Neese, Frank; Pantazis, Dimitrios A

    2016-05-10

    The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree-Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.

  12. 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.

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

    PubMed Central

    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

    2014-01-01

    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. PMID:26137540

  14. Effects of pyrethroid molecules on rat nerves in vitro: potential to reverse temperature-sensitive conduction block of demyelinated peripheral axons

    PubMed Central

    Lees, George

    1998-01-01

    neurotoxic actions and severely limit the clinical potential of this and related molecules. PMID:9504390

  15. 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.

  16. Dynamics of H2 Eley-Rideal abstraction from W(110): sensitivity to the representation of the molecule-surface potential.

    PubMed

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

    2014-07-14

    Dynamics of the Eley-Rideal (ER) abstraction of H2 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.

  17. Evaluation of the skin sensitization potential of chemicals using expression of co-stimulatory molecules, CD54 and CD86, on the naive THP-1 cell line.

    PubMed

    Yoshida, Y; Sakaguchi, H; Ito, Y; Okuda, M; Suzuki, H

    2003-04-01

    It has been known that dendritic cells (DCs) including Langerhans cells (LCs) play a critical role in the skin sensitization process. Many attempts have been made to develop in vitro sensitization tests that employ DCs derived from peripheral blood mononuclear cells (PBMC-DC) or CD34+ hematopoietic progenitor cells (CD34+ HPC) purified from cord blood or bone marrow. However, the use of the DCs in in vitro methods has been difficult due to the nature of these cells such as low levels in the source and/or donor-to-donor variability. In our studies, we employed the human monocytic leukemia cell line, THP-1, in order to avoid some of these difficulties. At the start, we examined whether treatment of the cells with various cytokines could produce DCs from THP-1. Treatment of THP-1 cells with cytokines such as GM-CSF, IL-4, TNF-alpha, and/or PMA did induce some phenotypic changes in THP-1 cells that were characteristic of DCs. Subsequently, responses to a known sensitizer, dinitrochlorobenzene (DNCB), and a non-sensitizer, dimethyl sulfoxide (DMSO) or sodium lauryl sulfate (SLS), on the expression of co-stimulatory molecules, CD54 and CD86, were examined between the naive cells and the cytokine-treated cells. Interestingly, the naive THP-1 cells responded only to DNCB and the response to the sensitizer was more distinct than cytokine-treated THP-1 cells. Similar phenomena were also observed in the human myeloid leukemia cell line, KG-1. Furthermore, with treatment of DNCB, naive THP-1 cells showed augmented expression of HLA, CD80 and secretion of IL-1 beta. The response of THP-1 cells to a sensitizer was similar to that of LCs/DCs. Upon demonstrating the differentiation of monocyte cells in our system, we then evaluated a series of chemicals, including known sensitizers and non-sensitizers, for their potential to augment CD54 and CD86 expression on naive THP-1 cells. Indeed, known sensitizers such as PPD and 2-MBT significantly augmented CD54 and CD86 expression in a

  18. 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)

  19. 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)

  20. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  1. 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.

  2. 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.

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

    PubMed

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

    2016-03-21

    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. PMID:27004887

  4. Imaging-Based High-Throughput Screening Assay To Identify New Molecules with Transmission-Blocking Potential against Plasmodium falciparum Female Gamete Formation

    PubMed Central

    Miguel-Blanco, Celia; Lelièvre, Joël; Delves, Michael J.; Bardera, Ana I.; Presa, Jesús L.; López-Barragán, María José; Ruecker, Andrea; Marques, Sara; Sinden, Robert E.

    2015-01-01

    In response to a call for the global eradication of malaria, drug discovery has recently been extended to identify compounds that prevent the onward transmission of the parasite, which is mediated by Plasmodium falciparum stage V gametocytes. Lately, metabolic activity has been used in vitro as a surrogate for gametocyte viability; however, as gametocytes remain relatively quiescent at this stage, their ability to undergo onward development (gamete formation) may be a better measure of their functional viability. During gamete formation, female gametocytes undergo profound morphological changes and express translationally repressed mRNA. By assessing female gamete cell surface expression of one such repressed protein, Pfs25, as the readout for female gametocyte functional viability, we developed an imaging-based high-throughput screening (HTS) assay to identify transmission-blocking compounds. This assay, designated the P. falciparum female gametocyte activation assay (FGAA), was scaled up to a high-throughput format (Z′ factor, 0.7 ± 0.1) and subsequently validated using a selection of 50 known antimalarials from diverse chemical families. Only a few of these agents showed submicromolar 50% inhibitory concentrations in the assay: thiostrepton, methylene blue, and some endoperoxides. To determine the best conditions for HTS, a robustness test was performed with a selection of the GlaxoSmithKline Tres Cantos Antimalarial Set (TCAMS) and the final screening conditions for this library were determined to be a 2 μM concentration and 48 h of incubation with gametocytes. The P. falciparum FGAA has been proven to be a robust HTS assay faithful to Plasmodium transmission-stage cell biology, and it is an innovative useful tool for antimalarial drug discovery which aims to identify new molecules with transmission-blocking potential. PMID:25801574

  5. Conditional ablation of the neural cell adhesion molecule reduces precision of spatial learning, long-term potentiation, and depression in the CA1 subfield of mouse hippocampus.

    PubMed

    Bukalo, Olena; Fentrop, Nikolas; Lee, Alan Y W; Salmen, Benedikt; Law, Janice W S; Wotjak, Carsten T; Schweizer, Michaela; Dityatev, Alexander; Schachner, Melitta

    2004-02-18

    NCAM, a neural cell adhesion molecule of the immunoglobulin superfamily, is involved in neuronal migration and differentiation, axon outgrowth and fasciculation, and synaptic plasticity. To dissociate the functional roles of NCAM in the adult brain from developmental abnormalities, we generated a mutant in which the NCAM gene is inactivated by cre-recombinase under the control of the calcium-calmodulin-dependent kinase II promoter, resulting in reduction of NCAM expression predominantly in the hippocampus. This mutant (NCAMff+) did not show the overt morphological and behavioral abnormalities previously observed in constitutive NCAM-deficient (NCAM-/-) mice. However, similar to the NCAM-/- mouse, a reduction in long-term potentiation (LTP) in the CA1 region of the hippocampus was revealed. Long-term depression was also abolished in NCAMff+ mice. The deficit in LTP could be rescued by elevation of extracellular Ca2+ concentrations from 1.5 or 2.0 to 2.5 mm, suggesting an involvement of NCAM in regulation of Ca2+-dependent signaling during LTP. Contrary to the NCAM-/- mouse, LTP in the CA3 region was normal, consistent with normal mossy fiber lamination in NCAMff+ as opposed to abnormal lamination in NCAM-/- mice. NCAMff+ mutants did not show general deficits in short- and long-term memory in global landmark navigation in the water maze but were delayed in the acquisition of precise spatial orientation, a deficit that could be overcome by training. Thus, mice conditionally deficient in hippocampal NCAM expression in the adult share certain abnormalities characteristic of NCAM-/- mice, highlighting the role of NCAM in the regulation of synaptic plasticity in the CA1 region.

  6. 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.

  7. 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.

  8. Study of the potential of stratum corneum lipids and exogenous molecules interaction by fluorescence spectroscopy for the estimation of percutaneous penetration.

    PubMed

    Jungman, Elsa; Laugel, Cécile; Kasselouri, Athéna; Baillet-Guffroy, Arlette

    2012-09-15

    Considering that the skin barrier properties are closely linked to the ceramides composition and conformation within the SC, our work focused on developing a new evaluation criterion in complement of the Log Pow and MW: lipids retentive role within the SC. We developed an in vitro model to study exogenous molecules (Mol) and SC lipids interaction by fluorescence spectroscopy. As ceramides do not fluoresce, fluorescence probes that emit a fluorescence signal in contact with lipidic chains were selected for the study. A protocol was developed based on the exogenous molecule (cosmetic actives) affinity for the SC lipids. A fluorescence criterion (ΔI) was calculated from our results and compared to ex vivo skin penetration measurements realized with a Franz cell device. Our results indicated that polarity seems to be very representative of the ceramide and exogenous molecule interaction for most of the molecules tested. However, the ΔI calculated highlighted the particular interaction of some exogenous molecules with ceramides and their skin distribution. This particular behavior was not initially possible to estimate with the Log Pow and MW. This work aimed to develop a new alternative method to enhance the percutaneous penetration estimation of exogenous molecules for the risk analysis.

  9. 'Escentric' molecules.

    PubMed

    Schön, Geza

    2008-06-01

    Can a fragrance be revolutionary? In this commentary, the creation of two unusual, extravagant fine fragrances, 'escentric01' and 'molecule01', is described. In response to the fantasy components found in release notes of many recent perfume launches, both center around a single real fragrance raw material, the transparent woody aroma chemical 'Iso E Super' (1+2). The perfume 'escentric01' contains 65% of it, accompanied by Trisamber (3), red pepper, lime oil, incense and musks, while 'molecule01' consists exclusively of 'Iso E Super' (1+2). The elegant woody note lives here its own eccentric life--the revolution starts.

  10. DFT study of adsorption of picric acid molecule on the surface of single-walled ZnO nanotube; as potential new chemical sensor

    NASA Astrophysics Data System (ADS)

    Farmanzadeh, Davood; Tabari, Leila

    2015-01-01

    Using density functional theory (DFT), we have investigated the adsorption of picric acid (PA) molecule on the surface of (8,0) single-walled ZnO nanotube (ZnONT). The results show that the PA molecule can be chemisorbed on the surface of ZnONT with adsorption energies of -82.01 and -75.26 kJ/mol in gas and aqueous phase, respectively. Frontier molecular orbital analysis show that HOMO/LUMO gap of ZnONT reduces from 1.66 and 1.75 eV in the pristine nanotube to 0.83 and 0.72 eV in PA-adsorbed form in gas and aqueous phase, respectively. It suggests that the process can affect the electronic properties of the studied nanotube which would lead to its conductance change upon the adsorption of PA molecule. The modifying effect on the electrical conductance of ZnONT underlies the working mechanism of gas sensors for detecting the PA molecules. Analyses of the adsorption behavior of the electrically charged ZnONT toward PA molecule in the gas phase show that the PA molecule can be strongly adsorbed on the negatively charged ZnONT surface with significant adsorption energy (-135.1 kJ/mol). However, from the HOMO/LUMO gap changes, it can be concluded that the positive ZnONT might sensitively detect the PA molecule in comparison to the negative tube. These results can provide helpful information for experimental investigation to develop novel nanotube-based sensors.

  11. Calculations of 21 Λ-S and 42 Ω states of BC molecule: Potential energy curves, spectroscopic parameters and spin-orbit coupling effect.

    PubMed

    Xing, Wei; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-01-15

    The potential energy curves (PECs) were calculated for the 42 Ω states generated from the 21 Λ-S states (X(4)Σ(-), A(4)Π, B(4)Σ(-), a(2)Π, b(2)Σ(-), c(2)Δ, d(2)Σ(+), e(2)Π, 3(2)Π, 4(2)Π, 5(2)Π, 2(2)Σ(-), 3(2)Σ(-), 2(2)Σ(+), 3(2)Σ(+), 2(2)Δ, 3(2)Δ, 1(4)Σ(+), 2(4)Π, 1(4)Δ and 1(2)Φ), which originated from the lowest two dissociation channels, B((2)Pu)+C((3)Pg) and B((2)Pu)+C((1)Dg), of the BC molecule. The PECs were calculated for internuclear separations from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV6Z basis set. Of these 21 Λ-S states, the e(2)Π, 2(2)Δ, 2(2)Σ(-), 4(2)Π, 1(2)Φ and 3(2)Δ possess the double wells. The A(4)Π, a(2)Π, c(2)Δ, 2(4)Π, 4(2)Π, 5(2)Π, 1(4)Δ and 1(2)Φ states are inverted with the spin-orbit coupling (SOC) effect taken into account. The first well of e(2)Π state and the second well of 4(2)Π and 2(2)Δ states do not have any vibrational states whether with or without the SOC effect included. All the Λ-S and Ω states involved in this paper are bound states. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pV5Z basis set. Core-valence correlation correction was included at the level of an aug-cc-pCV5Z basis set. The SOC effect was accounted for by the state interaction method with the Breit-Pauli Hamiltonian and the all-electron cc-pCV5Z basis set. The PECs of all the states were extrapolated to the complete basis set limit. The spectroscopic parameters were obtained. The vibrational properties of several Λ-S and Ω states with the relatively shallow wells were evaluated. The SOC effect on the spectroscopic parameters is not obvious for almost all the states. The spectroscopic properties reported in this paper can be expected to be reliably predicted ones.

  12. Calculations of 21 Λ-S and 42 Ω states of BC molecule: Potential energy curves, spectroscopic parameters and spin-orbit coupling effect

    NASA Astrophysics Data System (ADS)

    Xing, Wei; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-01-01

    The potential energy curves (PECs) were calculated for the 42 Ω states generated from the 21 Λ-S states (X4Σ-, A4Π, B4Σ-, a2Π, b2Σ-, c2Δ, d2Σ+, e2Π, 32Π, 42Π, 52Π, 22Σ-, 32Σ-, 22Σ+, 32Σ+, 22Δ, 32Δ, 14Σ+, 24Π, 14Δ and 12Φ), which originated from the lowest two dissociation channels, B(2Pu) + C(3Pg) and B(2Pu) + C(1Dg), of the BC molecule. The PECs were calculated for internuclear separations from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV6Z basis set. Of these 21 Λ-S states, the e2Π, 22Δ, 22Σ-, 42Π, 12Φ and 32Δ possess the double wells. The A4Π, a2Π, c2Δ, 24Π, 42Π, 52Π, 14Δ and 12Φ states are inverted with the spin-orbit coupling (SOC) effect taken into account. The first well of e2Π state and the second well of 42Π and 22Δ states do not have any vibrational states whether with or without the SOC effect included. All the Λ-S and Ω states involved in this paper are bound states. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pV5Z basis set. Core-valence correlation correction was included at the level of an aug-cc-pCV5Z basis set. The SOC effect was accounted for by the state interaction method with the Breit-Pauli Hamiltonian and the all-electron cc-pCV5Z basis set. The PECs of all the states were extrapolated to the complete basis set limit. The spectroscopic parameters were obtained. The vibrational properties of several Λ-S and Ω states with the relatively shallow wells were evaluated. The SOC effect on the spectroscopic parameters is not obvious for almost all the states. The spectroscopic properties reported in this paper can be expected to be reliably predicted ones.

  13. Walking molecules.

    PubMed

    von Delius, Max; Leigh, David A

    2011-07-01

    Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references). PMID:21416072

  14. 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

  15. Identification of EPAC (Exchange Protein Activated by cAMP) bioinformatically as a potential signalling biomarker in Cardiovascular Disease (CVD) and its molecular docking by a lead molecule.

    PubMed

    Bala, Saranya; Pathak, Ravi Kant; Mishra, Vachaspati

    2011-01-01

    The present work delineates the combinatorial approach of firstly, creation of a centralized data-set comprising signalling proteins identified on the basis of altered expression, such as over-expression or repression of a set of signalling protein(s) leading to the cause of the disease, which is based on published reports screened through Pubmed and secondly, in the in silico creation of novel lead (drug) molecules and docking of identified signalling biomarkers using such drugs to investigate possibility of their future application in the model systems eventually. EPAC (Exchange Protein Activated by cAMP) emerges as a signalling biomarker in cases studied presently. Brefeldin, the known inhibitor of EPAC, though the mechanism yet unexplored, has been the molecule used as the pharmacophore for creation of lead drug molecule. Various modifications have been incorporated into the pharmacophore to increase the hydrophobic interactions for increasing the binding efficiency of the generated lead molecule. Side-chain modifications of the pharmacophore and refinement of data through firedock upon docking of EPAC with the modified pharmacophore yielded best results on the bases of atomic contact energy, van der Waal and partial electrostatic interactions as well as additional estimations of the binding free energy. Modifications of CH3 at C15 with COOH and H at C2 with OH in brefeldin showed the best docking results on the basis of protein-drug interaction parameters. The present work provides a clue in rational design of EPAC inhibitors which could be developed as drug lead in combating CVD. PMID:21738308

  16. 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

  17. The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.

    PubMed

    Venkata, Chandrasekhar; Forster, Mark J; Howe, Peter W A; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.

  18. The Potential Utility of Predicted One Bond Carbon-Proton Coupling Constants in the Structure Elucidation of Small Organic Molecules by NMR Spectroscopy

    PubMed Central

    Venkata, Chandrasekhar; Forster, Mark J.; Howe, Peter W. A.; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation. PMID:25365289

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

    PubMed

    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

  20. 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.

  1. Comment on ``On the role of dissipation on the Casimir-Polder potential between molecules in dielectric media'' [J. Chem. Phys. 133, 164501 (2010)

    NASA Astrophysics Data System (ADS)

    Dalvit, D. A. R.; Milonni, P. W.

    2011-07-01

    J. J. Rodriguez and A. Salam [J. Chem. Phys. 133, 164501 (2010)], 10.1063/1.3495954 find discrepancies between their calculation and a previously published one [S. Spagnolo, D. A. R. Dalvit, and P. W. Milonni, Phys. Rev. A 75, 052117 (2007)], 10.1103/PhysRevA.75.052117 for the van der Waals interaction of two guest molecules in a host dielectric medium. We trace these discrepancies to what we regard as fundamental errors in the calculation by Rodriguez and Salam.

  2. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy.

    PubMed

    Lau, Pick-Chung; Norwood, Robert A; Mansuripur, Masud; Peyghambarian, Nasser

    2014-07-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × -3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme.

  3. An effective nanosensor for organic molecules based on water-soluble mercaptopropionic acid-capped CdTe nanocrystals with potential application in high-throughput screening and high-resolution optical microscopy

    PubMed Central

    Lau, Pick-Chung; Norwood, Robert A.; Mansuripur, Masud; Peyghambarian, Nasser

    2014-01-01

    Specially-treated glass substrates coated with a thin film of water soluble mercaptopropionic acid (MPA) capped CdTe nanocrystals (NCs) were prepared and found to undergo photoluminescence changes by as much as 40% when micro-droplets of organic molecules were placed in the nanometer-range proximity of the NCs. This imaging technique involving close proximity between a nano-crystal and an organic molecule is found to provide a 2 × –3 × enhanced contrast ratio over the conventional method of fluorescence imaging. Photoluminescence of NCs is recoverable upon removal of the organic molecules, therefore validating these NCs as potential all-optical organic molecular nanosensors. Upon optimization and with proper instrumentation, these nano-crystals could eventually serve as point-detectors for purposes of super-resolution optical microscopy. No solvents are required for the proposed sensing mechanism since all solutions were dried under argon flow. Fluorophores and fluorescent proteins were investigated, including fluorescein, Rhodamine 6G, and green fluorescent protein (GFP). Furthermore, NC photoluminescence changes were systematically quantified as a function of the solution pH and of the organic molecule concentration. Long duration (> 40 minutes) continuous excitation studies were conducted in order to evaluate the reliability of the proposed sensing scheme. PMID:25071975

  4. Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease.

    PubMed

    Tóth, Gergely; Gardai, Shyra J; Zago, Wagner; Bertoncini, Carlos W; Cremades, Nunilo; Roy, Susan L; Tambe, Mitali A; Rochet, Jean-Christophe; Galvagnion, Celine; Skibinski, Gaia; Finkbeiner, Steven; Bova, Michael; Regnstrom, Karin; Chiou, San-San; Johnston, Jennifer; Callaway, Kari; Anderson, John P; Jobling, Michael F; Buell, Alexander K; Yednock, Ted A; Knowles, Tuomas P J; Vendruscolo, Michele; Christodoulou, John; Dobson, Christopher M; Schenk, Dale; McConlogue, Lisa

    2014-01-01

    The misfolding of intrinsically disordered proteins such as α-synuclein, tau and the Aβ peptide has been associated with many highly debilitating neurodegenerative syndromes including Parkinson's and Alzheimer's diseases. Therapeutic targeting of the monomeric state of such intrinsically disordered proteins by small molecules has, however, been a major challenge because of their heterogeneous conformational properties. We show here that a combination of computational and experimental techniques has led to the identification of a drug-like phenyl-sulfonamide compound (ELN484228), that targets α-synuclein, a key protein in Parkinson's disease. We found that this compound has substantial biological activity in cellular models of α-synuclein-mediated dysfunction, including rescue of α-synuclein-induced disruption of vesicle trafficking and dopaminergic neuronal loss and neurite retraction most likely by reducing the amount of α-synuclein targeted to sites of vesicle mobilization such as the synapse in neurons or the site of bead engulfment in microglial cells. These results indicate that targeting α-synuclein by small molecules represents a promising approach to the development of therapeutic treatments of Parkinson's disease and related conditions. PMID:24551051

  5. 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.

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

    PubMed

    Karunakaran, V; Balachandran, V

    2014-07-15

    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 (1)H and (13)C 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.

  7. The Genetically Modified Polysialylated Form of Neural Cell Adhesion Molecule-Positive Cells for Potential Treatment of X-Linked Adrenoleukodystrophy

    PubMed Central

    Jang, Jiho; Kim, Han-Soo; Kang, Joon Won

    2013-01-01

    Purpose Cell transplantation of myelin-producing exogenous cells is being extensively explored as a means of remyelinating axons in X-linked adrenoleukodystrophy. We determined whether 3,3',5-Triiodo-L-thyronine (T3) overexpresses the ABCD2 gene in the polysialylated (PSA) form of neural cell adhesion molecule (NCAM)-positive cells and promotes cell proliferation and favors oligodendrocyte lineage differentiation. Materials and Methods PSA-NCAM+ cells from newborn Sprague-Dawley rats were grown for five days on uncoated dishes in defined medium with or without supplementation of basic fibroblast growth factor (bFGF) and/or T3. Then, PSA-NCAM+ spheres were prepared in single cells and transferred to polyornithine/fibronectin-coated glass coverslips for five days to determine the fate of the cells according to the supplementation of these molecules. T3 responsiveness of ABCD2 was analyzed using real-time quantitative polymerase chain reaction, the growth and fate of cells were determined using 5-bromo-2-deoxyuridine incorporation and immunocytochemistry, respectively. Results Results demonstrated that T3 induces overexpression of the ABCD2 gene in PSA-NCAM+ cells, and can enhance PSA-NCAM+ cell growth in the presence of bFGF, favoring an oligodendrocyte fate. Conclusion These results may provide new insights into investigation of PSA-NCAM+ cells for therapeutic application to X-linked adrenoleukodystrophy. PMID:23225827

  8. Spectroscopic and magnetic studies of erbium(III)-TEMPO complex as a potential single-molecule magnet: Interplay of the crystal-field and exchange coupling effects

    NASA Astrophysics Data System (ADS)

    Karbowiak, Mirosław; Rudowicz, Czesław; Nakamura, Takeshi; Murakami, Rina; Ishida, Takayuki

    2016-10-01

    Crystallographic, spectroscopic, and magnetic studies of three-center systems: lanthanoid-Ln3+ ions doubly-coordinated by TEMPO (2,2,6,6-tetramethylpiperidin-1-oxyl) radicals [Ln-TEMPO2] are reported. The temperature dependence of alternating-current magnetic susceptibility indicates the single-molecule-magnet behavior of Er-TEMPO2, exhibiting relatively slow magnetization relaxation. Well-resolved absorption spectra were obtained only for Er-TEMPO2. Other samples yielded spectra not amenable for meaningful interpretation. The crystal-field parameters (CFPs) determined from the measured Er3+-energy levels served as starting CFPs for fitting the direct-current magnetic susceptibility result. Compatibility of the so-determined and fine-tuned CFPs, and interplay between crystal-field-related effects and exchange-coupling effects are considered. Exchange couplings in Ln-TEMPO2 appear antiferromagnetic and unexpectedly large.

  9. Optimized production of ultracold ground-state molecules: Stabilization employing potentials with ion-pair character and strong spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Tomza, Michał; Goerz, Michael H.; Musiał, Monika; Moszynski, Robert; Koch, Christiane P.

    2012-10-01

    We discuss the production of ultracold molecules in their electronic ground state by photoassociation employing electronically excited states with ion-pair character and strong spin-orbit interaction. A short photoassociation laser pulse drives a nonresonant three-photon transition for alkali-metal atoms colliding in their lowest triplet state. The excited-state wave packet is transferred to the ground electronic state by a second laser pulse, driving a resonant two-photon transition. After analyzing the transition matrix elements governing the stabilization step, we discuss the efficiency of population transfer using transform-limited and linearly chirped laser pulses. Finally, we employ optimal control theory to determine the most efficient stabilization pathways. We find that the stabilization efficiency can be increased by one and two orders of magnitude when using linearly chirped and optimally shaped laser pulses, respectively.

  10. Enteral n-3 fatty acids and micronutrients enhance percentage of positive neutrophil and lymphocyte adhesion molecules: a potential mediator of pressure ulcer healing in critically ill patients.

    PubMed

    Theilla, Miriam; Schwartz, Betty; Zimra, Yael; Shapiro, Haim; Anbar, Ronit; Rabizadeh, Esther; Cohen, Jonathan; Singer, Pierre

    2012-04-01

    n-3 Fatty acids are recognised as influencing both wound healing and immunity. We assessed the impact of a fish oil- and micronutrient-enriched formula (study formula) on the healing of pressure ulcers and on immune function in critically ill patients in an intensive care unit. A total of forty patients with pressure ulcers and receiving nutritional support were enrolled (intervention group, n 20, received study formula; and a control group, n 20, received an isoenergetic formula). Total and differential leucocyte count and percentage of adhesion molecule positive granulocyte and lymphocyte cells (CD11a, CD11b, CD18 and CD49b) were measured on days 0, 7 and 14. Percentage of positive lymphocytes for CD54, CD49b, CD49d and CD8 were also measured on days 0, 7 and 14. The state of pressure ulcers was assessed by using the pressure ulcer scale for healing tool score on days 7, 14 and 28 of treatment. No between-group differences in patient demographics, anthropometry or diagnostic class were observed. Patients who received the study formula showed significant increases in the percentage of positive CD18 and CD11a lymphocytes and of CD49b granulocytes as compared to controls (P < 0·05). While the severity of pressure ulcers was not significantly different between the two groups on admission, severity increased significantly over time for the control group (P < 0·05), but not for the study group. The present study suggests that a fish oil- and micronutrient-enriched formula may prevent worsening of pressure ulcers and that this effect may be mediated by an effect on adhesion molecule expression.

  11. Structure-based screen identifies a potent small-molecule inhibitor of Stat5a/b with therapeutic potential for prostate cancer and chronic myeloid leukemia

    PubMed Central

    Liao, Zhiyong; Gu, Lei; Vergalli, Jenny; Mariani, Samanta A.; De Dominici, Marco; Lokareddy, Ravi K.; Dagvadorj, Ayush; Purushottamachar, Puranik; McCue, Peter A.; Trabulsi, Edouard; Lallas, Costas D.; Gupta, Shilpa; Ellsworth, Elyse; Blackmon, Shauna; Ertel, Adam; Fortina, Paolo; Leiby, Benjamin; Xia, Guanjun; Rui, Hallgeir; Hoang, David T.; Gomella, Leonard G.; Cingolani, Gino; Njar, Vincent; Pattabiraman, Nagarajan; Calabretta, Bruno; Nevalainen, Marja T.

    2015-01-01

    Bypassing tyrosine kinases responsible for Stat5a/b phosphorylation would be advantageous for therapy development for Stat5a/b-regulated cancers. Here, we sought to identify small-molecule inhibitors of Stat5a/b for lead optimization and therapy development for prostate cancer (PC) and Bcr-Abl-driven leukemias. In silico screening of chemical structure databases combined with medicinal chemistry was used for identification of a panel of small-molecule inhibitors to block SH2-domain-mediated docking of Stat5a/b to the receptor-kinase complex and subsequent phosphorylation and dimerization. We tested the efficacy of the lead-compound, IST5-002, in experimental models and patient samples of two known Stat5a/b-driven cancers, prostate cancer (PC) and chronic myeloid leukemia (CML). The lead compound Inhibitor of Stat5-002 (IST5-002) prevented both Jak2 and Bcr-Abl-mediated phosphorylation and dimerization of Stat5a/b, and selectively inhibited transcriptional activity of Stat5a (IC50 1.5 μM) and Stat5b (IC50 3.5 μM). IST5-002 suppressed nuclear translocation of Stat5a/b, binding to DNA and Stat5a/b target gene expression. IST5-002 induced extensive apoptosis of PC cells, impaired growth of PC xenograft tumors and induced cell death in patient-derived PCs when tested ex vivo in explant organ cultures. Importantly, IST5-002 induced robust apoptotic death not only of imatinib-sensitive but also imatinib-resistant chronic myeloid leukemia (CML) cell lines and primary CML cells from patients. IST5-002 provides a lead structure for further chemical modifications for clinical development for Stat5a/b-driven solid tumors and hematological malignancies. PMID:26026053

  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. Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules.

    PubMed

    Chawla, Mohit; Credendino, Raffaele; Oliva, Romina; Cavallo, Luigi

    2015-10-15

    Non-natural (synthetic) nucleobases, including 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenine, have been introduced in RNA molecules for targeted applications, and have been characterized experimentally. However, no theoretical characterization of the impact of these modifications on the structure and energetics of the corresponding H-bonded base pair is available. To fill this gap, we performed quantum mechanics calculations, starting with the analysis of the impact of the 8-aza-7-deaza modification of the adenine skeleton, and we moved then to analyze the impact of the specific substituents on the modified 8-aza-7-deazaadenine. Our analysis indicates that, despite of these severe structural modifications, the H-bonding properties of the modified base pair gratifyingly replicate those of the unmodified base pair. Similar behavior is predicted when the same skeleton modifications are applied to guanine when paired to cytosine. To stress further the H-bonding pairing in the modified adenine-uracil base pair, we explored the impact of strong electron donor and electron withdrawing substituents on the C7 position. Also in this case we found minimal impact on the base pair geometry and energy, confirming the validity of this modification strategy to functionalize RNAs without perturbing its stability and biological functionality.

  14. Characterization and complete sequence of lactonase enzyme from Bacillus weihenstephanensis isolate P65 with potential activity against acyl homoserine lactone signal molecules.

    PubMed

    Sakr, Masarra Mohammed; Aboshanab, Khaled Mohamed Anwar; Aboulwafa, Mohammad Mabrouk; Hassouna, Nadia Abdel-Haleem

    2013-01-01

    Acyl homoserine lactones (AHLs) are the most common class of quorum sensing signal molecules (autoinducers) that have been reported to be essential for virulence of many relevant pathogenic bacteria such as Pseudomonas aeruginosa. New approach for controlling infections of such bacteria is through quorum quenching. In this study, the acyl homoserine lactone inhibitory activity of the crude enzyme from a Bacillus weihenstephanensis-isolate P65 was characterized. The crude enzyme was found to have relatively high thermal stability and was stable in pH range 6 to 9. The crude enzyme extract was found to have lactonase activity of 36.3 U/mg total protein. Maximum enzyme activity was achieved within a range of 28-50°C and pH 6-9. None of the metals used enhanced the activity neither did EDTA inhibit it. However, a concentration of 10 mM Fe(+2) reduced the activity to 73.8%. Catalytic activity and kinetic constants were determined using hexanoyl homoserine lactone as a substrate. Studying enzyme substrate specificity using synthetic standard signals displayed broad spectrum of activity. The enzyme was found to be constitutive. Isolation and complete nucleotide sequence of the respective lactonase gene were done and submitted to the Genbank database under accession code KC823046.

  15. Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules.

    PubMed

    Chawla, Mohit; Credendino, Raffaele; Oliva, Romina; Cavallo, Luigi

    2015-10-15

    Non-natural (synthetic) nucleobases, including 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenine, have been introduced in RNA molecules for targeted applications, and have been characterized experimentally. However, no theoretical characterization of the impact of these modifications on the structure and energetics of the corresponding H-bonded base pair is available. To fill this gap, we performed quantum mechanics calculations, starting with the analysis of the impact of the 8-aza-7-deaza modification of the adenine skeleton, and we moved then to analyze the impact of the specific substituents on the modified 8-aza-7-deazaadenine. Our analysis indicates that, despite of these severe structural modifications, the H-bonding properties of the modified base pair gratifyingly replicate those of the unmodified base pair. Similar behavior is predicted when the same skeleton modifications are applied to guanine when paired to cytosine. To stress further the H-bonding pairing in the modified adenine-uracil base pair, we explored the impact of strong electron donor and electron withdrawing substituents on the C7 position. Also in this case we found minimal impact on the base pair geometry and energy, confirming the validity of this modification strategy to functionalize RNAs without perturbing its stability and biological functionality. PMID:26389789

  16. 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%.

  17. 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

    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.

  18. MicroRNA miR-29 modulates expression of immunoinhibitory molecule B7-H3: potential implications for immune based therapy of human solid tumors.

    PubMed

    Xu, Hong; Cheung, Irene Y; Guo, Hong-Fen; Cheung, Nai-Kong V

    2009-08-01

    B7-H3, a surface immunomodulatory glycoprotein, inhibits natural killer cells and T cells. The monoclonal antibody (mAb) 8H9 is specific for 4Ig-B7-H3, the long and principal form of B7-H3. Early results from radioimmunotherapy using 8H9 have shown promise in patients with metastatic solid tumors to the central nervous system. Whereas B7-H3 transcript was ubiquitously expressed in a wide spectrum of human solid tumors as well as human normal tissues, B7-H3 protein was preferentially expressed only in tumor tissues. By quantitative reverse transcription-PCR, all three isoforms of microRNA miR-29 (a, b, and c) were highly expressed in normal tissues. However, they were down-regulated in a broad spectrum of solid tumors, including neuroblastoma, sarcomas, brain tumors, and tumor cell lines. B7-H3 protein expression was inversely correlated with miR-29 levels in both cell lines and tumor tissues tested. Using luciferase reporter assay, miR-29a was shown to directly target B7-H3 3' untranslated region, and knock-in and knockdown of miR-29a led to down-regulation and up-regulation, respectively, of B7-H3 protein expression. The ability of miR-29 to control B7-H3 protein expression has implications in immune escape by solid tumors. Differential modulation of this key immunoinhibitory molecule in tumor versus normal tissues may advance both cell-mediated immunotherapy and antibody-based targeted strategies using the B7-H3-specific mAb 8H9.

  19. 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

  20. Generation of minor histocompatibility antigen HA-1-specific cytotoxic T cells restricted by nonself HLA molecules: a potential strategy to treat relapsed leukemia after HLA-mismatched stem cell transplantation.

    PubMed

    Mutis, Tuna; Blokland, Els; Kester, Michel; Schrama, Ellen; Goulmy, Els

    2002-07-15

    Successful stem cell transplantation (SCT) across HLA barriers can be performed with cord blood, megadoses of stem cells, or with nonmyeloablative conditioning strategies. Because the HLA-mismatched transplants are often T-cell depleted, leukemia relapse rates are high. Treatment of relapsed leukemia after HLA-mismatched SCT is difficult. A novel potential strategy to treat relapsed leukemia after HLA-mismatched SCT is the use of patients' mismatched HLA molecules as antigen-presenting molecules to generate hematopoietic system-specific cytotoxic T cells (CTLs) from the stem cell donor. Adoptive transfer of these hematopoietic system-specific CTLs that are restricted by nonself HLA molecules may eliminate leukemia without affecting the patient's nonhematopoietic cells or donor hematopoietic cells. We investigated the feasibility of this strategy using the hematopoietic system-specific minor histocompatibility antigen HA-1, which is known to induce HLA-A2-restricted CTLs. HLA-A2(-) peripheral blood mononuclear cells were stimulated with HLA-A2(+) T2 cells pulsed with synthetic HA-1 peptide or with dendritic cells transduced with the HA-1 cDNA. Tetrameric HLA-A2/HA-1 peptide complexes were used to monitor and enrich HA-1-specific CTLs. In the alloreactive cultures, HA-1-specific CTLs were enriched up to 7% by 3 rounds of antigen-specific stimulations and up to 87% by fluorescence-activated cell sorting of tetramer-positive T cells. The HA-1-specific CTLs showed specific lysis of the relevant target cells, including leukemic cells. Because the polyclonal CTL cultures also contained natural killer cells and allo-HLA-A2-specific CTLs, CTL clones were generated that showed the expected HA-1 specificity only. Thus, HA-1-specific CTLs restricted by nonself HLA-A2 molecules can be generated in an HLA-A2-mismatched setting. PMID:12091347

  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

    2013-07-01

    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. 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.

  4. Simulations of the fluid phase of nitrogen molecules adsorbed on the basal planes of graphite: structural and dynamical effects of the corrugation in the holding potential.

    NASA Astrophysics Data System (ADS)

    Hansen, F. Y.; Bruch, L. W.; Taub, H.

    1997-03-01

    A discrepancy between calculated (F. Y. Hansen, L.W. Bruch and H. Taub, Phys. Rev. B. 52), 8515 (1995) and experimental melting temperatures of submonolayer films was traced to the intermolecular potentials. These have been tested by comparing molecular dynamics simulations of isosteric heats of adsorption in fluid films with experimental measurements (J. Piper, J. A. Morrison, C. Peters and Y. Ozaki, J. Chem. Soc., Faraday Trans. 1, 79), 2863 (1983). The effect of the corrugation in the holding potential on the fluid phases has also been evaluated in a series of simulations. For films on a model uncorrugated graphite surface the melting temperature is lowered by 7 K. Contrary to what is found for films on the corrugated surface, these simulations show that there is a region of liquid--gas coexistence, demonstrating that this is a normal triple point system. Diffusion constants in these fluids are larger than for the fluids on the corrugated graphite surface. At low coverages, a crossover from activated diffusion to nonactivated diffusion is seen. The damping of the hydrodynamic modes causing the long--time tails in the velocity correlation function seems to be a little stronger on a corrugated surface than on a smooth surface.

  5. Nonsequential double ionization of molecules

    SciTech Connect

    Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Zakrzewski, Jakub; Eckhardt, Bruno

    2005-03-01

    Double ionization of diatomic molecules by short linearly polarized laser pulses is analyzed. We consider the final stage of the ionization process, that is the decay of a highly excited two electron molecule, which is formed after rescattering. The saddles of the effective adiabatic potential energy close to which simultaneous escape of electrons takes place are identified. Numerical simulations of the ionization of molecules show that the process can be dominated by either sequential or nonsequential events. In order to increase the ratio of nonsequential to sequential ionizations very short laser pulses should be applied.

  6. 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.

  7. Molecule-doped rare gas clusters: structure and stability of ArnNO(X2 Π potential energy surfaces of ArNO

    NASA Astrophysics Data System (ADS)

    Naumkin, F. Y.; Wales, D. J.

    High level ab initio calculations carried out for the 2A' and 2A'' states of ArNO(X2Π) predict a crossing near the T-shape configuration, with the 2A' minimum being slightly deeper. SΠn-orbit coupling is included through a model treatment and results in two potential energy surfaces with similar topologies, nearly parallel to each other and close to the averaged non-relativistic surface. These results are used to construct a DIM-like model for ArnNO clusters. The lowest energy cluster structures are found to resemble those for Arn+1 with NO lying in the surface. The set of major magic numbers (structures of pronounced stability) is also the same as for the Arn+1 clusters, and is emphasized further by the detachment of NO, which requires a larger energy than for detachment of a single Ar atom. The relations of the difference between the two dissociation energies and of the ArnNO(1/2 to 3/2) excitation energy to the magic numbers are discussed.

  8. DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules.

    PubMed

    Kumar, Anmol; Yeole, Sachin D; Gadre, Shridhar R; López, Rafael; Rico, Jaime F; Ramírez, Guillermo; Ema, Ignacio; Zorrilla, David

    2015-12-01

    DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

  9. 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.

  10. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules I. Reference Data at the CCSD(T) Complete Basis Set Limit.

    PubMed

    Richard, Ryan M; Marshall, Michael S; Dolgounitcheva, O; Ortiz, J V; Brédas, Jean-Luc; Marom, Noa; Sherrill, C David

    2016-02-01

    In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates. PMID:26731487

  11. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically.

  12. Amino Acid-Derived 1,2-Benzisothiazolinone Derivatives as Novel Small-Molecule Antifungal Inhibitors: Identification of Potential Genetic Targets

    PubMed Central

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William

    2012-01-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC50 values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  13. Amino acid-derived 1,2-benzisothiazolinone derivatives as novel small-molecule antifungal inhibitors: identification of potential genetic targets.

    PubMed

    Alex, Deepu; Gay-Andrieu, Francoise; May, Jared; Thampi, Linta; Dou, Dengfeng; Mooney, Aileen; Groutas, William; Calderone, Richard

    2012-09-01

    We have identified four synthetic compounds (DFD-VI-15, BD-I-186, DFD-V-49, and DFD-V-66) from an amino acid-derived 1,2-benzisothiazolinone (BZT) scaffold that have reasonable MIC(50) values against a panel of fungal pathogens. These compounds have no structural similarity to existing antifungal drugs. Three of the four compounds have fungicidal activity against Candida spp., Cryptococcus neoformans, and several dermatophytes, while one is fungicidal to Aspergillus fumigatus. The kill rates of our compounds are equal to those in clinical usage. The BZT compounds remain active against azole-, polyene-, and micafungin-resistant strains of Candida spp. A genetics-based approach, along with phenotype analysis, was used to begin mode of action (MOA) studies of one of these compounds, DFD-VI-15. The genetics-based screen utilized a homozygous deletion collection of approximately 4,700 Saccharomyces cerevisiae mutants. We identified mutants that are both hypersensitive and resistant. Using FunSpec, the hypersensitive mutants and a resistant ace2 mutant clustered within a category of genes related directly or indirectly to mitochondrial functions. In Candida albicans, the functions of the Ace2p transcription factor include the regulation of glycolysis. Our model is that DFD-VI-15 targets a respiratory pathway that limits energy production. Supporting this hypothesis are phenotypic data indicating that DFD-VI-15 causes increased cell-reactive oxidants (ROS) and a decrease in mitochondrial membrane potential. Also, the same compound has activity when cells are grown in a medium containing glycerol (mitochondrial substrate) but is much less active when cells are grown anaerobically. PMID:22687516

  14. Solvent-free MALDI-MS: developmental improvements in the reliability and the potential of MALDI in the analysis of synthetic polymers and giant organic molecules.

    PubMed

    Trimpin, S; Keune, S; Räder, H J; Müllen, K

    2006-05-01

    A dry sample preparation strategy was previously established as a new method for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS), so-called solvent-free MALDI-MS. In this contribution, we examine systems that have been shown problematic with conventional solvent-based MALDI approaches. Problems frequently encountered are solubility, miscibility, and segregation effects during crystallization as a result of unfavorable analyte and matrix polarities. In all cases studied, solvent-free MALDI-MS simplified the measurement and improved the analysis. Solvent-free MALDI-MS enables more reliable results in well-known problematic systems such as polydimethylsiloxane with its segregation effects. However, even in highly compatible analyte/matrix systems such as polystyrene and dithranol, there were undesirable suppression effects when employing THF as solvent. Generally, the solvent-free method allows for more homogeneous analyte/matrix mixtures as well as higher shot-to-shot and sample-to-sample reproducibility. As a result, less laser power has to be applied, which yields milder MALDI conditions, reduced background signals, and provides better resolution of the analyte signals. Solvent-free MALDI-MS proved valuable for the characterization of nanosized material, e.g., fullereno-based structures, which indicated having an increased fragmentation-susceptibility. New analyte/matrix combinations (e.g., polyvinylpyrrolidone/dithranol) are accessible independent of solubility and compatibility in common solvents. An improved quantitation potential is recognized (e.g., insoluble polycyclic aromatic hydrocarbon against soluble dendrite precursor). The rapid and easy measurement of industrial products demonstrates the solvent-free method capable for improved throughput analysis of a variety of compounds (e.g., poly(butylmethacrylate) diol) in routine industrial analysis. Hence, this new MALDI method leads to qualitative and quantitative improvements, making

  15. Up-regulation of IGF-1R by mutant RAS in leukemia and potentiation of RAS signaling inhibitors by small molecule inhibition of IGF-1R

    PubMed Central

    Weisberg, Ellen; Nonami, Atsushi; Chen, Zhao; Nelson, Erik; Chen, Yongfei; Liu, Feiyang; Cho, Haeyeon; Zhang, Jianming; Sattler, Martin; Mitsiades, Constantine; Wong, Kwok-Kin; Liu, Qingsong; Gray, Nathanael; Griffin, James D.

    2014-01-01

    Purpose Activating mutations in the RAS oncogene occur frequently in human leukemias. Direct targeting of RAS has proven to be challenging, although targeting of downstream RAS mediators, such as MEK, is currently being tested clinically. Given the complexity of RAS signaling, it is likely that combinations of targeted agents will be more effective than single agents. Experimental Design A chemical screen using RAS-dependent leukemia cells was developed to identify compounds with unanticipated activity in the presence of a MEK inhibitor, and led to identification of inhibitors of IGF-1R. Results were validated using cell-based proliferation assays and apoptosis, cell cycle, and gene knockdown assays, immunoprecipitation and immunoblotting, and a non-invasive in vivo bioluminescence model of acute myeloid leukemia (AML). Results Mechanistically, IGF-1R protein expression/activity was substantially increased in mutant RAS-expressing cells, and suppression of RAS led to decreases in IGF-1R. Synergy between MEK and IGF-1R inhibitors correlated with induction of apoptosis, inhibition of cell cycle progression, and decreased phospho-S6 and phospho-4E-BP1. In vivo, NSG mice tail vein-injected with OCI-AML3-luc+ cells showed significantly lower tumor burden following one week of daily oral administration of 50 mg/kg NVP-AEW541 (IGF-1R inhibitor) combined with 25 mg/kg AZD6244 (MEK inhibitor), as compared to mice treated with either agent alone. Drug combination effects observed in cell-based assays were generalized to additional mutant RAS-positive neoplasms. Conclusions The finding that downstream inhibitors of RAS signaling and IGF-1R inhibitors have synergistic activity warrants further clinical investigation of IGF-1R and RAS signaling inhibition as a potential treatment strategy for RAS-driven malignancies. PMID:25186968

  16. 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.

  17. 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 ...

  18. 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

  19. Phase structure of soliton molecules

    NASA Astrophysics Data System (ADS)

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

    2007-06-01

    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.

  20. 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.

  1. Formation of Ultracold Polar Molecules

    NASA Astrophysics Data System (ADS)

    Taylor-Juarros, E.; Côté, R.; Kirby, K.

    2002-05-01

    A variety of experimental techniques have been employed to create a number of ultracold molecules, including CaH, Na_2, K_2, Cs_2, Rb2 and CO. Novel effects are predicted to occur in samples of ultracold polar molecules.(L. Santos et al.), Phys. Rev. Lett. 85, 1791 (2000). We present calculations of the formation rate of ultracold hydrides (LiH, NaH, KH, RbH, and CsH), using the most accurate molecular potentials and dipole moments available. We show that these polar molecules can be produced in selected vibrational and rotational states by stimulated radiative association in a mixture of ultracold hydrogen and alkali metal atoms. We study the properties of these atomic mixtures as well as those of the hydrides, and explore the effect of shape resonances on the formation rates. [2ex] *Supported by NSF

  2. 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.

  3. 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.

  4. [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.

  5. 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)

  6. 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.

  7. Relating single-molecule measurements to thermodynamics.

    PubMed

    Keller, David; Swigon, David; Bustamante, Carlos

    2003-02-01

    Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and which are allowed to fluctuate. Thus an experiment in which the end-to-end distance of the polymer molecule is fixed and the tension fluctuates yields a different result than an experiment where the force is fixed and the end-to-end distance fluctuates. It is further shown that this difference is due to asymmetry in the distribution of end-to-end distances for a single molecule, and that the difference vanishes in the appropriate thermodynamic limit; that is, as the polymer molecule becomes long compared to its persistence length. Despite these differences, much of the thermodynamic formalism still applies on the single-molecule level if the thermodynamic free energies are replaced with appropriate potentials of mean force. The primary remaining differences are consequences of the fact that unlike the free energies, the potentials of mean force are not in general homogeneous functions of their variables. The basic thermodynamic concepts of an intensive or extensive quantity, and the thermodynamic relationships that follow from them, are therefore less useful for interpreting single-molecule experiments.

  8. Vertically coupled dipolar exciton molecules

    NASA Astrophysics Data System (ADS)

    Cohen, Kobi; Khodas, Maxim; Laikhtman, Boris; Santos, Paulo V.; Rapaport, Ronen

    2016-06-01

    While the interaction potential between two dipoles residing in a single plane is repulsive, in a system of two vertically adjacent layers of dipoles it changes from repulsive interaction in the long range to attractive interaction in the short range. Here we show that for dipolar excitons in semiconductor heterostructures, such a potential may give rise to bound states if two such excitons are excited in two separate layers, leading to the formation of vertically coupled dipolar exciton molecules. Our calculations prove the existence of such bound states and predict their binding energy as a function of the layers separation as well as their thermal distributions. We show that these molecules should be observed in realistic systems such as semiconductor coupled quantum well structures and the more recent van der Waals bound heterostructures. Formation of such molecules can lead to new effects such as a collective dipolar drag between layers and new forms of multiparticle correlations, as well as to the study of dipolar molecular dynamics in a controlled system.

  9. Linking ultracold polar molecules.

    PubMed

    Avdeenkov, A V; Bohn, John L

    2003-01-31

    We predict that pairs of polar molecules can be weakly bound together in an ultracold environment, provided that a dc electric field is present. The field that links the molecules together also strongly influences the basic properties of the resulting dimer, such as its binding energy and predissociation lifetime. Because of their long-range character, these dimers will be useful in disentangling cold collision dynamics of polar molecules. As an example, we estimate the microwave photoassociation yield for OH-OH cold collisions.

  10. Interlocked molecules: Aqueous assembly

    NASA Astrophysics Data System (ADS)

    Bai, Linyi; Zhao, Yanli

    2015-12-01

    The quantitative self-assembly of mechanically interlocked molecules in water, instead of organic solvents, opens up the possibility of such systems being used in a biological context where their functions can be interfaced with biomolecular systems.

  11. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  12. 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)

  13. Ultralong-range polyatomic Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Gonzalez-Ferez, Rosario

    2016-05-01

    Ultralong-range polyatomic Rydberg molecules are formed when a ground-state atom is bound to a Rydberg atom. The binding mechanism of these Rydberg molecules is based on the low-energy collisions between a Rydberg electron and a ground-state atom and leads to the unusual oscillatory behavior of the adiabatic potential energy curves. If the ground-state atom immersed into the Rydberg wave function is replaced by a heteronuclear diatomic molecule another type of polyatomic Rydberg molecules can form. In this case, the Rydberg electron is coupled to the internal states of the polar ground-state molecule. In this talk, we will explore the electronic structure and rovibrational properties of these ultralong-range polyatomic Rydberg molecule. For the second type of Rydberg molecules, the polar dimer is allowed to rotate in the electric fields generated by the Rydberg electron and Rydberg core as well as an additional external field. We will investigate the metamorphosis of the Born-Oppenheimer potential curves, essential for the binding mechanism, with varying electric field and analyze the resulting properties such as the vibrational structure and the alignment and orientation of the polar dimer.

  14. Circularly Polarized Luminescence from Simple Organic Molecules

    PubMed Central

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

    2015-01-01

    This article aims to show the identity of “CPL-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 nonaggregated) 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. PMID:26136234

  15. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  16. 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.

  17. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  18. Single Molecule Manipulation

    NASA Astrophysics Data System (ADS)

    Kiang, Ching-Hwa

    2011-10-01

    Single-molecule manipulation studies open a door for a close-up investigation of complex biological interactions at the molecular level. In these studies, single biomolecules are pulled while their force response is being monitored. The process is often nonequilibrium, and interpretation of the results has been challenging. We used the atomic force microscope to pull proteins and DNA, and determined the equilibrium properties of the molecules using the recently derived nonequilibrium work theorem. I will present applications of the technique in areas ranging from fundamental biological problems such as DNA mechanics, to complex medical processes such as the mechanical activation of von Willebrand Factor, a key protein in blood coagulation.

  19. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  20. Single-molecule junctions beyond electronic transport.

    PubMed

    Aradhya, Sriharsha V; Venkataraman, Latha

    2013-06-01

    The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications.

  1. 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.

  2. 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…

  3. Halley's polymeric organic molecules

    NASA Technical Reports Server (NTRS)

    Huebner, W. F.; Boice, D. C.; Korth, A.

    1989-01-01

    The detection of polymeric organic compounds in the mass spectrum of Comet Halley obtained with the Positive Ion Cluster Composition analyzer on Giotto are examined. It is found that, in addition to polyoxymethylene, other polymers and complex molecules may exist in the comet. It is suggested that polymerized hydrogen cyanide may be a source for the observed CN and NH2 jets.

  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. Nanoparticle bridges for studying electrical properties of organic molecules.

    PubMed

    Leifer, Klaus; Welch, Ken; Jafri, Syed Hassan Mujtaba; Blom, Tobias

    2012-01-01

    The use of single molecules as building blocks for practical electronic devices and sensors has high potential for novel applications due to the versatility of electronic properties of the molecules. Nano-sized molecules offer great potential for further miniaturization of electronic devices. We describe a method where such molecules are used to bridge a nanoparticles-nanoelectrode interface and thus determine the electrical properties of such a junction. We describe in detail the fabrication of the platform, its functionalization with molecules, and the basics of the electrical measurements. This platform has been shown to guide electrical current through a few molecules. The versatility of such nanoparticle-molecule-nanoelectrode heterojunctions makes this platform suitable for both basic molecular electronics measurements and also for molecular sensing devices in biological and medical applications. PMID:22791462

  6. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    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. PMID:22985496

  7. OMG: Open Molecule Generator.

    PubMed

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

    2012-01-01

    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. PMID:22985496

  8. 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.

  9. 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.

  10. 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

  11. Spin Hall separation of ultracold atom-molecule mixed gases

    NASA Astrophysics Data System (ADS)

    Ye, Chong; Fu, Li-Bin; Liu, Jie

    2016-05-01

    We propose a theoretical scheme to separate a molecular cloud from atoms in analogy to the spin Hall effect and to completely transfer Feshbach molecules to the ground state by applying a spatially modulated laser field to an atom-molecule mixed gas. In particular, the laser-molecule interaction induces a synthetic U(1) gauge potential for the dressed molecular dark state. Through numerical simulation, we demonstrate that such a gauge field leads to a spin Hall separation of atoms and molecules. In such a process, molecules can be transformed into the ground state completely.

  12. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  13. Cometary Parent Molecules

    NASA Astrophysics Data System (ADS)

    Feldman, Paul

    1990-12-01

    We propose to use HRS observations of a suitable target-of-opportunity comet to study two outstanding problems related to the composition of the volatile component of the cometary nucleus. These problems concern two species, CO and S2, which have been observed in the cometary coma and identified as "parent" molecules sublimating directly from the nucleus. Both of these molecules have their principal fluorescent emissions in the vaccuum ultraviolet. The high spectral resolution will allow the determination of the rotational temperature of CO, which is diagnostic of the source temperature and the excitation mechanism of the observed emission. The determination of the abundance of both CO and S2 in the primarily water ice of the nucleus can serve to constrain current models of comet formation in the primordial solar nebula.

  14. 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.

  15. Spacer conformation in biologically active molecules. Part 2. Structure and conformation of 4-[2-(diphenylmethylamino)ethyl]-1-(2-methoxyphenyl) piperazine and its diphenylmethoxy analog—potential 5-HT 1A receptor ligands

    NASA Astrophysics Data System (ADS)

    Karolak-Wojciechowska, J.; Fruziński, A.; Czylkowski, R.; Paluchowska, M. H.; Mokrosz, M. J.

    2003-09-01

    As a part of studies on biologically active molecule structures with aliphatic linking chain, the structures of 4-[2-diphenylmethylamino)ethyl]-1-(2-methoxyphenyl)piperazine dihydrochloride ( 1) and 4-[2-diphenylmethoxy)ethyl]-1-(2-methoxyphenyl)piperazine fumarate ( 2) have been reported. In both compounds, four atomic non-all-carbons linking chains (N)C-C-X-C are present. The conformation of that linking spacer depends on the nature of the X-atom. The preferred conformation for chain with XNH has been found to be fully extended while for that with XO—the bend one. It was confirmed by conformational calculations (strain energy distribution and random search) and crystallographic data, including statistics from CCDC.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. Single-molecule electronics: from chemical design to functional devices.

    PubMed

    Sun, Lanlan; Diaz-Fernandez, Yuri A; Gschneidtner, Tina A; Westerlund, Fredrik; Lara-Avila, Samuel; Moth-Poulsen, Kasper

    2014-11-01

    The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable us to continue the trend of aggressive downscaling of silicon-based electronic devices. More significantly, the fabrication, understanding and control of fully functional circuits at the single-molecule level could also open up the possibility of using molecules as devices with novel, not-foreseen functionalities beyond complementary metal-oxide semiconductor technology (CMOS). This review aims at highlighting the chemical design and synthesis of single molecule devices as well as their electrical and structural characterization, including a historical overview and the developments during the last 5 years. We discuss experimental techniques for fabrication of single-molecule junctions, the potential application of single-molecule junctions as molecular switches, and general physical phenomena in single-molecule electronic devices.

  1. Cold and ultracold molecules: spotlight on orbiting resonances.

    PubMed

    Chandler, David W

    2010-03-21

    There is great interest in the production of cold molecules, at temperatures below 1 K, and ultracold molecules, at temperatures below 1 mK. Such molecules have potential applications in areas ranging from precision measurement to quantum information storage and processing, and quantum gases of ultracold polar molecules are expected to exhibit novel quantum phases. In addition, cold molecules open up a new domain for collision physics, dominated by long-range forces and scattering resonances. There have been major recent advances both in cooling molecules from room temperature and in forming molecules in ultracold atomic gases. As these techniques mature, and cold and ultracold samples are more accessible, collision studies at previously unavailable energies will be possible. This spotlight article will highlight some of the background and motivation for studying collisions at low energies and will direct readers to recent articles on the recent experimental advancements.

  2. Single-Molecule Sensors: Challenges and Opportunities for Quantitative Analysis.

    PubMed

    Gooding, J Justin; Gaus, Katharina

    2016-09-12

    Measurement science has been converging to smaller and smaller samples, such that it is now possible to detect single molecules. This Review focuses on the next generation of analytical tools that combine single-molecule detection with the ability to measure many single molecules simultaneously and/or process larger and more complex samples. Such single-molecule sensors constitute a new type of quantitative analytical tool, as they perform analysis by molecular counting and thus potentially capture the heterogeneity of the sample. This Review outlines the advantages and potential of these new, quantitative single-molecule sensors, the measurement challenges in making single-molecule devices suitable for analysis, the inspiration biology provides for overcoming these challenges, and some of the solutions currently being explored.

  3. Single-Molecule Sensors: Challenges and Opportunities for Quantitative Analysis.

    PubMed

    Gooding, J Justin; Gaus, Katharina

    2016-09-12

    Measurement science has been converging to smaller and smaller samples, such that it is now possible to detect single molecules. This Review focuses on the next generation of analytical tools that combine single-molecule detection with the ability to measure many single molecules simultaneously and/or process larger and more complex samples. Such single-molecule sensors constitute a new type of quantitative analytical tool, as they perform analysis by molecular counting and thus potentially capture the heterogeneity of the sample. This Review outlines the advantages and potential of these new, quantitative single-molecule sensors, the measurement challenges in making single-molecule devices suitable for analysis, the inspiration biology provides for overcoming these challenges, and some of the solutions currently being explored. PMID:27444661

  4. 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

  5. Synthesis and characterization of various ruthenium small molecules and metallopolymers for potential use in photovoltaic devices and luminescence properties of N-heterocyclic carbenes and trifluoro methylated tris(pyrazolyl)borate silver (I) acid-base adducts

    NASA Astrophysics Data System (ADS)

    Chitikuri, Shylaja

    This thesis with its 66 pages, 1 table, 29 figures and 47 references, deals with two major topics involving structure and properties of selected metal complexes and their use in electronic devices. The first chapter discusses the development of ruthenium-based metallopolymer and small molecular complexes toward possible utilization as active materials for solar cells. Such complexes have been found to be good "black absorbers" with solid-state absorption that spans the entire visible region into the near-infrared, representing an impressive overlap with the solar radiation that is more favorable than common molecular solar cell active materials. The second chapter includes photophysical studies of different metallo N-heterocyclic carbenes and acid-base adducts comprising fluorinated tris(pyrazolyl)borate silver(I) complexes coordinated to different solvent and aromatic molecules. These species have been investigated and found to exhibit unusual photophysical properties, including metal-free phosphorescence at room temperature with high quantum yield, multi-color emission from a single compound, and selective sensing of temperature and hazardous vapors.

  6. Electrostatic propulsion using C60 molecules

    NASA Technical Reports Server (NTRS)

    Leifer, Stephanie D.; Rapp, Donald; Saunders, Winston A.

    1992-01-01

    An evaluation is made of the potential benefits of C60 molecules as a basis for ion propulsion. Because C60 is storable, its use may result in a larger usable propellant fraction than previous methods of cluster ion propulsion. C60 may also relax such engineering constraints as grid spacing, which restrict the performance of noble gas ion propulsion. The behavior of C60 in a plasma discharge environment, as well as various electron impact cross sections of the molecule, will greatly afftect the feasibility of the concept.

  7. Molecular spintronics using single-molecule magnets.

    PubMed

    Bogani, Lapo; Wernsdorfer, Wolfgang

    2008-03-01

    A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

  8. 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.

  9. Melatonin: a multitasking molecule.

    PubMed

    Reiter, Russel J; Tan, Dun-Xian; Fuentes-Broto, Lorena

    2010-01-01

    Melatonin (N-acetyl-5-methoxytryptamine) has revealed itself as an ubiquitously distributed and functionally diverse molecule. The mechanisms that control its synthesis within the pineal gland have been well characterized and the retinal and biological clock processes that modulate the circadian production of melatonin in the pineal gland are rapidly being unravelled. A feature that characterizes melatonin is the variety of mechanisms it employs to modulate the physiology and molecular biology of cells. While many of these actions are mediated by well-characterized, G-protein coupled melatonin receptors in cellular membranes, other actions of the indole seem to involve its interaction with orphan nuclear receptors and with molecules, for example calmodulin, in the cytosol. Additionally, by virtue of its ability to detoxify free radicals and related oxygen derivatives, melatonin influences the molecular physiology of cells via receptor-independent means. These uncommonly complex processes often make it difficult to determine specifically how melatonin functions to exert its obvious actions. What is apparent, however, is that the actions of melatonin contribute to improved cellular and organismal physiology. In view of this and its virtual absence of toxicity, melatonin may well find applications in both human and veterinary medicine.

  10. Ultracold triplet molecules in the rovibrational ground state.

    PubMed

    Lang, F; Winkler, K; Strauss, C; Grimm, R; Denschlag, J Hecker

    2008-09-26

    We report here on the production of an ultracold gas of tightly bound Rb2 triplet molecules in the rovibrational ground state, close to quantum degeneracy. This is achieved by optically transferring weakly bound Rb2 molecules to the absolute lowest level of the ground triplet potential with a transfer efficiency of about 90%. The transfer takes place in a 3D optical lattice which traps a sizeable fraction of the tightly bound molecules with a lifetime exceeding 200 ms. PMID:18851446

  11. 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.

  12. 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.

  13. Electron Transport Through Single Fullerene Molecules (abstract)

    NASA Astrophysics Data System (ADS)

    Stróżecka, Anna; Muthukumar, Kaliappan; Larsson, J. Andreas; Voigtländer, Bert

    2009-04-01

    Fullerenes show potential for applications in nanotechnology due to the possibility of tuning their properties by doping or functionalization. In particular, the endohedral doping of the hollow carbon cage with metal atoms allows changing the electronic and magnetic properties of the molecule without distorting the geometry of the outer shell. Here we present a low temperature scanning tunneling microscopy (STM) and spectroscopy study of the vibrational and transport properties of Ce2atC80 metallofullerenes. We observe that electron transport through the endohedral fullerene is strongly mediated by excitation of molecular vibrations, especially the dynamics of encapsulated atoms. We measure the conductance of the single-molecule junction upon contact between the molecule and the STM tip. To determine the role of doping atoms we compare the results obtained for the endohedrally doped species with those for a hollow fullerene. Analysis shows that localization of electron density on encapsulated atoms hinders the conduction process through the fullerene.

  14. Conformational dynamics of peptide T molecule

    NASA Astrophysics Data System (ADS)

    Akverdieva, Gulnare; Godjayev, Niftali; Akyuz, Sevim

    2002-05-01

    Using a method of the theoretical conformational analysis, a conformational dynamics of the side chains of the amino acid residues of peptide T, a competitor of the human immuno-deficiency virus in the binding to human T cells, was investigated. For this purpose, the conformational maps of the potential surfaces were constructed over the angles of the side chains for the preferable conformations of peptide T molecule. Permissible deviations of these angles from the optimal values were determined. It has been found that the angles of the side chains of the amino acid residues involved in physiologically active fragment Thr4-Thr8 are more rigid than in the other segment of the molecule. This fact confirms the existence of such a regular structure as β-turn revealed previously in studies of the spatial structure of the peptide T molecule.

  15. Genetically engineered antibody molecules and their application.

    PubMed

    Morrison, S L; Wims, L; Wallick, S; Tan, L; Oi, V T

    1987-01-01

    Immunoglobulin genes can be efficiently expressed following transfection into myeloma cells. Using protoplast fusion, transfection frequencies greater than 10(-3) can be achieved. Compatible plasmids containing two different selectible markers are used to simultaneously deliver heavy and light chain genes to the same cell. To produce molecules with differing specificities the rearranged and expressed variable regions can be cloned from the appropriate hybridoma. In some cases, variable regions from cDNAs can be inserted into the expression vectors. It is possible to manipulate the immunoglobulin genes and produce novel antibody molecules. Antibodies have been produced in which the variable regions from mouse antibodies have been joined to human constant regions. In addition, antibodies with altered constant regions have been produced. These genetically engineered antibodies provide a unique set of reagents to study structure-function relationships within the molecule. They also can potentially be used in the diagnosis and therapy of human disease.

  16. Profiling protein function with small molecule microarrays

    PubMed Central

    Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

    2002-01-01

    The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

  17. 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

  18. Analytic Empirical Potentials for BeH^+, BeD^+, and BeT^+ Including up to 4TH Order QED in the Long-Range and Predictions for the Halo Nucleonic Molecules 11BeH^+ and 14BeH^+.

    NASA Astrophysics Data System (ADS)

    Li Chun Fong, Lena C. M.; Lach, Grzegorz; Le Roy, Robert J.; Dattani, Nikesh S.

    2015-06-01

    The 13.81(8)s half-life of the halo nucleonic atom 11Be is orders of magnitude longer than those for any other halo nucleonic atom known, and makes Be-based diatomics the most promising candidates for the formation of the first halo nucleonic molecules. However, the 4e^- species LiH and BeH^+ are some of the first molecules for which the highest accuracy ab initio methods are not accessible, so empirical potential energy functions will be important for making predictions and for benchmarking how ab initio calculations break down at this transition from 3e^- to 4e^-. BeH^+ is also very light, and has one of the most extensive data sets involving a tritium isotopologue, making it a very useful benchmark for studying Born-Oppenheimer breakdown. We therefore seek to determine an empirical analytic potential energy function for BeH^+ that has as much precision as possible. To this end, all available spectroscopic data for all stable isotopologues of BeH^+ are analyzed in a standard direct-potential-fit procedure that uses least-squares fits to optimize the parameters defining an analytic potential. The ``Morse/Long-range'' (MLR) model used for the potential energy function incorporates the inverse-power long-range tail required by theory, and the calculation of the leading long-range coefficients C_4, C_6, C_7, and C_8 include non-adiabatic terms, and up to 4th order QED corrections. As a by-product, we have calculated some fundamental properties of 1e^- systems with unprecedented precision, such as the dipole, quadrupole, octupole, non-adiabatic, and mixed higher order polarizabilities of hydrogen, deuterium, and tritium. We provide good first estimates for the transition energies for the halo nucleonic species 11BeH^+ and 14BeH^+.

  19. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?

  20. 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.

  1. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another? PMID:17328425

  2. 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.

  3. Ultracold molecules from the bottom-up

    NASA Astrophysics Data System (ADS)

    Zhang, Jessie T.; Hutzler, Nicholas R.; Liu, Lee R.; Yu, Yichao; Ni, Kang-Kuen

    2016-05-01

    Ultracold polar molecules exhibit strong, long-range, and tunable dipole-dipole interactions that may be utilized for a wide range of studies in quantum simulation and quantum information processing. To realize the full potential of these studies, it is desirable to have a low entropy sample of ultracold polar molecules with full control over both internal and external states, as well as inter-particle interactions. We work toward this goal with a new, bottom-up approach using the highly polar NaCs molecule. The key steps of our scheme are trapping single Na and Cs atoms in optical dipole traps, cooling the atoms to their motional ground state using Raman sideband cooling, and finally coherently transferring them to ground state NaCs molecules via a two-photon process. This approach should enable creation of low entropy samples with full control over all degrees of freedom, as well as realizing the possibility of single-site read-out and manipulation of molecules.

  4. Lesser-Known Molecules in Ovarian Carcinogenesis

    PubMed Central

    Lozneanu, Ludmila; Cojocaru, Elena; Giuşcă, Simona Eliza; Cărăuleanu, Alexandru; Căruntu, Irina-Draga

    2015-01-01

    Currently, the deciphering of the signaling pathways brings about new advances in the understanding of the pathogenic mechanism of ovarian carcinogenesis, which is based on the interaction of several molecules with different biochemical structure that, consequently, intervene in cell metabolism, through their role as regulators in proliferation, differentiation, and cell death. Given that the ensemble of biomarkers in OC includes more than 50 molecules the interest of the researchers focuses on the possible validation of each one's potential as prognosis markers and/or therapeutic targets. Within this framework, this review presents three protein molecules: ALCAM, c-FLIP, and caveolin, motivated by the perspectives provided through the current limited knowledge on their role in ovarian carcinogenesis and on their potential as prognosis factors. Their structural stability, once altered, triggers the initiation of the sequences characteristic for ovarian carcinogenesis, through their role as modulators for several signaling pathways, contributing to the disruption of cellular junctions, disturbance of pro-/antiapoptotic equilibrium, and alteration of transmission of the signals specific for the molecular pathways. For each molecule, the text is built as follows: (i) general remarks, (ii) structural details, and (iii) particularities in expression, from different tumors to landmarks in ovarian carcinoma. PMID:26339605

  5. 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.

  6. 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.

  7. 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

  8. Coherent Transfer of Photoassociated Molecules into the Rovibrational Ground State

    NASA Astrophysics Data System (ADS)

    Inouye, Shin

    2011-05-01

    Recently, there have been impressive advances in methods of creating ultracold molecules from ultracold atomic gases. One of the key technologies used there is Stimulated Raman Adiabatic Passage (STIRAP), which has been successfully used for transferring Feshbach molecules into the rovibrational ground state. Since STIRAP relies on quantum coherence, it is unclear if STIRAP is also useful for non-polarized sample, like photo-associated molecules in a magneto-optical trap. Here we report on the SITRAP transfer of weakly bound molecules produced by photoassociation (PA). Laser cooled 41 K and 87 Rb atoms were first photo-associated into loosely-bound molecules in the X 1 Σ potential. Using v = 41, J = 1 level in the (3) 1 Σ potential as an intermediate level, we succeeded in transferring molecules in the v = 91, J = 0 level into the absolute ground state (X 1 Σ , v = 0, N = 0). High-resolution spectroscopy based on the coherent transfer revealed the hyperfine structure of both weakly-bound and tightly-bound molecules. Our results show that a pure sample of ultracold ground-state molecules is achieved via the all-optical association of laser-cooled atoms, opening possibilities to coherently manipulate a wide variety of molecules.In collaboration with Kiyotaka Aikawa, Kohei Oasa, University of Tokyo; Masahito Ueda, University of Tokyo, JST, ERATO; Jun Kobayashi, University of Tokyo; and Tetsuo Kishimoto, University of Electro-Communications.

  9. Collisions of molecules with clusters: A quasiclassical study

    SciTech Connect

    Jellinek, J.; Guevenc, Z.B.

    1993-08-01

    Presented are results of a quasiclassical simulation study of processes induced by a collision of a D{sub 2} molecule with a Ni{sub 13} cluster. Focus was on the reactive channel, i.e., dissociative adsorption of the molecule. Dependence on factors such as the collision energy, initial (quantized) rovibrational state of the molecule, and structure and temperature of cluster were analyzed. Direct and indirect (involving formation of transient complexes -- resonances) reaction pathways were considered and characterized quantitatively. We have illustrated how multidimensional potential energy surfaces describing cluster-molecule interactions can be analyzed in terms of a reduced set of relevant degrees of freedom and the topologies of these surfaces correlated with dynamical phenomena extracted from the calculations. The complex problem of ``tuning`` the cluster-molecule interaction potential using experimental data has also been addressed, and a specific example of such ``tuning`` has been given. It underscores the crucial role of the intimate interplay between theory and experiment, especially in the field of clusters where, because of the large number of degrees of freedom involved, first principle calculations are (and will remain) of limited feasibility. More generally, the analysis and the discussion presented show that the phenomena and problems relevant for cluster-molecule collisions -- a new research area by all accounts have much in common with those encountered in nucleus-nucleus, atom-atom, atom-molecule, and molecule-molecule collisions -- research fields with a considerable history.

  10. Molecular mechanism of CO2 and SO2 molecules binding to the air/liquid interface of 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid: A Molecular dynamics study with polarizable potential models

    SciTech Connect

    Wick, Collin D.; Chang, Tsun-Mei; Dang, Liem X.

    2010-11-25

    Molecular dynamics simulations with many-body interactions were carried out to understand the bulk and interfacial absorption of gases in 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF4). A new polarizable molecular model was developed for BMIMBF4, which was found to give the correct liquid density, but also had good agreement with experiment for its surface tension and X-ray reflectivity. The potential of mean force of CO2 and SO2 were calculated across the air-BMIMBF4 interface, and the bulk free energies were calculated with the free energy perturbation method. A new polarizable model was also developed for CO2. The air-BMIMBF4 interface had enhanced BMIM density, which was mostly related to its butyl group, followed by enhanced BF4 density a few angstroms towards the liquid bulk. The density profiles were observed to exhibit oscillations between high BMIM and BF4 density, indicating the presence of surface layering induced by the interface. The potential of mean force for CO2 and SO2 showed more negative free energies in regions of enhanced BF4 density, while more positive free energies in regions of high BMIM density. Moreover, these gases showed free energy minimums at the interface, where the BMIM alkyl groups were found to be most prevalent. Our results show the importance of ionic liquid interfacial ordering for understanding gas solvation in them. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  11. 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.

  12. 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.

  13. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  14. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole–dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  15. Energy Transfer Involving Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Gibbons, John Paul

    three colliding pairs, the experimental results lie between the results calculated for the same two sets of potential parameters. These parameters were those calculated to match the short range Lennard-Jones potential and a set obtained by a theoretical Thomas-Fermi treatment of the molecules.

  16. Tunneling, diffusion, and dissociation of Feshbach molecules in optical lattices

    NASA Astrophysics Data System (ADS)

    Bailey, Taylor; Bertulani, Carlos A.; Timmermans, Eddy

    2012-03-01

    The quantum dynamics of an ultracold diatomic molecule tunneling and diffusing in a one-dimensional optical lattice exhibits unusual features. While it is known that the process of quantum tunneling through potential barriers can break up a bound-state molecule into a pair of dissociated atoms, interference and reassociation produce intricate patterns in the time-evolving site-dependent probability distribution for finding atoms and bound-state molecules. We find that the bound-state molecule is unusually resilient against break up at ultralow binding energy Eb (Eb much smaller than the barrier height of the lattice potential). After an initial transient, the bound-state molecule spreads with a width that grows as the square root of time. Surprisingly, the width of the probability of finding dissociated atoms does not increase with time as a power law.

  17. 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.

  18. Engineering vascularized tissues using natural and synthetic small molecules

    PubMed Central

    Sefcik, Lauren S; Petrie Aronin, Caren E

    2008-01-01

    Vascular growth and remodeling are complex processes that depend on the proper spatial and temporal regulation of many different signaling molecules to form functional vascular networks. The ability to understand and regulate these signals is an important clinical need with the potential to treat a wide variety of disease pathologies. Current approaches have focused largely on the delivery of proteins to promote neovascularization of ischemic tissues, most notably VEGF and FGF. Although great progress has been made in this area, results from clinical trials are disappointing and safer and more effective approaches are required. To this end, biological agents used for therapeutic neovascularization must be explored beyond the current well-investigated classes. This review focuses on potential pathways for novel drug discovery, utilizing small molecule approaches to induce and enhance neovascularization. Specifically, four classes of new and existing molecules are discussed, including transcriptional activators, receptor selective agonists and antagonists, natural product-derived small molecules, and novel synthetic small molecules. PMID:19337401

  19. 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.

  20. ADAM metallopeptidase domain 17 (ADAM17) is naturally processed through major histocompatibility complex (MHC) class I molecules and is a potential immunotherapeutic target in breast, ovarian and prostate cancers

    PubMed Central

    Sinnathamby, G; Zerfass, J; Hafner, J; Block, P; Nickens, Z; Hobeika, A; Secord, A A; Lyerly, H K; Morse, M A; Philip, R

    2011-01-01

    Selection of suitable antigens is critical for the development of cancer vaccines. Most desirable are over-expressed cell surface proteins that may serve as targets for both antibodies and T cells, thus maximizing a concerted immune response. Towards this goal, we characterized the relevance of tumour necrosis factor-α-converting enzyme (ADAM17) for such targeted therapeutics. ADAM17 is one of the several metalloproteinases that play a key role in epidermal growth factor receptor (EGFR) signalling and has recently emerged as a new therapeutic target in several tumour types. In the present study, we analysed the expression profile of ADAM17 in a variety of normal and cancer cells of human origin and found that this protein is over-expressed on the surface of several types of cancer cells compared to the normal counterparts. Furthermore, we analysed the presentation of a human leucocyte antigen (HLA)-A2-restricted epitope from ADAM17 protein to specific T cells established from normal donors as well as ovarian cancer patients. Our analysis revealed that the HLA-A2-restricted epitope is processed efficiently and presented by various cancer cells and not by normal cells. Tumour-specific T cell activation results in the secretion of both interferon-γ and granzyme B that can be blocked by HLA-A2 specific antibodies. Collectively, our data present evidence that ADAM17 can be a potential target antigen to devise novel immunotherapeutic strategies against ovarian, breast and prostate cancer. PMID:21175594

  1. ADAM metallopeptidase domain 17 (ADAM17) is naturally processed through major histocompatibility complex (MHC) class I molecules and is a potential immunotherapeutic target in breast, ovarian and prostate cancers.

    PubMed

    Sinnathamby, G; Zerfass, J; Hafner, J; Block, P; Nickens, Z; Hobeika, A; Secord, A A; Lyerly, H K; Morse, M A; Philip, R

    2011-03-01

    Selection of suitable antigens is critical for the development of cancer vaccines. Most desirable are over-expressed cell surface proteins that may serve as targets for both antibodies and T cells, thus maximizing a concerted immune response. Towards this goal, we characterized the relevance of tumour necrosis factor-α-converting enzyme (ADAM17) for such targeted therapeutics. ADAM17 is one of the several metalloproteinases that play a key role in epidermal growth factor receptor (EGFR) signalling and has recently emerged as a new therapeutic target in several tumour types. In the present study, we analysed the expression profile of ADAM17 in a variety of normal and cancer cells of human origin and found that this protein is over-expressed on the surface of several types of cancer cells compared to the normal counterparts. Furthermore, we analysed the presentation of a human leucocyte antigen (HLA)-A2-restricted epitope from ADAM17 protein to specific T cells established from normal donors as well as ovarian cancer patients. Our analysis revealed that the HLA-A2-restricted epitope is processed efficiently and presented by various cancer cells and not by normal cells. Tumour-specific T cell activation results in the secretion of both interferon-γ and granzyme B that can be blocked by HLA-A2 specific antibodies. Collectively, our data present evidence that ADAM17 can be a potential target antigen to devise novel immunotherapeutic strategies against ovarian, breast and prostate cancer. PMID:21175594

  2. Pyridine sulfonamide as a small key organic molecule for the potential treatment of type-II diabetes mellitus and Alzheimer's disease: In vitro studies against yeast α-glucosidase, acetylcholinesterase and butyrylcholinesterase.

    PubMed

    Riaz, Sadaf; Khan, Islam Ullah; Bajda, Marek; Ashraf, Muhammad; Qurat-Ul-Ain; Shaukat, Ayesha; Rehman, Tanzeel Ur; Mutahir, Sadaf; Hussain, Sajjad; Mustafa, Ghulam; Yar, Muhammad

    2015-12-01

    This paper presents the efficient high yield synthesis of novel pyridine 2,4,6-tricarbohydrazide derivatives (4a-4i) along with their α-glucosidase, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition activities. The enzymes inhibition results showed the potential of synthesized compounds in controlling both type-II diabetes mellitus and Alzheimer's disease. In vitro biological investigations revealed that most of compounds were more active against yeast α-glucosidase than the reference compound acarbose (IC50 38.25±0.12μM). Among the tested series the compound 4c bearing 4-flouro benzyl group was noted to be the most active (IC50 25.6±0.2μM) against α-glucosidase, and it displayed weak inhibition activities against AChE and BChE. Compound 4a exhibited the most desired results against all three enzymes, as it was significantly active against all the three enzymes; α-glucosidase (IC50 32.2±0.3μM), AChE (IC50 50.2±0.8μM) and BChE (IC50 43.8±0.8μM). Due to the most favorable activity of 4a against the tested enzymes, for molecular modeling studies this compound was selected to investigate its pattern of interaction with α-glucosidase and AChE targets.

  3. Aromatic molecules as spintronic devices

    SciTech Connect

    Ojeda, J. H.; Orellana, P. A.; Laroze, D.

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  4. Part I. Evaluation of thermodynamic and kinetic parameters for electron transfer and following chemical reaction from a global analysis of current-potential-time data. Part II. Electro-catalytic detection in high-performance liquid chromatography of vitamin B[sub 12] and other molecules of biological and environmental interest

    SciTech Connect

    Kumar, V.T.

    1992-01-01

    Simultaneous evaluation of electron transfer rate constant, k[sup 0], following chemical reaction rate constant, k[sub f], electron transfer coefficient, [alpha] and standard potential, E[sup 0][prime] for an electrochemical reaction following the EC mechanism is described. A mathematical model for the current response to a potential step is developed, starting with the Butler-Volmer equation for electrode kinetics and concentration expressions for the redox couple. The resulting integral equations are solved numerically via the Step Function method. Current-potential and current-time curves are simulated and tested under limiting conditions. The four parameters of the system are evaluated by fitting simulated current-voltage-time (i-E-t) surface to the theoretical equation. The method is applied to study an important biological molecule, viz., methyl cobalamin, in DMSO. Included in the discussion part is the use of kinetic zone diagrams to depict chronoamperometric current response as a function of dimensionless rate constants for the EC reaction scheme. This compact display of the influence of the two rate constants on current in all time windows can be used to select the best data for analysis. Theoretical limits of measurable rate constants can be estimated from the zone diagram. The development of a dropping mercury electrode detector for High Performance Liquid Chromatography (HPLC) and its application to analysis of B[sub 12] and other vitamins is described. This EC detector is able to achieve high levels of sensitivity by exploiting the catalytic hydrogen evolution undergone by many nitrogenous organic molecules. Vitamin B[sub 12], thiamine, riboflavin and niacinamide were analyzed individually and in mixtures on reverse phase C18 column. Preliminary results from the analysis of commercial multivitamin preparations are also discussed.

  5. Evaluating enzymatic synthesis of small molecule drugs.

    PubMed

    Moura, Matthew; Finkle, Justin; Stainbrook, Sarah; Greene, Jennifer; Broadbelt, Linda J; Tyo, Keith E J

    2016-01-01

    There have been many achievements in applying biochemical synthetic routes to the synthesis of commodity chemicals. However, most of these endeavors have focused on optimizing and increasing the yields of naturally existing pathways. We sought to evaluate the potential for biosynthesis beyond the limits of known biochemistry towards the production of small molecule drugs that do not exist in nature. Because of the potential for improved yields compared to total synthesis, and therefore lower manufacturing costs, we focused on drugs for diseases endemic to many resource poor regions, like tuberculosis and HIV. Using generalized biochemical reaction rules, we were able to design biochemical pathways for the production of eight small molecule drugs or drug precursors and identify potential enzyme-substrate pairs for nearly every predicted reaction. All pathways begin from native metabolites, abrogating the need for specialized precursors. The simulated pathways showed several trends with the sequential ordering of reactions as well as the types of chemistries used. For some compounds, the main obstacles to finding feasible biochemical pathways were the lack of appropriate, natural starting compounds and a low diversity of biochemical coupling reactions necessary to synthesize molecules with larger molecular size.

  6. 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.

  7. 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.

  8. Proregenerative Properties of ECM Molecules

    PubMed Central

    Plantman, Stefan

    2013-01-01

    After traumatic injuries to the nervous system, regrowing axons encounter a complex microenvironment where mechanisms that promote regeneration compete with inhibitory processes. Sprouting and axonal regrowth are key components of functional recovery but are often counteracted by inhibitory molecules. This review covers extracellular matrix molecules that support neuron axonal outgrowth. PMID:24195084

  9. 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.

  10. 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)

  11. 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.

  12. Molecule-hugging graphene nanopores.

    PubMed

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

    2013-07-23

    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

  13. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  14. Molecules within molecules: Recognition through self-assembly

    PubMed Central

    Hof, Fraser; Rebek, Julius

    2002-01-01

    Synthetic molecular receptors that completely surround their target molecules can be created through the use of noncovalent interactions. These molecular capsules selectively sequester guest molecules from the influence of bulk solvent and other molecules on the basis of size, shape, and chemical complementarity. This reversible isolation spawns unique behavior within the confines of the host; the catalysis of chemical reactions and the stabilization of reactive species are possible outcomes that have been recently demonstrated. Compartmentalization of reagents can also have a dramatic effect on reactions that take place outside of the capsule, producing nonlinear kinetics in relatively simple reaction systems. PMID:11880604

  15. 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

  16. 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

  17. 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.

  18. Challenges in quantitative single molecule localization microscopy.

    PubMed

    Shivanandan, A; Deschout, H; Scarselli, M; Radenovic, A

    2014-10-01

    Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.

  19. Multichannel quantum defect theory for polar molecules

    NASA Astrophysics Data System (ADS)

    Elfimov, Sergei V.; Dorofeev, Dmitrii L.; Zon, Boris A.

    2014-02-01

    Our work is devoted to developing a general approach for nonpenetrating Rydberg states of polar molecules. We propose a method to estimate the accuracy of calculation of their wave functions and quantum defects. Basing on this method we estimate the accuracy of Born-Oppenheimer (BO) and inverse Born-Oppenheimer (IBO) approximations for these states. This estimation enables us to determine the space and energy regions where BO and IBO approximations are valid. It depends on the interplay between l coupling (due to dipole potential of the core) and l uncoupling (due to rotation the core). Next we consider the intermediate region where both BO and IBO are not valid. For this intermediate region we propose a modification of Fano's multichannel quantum defect theory to match BO and IBO wave functions and show that it gives more reliable results. They are demonstrated on the example of SO molecule.

  20. 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

  1. Quantum transport through aromatic molecules

    SciTech Connect

    Ojeda, J. H.; Rey-González, R. R.; Laroze, D.

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  2. 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)

  3. Organic heterocyclic molecules become superalkalis.

    PubMed

    Reddy, G Naaresh; Giri, Santanab

    2016-09-21

    An organic molecule which behaves like a superalkali has been designed from an aromatic heterocyclic molecule, pyrrole. Using first-principles calculation and a systematic two-step approach, we can have superalkali molecules with a low ionization energy, even lower than that of Cs. Couple cluster (CCSD) calculation reveals that a new heterocycle, C3N2(CH3)5 derived from a well-known aromatic heterocycle, pyrrole (C4H5N) has an ionization energy close to 3.0 eV. A molecular dynamics calculation on C3N2(CH3)5 reveals that the structure is dynamically stable. PMID:27530344

  4. [Using shock waves for transfer of molecules in cells].

    PubMed

    Ueberle, Friedrich; Delius, Michael; Guo, Lei

    2002-01-01

    A mixture of human lymphocytes (L1210) and fluorescent marker molecules are subjected to shockwaves in vitro. Due to the transient cavitation generated by the shockwaves, the cells take up the marker molecules. Cavitation is characterized by the bubble collapse times. An electrohydraulic generator XL-1 and a piezoelectric generator PR-II were used; PR-II was more effective. Depending on the pulse energy and number of pulses, up to 70% of the surviving cells took up the molecules. Shockwave-mediated molecule transfer provides a useful tool for the transfer of molecules into cells, which can be used as a research tool in the medical and biotechnological fields. Due to the large penetration potential of shock-waves into the body, the method may be further developed for in vivo transfer of drugs and cell transfection use.

  5. Antibody-enabled small-molecule drug discovery.

    PubMed

    Lawson, Alastair D G

    2012-06-29

    Although antibody-based therapeutics have become firmly established as medicines for serious diseases, the value of antibodies as tools in the early stages of small-molecule drug discovery is only beginning to be realized. In particular, antibodies may provide information to reduce risk in small-molecule drug discovery by enabling the validation of targets and by providing insights into the design of small-molecule screening assays. Moreover, antibodies can act as guides in the quest for small molecules that have the ability to modulate protein-protein interactions, which have traditionally only been considered to be tractable targets for biological drugs. The development of small molecules that have similar therapeutic effects to current biologics has the potential to benefit a broader range of patients at earlier stages of disease.

  6. Sperm specific proteins-potential candidate molecules for fertility control.

    PubMed

    Suri, Anil

    2004-03-10

    The increase in population growth rate warrants the development of additional contraceptive methods that are widely acceptable, free from side effects and less expensive. Immunocontraception, and in particular the targeting of antibodies to gamete-specific antigens implicated in sperm egg binding and fertilization, offers an attractive approach to control fertility. The development of a contraceptive vaccine based on sperm antigen represents a promising approach to contraception. In mammals, fertilization is completed by the direct interaction of sperm and egg, a process mediated primarily by sperm surface proteins. Sperm have proteins that are unique, cell specific, immunogenic and accessible to antibodies. A few of the sperm specific proteins have been isolated and characterized. The antibodies raised against the sperm specific antigens have proved to be extremely effective at reducing sperm-egg interaction in vitro; fertility trials in sub-human primates would eventually prove the effectiveness of the sperm antigens in terms of contraceptive efficacy.

  7. Sperm specific proteins-potential candidate molecules for fertility control

    PubMed Central

    Suri, Anil

    2004-01-01

    The increase in population growth rate warrants the development of additional contraceptive methods that are widely acceptable, free from side effects and less expensive. Immunocontraception, and in particular the targeting of antibodies to gamete-specific antigens implicated in sperm egg binding and fertilization, offers an attractive approach to control fertility. The development of a contraceptive vaccine based on sperm antigen represents a promising approach to contraception. In mammals, fertilization is completed by the direct interaction of sperm and egg, a process mediated primarily by sperm surface proteins. Sperm have proteins that are unique, cell specific, immunogenic and accessible to antibodies. A few of the sperm specific proteins have been isolated and characterized. The antibodies raised against the sperm specific antigens have proved to be extremely effective at reducing sperm-egg interaction in vitro; fertility trials in sub-human primates would eventually prove the effectiveness of the sperm antigens in terms of contraceptive efficacy. PMID:15012833

  8. 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.

  9. 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)

  10. 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

  11. Cobalt single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Yang, En-Che; Hendrickson, David N.; Wernsdorfer, Wolfgang; Nakano, Motohiro; Zakharov, Lev N.; Sommer, Roger D.; Rheingold, Arnold L.; Ledezma-Gairaud, Marisol; Christou, George

    2002-05-01

    A cobalt molecule that functions as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atom ions at the corners of a cube. Variable-field and variable-temperature magnetization data have been analyzed to establish that the molecule has a S=6 ground state with considerable negative magnetoanisotropy. Single-ion zero-field interactions (DSz2) at each cobalt ion are the origin of the negative magnetoanisotropy. A single crystal of the compound was studied by means of a micro-superconducting quantum interference device magnetometer in the range of 0.040-1.0 K. Hysteresis was found in the magnetization versus magnetic field response of this single crystal.

  12. Surface chemistry of deuterated molecules

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    1983-03-01

    The chemical composition of grain mantles is calculated in order to determine the concentration of deuterated molecules relative to their hydrogenated counterparts in grain mantles. The computation takes into account reactions involving deuterium in the gas phase and on grain surfaces. The results show that the abundance of deuterium molecules in grain mantles is much higher than expected on the basis of the cosmic abundance ratio of D to H. HDCO has a relatively high abundance in grain mantles as compared to other deuterated molecules, due to the fact that H abstraction from HDCO has a lower activation barrier than D abstraction. The infrared characteristics of the calculated grain mantles are discussed and observational tests of the model calcultions are suggested. The contribution of grain surface chemistry to the concentration of molecules in the gas phase is briefly considered.

  13. Traversing the polymorphic landscape through tuning molecule-molecule, molecule-substrate and molecule-solvent interactions

    NASA Astrophysics Data System (ADS)

    Purdum, Geoffrey; Gessner, Thomas; Weitz, R. Thomas; Loo, Yueh-Lin

    As subtle changes in the crystalline packing motif of molecular semiconductors can have a large impact on charge transport, a thorough understanding of the accessibility of polymorphs in thin films is needed. Using a series of core-chlorinated naphthalene tetracarboxylic diimides, we demonstrate that the choice of the alkyl substituents at the imide functionalities, as well as the choice of substrate and post-deposition processing conditions, tune the relative strengths of molecule-molecule, molecule-substrate and molecule-solvent interactions, providing a handle over polymorphic selection. We access the triclinic polymorph of NTCDI-CH2C3F7 in thermally evaporated thin films; solvent-vapor annealing induces a reversible transformation to its monoclinic polymorph. The addition of a fluoromethylene group in the alkyl substituent increases molecule-molecule interactions and, accordingly, improves the stability of its triclinic polymorph; this derivative does not undergo a polymorphic transformation with any of the post-deposition conditions we have explored.

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Cheng, Fei; Yang, Xiaodong; Gao, Jie

    2015-09-01

    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.

  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. Strongly driven quantum pendulum of the carbonyl sulfide molecule

    NASA Astrophysics Data System (ADS)

    Trippel, Sebastian; Mullins, Terry; Müller, Nele L. M.; Kienitz, Jens S.; Omiste, Juan J.; Stapelfeldt, Henrik; González-Férez, Rosario; Küpper, Jochen

    2014-05-01

    We demonstrate and analyze a strongly driven quantum pendulum in the angular motion of state-selected and laser-aligned carbonyl sulfide molecules. Raman couplings during the rising edge of a 50-ps laser pulse create a wave packet of pendular states, which propagates in the confining potential formed by the polarizability interaction between the molecule and the laser field. This wave-packet dynamics manifests itself as pronounced oscillations in the degree of alignment with a laser-intensity-dependent period.

  19. 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.

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

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    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.

  2. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jose, K V Jovan; Beckett, Daniel; Raghavachari, Krishnan

    2015-09-01

    We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules.

  3. Measuring an antibody affinity distribution molecule by molecule.

    PubMed

    Temirov, Jamshid P; Bradbury, Andrew R M; Werner, James H

    2008-11-15

    Single molecule fluorescence microscopy was used to observe the binding and unbinding of hapten decorated quantum dots to individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  4. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  5. Spectroscopic modeling of water molecule

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.

    2013-12-01

    This research is devoted to the vibrational spectroscopy inverse problem solution that gives a possibility to design a molecule and make conclusions about its geometry. The valence angle finding based on the usage of inverse spectral vibrational spectroscopy problem is a well-known task. 3N-matrix method was chosen to solve the proposed task. The usage of this method permits to make no assumptions about the molecule force field, besides it can be applied to molecules of matter in liquid state. Anharmonicity constants assessment is an important part of the valence angle finding. The reduction to zero vibrations is necessary because used matrix analytical expression were found in the harmonic approach. In order to find the single-valued inverse spectral problem of vibrational spectroscopy solution a shape parameter characterizing "mixing" of ω1 and ω2 vibrations forms must be found. The minimum of such a function Υ called a divergence parameter was found. This function characterizes method's accuracy. The valence angle assessment was reduced to the divergence parameter minimization. The β value concerning divergence parameter minimum was interpreted as the desired valence angle. The proposed method was applied for water molecule in liquid state: β = (88,8 ±1,7)° . The found angle fits the water molecule nearest surrounding tetrahedral model including hydrogen bond curvature in the first approximation.

  6. The entropies of adsorbed molecules.

    PubMed

    Campbell, Charles T; Sellers, Jason R V

    2012-10-31

    Adsorbed molecules are involved in many reactions on solid surface that are of great technological importance. As such, there has been tremendous effort worldwide to learn how to predict reaction rates and equilibrium constants for reactions involving adsorbed molecules. Theoretical calculation of both the rate and equilibrium constants for such reactions requires knowing the entropy and enthalpy of the adsorbed molecule. While much effort has been devoted to measuring and calculating the enthalpies of well-defined adsorbates, few measurements of the entropies of adsorbates have been reported. We present here a new way to determine the standard entropies of adsorbed molecules (S(ad)(0)) on single crystal surfaces from temperature programmed desorption data, prove its accuracy by comparison to entropies measured by equilibrium methods, and apply it to published data to extract new entropies. Most importantly, when combined with reported entropies, we find that at high coverage, they linearly track the entropy of the gas-phase molecule at the same temperature (T), such that S(ad)(0)(T) = 0.70 S(gas)(0)(T) - 3.3R (R = the gas constant), with a standard deviation of only 2R over a range of 50R. These entropies, which are ~2/3 of the gas, are huge compared to most theoretical predictions. This result can be extended to reliably predict prefactors in the Arrhenius rate constant for surface reactions involving such species, as proven here for desorption. PMID:23033909

  7. Electronic Transport in Organic Molecules

    NASA Astrophysics Data System (ADS)

    Tian, W.; Samanta, M. P.; Henderson, J. I.; Kubiak, C. P.; Datta, S.

    1996-03-01

    A systematic theoretical study of the conductance of a class of organic molecules connected between two gold cantact pads will be presented. This class of molecules consists of oligomers of benzene rings linked at their para-positions and terminated with suitable ligand end groups designed to bond to gold substrates. Such molecules are currently being investigated experimentally for use as interconnectors in nanoscale electronic devices (J.Guay et al, J.Am.Chem.Soc., 115,1869, (1993); M.Dorogi et al, Phys. Rev. B52,9071,(1995); D.B.Janes et al, Superlatt. and Microstruc., in press). Analytical and numerical results will be presented illustrating effects of Metal Induced Gap States (MIGS), end group atoms, geometric and molecular structure on the measured conductance.

  8. Room temperature single molecule microscopes

    SciTech Connect

    Ambrose, W.P.; Goodwin, P.M.; Enderlein, G.; Semin, D.J.; Keller, R.A.

    1997-12-31

    We have developed three capabilities to image the locations of and interrogate immobilized single fluorescent molecules: near-field scanning optical, confocal scanning optical, and wide-field epi-fluorescence microscopy. Each microscopy has its own advantages. Near-field illumination can beat the diffraction limit. Confocal microscopy has high brightness and temporal resolution. Wide-field has the quickest (parallel) imaging capability. With confocal microscopy, we have verified that single fluorescent spots in our images are due to single molecules by observing photon antibunching. Using all three microscopies, we have observed that xanthene molecules dispersed on dry silica curiously exhibit intensity fluctuations on millisecond to minute time scales. We are exploring the connection between the intensity fluctuations and fluctuations in individual photophysical parameters. The fluorescence lifetimes of Rhodamine 6G on silica fluctuate. The complex nature of the intensity and lifetime fluctuations is consistent with a mechanism that perturbs more than one photophysical parameter.

  9. Proton affinities of hydrated molecules

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes

    2016-09-01

    Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

  10. Interstellar molecules and dense clouds.

    NASA Technical Reports Server (NTRS)

    Rank, D. M.; Townes, C. H.; Welch, W. J.

    1971-01-01

    Current knowledge of the interstellar medium is discussed on the basis of recent published studies. The subjects considered include optical identification of interstellar molecules, radio molecular lines, interstellar clouds, isotopic abundances, formation and disappearance of interstellar molecules, and interstellar probing techniques. Diagrams are plotted for the distribution of galactic sources exhibiting molecular lines, for hydrogen molecule, hydrogen atom and electron abundances due to ionization, for the densities, velocities and temperature of NH3 in the direction of Sagitarius B2, for the lower rotational energy levels of H2CO, and for temporal spectral variations in masing H2O clouds of the radio source W49. Future applications of the maser and of molecular microscopy in this field are visualized.

  11. A quantum gas of polar molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Moses, Steven A.

    Ultracold polar molecules, because of their long-range, spatially anisotropic interactions, are a new quantum system in which to study novel many-body phenomena. In our lab, we have produced the first quantum gas of 40K 87Rb polar molecules. These molecules were found to undergo exothermic chemical reactions, and this led to interesting studies of chemistry near absolute zero. By creating the molecules at individual sites of a 3D optical lattice, we completely suppress these chemical reactions, and the polar molecule gas becomes stable and lives for tens of seconds. This thesis documents our efforts to explore coherent, many-body phenomena resulting from long-range dipolar interactions in the lattice. By encoding a spin-1/2 system in the rotational states of the molecules, we were able to realize spin-exchange interactions based on a spin Hamiltonian, which is one of the first steps in studying quantum magnetism with polar molecules. While this study was the first realization of such coherent dipolar interactions with polar molecules in a lattice, its full potential was limited by the low lattice filling fractions. Using our ability to exquisitely control the initial atomic gas mixture, we loaded a Mott insulator of Rb and a band insulator of K into the lattice. This quantum synthesis approach led to significantly higher molecular filling fractions and represents the first fully connected system of polar molecules in an optical lattice. This low-entropy quantum gas of polar molecules opens the door to interesting quantum simulations, which should be attainable in the next generation of the experiment.

  12. Orbital molecules in electronic materials

    SciTech Connect

    Attfield, J. Paul

    2015-04-01

    Orbital molecules are made up of coupled orbital states on several metal ions within an orbitally ordered (and sometimes also charge-ordered) solid such as a transition metal oxide. Spin-singlet dimers are known in many materials, but recent discoveries of more exotic species such as 18-electron heptamers in AlV{sub 2}O{sub 4} and magnetic 3-atom trimerons in magnetite (Fe{sub 3}O{sub 4}) have shown that orbital molecules constitute a general new class of quantum electronic states in solids.

  13. Extracellular movement of signaling molecules

    PubMed Central

    Müller, Patrick; Schier, Alexander F.

    2011-01-01

    Extracellular signaling molecules have crucial roles in development and homeostasis, and their incorrect deployment can lead to developmental defects and disease states. Signaling molecules are released from sending cells, travel to target cells and act over length scales of several orders of magnitude, from morphogen-mediated patterning of small developmental fields to hormonal signaling throughout the organism. We discuss how signals are modified and assembled for transport, which routes they take to reach their targets and how their range is affected by mobility and stability. PMID:21763615

  14. Extracellular movement of signaling molecules.

    PubMed

    Müller, Patrick; Schier, Alexander F

    2011-07-19

    Extracellular signaling molecules have crucial roles in development and homeostasis, and their incorrect deployment can lead to developmental defects and disease states. Signaling molecules are released from sending cells, travel to target cells, and act over length scales of several orders of magnitude, from morphogen-mediated patterning of small developmental fields to hormonal signaling throughout the organism. We discuss how signals are modified and assembled for transport, which routes they take to reach their targets, and how their range is affected by mobility and stability.

  15. 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

  16. Slow beams of massive molecules

    NASA Astrophysics Data System (ADS)

    Deachapunya, S.; Fagan, P. J.; Major, A. G.; Reiger, E.; Ritsch, H.; Stefanov, A.; Ulbricht, H.; Arndt, M.

    2008-02-01

    Slow beams of neutral molecules are of great interest for a wide range of applications, from cold chemistry through precision measurements to tests of the foundations of quantum mechanics. We report on the quantitative observation of thermal beams of perfluorinated macromolecules with masses up to 6000 amu, reaching velocities down to 11 m/s. Such slow, heavy and neutral molecular beams are of importance for a new class of experiments in matter-wave interferometry and we also discuss the requirements for further manipulation and cooling schemes with molecules in this unprecedented mass range.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Control of vascular permeability by adhesion molecules

    PubMed Central

    Sarelius, Ingrid H; Glading, Angela J

    2014-01-01

    Vascular permeability is a vital function of the circulatory system that is regulated in large part by the limited flux of solutes, water, and cells through the endothelial cell layer. One major pathway through this barrier is via the inter-endothelial junction, which is driven by the regulation of cadherin-based adhesions. The endothelium also forms attachments with surrounding proteins and cells via 2 classes of adhesion molecules, the integrins and IgCAMs. Integrins and IgCAMs propagate activation of multiple downstream signals that potentially impact cadherin adhesion. Here we discuss the known contributions of integrin and IgCAM signaling to the regulation of cadherin adhesion stability, endothelial barrier function, and vascular permeability. Emphasis is placed on known and prospective crosstalk signaling mechanisms between integrins, the IgCAMs- ICAM-1 and PECAM-1, and inter-endothelial cadherin adhesions, as potential strategic signaling nodes for multipartite regulation of cadherin adhesion. PMID:25838987

  2. Control of vascular permeability by adhesion molecules.

    PubMed

    Sarelius, Ingrid H; Glading, Angela J

    2015-01-01

    Vascular permeability is a vital function of the circulatory system that is regulated in large part by the limited flux of solutes, water, and cells through the endothelial cell layer. One major pathway through this barrier is via the inter-endothelial junction, which is driven by the regulation of cadherin-based adhesions. The endothelium also forms attachments with surrounding proteins and cells via 2 classes of adhesion molecules, the integrins and IgCAMs. Integrins and IgCAMs propagate activation of multiple downstream signals that potentially impact cadherin adhesion. Here we discuss the known contributions of integrin and IgCAM signaling to the regulation of cadherin adhesion stability, endothelial barrier function, and vascular permeability. Emphasis is placed on known and prospective crosstalk signaling mechanisms between integrins, the IgCAMs- ICAM-1 and PECAM-1, and inter-endothelial cadherin adhesions, as potential strategic signaling nodes for multipartite regulation of cadherin adhesion. PMID:25838987

  3. 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.

  4. Monitoring Molecules: Insights and Progress

    PubMed Central

    2015-01-01

    In August, 2014, neuroscientists and physical scientists gathered together on the campus of the University of California, Los Angeles to discuss how to monitor molecules in neuroscience. This field has seen significant growth since its inception in the 1970s. Here, the advances in this field are documented, including its advance into understanding the actions that specific neurotransmitters mediate during behavior. PMID:25514501

  5. 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)

  6. Ultrafast dynamics of single molecules.

    PubMed

    Brinks, Daan; Hildner, Richard; van Dijk, Erik M H P; Stefani, Fernando D; Nieder, Jana B; Hernando, Jordi; van Hulst, Niek F

    2014-04-21

    The detection of individual molecules has found widespread application in molecular biology, photochemistry, polymer chemistry, quantum optics and super-resolution microscopy. Tracking of an individual molecule in time has allowed identifying discrete molecular photodynamic steps, action of molecular motors, protein folding, diffusion, etc. down to the picosecond level. However, methods to study the ultrafast electronic and vibrational molecular dynamics at the level of individual molecules have emerged only recently. In this review we present several examples of femtosecond single molecule spectroscopy. Starting with basic pump-probe spectroscopy in a confocal detection scheme, we move towards deterministic coherent control approaches using pulse shapers and ultra-broad band laser systems. We present the detection of both electronic and vibrational femtosecond dynamics of individual fluorophores at room temperature, showing electronic (de)coherence, vibrational wavepacket interference and quantum control. Finally, two colour phase shaping applied to photosynthetic light-harvesting complexes is presented, which allows investigation of the persistent coherence in photosynthetic complexes under physiological conditions at the level of individual complexes. PMID:24473271

  7. 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.

  8. 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.

  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. Rotation of methane molecules in dimers and small clusters.

    PubMed

    Hoshina, Hiromichi; Skvortsov, Dmitri; Slipchenko, Mikhail N; Sartakov, Boris G; Vilesov, Andrey F

    2015-08-28

    This work reports on the study of the internal rotation of methane molecules in small clusters containing up to about five molecules. The clusters were assembled in helium droplets at T = 0.38 K by successive capture of single methane molecules and studied by infrared laser spectroscopy of the fundamental CH4 ν3 vibration around 3030 cm(-1). The spectra demonstrate well resolved structure due to internal rotation of the constituent molecules in the clusters. The most resolved spectrum for the dimers shows characteristic splitting of the lines due to anisotropic intermolecular interaction. The magnitude of the splitting is found to be in a good quantitative agreement with the recent theoretical anisotropic intermolecular potentials. PMID:26328841

  11. 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. PMID:26283245

  12. 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

  13. A New Approach to the Architecture of Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Yarman, Tolga

    2001-05-01

    In our previous work, we established that, in an atomic or molecular wave-like description embodying a potential energy term made of Coulomb Potentials, if the mass M of the object (or different masses the object involves) is multiplied by the hypothetical number γ, then the size of space R in which this object is installed, shrinks as much, and the total energy E of the object, is increased as much [1]. This occurance yields at once the “quantum mechanical invariance” of the quantity EMR^2; furthermore this quantity happens to be girdled to h^2, so that we end up with the relationship EMR^2 h^2 [1]. Note that this is in no way a “dimension analysis”. Anyhow, the occurance we disclose would not work, if the wave-like description embodies other potentials than Coulomb Potentials, though of course, there still would be no problem in regards to a dimension analysis. Herein, we consider the above relationship, together with the equation related to the electronic motion of the molecule (for fixed nuclei), obtained through the Born and Oppenheimer Approximation [2], when this is applied to the Schrodinger description of a diatomic molecule. Our approach thus leads to an essential relationship for the vibrational period of the diatomic molecule in hand, namely T=4π ^2/[h(n_in_j)^1/2][gM_redm_e]^1/2R^2, where M_red is the reduced mass of the nuclei of the diatomic molecule of concern, me the mass of the electron, and g, a dimensionless coefficient; ni and nj (essentially on the basis of the study of the hydrogen molecule vibrational excited electronic data together with the study of the ground state vibrational data related to alkali hydrides and alkali molecules), are disclosed to be the numbers identifying the rows of The Periodic Table of The Elements, to which the atoms making up the molecule belong; this finding is further checked throughout the entire body of diatomic molecules. From the above relationship, it appears immediately that g, necessesarily

  14. Nonlinear Optical Properties of Molecules.

    NASA Astrophysics Data System (ADS)

    Elliott, Daniel Scott

    The measurement of the hyperpolarizabilities of atoms and molecules serves as a test of molecular wave function computational techniques. In this thesis, hyperpolarizabilities for the three processes dc electric-field induced second -harmonic generation, third-harmonic generation and intensity -dependent refractive index are determined. Measurements are performed on gases so that intermolecular interactions can be neglected. We have measured the third-order polarizability of the conjugated molecules ethylene, 1,3-butadiene, 1,3,5 -hexatriene, and benzene with the technique of dc electric -field induced second-harmonic generation. These experiments were motivated by recent theoretical results which indicated that the hyperpolarizabilities of two of these molecules were negative. Had this proven to be true, it would have been the first such case for a nonresonant hyperpolarizability. Our results for benzene are in good agreement with previous measurements made on benzene in the liquid phase, lending added confidence to the use of local field factors needed for that work. We also report results for the hyperpolarizabilities of chlorodifluoromethane. The third-order polarizability is in reasonable agreement with estimates by the bond additivity approximation. An examination of the electronic dispersion of and vibrational contributions to the third-order polarizability for various processes is presented. New data for the third -harmonic polarizability for the fluorinated methanes and sulfur hexafluoride is included. Currently, ab initio calculations of molecular hyperpolarizabilities do not include any consideration of vibrational motion of the molecule. Our estimates indicate that the vibrational contributions are very important in the case of the Kerr effect. This is an important matter of principle, and should be further investigated. We have also devised an interferometric technique for the measurement of the intensity-dependent dispersion in the refractive index

  15. Pair Tunneling through Single Molecules

    NASA Astrophysics Data System (ADS)

    Raikh, Mikhail

    2007-03-01

    Coupling to molecular vibrations induces a polaronic shift, and can lead to a negative charging energy, U. For negative U, the occupation of the ground state of the molecule is even. In this situation, virtual pair transitions between the molecule and the leads can dominate electron transport. At low temperature, T, these transitions give rise to the charge-Kondo effect [1]. We developed the electron transport theory through the negative-U molecule [2] at relatively high T, when the Kondo correlations are suppressed. Two physical ingredients distinguish our theory from the transport through a superconducting grain coupled to the normal leads [3]: (i) in parallel with sequential pair-tunneling processes, single-particle cotunneling processes take place; (ii) the electron pair on the molecule can be created (or annihilated) by two electrons tunneling in from (or out to) opposite leads. We found that, even within the rate-equation description, the behavior of differential conductance through the negative-U molecule as function of the gate voltage is quite peculiar: the height of the peak near the degeneracy point is independent of temperature, while its width is proportional to T. This is in contrast to the ordinary Coulomb-blockade conductance peak, whose integral strength is T-independent. At finite source-drain bias, V>>T, the width of the conductance peak is ˜V, whereas the conventional Coulomb-blockade peak at finite V splits into two sharp peaks at detunings V/2, and -V/2. Possible applications to the gate-controlled current rectification and switching will be discussed. [1] A. Taraphder and P. Coleman, Phys. Rev. Lett. 66, 2814 (1991). [2] J. Koch, M. E. Raikh, and F. von Oppen, Phys. Rev. Lett. 96, 056803 (2006). [3] F. W. J. Hekking, L. I. Glazman, K. A. Matveev, and R. I. Shekhter, Phys. Rev. Lett. 70, 4138 (1993).

  16. Collisional quenching dynamics and reactivity of highly vibrationally excited molecules

    NASA Astrophysics Data System (ADS)

    Liu, Qingnan

    Highly excited molecules are of great importance in many areas of chemistry including photochemistry. The dynamics of highly excited molecules are affected by the intermolecular and intramolecular energy flow between many different kinds of motions. This thesis reports investigations of the collisional quenching and reactivity of highly excited molecules aimed at understanding the dynamics of highly excited molecules. There are several important questions that are addressed. How do molecules behave in collisions with a bath gas? How do the energy distributions evolve in time? How is the energy partitioned for both the donor and bath molecules after collisions? How do molecule structure, molecule state density and intermolecular potential play the role during collisional energy transfer? To answer these questions, collisional quenching dynamics and reactivity of highly vibrationally excited azabenzene molecules have been studied using high resolution transient IR absorption spectroscopy. The first study shows that the alkylated pyridine molecules that have been excited with Evib˜38,800 cm-1 impart less rotational and translational energy to CO2 than pyridine does. Comparison between the alkylated donors shows that the strong collisions are reduced for donors with longer alkyl chains by lowering the average energy per mode but longer alkyl chain have increased flexibility and higher state densities that enhance energy loss via strong collisions. In the second study, the role of hydrogen bonding interactions is explored in collision of vibrationally excited pyridines with H2O. Substantial difference in the rotational energy of H 2O is correlated with the structure of the global energy minimum. A torque-inducing mechanism is proposed that involves directed movement of H 2O between sigma and pi-hydrogen bonding interactions with the pyridine donors. In the third study the dynamics of strong and weak collisions for highly vibrationally excited methylated pyridine

  17. 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

  18. Localized atomic orbitals for atoms in molecules. III. Polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Aufderheide, Keith H.; Chung-Phillips, Alice

    1982-02-01

    Using a previously described method, localized atomic orbitals (LAOs) for atoms in molecules are constructed for the atoms C, N, O, and F in the polyatomic molecules CH4, NH3, OH2, CH3CH3, CH3NH2, CH3OH, CH3F, CH2CH2, C6H6, CO2, and CHCH. As in our prior studies, LAOs partition into sets of core, lone pair, and bonding orbitals. Ordinarily, both core and lone pair LAOs are doubly occupied and bonding is described principally as the interaction of bonding LAOs on adjacent, bonded atoms. Angles between valence LAOs on a given atom continue to vary in a manner reminiscent of trends common to simple valence shell electron pair repulsion theory. Of special interest are the systems CO2, C6H6, and CH3F: The peculiarities germane to these molecules are discussed fully in the text. Finally, certain properties (orbital populations, intra-atomic orbital angles, etc.) of groups (-CH3, -NH2, -OH, etc.) common to several systems studied show a remarkable transferability.

  19. Molecule-optimized basis sets and Hamiltonians for accelerated electronic structure calculations of atoms and molecules.

    PubMed

    Gidofalvi, Gergely; Mazziotti, David A

    2014-01-16

    Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multireferenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schrödinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACSE improves the accuracy of the equivalent standard atom-optimized basis set at little additional computational cost. We illustrate the method with the potential energy curves of hydrogen fluoride and diatomic nitrogen. Relative to the hydrogen fluoride potential energy curve from the ACSE in a polarized triple-ζ basis set, the ACSE curve in a molecule-optimized basis set, equivalent in size to a polarized double-ζ basis, has a nonparallelity error of 0.0154 au, which is significantly better than the nonparallelity error of 0.0252 au from the polarized double-ζ basis set.

  20. Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge

    NASA Astrophysics Data System (ADS)

    Korobenko, A.; Milner, V.

    2016-05-01

    We use an optical centrifuge to align asymmetric top SO2 molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.

  1. Adiabatic field-free alignment of asymmetric top molecules with an optical centrifuge

    NASA Astrophysics Data System (ADS)

    Korobenko, Aleksey; Milner, Valery

    2016-05-01

    We use an optical centrifuge to align asymmetric top SO2 molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment which persists after the molecules are released from the centrifuge. Periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 degrees, permanent field-free alignment offers new ways of controlling molecules with laser light.

  2. Fluorescent Biosensors Based on Single-Molecule Counting.

    PubMed

    Ma, Fei; Li, Ying; Tang, Bo; Zhang, Chun-Yang

    2016-09-20

    Biosensors for highly sensitive, selective, and rapid quantification of specific biomolecules make great contributions to biomedical research, especially molecular diagnostics. However, conventional methods for biomolecular assays often suffer from insufficient sensitivity and poor specificity. In some case (e.g., early disease diagnostics), the concentration of target biomolecules is too low to be detected by these routine approaches, and cumbersome procedures are needed to improve the detection sensitivity. Therefore, there is an urgent need for rapid and ultrasensitive analytical tools. In this respect, single-molecule fluorescence approaches may well satisfy the requirement and hold promising potential for the development of ultrasensitive biosensors. Encouragingly, owing to the advances in single-molecule microscopy and spectroscopy over past decades, the detection of single fluorescent molecule comes true, greatly boosting the development of highly sensitive biosensors. By in vitro/in vivo labeling of target biomolecules with proper fluorescent tags, the quantification of certain biomolecule at the single-molecule level is achieved. In comparison with conventional ensemble measurements, single-molecule detection-based analytical methods possess the advantages of ultrahigh sensitivity, good selectivity, rapid analysis time, and low sample consumption. Consequently, single-molecule detection may be potentially employed as an ideal analytical approach to quantify low-abundant biomolecules with rapidity and simplicity. In this Account, we will summarize our efforts for developing a series of ultrasensitive biosensors based on single-molecule counting. Single-molecule counting is a member of single-molecule detection technologies and may be used as a very simple and ultrasensitive method to quantify target molecules by simply counting the individual fluorescent bursts. In the fluorescent sensors, the signals of target biomolecules may be translated to the

  3. Fluorescent Biosensors Based on Single-Molecule Counting.

    PubMed

    Ma, Fei; Li, Ying; Tang, Bo; Zhang, Chun-Yang

    2016-09-20

    Biosensors for highly sensitive, selective, and rapid quantification of specific biomolecules make great contributions to biomedical research, especially molecular diagnostics. However, conventional methods for biomolecular assays often suffer from insufficient sensitivity and poor specificity. In some case (e.g., early disease diagnostics), the concentration of target biomolecules is too low to be detected by these routine approaches, and cumbersome procedures are needed to improve the detection sensitivity. Therefore, there is an urgent need for rapid and ultrasensitive analytical tools. In this respect, single-molecule fluorescence approaches may well satisfy the requirement and hold promising potential for the development of ultrasensitive biosensors. Encouragingly, owing to the advances in single-molecule microscopy and spectroscopy over past decades, the detection of single fluorescent molecule comes true, greatly boosting the development of highly sensitive biosensors. By in vitro/in vivo labeling of target biomolecules with proper fluorescent tags, the quantification of certain biomolecule at the single-molecule level is achieved. In comparison with conventional ensemble measurements, single-molecule detection-based analytical methods possess the advantages of ultrahigh sensitivity, good selectivity, rapid analysis time, and low sample consumption. Consequently, single-molecule detection may be potentially employed as an ideal analytical approach to quantify low-abundant biomolecules with rapidity and simplicity. In this Account, we will summarize our efforts for developing a series of ultrasensitive biosensors based on single-molecule counting. Single-molecule counting is a member of single-molecule detection technologies and may be used as a very simple and ultrasensitive method to quantify target molecules by simply counting the individual fluorescent bursts. In the fluorescent sensors, the signals of target biomolecules may be translated to the

  4. 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.

  5. 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.

  6. Simple molecules as complex systems.

    PubMed

    Furtenbacher, Tibor; Arendás, 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 H2(16)O, 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.

  7. 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

  8. Small Molecules Take A Big Step Against Clostridium difficile.

    PubMed

    Beilhartz, Greg L; Tam, John; Melnyk, Roman A

    2015-12-01

    Effective treatment of Clostridium difficile infections demands a shift away from antibiotics towards toxin-neutralizing agents. Work by Bender et al., using a drug that attenuates toxin action in vivo without affecting bacterial survival, demonstrates the exciting potential of small molecules as a new modality in the fight against C. difficile. PMID:26547239

  9. Single Molecule and Single Cell Epigenomics

    PubMed Central

    Hyun, Byung-Ryool; McElwee, John L.; Soloway, Paul D.

    2014-01-01

    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. PMID:25204781

  10. A single-molecule optical transistor.

    PubMed

    Hwang, J; Pototschnig, M; Lettow, R; Zumofen, G; Renn, A; Götzinger, S; Sandoghdar, V

    2009-07-01

    The transistor is one of the most influential inventions of modern times and is ubiquitous in present-day technologies. In the continuing development of increasingly powerful computers as well as alternative technologies based on the prospects of quantum information processing, switching and amplification functionalities are being sought in ultrasmall objects, such as nanotubes, molecules or atoms. Among the possible choices of signal carriers, photons are particularly attractive because of their robustness against decoherence, but their control at the nanometre scale poses a significant challenge as conventional nonlinear materials become ineffective. To remedy this shortcoming, resonances in optical emitters can be exploited, and atomic ensembles have been successfully used to mediate weak light beams. However, single-emitter manipulation of photonic signals has remained elusive and has only been studied in high-finesse microcavities or waveguides. Here we demonstrate that a single dye molecule can operate as an optical transistor and coherently attenuate or amplify a tightly focused laser beam, depending on the power of a second 'gating' beam that controls the degree of population inversion. Such a quantum optical transistor has also the potential for manipulating non-classical light fields down to the single-photon level. We discuss some of the hurdles along the road towards practical implementations, and their possible solutions. PMID:19571881

  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. 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

  14. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions.

    PubMed

    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

  15. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions.

    PubMed

    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.

  16. Light Switching of Molecules on Surfaces

    NASA Astrophysics Data System (ADS)

    Browne, Wesley R.; Feringa, Ben L.

    2009-05-01

    Smart surfaces, surfaces that respond to an external stimulus in a defined manner, hold considerable potential as components in molecular-based devices, not least as discrete switching elements. Many stimuli can be used to switch surfaces between different states, including redox, light, pH, and ion triggers. The present review focuses on molecular switching through the electronic excitation of molecules on surfaces with light. In developing light-responsive surfaces, investigators face several challenges, not only in achieving high photostationary states and fully reversible switching, but also in dealing with fatigue resistance and the effect of immobilization itself on molecular properties. The immobilization of light-responsive molecules requires the design and synthesis of functional molecular components both to achieve light switching and to anchor the molecular entity onto a surface. This review discusses several demonstrative examples of photoswitchable molecular systems in which the photochemistry has been explored in the immobilized state under ambient conditions and especially on electroactive surfaces, including self-assembled monolayers, bilayers, and polymer films.

  17. Experimental and theoretical studies of plasmon-molecule interactions.

    PubMed

    Chen, Hanning; Schatz, George C; Ratner, Mark A

    2012-09-01

    Plasmon-molecule interactions are widely believed to involve photo-induced interferences between the localized excitation of individual electrons in molecules and the large collective excitation of conduction electrons in metal particles. The intrinsic multi-scale characteristics of plasmon-molecule interactions not only offer great opportunities for realizing precise top-down control of the optical properties of individual molecules, but also allow for accurate bottom-up manipulation of light polarization and propagation as a result of molecular excitation. However, the temporal and spatial complexity of plasmon-molecule experiments severely limits our interpretation and understanding of interactions that have important applications in dye-sensitized solar cells, single-molecule detectors, photoconductive molecular electronics, all-optical switching and photo-catalytic water splitting. This review aims to outline recent progress in experimental practice and theory for probing and exploiting the subtle coupling between discrete molecular orbitals and continuous metallic bands. For each experimental technique or theoretical model, the fundamental mechanisms and relevant applications are discussed in detail with specific examples. In addition, the experimental validation of theoretical models and the computational design of functional devices are both highlighted. Finally, a brief summary is presented together with an outlook for potential future directions of this emerging interdisciplinary research field. PMID:22935744

  18. Vibrationally Averaged Long-Range Molecule-Molecule Dispersion Coefficients from Coupled-Cluster Calculations

    NASA Astrophysics Data System (ADS)

    Schmidt, Matthew; Nooijen, Marcel

    2011-06-01

    Recent years have seen increasing interest in the structure and dynamics of molecular clusters formed when a chromophore molecule such as CO_2, OCS or N_2O is solvated by number of He atoms and/or para-H_2 molecules. A key experimental probe of their behaviour is the shift of a chromophore's vibrational transition frequency which occurs when the solvent species are attached to it. Such shifts are driven by the changes in the solvent-chromophore interaction potential upon vibrational excitation of the probe molecule. While `conventional' supermolecule calculations can often provide realistic predictions of such changes in the potential well and repulsive wall region, they become increasingly unreliable for describing the weak interactions at long range where most of the solvent species in a large cluster are located. It is therefore important to have accurate relative-orientation and monomer-stretching dependent long-range C_6, C_8 and C10 dispersion coefficients to incorporate into the models for the interaction potential and for its dependence on the chromophore's vibrational state. This paper describes how those coefficients can be obtained from calculated monomer dipole, quadrupole, and octupole polarizabilities for imaginary frequencies, and by making use of the Casimir-Polder relation and angular momentum coupling to extract orientation-dependent quantities. The calculations are performed using a modified version of the ACES2 program system which allows the calculation of dipole, quadrupole and octupole polarizabilities at the EOM-CCSD level, and of static multipole moments using CCSD(T) calculations and adequate basis sets. For each relevant level of the chromophore, vibrational averaging is performed by calculating the imaginary frequency polarizabilities at judiciously chosen geometries and performing a numerical integration using the free-molecule vibrational wavefunction. Subsequent work will involve merging this long-range part of the potential with a

  19. New antimicrobial molecules and new antibiotic strategies.

    PubMed

    Rodríguez de Castro, Felipe; Naranjo, Olga Rajas; Marco, Javier Aspa; Violán, Jordi Solé

    2009-04-01

    Drug options for treatment of infections are increasingly limited. The pharmaceutical industry has found it difficult to discover new antimicrobial agents, and only two novel classes of antibiotics, the oxazolidinones and the cyclic lipopeptides, have entered the market since the late 1960s. Few new agents have reached the market in the last decade with potential interest for community-acquired pneumonia (CAP) treatment, including linezolid (the first oxazolidinone in clinical use), new fluoroquinolones, cefditoren, ertapenem, and telithromycin. Agents currently in clinical development include other novel quinolones and ketolides, broad-spectrum cephalosporin derivatives, faropenem, several glycopeptides, and iclaprim. Other molecules are considered to be promising candidates for the future. In addition to the foregoing agents, alternative treatment approaches have also been introduced into clinical practice, which include the administration of the appropriate antimicrobials in a timely manner and the consideration of the pharmacokinetic-pharmacodynamic properties of the agent(s). PMID:19296416

  20. Microemulsions as carriers for therapeutic molecules.

    PubMed

    Mehta, Surinder K; Kaur, Gurpreet

    2010-01-01

    The thrust for finding newer drug delivery systems for exiting therapeutic molecules has opened a wide window for colloidal systems. Due to the presence of different domains of variable polarity in the microemulsion systems, they show a huge potential to be used as drug delivery vehicles for a variety of drugs. The use of microemulsion as drug delivery vehicles through a number of routes has engaged a large number of research groups in this area. Microemulsion media finds several applications ranging from drug delivery to drug nanoparticle templating due to its ability to enhance solubility, stability and bioavailability. This review on patent articles recounts the patent literature dealing with different kind of microemulsion carriers used via different routes, solubility and permeability enhancement and its use as a template for nanoparticle synthesis. PMID:19807681

  1. Small-Molecule Inhibitors of Urea Transporters

    PubMed Central

    Verkman, Alan S.; Esteva-Font, Cristina; Cil, Onur; Anderson, Marc O.; Li, Fei; Li, Min; Lei, Tianluo; Ren, Huiwen; Yang, Baoxue

    2015-01-01

    Urea transporter (UT) proteins, which include isoforms of UT-A in kidney tubule epithelia and UT-B in vasa recta endothelia and erythrocytes, facilitate urinary concentrating function. Inhibitors of urea transporter function have potential clinical applications as sodium-sparing diuretics, or ‘urearetics,’ in edema from different etiologies, such as congestive heart failure and cirrhosis, as well as in syndrome of inappropriate antidiuretic hormone (SIADH). High-throughput screening of drug-like small molecules has identified UT-A and UT-B inhibitors with nanomolar potency. Inhibitors have been identified with different UT-A versus UT-B selectivity profiles and putative binding sites on UT proteins. Studies in rodent models support the utility of UT inhibitors in reducing urinary concentration, though testing in clinically relevant animal models of edema has not yet been done. PMID:25298345

  2. [Ants: a chemical library of anticancer molecules].

    PubMed

    Vétillard, Angélique; Bouzid, Wafa

    2016-01-01

    Animal venoms are complex mixtures containing simple organic molecules, proteins, peptides, and other bioactive elements with extraordinary biological properties associated with their ability to act on a number of molecular receptors in the process of incapacitating their target organisms. In such a context, arthropod venoms are invaluable sources of bioactive substances, with therapeutic interest but the limited availability of some venom such as those from ants, has restricted the potential that these biomolecules could represent. We investigated for the first time transcriptomic expression from the ant species Tetramorium bicarinatum. Four hundred randomly selected clones from cDNA libraries were sequenced and a total of 374 expressed sequence tags (ESTs) were generated. Based on the results of BLAST searches, these sequences were clustered and assembled into 269 contigs. About 72% (269) of these matched BLASTx hits with an interesting diversity and unusual abundance of cellular transcripts (48%) related to gene and protein expression reflecting the specialization of this tissue. In addition, transcripts encoding transposases were relatively highly expressed (14%). It may be that transposable elements are present and that their presence accounts for some of the variation in venom toxins. About twenty per cent of the ESTs were categorized as putative toxins, the major part represented by allergens (48% of the total venom toxins) such as pilosulin 5, sol i 3 and Myp p I and II. Several contigs encoding enzymes, including zinc-metalloproteases (17%) that are likely involved in the processing and activation of venom proteins/peptides, were also identified from the library. In addition, a number of sequences (8%) had no significant similarity to any known sequence which indicates a potential source of for the discovery of new toxins. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium

  3. Single-molecule observations of ribosome function.

    PubMed

    Blanchard, Scott C

    2009-02-01

    Single-molecule investigations promise to greatly advance our understanding of basic and regulated ribosome functions during the process of translation. Here, recent progress towards directly imaging the elemental translation elongation steps using fluorescence resonance energy transfer (FRET)-based imaging methods is discussed, which provide striking evidence of the highly dynamic nature of the ribosome. In this view, global rates and fidelities of protein synthesis reactions may be regulated by interactions of the ribosome with mRNA, tRNA, translation factors and potentially many other cellular ligands that modify intrinsic conformational equilibria in the translating particle. Future investigations probing this model must aim to visualize translation processes from multiple structural and kinetic perspectives simultaneously, to provide direct correlations between factor binding and conformational events.

  4. [Ants: a chemical library of anticancer molecules].

    PubMed

    Vétillard, Angélique; Bouzid, Wafa

    2016-01-01

    Animal venoms are complex mixtures containing simple organic molecules, proteins, peptides, and other bioactive elements with extraordinary biological properties associated with their ability to act on a number of molecular receptors in the process of incapacitating their target organisms. In such a context, arthropod venoms are invaluable sources of bioactive substances, with therapeutic interest but the limited availability of some venom such as those from ants, has restricted the potential that these biomolecules could represent. We investigated for the first time transcriptomic expression from the ant species Tetramorium bicarinatum. Four hundred randomly selected clones from cDNA libraries were sequenced and a total of 374 expressed sequence tags (ESTs) were generated. Based on the results of BLAST searches, these sequences were clustered and assembled into 269 contigs. About 72% (269) of these matched BLASTx hits with an interesting diversity and unusual abundance of cellular transcripts (48%) related to gene and protein expression reflecting the specialization of this tissue. In addition, transcripts encoding transposases were relatively highly expressed (14%). It may be that transposable elements are present and that their presence accounts for some of the variation in venom toxins. About twenty per cent of the ESTs were categorized as putative toxins, the major part represented by allergens (48% of the total venom toxins) such as pilosulin 5, sol i 3 and Myp p I and II. Several contigs encoding enzymes, including zinc-metalloproteases (17%) that are likely involved in the processing and activation of venom proteins/peptides, were also identified from the library. In addition, a number of sequences (8%) had no significant similarity to any known sequence which indicates a potential source of for the discovery of new toxins. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Flux-bubble models and mesonic molecules

    NASA Astrophysics Data System (ADS)

    Boyce, M. M.; Treurniet, J.; Watson, P. J. S.

    1999-06-01

    It has been shown that the string-flip potential model reproduces most of the bulk properties of nuclear matter, with the exception of nuclear binding. Furthermore, it was postulated that this model with the inclusion of the colour-hyperfine interaction should produce binding. In some recent work a modified version of the string-flip potential model was developed, called the flux-bubble model, which would allow for the addition of perturbative QCD interactions. In attempts to construct a simple q overlineq nucleon system using the flux-bubble model (which only included colour-Coulomb interactions) difficulties arise with trying to construct a many-body variational wave function that would take into account the locality of the flux-bubble interactions. In this paper we look at a toy system, a mesonic molecule, in order to understand these difficulties. En route, a new variational wave function is proposed that may have a sufficient impact on the old string-flip potential model results that the inclusion of perturbative effects may not be needed.

  10. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin-orbit, angular momenta, spin-rotational and spin-spin. Introducing the relevant couplings using so-called Born-Oppenheimer breakdown curves can correct non-adiabatic effects.

  11. XUV ionization of aligned molecules

    NASA Astrophysics Data System (ADS)

    Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

    2011-11-01

    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 CO2 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.

  12. 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.

  13. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin–orbit, angular momenta, spin-rotational and spin–spin. Introducing the relevant couplings using so-called Born–Oppenheimer breakdown curves can correct non-adiabatic effects.

  14. Nanoelectronics of a DNA molecule

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Fulco, U. L.; Caetano, E. W. S.; Freire, V. N.; Lyra, M. L.; Moura, F. A. B. F.

    2014-03-01

    We investigate the nanoelectronic properties of a double-strand quasiperiodic DNA molecule, modeled by a tight-binding effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, to investigate the electronic density of states, the electronic transmissivity, and the current-voltage characteristic curves of sequences of a DNA finite segment.We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.

  15. Silicene as a highly sensitive molecule sensor for NH3, NO and NO2.

    PubMed

    Hu, Wei; Xia, Nan; Wu, Xiaojun; Li, Zhenyu; Yang, Jinlong

    2014-04-21

    On the basis of first-principles calculations, we demonstrate the potential application of silicene as a highly sensitive molecule sensor for NH3, NO, and NO2 molecules. NH3, NO and NO2 molecules chemically adsorb on silicene via strong chemical bonds. With distinct charge transfer from silicene to molecules, silicene and chemisorbed molecules form charge-transfer complexes. The adsorption energy and charge transfer in NO2-adsorbed silicene are larger than those of NH3- and NO-adsorbed silicones. Depending on the adsorbate types and concentrations, the silicene-based charge-transfer complexes exhibit versatile electronic properties with tunable band gap opening at the Dirac point of silicene. The calculated charge carrier concentrations of NO2-chemisorbed silicene are 3 orders of magnitude larger than intrinsic charge carrier concentration of graphene at room temperature. The results present a great potential of silicene for application as a highly sensitive molecule sensor.

  16. 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.

  17. Ab Initio Study of Electronic States of Astrophysically Important Molecules

    NASA Astrophysics Data System (ADS)

    Valiev, R. R.; Berezhnoy, A. A.; Minaev, B. F.; Chernov, V. E.; Cherepanov, V. N.

    2016-08-01

    A study of electronic states of LiO, NaO, KO, MgO, and CaO molecules has been performed. Potential energy curves of the investigated molecules have been constructed within the framework of the XMC-QDPT2 method. Lifetimes and efficiencies of photolysis mechanisms of these monoxides have been estimated within the framework of an analytical model of photolysis. The results obtained show that oxides of the considered elements in the exospheres of the Moon and Mercury are destroyed by solar photons during the first ballistic flight.

  18. 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.

  19. Dual band metamaterial perfect absorber based on artificial dielectric "molecules".

    PubMed

    Liu, Xiaoming; Lan, Chuwen; Li, Bo; Zhao, Qian; Zhou, Ji

    2016-01-01

    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. PMID:27406699

  20. Metal/molecule interfaces: Dispersion forces unveiled

    NASA Astrophysics Data System (ADS)

    van Ruitenbeek, Jan

    2012-10-01

    The role of dispersion forces in molecule-metal bonding has often been underestimated or ignored. Two groups now report independent single-molecule experiments that illustrate and quantify the effect of such interactions on bonding strength.

  1. Symmetry of electrostatic interaction between pyrophosphate DNA molecules.

    PubMed

    Golo, V L; Kats, E I; Kuznetsova, S A; Volkov, Yu S

    2010-01-01

    We study chiral electrostatic interaction between artificial ideal homopolymer DNA-like molecules in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a one-dimensional lattice of dipoles and charges corresponding to base pairs and (pyro)phosphate groups, respectively. The interaction between molecules of the DNA is described by a pair potential U of electrostatic forces between the two sets of dipoles and charges belonging to respective lattices describing the molecules. Minima of the potential U indicate orientational ordering of the molecules and thus liquid crystalline phases of the DNA. We use numerical methods for finding the set of minima in conjunction with symmetries verified by the potential U . The symmetries form a non-commutative group of 8th order, S . Using the group S we suggest a classification of liquid crystalline phases of the DNA, which allows several cholesteric phases, that is polymorphism. Pyrophosphate forms of the DNA could clarify the role played by charges in their liquid crystalline phases, and open experimental research, important for nano-technological and bio-medical applications.

  2. Spin squeezing a cold molecule

    NASA Astrophysics Data System (ADS)

    Bhattacharya, M.

    2015-12-01

    In this article we present a concrete proposal for spin squeezing the cold ground-state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. In contrast to existing work, we consider a single, noninteracting molecule with angular momentum greater than 1 /2 . Starting from an experimentally relevant effective Hamiltonian, we identify an adiabatic regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993), 10.1103/PhysRevA.47.5138], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T. Ng, and P. T. Leung, Phys. Rev. A 63, 055601 (2001), 10.1103/PhysRevA.63.055601], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989), 10.1103/PhysRevA.39.2969]. We then consider the situation in which nonadiabatic effects are quite large and show that the effective Hamiltonian supports spin squeezing even in this case. We provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounting for the effects of field misalignment. Our results have consequences for applications such as precision spectroscopy, techniques such as magnetometry, and stereochemical effects such as the orientation-to-alignment transition.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Analytical design of soliton molecules in fibers

    NASA Astrophysics Data System (ADS)

    Moubissi, A.-B.; Nse Biyoghe, S.; Mback, C. B. L.; Ekogo, T. B.; Ben-Bolie, G. H.; Kofane, T. C.; Tchofo Dinda, P.

    2016-09-01

    We present an analytical method for designing fiber systems for a highly stable propagation of soliton molecules. This analytical design uses the variational equations of the soliton molecule to determine the parameters of the most suitable fiber system for any desired soliton, thus reducing dramatically the cost of the whole procedure of design, for both the appropriate fiber system and the desired soliton molecule.

  9. Force-induced tautomerization in a single molecule.

    PubMed

    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.

  10. Force-induced tautomerization in a single molecule.

    PubMed

    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. PMID:27657869

  11. Prediction of binding to MHC class I molecules.

    PubMed

    Adams, H P; Koziol, J A

    1995-09-25

    The binding of antigenic peptide sequences to major histocompatibility complex (MHC) molecules is a prerequisite for stimulation of cytotoxic T cell responses. Neural networks are here used to predict the binding capacity of polypeptides to MHC class I molecules encoded by the gene HLA-A*0201. Given a large database of 552 nonamers and 486 decamers and their known binding capacities, the neural networks achieve a predictive hit rate of 0.78 for classifying peptides which might induce an immune response (good or intermediate binders) vs. those which cannot (weak or non-binders). The neural nets also depict specific motifs for different binding capacities. This approach is in principle applicable to all MHC class I and II molecules, given a suitable set of known binding capacities. The trained networks can then be used to perform a systematic search through all pathogen or tumor antigen protein sequences for potential cytotoxic T lymphocyte epitopes.

  12. Hovering and Twirling of Tethered Molecules by Confinement between Surfaces.

    PubMed

    Rios, Laura; Lee, Joonhee; Tallarida, Nicholas; Apkarian, V Ara

    2016-07-01

    Through STM images, we show that azobenzene-terminated alkanethiols hover and twirl when confined between the Ag tip and Au(111) substrate of an STM junction. In contrast with mechanisms of activation used to drive molecular rotors, twirling is induced by the effective elimination of lateral corrugation in the energy landscape when molecules hover by their van der Waals attraction to the approaching tip. While in the stationary state the benzenes of the head group lie flat with an inter-ring separation of 7.5 Å, they stand on-edge as the molecule twirls and their separation contracts to 5.2 Å, close to the value of the free molecule. The captured images of motion allow the characterization of physisorption potentials.

  13. Single-molecule decoding of combinatorially modified nucleosomes.

    PubMed

    Shema, Efrat; Jones, Daniel; Shoresh, Noam; Donohue, Laura; Ram, Oren; Bernstein, Bradley E

    2016-05-01

    Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation. PMID:27151869

  14. 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

  15. Cancer Immunotherapy: Selected Targets and Small-Molecule Modulators.

    PubMed

    Weinmann, Hilmar

    2016-03-01

    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.

  16. 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. PMID:26537401

  17. 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.

  18. Electrostatic spin crossover effect in polar magnetic molecules.

    PubMed

    Baadji, Nadjib; Piacenza, Manuel; Tugsuz, Tugba; Della Sala, Fabio; Maruccio, Giuseppe; Sanvito, Stefano

    2009-10-01

    The magnetic configuration of a nanostructure can be altered by an external magnetic field, by spin-transfer torque or by its magnetoelastic response. Here, we explore an alternative route, namely the possibility of switching the sign of the exchange coupling between two magnetic centres by means of an electric potential. This general effect, which we name electrostatic spin crossover, occurs in insulating molecules with super-exchange magnetic interaction and inversion symmetry breaking. As an example we present the case of a family of di-cobaltocene-based molecules. The critical fields for switching, calculated from first principles, are of the order of 1 V nm(-1) and can be achieved in two-terminal devices. More crucially, such critical fields can be engineered with an appropriate choice of substituents to add to the basic di-cobaltocene unit. This suggests that an easy chemical strategy for achieving the synthesis of suitable molecules is possible.

  19. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling.

    PubMed

    Osorio, Henrry M; Catarelli, Samantha; Cea, Pilar; Gluyas, Josef B G; Hartl, František; Higgins, Simon J; Leary, Edmund; Low, Paul J; Martín, Santiago; Nichols, Richard J; Tory, Joanne; Ulstrup, Jens; Vezzoli, Andrea; Milan, David C; Zeng, Qiang

    2015-11-18

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media.

  20. Photochemistry and Astrochemistry: Photochemical Pathways to Interstellar Complex Organic Molecules.

    PubMed

    Öberg, Karin I

    2016-09-14

    The interstellar medium is characterized by a rich and diverse chemistry. Many of its complex organic molecules are proposed to form through radical chemistry in icy grain mantles. Radicals form readily when interstellar ices (composed of water and other volatiles) are exposed to UV photons and other sources of dissociative radiation, and if sufficiently mobile the radicals can react to form larger, more complex molecules. The resulting complex organic molecules (COMs) accompany star and planet formation and may eventually seed the origins of life on nascent planets. Experiments of increasing sophistication have demonstrated that known interstellar COMs as well as the prebiotically interesting amino acids can form through ice photochemistry. We review these experiments and discuss the qualitative and quantitative kinetic and mechanistic constraints they have provided. We finally compare the effects of UV radiation with those of three other potential sources of radical production and chemistry in interstellar ices: electrons, ions, and X-rays.

  1. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling.

    PubMed

    Osorio, Henrry M; Catarelli, Samantha; Cea, Pilar; Gluyas, Josef B G; Hartl, František; Higgins, Simon J; Leary, Edmund; Low, Paul J; Martín, Santiago; Nichols, Richard J; Tory, Joanne; Ulstrup, Jens; Vezzoli, Andrea; Milan, David C; Zeng, Qiang

    2015-11-18

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media. PMID:26488257

  2. 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.

  3. Cosmic ray synthesis of organic molecules in Titan's atmosphere

    NASA Technical Reports Server (NTRS)

    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.

  4. 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

  5. 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.

  6. Laboratory studies of astrophysical molecules

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan

    There is growing evidence that the molecules necessary for the evolution of life on earth arrived from the interstellar medium. The study of these molecules is therefore of great current interest. Two major types of signals from interstellar space, so-called unidentified interstellar infrared emission bands and the diffuse interstellar absorption bands, have intrigued and puzzled astrochemists for decades. This work has been concentrated on how to contribute to an understanding of the origins of these perplexing signals from space and help identify other molecules that may exist in outer space. Matrix isolation spectroscopy (infrared and ultraviolet-visible) combined with theoretical calculations has been employed throughout this research. Fourier transform infrared absorption spectroscopic measurements, aided by theoretical calculations and 13 C-isotope shifts, have led to the identification of eight heretofore unknown C n S m clusters: C 2 S, C 6 S, C 7 S, C 7 S 2 , C 9 S 2 , C 11 S 2 , C 13 S 2 , and C 15 S 2 . Infrared absorption studies of xenon polycarbon clusters aid in understanding the special electronic structure and reactivity of carbon clusters, which might be associated with the formation mechanism of Buckyball (C 60 ). Reaction of C3 with benzene and ammonia might be involved in the formation of more complex molecular structures, including polycyclic aromatic hydrocarbons (PAHs) and biomolecules such as the amino acids. High resolution vibrational and electronic spectra of neutral dibenzo [b,def]chrysene and its ions in 12 K argon matrices have been recorded. Spectral assignments were supported by high level theoretical calculations. A mixture of the neutral and ionic infrared spectra of dibenzo[b,def]chrysene resembles the unidentified IR bands in the reflection nebula NGC 7023. Anharmonic frequency calculations for neutral and cationic naphthalene, phenanthrene and anthracene using density functional theory have been carried out for the first time

  7. 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 .

  8. Photoluminescence of a Plasmonic Molecule.

    PubMed

    Huang, Da; Byers, Chad P; Wang, Lin-Yung; Hoggard, Anneli; Hoener, Ben; Dominguez-Medina, Sergio; Chen, Sishan; Chang, Wei-Shun; Landes, Christy F; Link, Stephan

    2015-07-28

    Photoluminescent Au nanoparticles are appealing for biosensing and bioimaging applications because of their non-photobleaching and non-photoblinking emission. The mechanism of one-photon photoluminescence from plasmonic nanostructures is still heavily debated though. Here, we report on the one-photon photoluminescence of strongly coupled 50 nm Au nanosphere dimers, the simplest plasmonic molecule. We observe emission from coupled plasmonic modes as revealed by single-particle photoluminescence spectra in comparison to correlated dark-field scattering spectroscopy. The photoluminescence quantum yield of the dimers is found to be surprisingly similar to the constituent monomers, suggesting that the increased local electric field of the dimer plays a minor role, in contradiction to several proposed mechanisms. Aided by electromagnetic simulations of scattering and absorption spectra, we conclude that our data are instead consistent with a multistep mechanism that involves the emission due to radiative decay of surface plasmons generated from excited electron-hole pairs following interband absorption. PMID:26165983

  9. 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.

  10. New molecules for hippocampal development.

    PubMed

    Skutella, T; Nitsch, R

    2001-02-01

    Pathfinding by developing axons towards their proper targets is an essential step in establishing appropriate neuronal connections. Recent work involving cell culture assays and molecular biology strategies, including knockout animals, strongly indicates that a complex network of guidance signals regulates the formation of hippocampal connections during development. Outgrowing axons are routed towards the hippocampal formation by specific expression of long-range cues, which include secreted class 3 semaphorins, netrin 1 and Slit proteins. Local membrane- or substrate-anchored molecules, such as ligands of the ephrin A subclass, provide layer-specific positional information. Understanding the molecular mechanisms that underlie axonal guidance during hippocampal development might be of importance in making therapeutic use of sprouting fibers, which are produced following the loss of afferents in CNS lesion. PMID:11164941

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Small-Molecule Regulators of MicroRNAs in Biomedicine.

    PubMed

    Xia, Tingting; Li, Jinbo; Cheng, Hao; Zhang, Chenyu; Zhang, Yan

    2015-11-01

    Preclinical Research MicroRNAs (miRNAs) can regulate gene expression at the post-transcriptional level and have been implicated in the development of various human diseases, including cancer. The regulatory networks of miRNAs play a vital role not only in normal physiology but also in pathology and may represent novel targets for drug discovery. Regulation of miRNAs and the elucidation of miRNA networks will advance miRNA-targeted research but are challenging due to a shortage of appropriate tools. Using different assay systems, diverse small molecules with unique miRNA regulatory activity have been identified. These bioactive small molecules not only showed regulation on different miRNAs but revealed previously unknown miRNA networks. Treatment of cancer both in vitro and in vivo with small-molecule regulators of miRNAs has demonstrated their therapeutic potential. In this review, we discuss assay systems for the identification of small-molecule regulators of miRNAs and reported small molecules, and discuss their applications as probes and candidate drug leads.

  17. 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.

  18. 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

  19. 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.

  20. Manipulation of Costimulatory Molecules by Intracellular Pathogens: Veni, Vidi, Vici!!

    PubMed Central

    Pahari, Susanta; Agrewala, Javed N.

    2012-01-01

    Some of the most successful pathogens of human, such as Mycobacterium tuberculosis (Mtb), HIV, and Leishmania donovani not only establish chronic infections but also remain a grave global threat. These pathogens have developed innovative strategies to evade immune responses such as antigenic shift and drift, interference with antigen processing/presentation, subversion of phagocytosis, induction of immune regulatory pathways, and manipulation of the costimulatory molecules. Costimulatory molecules expressed on the surface of various cells play a decisive role in the initiation and sustenance of immunity. Exploitation of the “code of conduct” of costimulation pathways provides evolutionary incentive to the pathogens and thereby abates the functioning of the immune system. Here we review how Mtb, HIV, Leishmania sp., and other pathogens manipulate costimulatory molecules to establish chronic infection. Impairment by pathogens in the signaling events delivered by costimulatory molecules may be responsible for defective T-cell responses; consequently organisms grow unhindered in the host cells. This review summarizes the convergent devices that pathogens employ to tune and tame the immune system using costimulatory molecules. Studying host-pathogen interaction in context with costimulatory signals may unveil the molecular mechanism that will help in understanding the survival/death of the pathogens. We emphasize that the very same pathways can potentially be exploited to develop immunotherapeutic strategies to eliminate intracellular pathogens. PMID:22719245

  1. 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.

  2. Single-molecule imaging by optical absorption

    NASA Astrophysics Data System (ADS)

    Celebrano, Michele; Kukura, Philipp; Renn, Alois; Sandoghdar, Vahid

    2011-02-01

    To date, optical studies of single molecules at room temperature have relied on the use of materials with high fluorescence quantum yield combined with efficient spectral rejection of background light. To extend single-molecule studies to a much larger pallet of substances that absorb but do not fluoresce, scientists have explored the photothermal effect, interferometry, direct attenuation and stimulated emission. Indeed, very recently, three groups have succeeded in achieving single-molecule sensitivity in absorption. Here, we apply modulation-free transmission measurements known from absorption spectrometers to image single molecules under ambient conditions both in the emissive and strongly quenched states. We arrive at quantitative values for the absorption cross-section of single molecules at different wavelengths and thereby set the ground for single-molecule absorption spectroscopy. Our work has important implications for research ranging from absorption and infrared spectroscopy to sensing of unlabelled proteins at the single-molecule level.

  3. 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.

  4. 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.

  5. 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

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

    SciTech Connect

    Rizzo, T.R.

    1992-03-01

    These experiments apply multiple-laser spectroscopic techniques to investigate the bond energies, potential surface topologies, and dissociation dynamics of highly vibrationally excited molecules. Infrared-optical double resonance pumping of light atom stretch vibrations in H{sub 2}O{sub 2} and HN{sub 3} prepares reactant molecules in single rovibrational states above the unimolecular dissociation threshold on the ground potential surface, and laser induced fluorescence detection of the OH or NH fragments monitors the partitioning of energy into individual product quantum states. Product energy partitioning data from H{sub 2}O{sub 2} dissociation provide a stringent test of statistical theories as well as potential energy surface calculations. Ongoing work on HN{sub 3} seeks to determine the height of the barrier to dissociation on the singlet potential energy surface. Our most recently developed spectroscopic scheme allows the measurement of high vibrational overtone spectra of jet-cooled molecules. This approach uses CO{sub 2} laser infrared multiphoton dissociation followed by laser induced fluorescence product detection to measure weak vibrational overtone transitions in low pressure environments. Application of this scheme to record the {Delta}V{sub OH}=4 and {Delta}V{sub OH}=5 transitions of CH{sub 3}OH cooled in a supersonic free-jet demonstrates both its feasibility and its utility for simplifying high vibrational overtone spectra.

  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. Towards composite spheres as building blocks for structured molecules.

    PubMed

    Lee, Lloyd L; Pellicane, Giuseppe

    2016-10-19

    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. PMID:27546819

  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. Two-Photon Small Molecule Enzymatic Probes.

    PubMed

    Qian, Linghui; Li, Lin; Yao, Shao Q

    2016-04-19

    Enzymes are essential for life, especially in the development of disease and on drug effects, but as we cannot yet directly observe the inside interactions and only partially observe biochemical outcomes, tools "translating" these processes into readable information are essential for better understanding of enzymes as well as for developing effective tools to fight against diseases. Therefore, sensitive small molecule probes suitable for direct in vivo monitoring of enzyme activities are ultimately desirable. For fulfilling this desire, two-photon small molecule enzymatic probes (TSMEPs) producing amplified fluorescent signals based on enzymatic conversion with better photophysical properties and deeper penetration in intact tissues and whole animals have been developed and demonstrated to be powerful in addressing the issues described above. Nonetheless, currently available TSMEPs only cover a small portion of enzymes despite the distinct advantages of two-photon fluorescence microscopy. In this Account, we would like to share design principles for TSMEPs as potential indicators of certain pathology-related biomarkers together with their applications in disease models to inspire more elegant work to be done in this area. Highlights will be addressed on how to equip two-photon fluorescent probes with features amenable for direct assessment of enzyme activities in complex pathological environments. We give three recent examples from our laboratory and collaborations in which TSMEPs are applied to visualize the distribution and activity of enzymes at cellular and organism levels. The first example shows that we could distinguish endogenous phosphatase activity in different organelles; the second illustrates that TSMEP is suitable for specific and sensitive detection of a potential Parkinson's disease marker (monoamine oxidase B) in a variety of biological systems from cells to patient samples, and the third identifies that TSMEPs can be applied to other enzyme

  11. 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

  12. Assessment of a New Semilocal Density Functional on Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Tao, Jianmin

    We have recently developed a new semilocal density functional based on the exchange hole (localized under a general coordinate transformation) from density matrix expansion, instead of imposing energy constraints to the functional or fitting it to a training set of properties. This functional is comprehensively evaluated on diverse properties of molecules and solids, including atomization energies for G2/97 (148 molecules), enthalpies of formation for G3-3 (75 molecules), ionization potentials for G3/99 (86 species), electron affinities for G3/99 (58 species), proton affinities (8 molecules), bond lengths for T-96R (96 molecules), vibrational frequencies for T-82F (82 molecules), 10 hydrogen bonded complexes, as well as lattice constants, bulk moduli, and cohesive energies for solids. Our tests show that the functional is remarkably accurate for these wide-ranging properties. This work was supported by NSF under Grant No. CHE-1261918.

  13. Cooling and trapping of atoms and molecules by counterpropagating pulse trains

    NASA Astrophysics Data System (ADS)

    Romanenko, V. I.; Udovitskaya, Ye. G.; Romanenko, A. V.; Yatsenko, L. P.

    2014-11-01

    We discuss a possible one-dimensional trapping and cooling of atoms and molecules due to their nonresonant interaction with counterpropagating light pulse trains. The counterpropagating pulses form a one-dimensional trap for atoms and molecules and a properly chosen carrier frequency detuning from the transition frequency of the atoms or molecules keeps the temperature of the atomic or molecular ensemble close to the Doppler cooling limit. The calculation by the Monte Carlo wave-function method is carried out for the two-level and three-level schemes of the atom's and the molecule's interaction with the field, respectively. The models discussed are applicable to atoms and molecules with almost diagonal Frank-Condon factor arrays. Illustrative calculations are carried out for ensemble-averaged characteristics for sodium atoms and SrF molecules in the trap. The potential for the nanoparticle light pulses's trap formed by counterpropagating light pulse trains is also discussed.

  14. 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.

  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. 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

  17. Modulation of Immunity by Antiangiogenic Molecules in Cancer

    PubMed Central

    Terme, Magali; Colussi, Orianne; Marcheteau, Elie; Tanchot, Corinne; Tartour, Eric; Taieb, Julien

    2012-01-01

    In the last decades a new class of therapeutic drugs have been developed that block tumor angiogenesis. These antiangiogenic molecules, which target VEGF or VEGFR, PDGFR, and c-kit, can act not only on endothelial cells but also on immune cells. Some antiangiogenic molecules inhibit the development of immunosuppressive mechanisms developed by the tumors to escape the immune system (such as regulatory T cells, myeloid-derived suppressor cells, and immunosuppressive cytokines). These immunomodulatory effects must be characterized in detail to enable a better prescription of these treatments. In this paper we will focus on the impact of anti-angiogenic drugs on immunosuppression and their potential combination with immunotherapeutic strategies. Interestingly, immune parameters or their modulation during treatment could serve as potential biomarkers of response or resistance to anti-angiogenic therapies. PMID:23320019

  18. 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

  19. Broadband single-molecule excitation spectroscopy

    NASA Astrophysics Data System (ADS)

    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.

  20. Rotational Cooling of Trapped Polyatomic Molecules.

    PubMed

    Glöckner, Rosa; Prehn, Alexander; Englert, Barbara G U; Rempe, Gerhard; Zeppenfeld, Martin

    2015-12-01

    Controlling the internal degrees of freedom is a key challenge for applications of cold and ultracold molecules. Here, we demonstrate rotational-state cooling of trapped methyl fluoride molecules (CH_{3}F) by optically pumping the population of 16 M sublevels in the rotational states J=3, 4, 5 and 6 into a single level. By combining rotational-state cooling with motional cooling, we increase the relative number of molecules in the state J=4, K=3, M=4 from a few percent to over 70%, thereby generating a translationally cold (≈30  mK) and nearly pure state ensemble of about 10^{6} molecules. Our scheme is extendable to larger sets of initial states, other final states, and a variety of molecule species, thus paving the way for internal-state control of ever-larger molecules.