Статті в журналах: "Prototypical molecules"

1

Borodin, Dmitriy, Igor Rahinov, Pranav R. Shirhatti, Meng Huang, Alexander Kandratsenka, Daniel J. Auerbach, Tianli Zhong, et al. "Following the microscopic pathway to adsorption through chemisorption and physisorption wells." Science 369, no. 6510 (September 17, 2020): 1461–65. http://dx.doi.org/10.1126/science.abc9581.

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Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.

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2

Shao, Beiyue, and David A. Vanden Bout. "Probing the molecular weight dependent intramolecular interactions in single molecules of PCDTBT." Journal of Materials Chemistry C 5, no. 37 (2017): 9786–91. http://dx.doi.org/10.1039/c7tc02255g.

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Push–pull conjugated polymers have shown high performance in organic photovoltaic devices and yet, there have been fewer studies of the fundamental structure–property relationship in this class of materials compared to prototypical conjugated homopolymers MEH-PPV and P3HT.

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3

Hoffmann-Vogel, R. "Imaging prototypical aromatic molecules on insulating surfaces: a review." Reports on Progress in Physics 81, no. 1 (December 13, 2017): 016501. http://dx.doi.org/10.1088/1361-6633/aa8fda.

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4

Pitzer, Martin, Maksim Kunitski, Allan S. Johnson, Till Jahnke, Hendrik Sann, Felix Sturm, Lothar Ph H. Schmidt, et al. "Direct Determination of Absolute Molecular Stereochemistry in Gas Phase by Coulomb Explosion Imaging." Science 341, no. 6150 (September 5, 2013): 1096–100. http://dx.doi.org/10.1126/science.1240362.

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Bijvoet’s method, which makes use of anomalous x-ray diffraction or dispersion, is the standard means of directly determining the absolute (stereochemical) configuration of molecules, but it requires crystalline samples and often proves challenging in structures exclusively comprising light atoms. Herein, we demonstrate a mass spectrometry approach that directly images the absolute configuration of individual molecules in the gas phase by cold target recoil ion momentum spectroscopy after laser ionization–induced Coulomb explosion. This technique is applied to the prototypical chiral molecule bromochlorofluoromethane and the isotopically chiral methane derivative bromodichloromethane.

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5

Plehn, Thomas, Dirk Ziemann, and Volkhard May. "Charge separation at an organic/inorganic nano-hybrid interface: atomistic simulations of a para-sexiphenyl ZnO system." Physical Chemistry Chemical Physics 20, no. 42 (2018): 26870–84. http://dx.doi.org/10.1039/c8cp03978j.

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6

Ashfold, Michael N. R., Rebecca A. Ingle, Tolga N. V. Karsili, and Jingsong Zhang. "Photoinduced C–H bond fission in prototypical organic molecules and radicals." Physical Chemistry Chemical Physics 21, no. 26 (2019): 13880–901. http://dx.doi.org/10.1039/c8cp07454b.

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7

Kennedy, Linda M., and Kristina M. Gonzalez. "Taste quality coding in vertebrate receptor molecules and cells." Behavioral and Brain Sciences 31, no. 1 (February 2008): 82–83. http://dx.doi.org/10.1017/s0140525x08003439.

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AbstractRecent work on receptor molecules and cells used prototypical sweet, salty, sour, bitter, and umami stimuli. Labeled-line coding was supported, but it remains possible that the molecules and cells could respond to other tastants. Studies with other tastants are needed. The sensory message might contain two codes – one for attraction or aversion, the other, across-fiber patterning of stimulus quality.

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8

Endo, Tomoyuki, Simon P. Neville, Vincent Wanie, Samuel Beaulieu, Chen Qu, Jude Deschamps, Philippe Lassonde, et al. "Capturing roaming molecular fragments in real time." Science 370, no. 6520 (November 26, 2020): 1072–77. http://dx.doi.org/10.1126/science.abc2960.

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Since the discovery of roaming as an alternative molecular dissociation pathway in formaldehyde (H2CO), it has been indirectly observed in numerous molecules. The phenomenon describes a frustrated dissociation with fragments roaming at relatively large interatomic distances rather than following conventional transition-state dissociation; incipient radicals from the parent molecule self-react to form molecular products. Roaming has been identified spectroscopically through static product channel–resolved measurements, but not in real-time observations of the roaming fragment itself. Using time-resolved Coulomb explosion imaging (CEI), we directly imaged individual “roamers” on ultrafast time scales in the prototypical formaldehyde dissociation reaction. Using high-level first-principles simulations of all critical experimental steps, distinctive roaming signatures were identified. These were rendered observable by extracting rare stochastic events out of an overwhelming background using the highly sensitive CEI method.

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9

Thebeau, Lydia G., Sri P. Vagvala, Yee M. Wong, and Lynda A. Morrison. "B7 Costimulation Molecules Expressed from the Herpes Simplex Virus 2 Genome Rescue Immune Induction in B7-Deficient Mice." Journal of Virology 81, no. 22 (September 5, 2007): 12200–12209. http://dx.doi.org/10.1128/jvi.01224-07.

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ABSTRACT The interaction between B7 costimulation molecules on antigen-presenting cells and CD28 on antigen-responsive T cells is essential for T-cell activation and maturation of immune responses to herpes simplex virus (HSV) infection. Vaccine-induced immune responses also depend upon adequate upregulation of B7 costimulation molecules, but this signal may be limiting for replication-defective virus vaccines. We investigated whether expression of B7 costimulation molecules by a prototypical replication-defective antiviral vaccine could enhance immune responses to the vaccine and whether B7-1 and B7-2 would be similarly effective. We altered an ICP8− replication-defective strain of HSV type 2 (HSV-2), 5BlacZ, to encode either murine B7-1 or B7-2. B7 molecule expression was detected on the surface of cells infected in vitro and at the RNA level in tissue of immunized mice. Immunization of B7-1/B7-2 knockout mice with B7-encoding virus modestly expanded the number of gamma interferon-producing T cells and significantly augmented class-switched HSV-specific antibody responses compared with the parental virus. Mice immunized with either B7-expressing virus showed less replication of challenge virus in the genital mucosa than mice immunized with 5BlacZ, markedly fewer signs of genital and neurological disease, and little weight loss. Virtually all mice immunized with B7-encoding virus survived challenge with a large dose of HSV-2, whereas most 5BlacZ-immunized mice succumbed to infection. These results indicate that protective immune responses can be enhanced by the inclusion of host B7 costimulation molecules in a prototypical replication-defective HSV vaccine against HSV-2 genital infection and that B7-1 and B7-2 induce immune responses with similar capacities to fight HSV-2 infection.

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10

Prauzner-Bechcicki, Jakub S., Lukasz Zajac, Piotr Olszowski, Res Jöhr, Antoine Hinaut, Thilo Glatzel, Bartosz Such, Ernst Meyer, and Marek Szymonski. "Scanning probe microscopy studies on the adsorption of selected molecular dyes on titania." Beilstein Journal of Nanotechnology 7 (November 9, 2016): 1642–53. http://dx.doi.org/10.3762/bjnano.7.156.

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Titanium dioxide, or titania, sensitized with organic dyes is a very attractive platform for photovoltaic applications. In this context, the knowledge of properties of the titania–sensitizer junction is essential for designing efficient devices. Consequently, studies on the adsorption of organic dyes on titania surfaces and on the influence of the adsorption geometry on the energy level alignment between the substrate and an organic adsorbate are necessary. The method of choice for investigating the local environment of a single dye molecule is high-resolution scanning probe microscopy. Microscopic results combined with the outcome of common spectroscopic methods provide a better understanding of the mechanism taking place at the titania–sensitizer interface. In the following paper, we review the recent scanning probe microscopic research of a certain group of molecular assemblies on rutile titania surfaces as it pertains to dye-sensitized solar cell applications. We focus on experiments on adsorption of three types of prototypical dye molecules, i.e., perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA), phtalocyanines and porphyrins. Two interesting heteromolecular systems comprising molecules that are aligned with the given review are discussed as well.

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11

Kłos, Jacek, Hui Li, Eite Tiesinga, and Svetlana Kotochigova. "Prospects for assembling ultracold radioactive molecules from laser-cooled atoms." New Journal of Physics 24, no. 2 (February 1, 2022): 025005. http://dx.doi.org/10.1088/1367-2630/ac50ea.

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Abstract Molecules with unstable isotopes often contain heavy and deformed nuclei and thus possess a high sensitivity to parity-violating effects, such as the Schiff moments. Currently the best limits on Schiff moments are set with diamagnetic atoms. Polar molecules with quantum-enhanced sensing capabilities, however, can offer better sensitivity. In this work, we consider the prototypical 223Fr107Ag molecule, as the octupole deformation of the unstable 223Fr francium nucleus amplifies the nuclear Schiff moment of the molecule by two orders of magnitude relative to that of spherical nuclei and as the silver atom has a large electron affinity. To develop a competitive experimental platform based on molecular quantum systems, 223Fr atoms and 107Ag atoms have to be brought together at ultracold temperatures. That is, we explore the prospects of forming 223Fr107Ag from laser-cooled Fr and Ag atoms. We have performed fully relativistic electronic-structure calculations of ground and excited states of FrAg that account for the strong spin-dependent relativistic effects of Fr and the strong ionic bond to Ag. In addition, we predict the nearest-neighbor densities of magnetic-field Feshbach resonances in ultracold 223Fr + 107Ag collisions with coupled-channel calculations. These resonances can be used for magneto-association into ultracold, weakly-bound FrAg. We also determine the conditions for creating 223Fr107Ag molecules in their absolute ground state from these weakly-bound dimers via stimulated Raman adiabatic passage using our calculations of the relativistic transition electric dipole moments.

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12

Rice, G. W., and R. L. Woodin. "Kinetics and mechanism of laser-driven powder synthesis from organosilane precursors." Journal of Materials Research 4, no. 6 (December 1989): 1538–48. http://dx.doi.org/10.1557/jmr.1989.1538.

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Laser-driven synthesis of refractory powders from the organosilicon compounds ((CH3)3Si)2NH and ((CH3)3Si)2O has been studied as prototypical of powder syntheses from large molecules. A cw CO2 laser is used for powder syntheses and pulsed TEA CO2 laser-driven homogeneous pyrolysis is used to study the initiation chemistry. Initial decomposition of the organosilanes by Si–C bond cleavage initiates free radical chain reactions which produce organosilicon polymers and subsequent refractory phases. A qualitative model is proposed which provides a framework for understanding the parameters influencing powder synthesis from large molecules.

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13

Tag El Din, El Sayed M., Faisal Sultan, Muhammad Usman Ghani, Jia-Bao Liu, Sanaullah Dehraj, Murat Cancan, Fahad M. Alharbi, and Abdullah Alhushaybari. "Some Novel Results Involving Prototypical Computation of Zagreb Polynomials and Indices for SiO4 Embedded in a Chain of Silicates." Molecules 28, no. 1 (December 26, 2022): 201. http://dx.doi.org/10.3390/molecules28010201.

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A topological index as a graph parameter was obtained mathematically from the graph’s topological structure. These indices are useful for measuring the various chemical characteristics of chemical compounds in the chemical graph theory. The number of atoms that surround an atom in the molecular structure of a chemical compound determines its valency. A significant number of valency-based molecular invariants have been proposed, which connect various physicochemical aspects of chemical compounds, such as vapour pressure, stability, elastic energy, and numerous others. Molecules are linked with numerical values in a molecular network, and topological indices are a term for these values. In theoretical chemistry, topological indices are frequently used to simulate the physicochemical characteristics of chemical molecules. Zagreb indices are commonly employed by mathematicians to determine the strain energy, melting point, boiling temperature, distortion, and stability of a chemical compound. The purpose of this study is to look at valency-based molecular invariants for SiO4 embedded in a silicate chain under various conditions. To obtain the outcomes, the approach of atom–bond partitioning according to atom valences was applied by using the application of spectral graph theory, and we obtained different tables of atom—bond partitions of SiO4. We obtained exact values of valency-based molecular invariants, notably the first Zagreb, the second Zagreb, the hyper-Zagreb, the modified Zagreb, the enhanced Zagreb, and the redefined Zagreb (first, second, and third). We also provide a graphical depiction of the results that explains the reliance of topological indices on the specified polynomial structure parameters.

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14

Politzer, Peter, Jane S. Murray, and Pat Lane. "Computational determination of effects of electric fields upon “trigger linkages” of prototypical energetic molecules." International Journal of Quantum Chemistry 109, no. 3 (2009): 534–39. http://dx.doi.org/10.1002/qua.21800.

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15

Sroczyńska, Marta, Anna Dawid, Michał Tomza, Zbigniew Idziaszek, Tommaso Calarco, and Krzysztof Jachymski. "Controlling the dynamics of ultracold polar molecules in optical tweezers." New Journal of Physics 24, no. 1 (December 30, 2021): 015001. http://dx.doi.org/10.1088/1367-2630/ac434b.

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Abstract Ultracold molecules trapped in optical tweezers show great promise for the implementation of quantum technologies and precision measurements. We study a prototypical scenario where two interacting polar molecules placed in separate traps are controlled using an external electric field. This, for instance, enables a quantum computing scheme in which the rotational structure is used to encode the qubit states. We estimate the typical operation timescales needed for state engineering to be in the range of few microseconds. We further underline the important role of the spatial structure of the two-body states, with the potential for significant gate speedup employing trap-induced resonances.

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16

Ferrer, Sofia, and Antonio Echavarren. "Synthesis of Bullvalenes: Classical Approaches and Recent Developments." Synthesis 51, no. 05 (January 14, 2019): 1037–48. http://dx.doi.org/10.1055/s-0037-1611637.

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The goal of this short review is to provide an overview of the different synthetic methodologies applied along the years for the synthesis of bullvalenes, prototypical fluxional molecules that were key in the understanding of valence tautomerism phenomena. Some interesting applications of these unique shapeshifting compounds are also presented.1 Introduction2 Classical Syntheses of Bullvalenes3 Recent Developments in the Synthesis of Bullvalenes4 Applications of Bullvalenes5 Conclusion

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17

Kay, Euan R., and David A. Leigh. "Beyond switches: Rotaxane- and catenane-based synthetic molecular motors." Pure and Applied Chemistry 80, no. 1 (January 1, 2008): 17–29. http://dx.doi.org/10.1351/pac200880010017.

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Nature uses molecular motors and machines in virtually every significant biological process, but learning how to design and assemble simpler artificial structures that function through controlled molecular-level motion is a major challenge for contemporary physical science. The established engineering principles of the macroscopic world can offer little more than inspiration to the molecular engineer who creates devices for an environment where everything is constantly moving and being buffeted by other atoms and molecules. Rather, experimental designs for working molecular machines must follow principles derived from chemical kinetics, thermodynamics, and nonequilibrium statistical physics. The remarkable characteristics of interlocked molecules make them particularly useful for investigating the control of motion at the molecular level. Yet, the vast majority of synthetic molecular machines studied to date are simple two-state switches. Here we outline recent developments from our laboratory that demonstrate more complex molecular machine functions. This new generation of synthetic molecular machines can move continuously and progressively away from equilibrium, and they may be considered true prototypical molecular motors. The examples discussed exemplify two, fundamentally different, "Brownian ratchet" mechanisms previously developed in theoretical statistical physics and realized experimentally in molecular-level devices for the first time in these systems.

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18

Langewisch, Gernot, Jens Falter, André Schirmeisen, and Harald Fuchs. "Influence of the adsorption geometry of PTCDA on Ag(111) on the tip–molecule forces in non-contact atomic force microscopy." Beilstein Journal of Nanotechnology 5 (January 27, 2014): 98–104. http://dx.doi.org/10.3762/bjnano.5.9.

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Perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) adsorbed on a metal surface is a prototypical organic–anorganic interface. In the past, scanning tunneling microscopy and scanning tunneling spectroscopy studies of PTCDA adsorbed on Ag(111) have revealed differences in the electronic structure of the molecules depending on their adsorption geometry. In the work presented here, high-resolution 3D force spectroscopy measurements at cryogenic temperatures were performed on a surface area that contained a complete PTCDA unit cell with the two possible geometries. At small tip-molecule separations, deviations in the tip-sample forces were found between the two molecule orientations. These deviations can be explained by a different electron density in both cases. This result demonstrates the capability of 3D force spectroscopy to detect even small effects in the electronic properties of organic adsorbates.

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19

Bussolotti, F., and R. Friedlein. "Hybrid interfaces of biological molecules and metals: The prototypical case of adenine on Cu(110)." Journal of Chemical Physics 132, no. 18 (May 14, 2010): 184705. http://dx.doi.org/10.1063/1.3430743.

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20

Wells, J. R., P. G. House, and Eric Weitz. "Interaction of H2 and Prototypical Solvent Molecules with Cr(CO)5 in the Gas Phase." Journal of Physical Chemistry 98, no. 34 (August 1994): 8343–51. http://dx.doi.org/10.1021/j100085a014.

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21

Hamilton, Tracy P., and Henry F. Schaefer. "The prototypical zinc carbene and zinc carbyne molecules ZnCH2 and HZnCH: triplet electronic ground states." Journal of the Chemical Society, Chemical Communications, no. 9 (1991): 621. http://dx.doi.org/10.1039/c39910000621.

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22

Chaudhry, Shafqat Rasul, Sumaira Shafique, Saba Sajjad, Daniel Hänggi, and Sajjad Muhammad. "Janus Faced HMGB1 and Post-Aneurysmal Subarachnoid Hemorrhage (aSAH) Inflammation." International Journal of Molecular Sciences 23, no. 19 (September 23, 2022): 11216. http://dx.doi.org/10.3390/ijms231911216.

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Aneurysmal subarachnoid hemorrhage (aSAH), resulting majorly from the rupture of intracranial aneurysms, is a potentially devastating disease with high morbidity and mortality. The bleeding aneurysms can be successfully secured; however, the toxic and mechanical impact of the blood extravasation into the subarachnoid space damages the brain cells leading to the release of different damage-associated molecular pattern molecules (DAMPs). DAMPs upregulate the inflammation after binding their cognate receptors on the immune cells and underlies the early and delayed brain injury after aSAH. Moreover, these molecules are also associated with different post-aSAH complications, which lead to poor clinical outcomes. Among these DAMPs, HMGB1 represents a prototypical protein DAMP that has been well characterized for its proinflammatory role after aSAH and during different post-aSAH complications. However, recent investigations have uncovered yet another face of HMGB1, which is involved in the promotion of brain tissue remodeling, neurovascular repair, and anti-inflammatory effects after SAH. These different faces rely on different redox states of HMGB1 over the course of time after SAH. Elucidation of the dynamics of these redox states of HMGB1 has high biomarker as well as therapeutic potential. This review mainly highlights these recent findings along with the conventionally described normal role of HMGB1 as a nuclear protein and as a proinflammatory molecule during disease (aSAH).

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23

Russo, Mattia, Kirsty E. McGhee, Tersilla Virgili, David G. Lidzey, Giulio Cerullo, and Margherita Maiuri. "Dephasing Processes in the Molecular Dye Lumogen-F Orange Characterized by Two-Dimensional Electronic Spectroscopy." Molecules 27, no. 20 (October 20, 2022): 7095. http://dx.doi.org/10.3390/molecules27207095.

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Molecular dyes are finding more and more applications in photonics and quantum technologies, such as polaritonic optical microcavities, organic quantum batteries and single-photon emitters for quantum sensing and metrology. For all these applications, it is of crucial importance to characterize the dephasing mechanisms. In this work we use two-dimensional electronic spectroscopy (2DES) to study the temperature dependent dephasing processes in the prototypical organic dye Lumogen-F orange. We model the 2DES maps using the Bloch equations for a two-level system and obtain a dephasing time T2 = 53 fs at room temperature, which increases to T2 = 94 fs at 86 K. Furthermore, spectral diffusion processes are observed and modeled by a combination of underdamped and overdamped Brownian oscillators. Our results provide useful design parameters for advanced optoelectronic and photonic devices incorporating dye molecules.

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24

Li, Hui, Bohan Zhang, Xueguang Lu, Xuyu Tan, Fei Jia, Yue Xiao, Zehong Cheng, et al. "Molecular spherical nucleic acids." Proceedings of the National Academy of Sciences 115, no. 17 (April 9, 2018): 4340–44. http://dx.doi.org/10.1073/pnas.1801836115.

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Herein, we report a class of molecular spherical nucleic acid (SNA) nanostructures. These nano-sized single molecules are synthesized from T8 polyoctahedral silsesquioxane and buckminsterfullerene C60 scaffolds, modified with 8 and 12 pendant DNA strands, respectively. These conjugates have different DNA surface densities and thus exhibit different levels of nuclease resistance, cellular uptake, and gene regulation capabilities; the properties displayed by the C60 SNA conjugate are closer to those of conventional and prototypical gold nanoparticle SNAs. Importantly, the C60 SNA can serve as a single entity (no transfection agent required) antisense agent to efficiently regulate gene expression. The realization of molecularly pure forms of SNAs will open the door for studying the interactions of such structures with ligands and living cells with a much greater degree of control than the conventional polydisperse forms of SNAs.

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25

Barracchia, Carlo Giorgio, Roberto Tira, Francesca Parolini, Francesca Munari, Luigi Bubacco, Georgios A. Spyroulias, Mariapina D’Onofrio, and Michael Assfalg. "Unsaturated Fatty Acid-Induced Conformational Transitions and Aggregation of the Repeat Domain of Tau." Molecules 25, no. 11 (June 11, 2020): 2716. http://dx.doi.org/10.3390/molecules25112716.

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Background: The intrinsically disordered, amyloidogenic protein Tau associates with diverse classes of molecules, including proteins, nucleic acids, and lipids. Mounting evidence suggests that fatty acid molecules could play a role in the dysfunction of this protein, however, their interaction with Tau remains poorly characterized. Methods: In a bid to elucidate the association of Tau with unsaturated fatty acids at the sub-molecular level, we carried out a variety of solution NMR experiments in combination with circular dichroism and fluorescence measurements. Our study shows that Tau4RD, the highly basic four-repeat domain of Tau, associates strongly with arachidonic and oleic acid assemblies in a high lipid/protein ratio, perturbing their supramolecular states and itself undergoing time-dependent structural adaptation. The structural signatures of Tau4RD/fatty acid aggregates appear similar for arachidonic acid and oleic acid, however, they are distinct from those of another prototypical intrinsically disordered protein, α-synuclein, when bound to these lipids, revealing protein-specific conformational adaptations. Both fatty acid molecules are found to invariably promote the self-aggregation of Tau4RD and of α-synuclein. Conclusions: This study describes the reciprocal influence that Tau4RD and fatty acids exert on their conformational states, contributing to our understanding of fundamental aspects of Tau/lipid co-assembly.

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26

Lebeer, S., J. Vanderleyden, and S. De Keersmaecker. "Adaptation factors of the probiotic Lactobacillus rhamnosus GG." Beneficial Microbes 1, no. 4 (November 1, 2010): 335–42. http://dx.doi.org/10.3920/bm2010.0032.

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Probiotic bacteria are administered as live micro-organisms to provide a health benefit to the host. Knowledge on adaptation factors that promote the survival and persistence of probiotics in the intestine is key to understand and improve their ecological and probiotic performance. Adaptation factors include adhesins, molecules conferring stress tolerance and nutritional versatility, antimicrobial products against competing microbes, and factors promoting resistance against the host immune system. Here, we present an overview of the current knowledge on adaptation factors of probiotic lactobacilli, with focus on the prototypical and widely documented probiotic strain Lactobacillus rhamnosus GG.

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27

Fischer, Michael. "First-Principles Study of AlPO4-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules." Molecules 24, no. 5 (March 6, 2019): 922. http://dx.doi.org/10.3390/molecules24050922.

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Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two “types” of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO4-H3 contains both types of H2O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO4-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO4-C, leading to the identification of a few “fingerprint” modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO4-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.

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28

Bianchi, Eleonora. "Interstellar complex organic molecules in the prototypical Class I protostar SVS13-A: From large scales to planet forming disks." EPJ Web of Conferences 265 (2022): 00028. http://dx.doi.org/10.1051/epjconf/202226500028.

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We present a chemical systematic study of the Class I object SVS13- A obtained in the framework of two IRAM Large Programs: ASAI (Astrochemical Survey At IRAM-30m) with the 30m and SOLIS (Seeds Of Life In Space) with NOEMA. Thanks to the ASAI high-sensitivity unbiased spectral survey of the 3, 2 and 1.3mm bands, we detect and analyse several emission lines from deuterated species and interstellar complex organic molecules (iCOMs, e.g. molecules composed by 6 or more atoms and based on carbon). Within SOLIS, we obtain high-sensitivity and high-spatial resolution (∼ 180 au) maps of crucial iCOMs. As a follow up, thanks to ALMA we explore the chemistry in the planet forming region (∼ 50 au). We image emission lines from methanol (CH3OH), acetaldehyde (CH3CHO), formamide (NH2CHO) and dimethyl ether (CH3OCH3). The different spatial distributions suggest a chemical differentiation inside the binary system or a different continuum opacity in the two protostellar disks.

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29

Catellani, A., G. Cicero, M. C. Righi, and C. A. Pignedoli. "First Principles Simulations of SiC-Based Interfaces." Materials Science Forum 483-485 (May 2005): 541–46. http://dx.doi.org/10.4028/www.scientific.net/msf.483-485.541.

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We review some recent investigations on prototypical SiC-based interfaces, as obtained from first-principles molecular dynamics. We discuss the interface with vacuum, and the role played by surface reconstruction in SiC homoepitaxy, and adatom diffusion. Then we move to the description of a buried, highly mismatched semiconductor interface, the one which occurs between SiC and Si, its natural substrate for growth: in this case, the mechanism governing the creation of a network of dislocations at the SiC/Si interface is presented, along with a microscopic description of the dislocation core. Finally, we describe a template solid/liquid interface, water on SiC: based on the predicted structure of SiC surfaces covered with water molecules, we propose (i) a way of nanopatterning cubic SiC(001) for the attachment of biomolecules and (ii) experiments to reveal the local geometry of adsorbed water.

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Boger, Dale L., Steven J. Henriksen, and Benjamin F. Cravatt. "Oleamide: An Endogenous Sleep-inducing Lipid and Prototypical Member of a New Class of Biological Signaling Molecules." Current Pharmaceutical Design 4, no. 4 (August 1998): 303–14. http://dx.doi.org/10.2174/138161280404221010152220.

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Abstract: Oleamide is an endogenous fatty acid primary amide that accumulates in the cerebrospinal fluid under conditions of sleep deprivation and induces physiological sleep in animals. A review covering its discovery, its implications, and the emerging biology surrounding its discovery is presented. Consistent with its role as a prototypical member of a new class of biological signaling molecules, enzymatic regulation of endogenous concentrations of oleamide have been characterized or proposed. Fatty acid amide hydrolase (FAAH) is an integral membrane protein that degrades oleamide and potent inhibitors with physiological sleep-inducing properties have been disclosed. The characterization, cloning, and neuronal distribution of FAAH have been detailed and the enzyme was found to possess the ability to hydrolyze a range of fatty acid amides including anandamide which serves as the endogenous ligand for the cannabinoid receptor. An additional endogenous substance with REM sleep-inducing properties, 2-octyl y-bromoacetoacetate, was characterized as a potent FAAH inhibitor. Oleamide has been shown to modulate serotonergic neurotransmission and inhibit intercellular gap junction communication and detailed studies of its well defined and selective structural features required for activity have been disclosed.

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31

Zhang, Chi, Benoit Coasne, Robert Guyer, Dominique Derome, and Jan Carmeliet. "Moisture-induced crossover in the thermodynamic and mechanical response of hydrophilic biopolymer." Cellulose 27, no. 1 (October 31, 2019): 89–99. http://dx.doi.org/10.1007/s10570-019-02808-z.

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Abstract The use of natural sustainable resources such as wood in green industrial processes is currently limited by our poor understanding of the impact of moisture on their thermodynamic and mechanical behaviors. Here, a molecular dynamics approach is used to investigate the physical response of a typical hydrophilic biopolymer in softwood hemicellulose—xylan—when subjected to moisture adsorption. A unique moisture-induced crossover is found in the thermodynamic and mechanical properties of this prototypical biopolymer with many quantities such as the heat of adsorption, heat capacity, thermal expansion and elastic moduli exhibiting a marked evolution change for a moisture content about 30 wt%. By investigating the microscopic structure of the confined water molecules and the polymer–water interfacial area, the molecular mechanism responsible for this crossover is shown to correspond to the formation of a double-layer adsorbed film along the amorphous polymeric chains. In addition to this moisture-induced crossover, many properties of the hydrated biopolymer are found to obey simple material models.

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32

Gras, Stephanie. "CD4+ T cell mediated HLA class II cross-restriction in HIV controllers." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 217.9. http://dx.doi.org/10.4049/jimmunol.204.supp.217.9.

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Abstract Rare individuals, termed HIV controllers, spontaneously control HIV infection by mounting efficient T cell responses against the virus. Protective CD4+ T cell responses from HIV controllers involve high affinity public T cell receptors (TCRs) recognizing an immunodominant capsid epitope (Gag293) presented by a remarkably broad array of HLA class II molecules. Here we determine the structures of a prototypical public TCR bound to HLAD-R1, –DR11, and –DR15 molecules presenting the Gag293 epitope. TCR recognition was driven by contacts with the Gag293 epitope, a feature that underpinned the extensive HLA cross-restriction. These high affinity TCRs promoted mature immunological synapse formation and cytotoxic capacity in both CD4+ and CD8+ T cells. The public TCRs suppressed HIV replication in multiple genetic backgrounds ex vivo, emphasizing the functional advantage conferred by broad HLA class II cross-restriction.

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33

Crippa, Luca, Francesco Tacchino, Mario Chizzini, Antonello Aita, Michele Grossi, Alessandro Chiesa, Paolo Santini, Ivano Tavernelli, and Stefano Carretta. "Simulating Static and Dynamic Properties of Magnetic Molecules with Prototype Quantum Computers." Magnetochemistry 7, no. 8 (August 12, 2021): 117. http://dx.doi.org/10.3390/magnetochemistry7080117.

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Magnetic molecules are prototypical systems to investigate peculiar quantum mechanical phenomena. As such, simulating their static and dynamical behavior is intrinsically difficult for a classical computer, due to the exponential increase of required resources with the system size. Quantum computers solve this issue by providing an inherently quantum platform, suited to describe these magnetic systems. Here, we show that both the ground state properties and the spin dynamics of magnetic molecules can be simulated on prototype quantum computers, based on superconducting qubits. In particular, we study small-size anti-ferromagnetic spin chains and rings, which are ideal test-beds for these pioneering devices. We use the variational quantum eigensolver algorithm to determine the ground state wave-function with targeted ansatzes fulfilling the spin symmetries of the investigated models. The coherent spin dynamics are simulated by computing dynamical correlation functions, an essential ingredient to extract many experimentally accessible properties, such as the inelastic neutron cross-section.

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Xiang, Yepeng, Pan Li, Shaolong Gong, Yu-Hsin Huang, Chun-Yu Wang, Cheng Zhong, Weixuan Zeng, et al. "Acceptor plane expansion enhances horizontal orientation of thermally activated delayed fluorescence emitters." Science Advances 6, no. 41 (October 2020): eaba7855. http://dx.doi.org/10.1126/sciadv.aba7855.

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Manipulating orientation of organic emitters remains a formidable challenge in organic light-emitting diodes (OLEDs). Here, expansion of the acceptor plane of thermally activated delayed fluorescence (TADF) emitters was demonstrated to selectively modulate emitting dipole orientation. Two proof-of-the-concept molecules, PXZPyPM and PXZTAZPM, were prepared by introducing a planar 2-phenylpyridine or 2,4,6-triphenyl-1,3,5-triazine substituent into a prototypical molecule (PXZPM) bearing a pyrimidine core and two phenoxazine donors. This design approach suppressed the influence of substituents on electronic structures and associated optoelectronic properties. Accordingly, PXZPyPM and PXZTAZPM preserved almost the same excited states and similar emission characteristics as PXZPM. The expanded acceptor plane of PXZPyPM and PXZTAZPM resulted in a 15 to 18% increase in horizontal ratios of emitting dipole orientation. PXZPyPM supported its green device exhibiting an external quantum efficiency of 33.9% and a power efficiency of 118.9 lumen per watt, competitive with the most efficient green TADF OLEDs reported so far.

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35

Ma'ayan, Avi. "Complex systems biology." Journal of The Royal Society Interface 14, no. 134 (September 2017): 20170391. http://dx.doi.org/10.1098/rsif.2017.0391.

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Complex systems theory is concerned with identifying and characterizing common design elements that are observed across diverse natural, technological and social complex systems. Systems biology, a more holistic approach to study molecules and cells in biology, has advanced rapidly in the past two decades. However, not much appreciation has been granted to the realization that the human cell is an exemplary complex system. Here, I outline general design principles identified in many complex systems, and then describe the human cell as a prototypical complex system. Considering concepts of complex systems theory in systems biology can illuminate our overall understanding of normal cell physiology and the alterations that lead to human disease.

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Beard, Dylan K., Seonna Bristol, Kayla Cosby, Amber Davis, Courtney Manning, Lionel Perry, Lauren Snapp, et al. "Crystal structure of a hypothetical protein from Giardia lamblia." Acta Crystallographica Section F Structural Biology Communications 78, no. 2 (January 28, 2022): 59–65. http://dx.doi.org/10.1107/s2053230x21013595.

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Giardiasis is the most prevalent diarrheal disease globally and affects humans and animals. It is a significant problem in developing countries, the number one cause of travelers' diarrhea and affects children and immunocompromised individuals, especially HIV-infected individuals. Giardiasis is treated with antibiotics (tinidazole and metronidazole) that are also used for other infections such as trichomoniasis. The ongoing search for new therapeutics for giardiasis includes characterizing the structure and function of proteins from the causative protozoan Giardia lamblia. These proteins include hypothetical proteins that share 30% sequence identity or less with proteins of known structure. Here, the atomic resolution structure of a 15.6 kDa protein was determined by molecular replacement. The structure has the two-layer αβ-sandwich topology observed in the prototypical endoribonucleases L-PSPs (liver perchloric acid-soluble proteins) with conserved allosteric active sites containing small molecules from the crystallization solution. This article is an educational collaboration between Hampton University and the Seattle Structural Genomics Center for Infectious Disease.

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37

Foss, Dennis L., and Michael P. Murtaugh. "Mechanisms of vaccine adjuvanticity at mucosal surfaces." Animal Health Research Reviews 1, no. 1 (June 2000): 3–24. http://dx.doi.org/10.1017/s1466252300000025.

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AbstractThe vast majority of pathogens invade via mucosal surfaces, including those of the intestine. Vaccination directly on these surfaces may induce local protective immunity and prevent infection and disease. Although vaccine delivery to the gut mucosa is fraught with obstacles, immunization can be enhanced using adjuvants with properties specific to intestinal immunity. In this review, we present three general mechanisms of vaccine adjuvant function as originally described by Freund, and we discuss these principles with respect to intestinal adjuvants in general and to the prototypical mucosal adjuvant, cholera toxin. The key property of intestinal adjuvants is to induce an immunogenic context for the presentation of the vaccine antigen. The success of oral vaccine adjuvants is determined by their ability to induce a controlled inflammatory response in the gut-associated lymphoid tissues, characterized by the expression of various costimulatory molecules and cytokines. An understanding of the specific molecular mechanisms of adjuvanticity in the gut will allow the rational development of safe and effective oral vaccines.

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38

Nejad, Arman, and Martin A. Suhm. "Concerted Pair Motion Due to Double Hydrogen Bonding: The Formic Acid Dimer Case." Journal of the Indian Institute of Science 100, no. 1 (November 22, 2019): 5–19. http://dx.doi.org/10.1007/s41745-019-00137-5.

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AbstractFormic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.

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39

Richter, Ferdinand, Nicholas Birchall, Christoph M. Feil, Martin Nieger, and Dietrich Gudat. "Annellated 1,3,4,2-Triazaphospholenes-Simple Modular Synthesis and a First Exploration of Ligand Properties." Molecules 27, no. 15 (July 25, 2022): 4747. http://dx.doi.org/10.3390/molecules27154747.

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The successful use of 1,3,4,2-triazaphospholenes (TAPs) as organo-catalysts stresses the need for efficient synthetic routes to these molecules. In this study, we establish the [1 + 4]-cycloaddition of PBr3 to azo-pyridines as a new approach to preparing pyrido-annellated TAPs in a single step from easily available precursors. The modular assembly of the azo-component via condensation of primary amines and nitroso compounds along with the feasibility of post-functionalization at the P–Br bond under conservation of the heterocyclic structure allows, in principle, to address a wide range of target molecules, which is illustrated by prototypical examples. The successful synthesis of a transition metal complex confirms for the first time the ability of a TAP to act as a P-donor ligand. Crystallographic studies suggest that hyperconjugation effects and intermolecular interactions induce a qualitatively similar ionic polarization of the P–Br bonds in TAPs as in better known isoelectronic diazaphospholenes.

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40

Drechsel, Carl, Philipp D’Astolfo, Jung-Ching Liu, Thilo Glatzel, Rémy Pawlak, and Ernst Meyer. "Topographic signatures and manipulations of Fe atoms, CO molecules and NaCl islands on superconducting Pb(111)." Beilstein Journal of Nanotechnology 13 (January 3, 2022): 1–9. http://dx.doi.org/10.3762/bjnano.13.1.

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Topological superconductivity emerging in one- or two-dimensional hybrid materials is predicted as a key ingredient for quantum computing. However, not only the design of complex heterostructures is primordial for future applications but also the characterization of their electronic and structural properties at the atomic scale using the most advanced scanning probe microscopy techniques with functionalized tips. We report on the topographic signatures observed by scanning tunneling microscopy (STM) of carbon monoxide (CO) molecules, iron (Fe) atoms and sodium chloride (NaCl) islands deposited on superconducting Pb(111). For the CO adsorption a comparison with the Pb(110) substrate is demonstrated. We show a general propensity of these adsorbates to diffuse at low temperature under gentle scanning conditions. Our findings provide new insights into high-resolution probe microscopy imaging with terminated tips, decoupling atoms and molecules by NaCl islands or tip-induced lateral manipulation of iron atoms on top of the prototypical Pb(111) superconducting surface.

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Wu, Baodong, and K. Andrew White. "Formation and Amplification of a Novel Tombusvirus Defective RNA Which Lacks the 5′ Nontranslated Region of the Viral Genome." Journal of Virology 72, no. 12 (December 1, 1998): 9897–905. http://dx.doi.org/10.1128/jvi.72.12.9897-9905.1998.

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ABSTRACT Defective interfering (DI) RNAs of tomato bushy stunt virus (TBSV) are small, subgenomic, helper-dependent replicons that are believed to be generated primarily by aberrant events during replication of the plus-sense RNA genome. Prototypical TBSV DI RNAs contain four noncontiguous segments (regions I through IV) derived from the 5′ nontranslated region (NTR) (I), an internal section (II), and the 3′-terminal portion (III and IV) of the viral genome. We have studied the formation of these molecules by using engineered precursor DI RNA transcripts and report here the consistent accumulation of a novel defective RNA species, designated RNA B. Northern blot, primer extension, and sequence analyses indicated that, unlike prototypical DI RNAs, RNA B lacks region I. In vitro transcripts corresponding to the region II-III-IV structure of RNA B were amplified when coinoculated with helper, indicating that the 5′ NTR of the genome does not harborcis-acting replication elements essential for viral RNA replication. Region I is, however, important for DI RNA fitness, since molecules lacking it accumulated to significantly lower levels (∼10-fold reduction). Analysis of the minus-strand sequence of region I led to the identification of an RNA undecamer sequence, arranged in tandem, at its very 3′ terminus. Additional variants of the undecamer motif were also identified at internal positions in region I and in the negative strands of regions II, III, and IV. Features of the undecamer motif, the consensus of which is (−)3′-CCCAAAGAGAG, are consistent with a role as a cis-acting replication element. It is proposed that the ability of RNA B to be amplified is due, in part, to compensatory effects of a strategically positioned undecamer motif in region II. Possible replicase-mediated mechanisms for the generation of this novel viral RNA are also presented.

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42

Jacobsen, Heiko. "Localized-orbital locator (LOL) profiles of chemical bonding." Canadian Journal of Chemistry 86, no. 7 (July 1, 2008): 695–702. http://dx.doi.org/10.1139/v08-052.

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We examine a recently introduced descriptor of chemical bonding, the localized-orbital locator (LOL), which is based on the kinetic-energy density (τ). Examples are presented for prototypical chemical bonds, such as single, double, and triple bonds, for bonding in transition metal complexes, for three-center two-electron bonds, as well as for hypervalent molecules. The topology of LOL is analyzed in terms of (3,–3) attractors (Γ). The influence of core electrons for chemical bonding is investigated, and a LOL-VSEPR (valence shell electron pair repulstion) relationship is established. Further, we compare LOL to the related electron localization function (ELF).Key words: chemical bonding, kinetic-energy density, localized-electron locator, VSEPR theory.

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43

Wu, Yangjun, Xiansong Xu, Dario Poletti, Yi Fan, Chu Guo, and Honghui Shang. "A Real Neural Network State for Quantum Chemistry." Mathematics 11, no. 6 (March 15, 2023): 1417. http://dx.doi.org/10.3390/math11061417.

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The restricted Boltzmann machine (RBM) has recently been demonstrated as a useful tool to solve the quantum many-body problems. In this work we propose tanh-FCN, which is a single-layer fully connected neural network adapted from RBM, to study ab initio quantum chemistry problems. Our contribution is two-fold: (1) our neural network only uses real numbers to represent the real electronic wave function, while we obtain comparable precision to RBM for various prototypical molecules; (2) we show that the knowledge of the Hartree-Fock reference state can be used to systematically accelerate the convergence of the variational Monte Carlo algorithm as well as to increase the precision of the final energy.

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Manrubia, Susanna, and José A. Cuesta. "Distribution of genotype network sizes in sequence-to-structure genotype–phenotype maps." Journal of The Royal Society Interface 14, no. 129 (April 2017): 20160976. http://dx.doi.org/10.1098/rsif.2016.0976.

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An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype–phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes.

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45

MALBON, Craig C., Jiangchuan TAO, and Hsien-yu WANG. "AKAPs (A-kinase anchoring proteins) and molecules that compose their G-protein-coupled receptor signalling complexes." Biochemical Journal 379, no. 1 (April 1, 2004): 1–9. http://dx.doi.org/10.1042/bj20031648.

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Cell signalling mediated via GPCRs (G-protein-coupled receptors) is a major paradigm in biology, involving the assembly of receptors, G-proteins, effectors and downstream elements into complexes that approach in design ‘solid-state’ signalling devices. Scaffold molecules, such as the AKAPs (A-kinase anchoring proteins), were discovered more than a decade ago and represent dynamic platforms, enabling multivalent signalling. AKAP79 and AKAP250 were the first to be shown to bind to membrane-embedded GPCRs, orchestrating the interactions of various protein kinases (including tyrosine kinases), protein phosphatases (e.g. calcineurin) and cytoskeletal elements with at least one member of the superfamily of GPCRs, the prototypical β2-adrenergic receptor. In this review, the multivalent interactions of AKAP250 with the cell membrane, receptor, cytoskeleton and constituent components are detailed, providing a working model for AKAP-based GPCR signalling complexes. Dynamic regulation of the AKAP–receptor complex is mediated by ordered protein phosphorylation.

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46

Redaelli, E., L. Bizzocchi, P. Caselli, O. Sipilä, V. Lattanzi, B. M. Giuliano, and S. Spezzano. "High-sensitivity maps of molecular ions in L1544." Astronomy & Astrophysics 629 (August 26, 2019): A15. http://dx.doi.org/10.1051/0004-6361/201935314.

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Context. The deuterium fraction in low-mass prestellar cores is a good diagnostic indicator of the initial phases of star formation, and is also a fundamental quantity to infer the ionisation degree in these objects. Aims. With the analysis of multiple transitions of N2H+, N2D+, HC18O+, and DCO+ we are able to determine the molecular column density maps and the deuterium fraction in N2H+ and HCO+ toward the prototypical prestellar core L1544. This is the preliminary step to derive the ionisation degree in the source. Methods. We used a non-local thermodynamic equilibrium (non-LTE) radiative transfer code combined with the molecular abundances derived from a chemical model to infer the excitation conditions of all the observed transitions. This allowed us to derive reliable maps of the column density of each molecule. The ratio between the column density of a deuterated species and its non-deuterated counterpart gives the sought-after deuteration level. Results. The non-LTE analysis confirms that, for the molecules analysed, higher-J transitions are characterised by excitation temperatures that are ≈1–2 K lower than those of the lower-J transitions. The chemical model that provides the best fit to the observational data predicts the depletion of N2H+ and to a lesser extent of N2D+ in the innermost region. The peak values for the deuterium fraction that we find are D/HN2H+ = 0.26−0.14+0.15 and D/HHCO+=0.035−0.012+0.015, in good agreement with previous estimates in the source.

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47

Ruan, Wenjing, Christopher T. Lee, and Julie Desbarats. "A Novel Juxtamembrane Domain in Tumor Necrosis Factor Receptor Superfamily Molecules Activates Rac1 and Controls Neurite Growth." Molecular Biology of the Cell 19, no. 8 (August 2008): 3192–202. http://dx.doi.org/10.1091/mbc.e08-02-0161.

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Members of the tumor necrosis factor receptor (TNFR) superfamily control cell fate determination, including cell death and differentiation. Fas (CD95) is the prototypical “death receptor” of the TNFR superfamily and signals apoptosis through well established pathways. In the adult nervous system, Fas induces apoptosis in the context of neuropathology such as stroke or amyotrophic lateral sclerosis. However, during nervous system development, Fas promotes neurite growth and branching. The molecular mechanisms underlying Fas-induced process formation and branching have remained unknown to date. Here, we define the molecular pathway linking Fas to process growth and branching in cell lines and in developing neurons. We describe a new cytoplasmic membrane proximal domain (MPD) that is essential for Fas-induced process growth and that is conserved in members of the TNFR superfamily. We show that the Fas MPD recruits ezrin, a molecule that links transmembrane proteins to the cytoskeleton, and activates the small GTPase Rac1. Deletion of the MPD, but not the death domain, abolished Rac1 activation and process growth. Furthermore, an ezrin-derived inhibitory peptide prevented Fas-induced neurite growth in primary neurons. Our results define a new domain, topologically and functionally distinct from the death domain, which regulates neuritogenesis via recruitment of ezrin and activation of Rac1.

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48

Trimble, William S., and Sergio Grinstein. "Barriers to the free diffusion of proteins and lipids in the plasma membrane." Journal of Cell Biology 208, no. 3 (February 2, 2015): 259–71. http://dx.doi.org/10.1083/jcb.201410071.

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Biological membranes segregate into specialized functional domains of distinct composition, which can persist for the entire life of the cell. How separation of their lipid and (glyco)protein components is generated and maintained is not well understood, but the existence of diffusional barriers has been proposed. Remarkably, the physical nature of such barriers and the manner whereby they impede the free diffusion of molecules in the plane of the membrane has rarely been studied in depth. Moreover, alternative mechanisms capable of generating membrane inhomogeneity are often disregarded. Here we describe prototypical biological systems where membrane segregation has been amply documented and discuss the role of diffusional barriers and other processes in the generation and maintenance of their structural and functional compartmentalization.

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Schilke, Peter, Karl M. Menten, Friedrich Wyrowski, and C. M. Walmsley. "Interferometric Observations of Chemistry in High-Mass Star-Forming Regions." Symposium - International Astronomical Union 197 (2000): 125–33. http://dx.doi.org/10.1017/s0074180900164733.

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Single dish spectral line surveys of high mass star-forming regions provide spectra with a very high line density, and reveal the presence of many complex molecules. Besides the prototypical Orion BN/KL region, more and more regions get surveyed and we start to get a better idea of the chemical similarities and differences. Yet, single dish studies miss an important aspect of hot cores, which is revealed by higher resolution studies with interferometers: the cores are not chemically homogeneous, but a pronounced chemical substructure exists. As an example of such an interferometric study, we will present one particular set of objects, the UC HII W3(OH) and its neighboring hot core W3(H2O) (otherwise known as the Turner-Welch object), and discuss their chemical properties.

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50

Partovi-Azar, Pouya, and Daniel Sebastiani. "Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation." Micromachines 12, no. 6 (June 10, 2021): 679. http://dx.doi.org/10.3390/mi12060679.

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Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

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