Academic literature on the topic 'Complex organic molecules'
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Journal articles on the topic "Complex organic molecules"
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Herbst, Eric, and Ewine F. van Dishoeck. "Complex Organic Interstellar Molecules." Annual Review of Astronomy and Astrophysics 47, no. 1 (September 2009): 427–80. http://dx.doi.org/10.1146/annurev-astro-082708-101654.
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Öberg, Karin I., Edith C. Fayolle, John B. Reiter, and Claudia Cyganowski. "Complex molecule formation around massive young stellar objects." Faraday Discuss. 168 (2014): 81–101. http://dx.doi.org/10.1039/c3fd00146f.
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Interstellar complex organic molecules were first identified in the hot inner regions of massive young stellar objects (MYSOs), but have more recently been found in many colder sources, indicating that complex molecules can form at a range of temperatures. However, individually these observations provide limited constraints on how complex molecules form, and whether the same formation pathways dominate in cold, warm and hot environments. To address these questions, we use spatially resolved observations from the Submillimeter Array of three MYSOs together with mostly unresolved literature data to explore how molecular ratios depend on environmental parameters, especially temperature. Towards the three MYSOs, we find multiple complex organic emission peaks characterized by different molecular compositions and temperatures. In particular, CH3CCH and CH3CN seem to always trace a lukewarm (T ≈ 60 K) and a hot (T > 100 K) complex chemistry, respectively. These spatial trends are consistent with abundance–temperature correlations of four representative complex organics – CH3CCH, CH3CN, CH3OCH3 and CH3CHO – in a large sample of complex molecule hosts mined from the literature. Together, these results indicate a general chemical evolution with temperature, i.e. that new complex molecule formation pathways are activated as a MYSO heats up. This is qualitatively consistent with model predictions. Furthermore, these results suggest that ratios of complex molecules may be developed into a powerful probe of the evolutionary stage of a MYSO, and may provide information about its formation history.
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Soma, Tatsuya, Nami Sakai, Yoshimasa Watanabe, and Satoshi Yamamoto. "Complex Organic Molecules in Taurus Molecular Cloud-1." Astrophysical Journal 854, no. 2 (February 16, 2018): 116. http://dx.doi.org/10.3847/1538-4357/aaa70c.
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Dartois, E., M. Chabot, T. Id Barkach, H. Rothard, B. Augé, A. N. Agnihotri, A. Domaracka, and P. Boduch. "Non-thermal desorption of complex organic molecules." Astronomy & Astrophysics 627 (July 2019): A55. http://dx.doi.org/10.1051/0004-6361/201834787.
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Context. The occurrence of complex organic molecules (COMs) in the gas phase at low temperature in the dense phases of the interstellar medium suggests that a non-thermal desorption mechanism is at work because otherwise, COMs should condense within a short timescale onto dust grains. Vacuum ultraviolet (VUV) photodesorption has been shown to be much less efficient for complex organic molecules, such as methanol, because mostly photoproducts are ejected. The induced photolysis competes with photodesorption for large COMs, which considerably lowers the efficiency to desorb intact molecules. Aims. We pursue an experimental work that has already shown that water molecules, the dominant ice mantle species, can be efficiently sputtered by cosmic rays. We investigate the sputtering efficiency of complex organic molecules that are observed either in the ice mantles of interstellar dense clouds directly by infrared spectroscopy (CH3OH), or that are observed in the gas phase by millimeter telescopes (CH3COOCH3) and that could be released from interstellar grain surfaces. Methods. We irradiated ice films containing complex organic molecules (methanol and methyl acetate) and water with swift heavy ions in the electronic sputtering regime. We monitored the infrared spectra of the film as well as the species released to the gas phase with a mass spectrometer. Results. We demonstrate that when methanol or methyl acetate is embedded in a water-ice mantle exposed to cosmic rays, a large portion is sputtered as an intact molecule, with a sputtering yield close to that of the main water-ice matrix. This must be even more true for the case of more volatile ice matrices, such as those that are embedded in carbon monoxide. Conclusions. Cosmic rays penetrating deep into dense clouds provide an efficient mechanism to desorb complex organic molecules. Compared to the VUV photons, which are induced by the interaction of cosmic rays, a large portion desorb as intact molecules with a proportion corresponding to the time-dependent bulk composition of the ice mantle, the latter evolving with time as a function of fluence due to the radiolysis of the bulk.
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Walsh, Catherine, Tom J. Millar, Hideko Nomura, Eric Herbst, Susanna Widicus Weaver, Yuri Aikawa, Jacob C. Laas, and Anton I. Vasyunin. "Complex organic molecules in protoplanetary disks." Astronomy & Astrophysics 563 (February 28, 2014): A33. http://dx.doi.org/10.1051/0004-6361/201322446.
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Faure, Alexandre, Eric Josselin, Laurent Wiesenfeld, and Cecilia Ceccarelli. "Collisional excitation of complex organic molecules." Proceedings of the International Astronomical Union 4, S251 (February 2008): 137–38. http://dx.doi.org/10.1017/s1743921308021376.
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AbstractA major difficulty in modelling the infrared and (sub)millimeter spectra of gas-phase complex organic molecules is the lack of state-to-state collisional rate coefficients. Accurate quantum or classical scattering calculations for large polyatomic species are indeed computationally highly challenging, particularly when both rotation and low frequency vibrations such as bending and torsional modes are involved. We briefly present here an approximate approach to estimate and/or extrapolate rotational and rovibrational rates for polyatomic molecules with many degrees of freedom.
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Liu, Sheng-Yuan. "Interferometric Observations of Complex Organic Molecules." Proceedings of the International Astronomical Union 1, S231 (March 21, 2006): 217. http://dx.doi.org/10.1017/s1743921306007216.
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Cruikshank, D. P. "Complex Organic Solid Matter in the Outer Solar System." Highlights of Astronomy 13 (2005): 902–3. http://dx.doi.org/10.1017/s1539299600017482.
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Complex organic molecular material of non-biological origin is found in abundance in the interstellar dust in our Galaxy, and is also detected in other galaxies. Some of this material was incorporated into the solar nebula and is now found in some Solar System bodies. While some pre-solar organic material has been preserved, synthesis of complex organics in planetary atmospheres and on icy surfaces has been in progress for the entire age of the Solar System. Refractory organic solids have proven difficult to detect by traditional spectroscopic techniques, and their presence is usually inferred from the low albedo and (often) red color of the surfaces of small bodies in the outer Solar System (OSS). Color in complex organic molecules, such as polymers and polycyclic aromatic hydrocarbons, is caused by absorption in the UV and visible spectral regions arising from electronic transitions connected primarily with C-C and C-0 bonding. In particular, large hydrocarbon molecules with conjugated (alternating pairs of double and single) C-C bonds have color because the electronic transitions of the de-localized pi electrons extend into the visible spectral region; the longer the conjugated chain, the further is the extension to longer wavelength, with the result that especially large molecular material appears black.
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Choudhury, R., P. Schilke, G. Stéphan, E. Bergin, T. Möller, A. Schmiedeke, and A. Zernickel. "Evolution of complex organic molecules in hot molecular cores." Astronomy & Astrophysics 575 (February 25, 2015): A68. http://dx.doi.org/10.1051/0004-6361/201424499.
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Ceccarelli, Cecilia. "Organic molecules in protostellar environments." Proceedings of the International Astronomical Union 4, S251 (February 2008): 79–88. http://dx.doi.org/10.1017/s174392130802125x.
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AbstractThe sequence that brings matter from a molecular cloud to a fully developed star plus planetary system seems to be a unique and rich chemistry laboratory where, step by step, molecular complexity increases. During the cold pre-collapse phase, atoms and simple molecules, like CO, freeze out onto the dust grains, forming icy mantles. Reactions on the grain surfaces likely form hydrogenated molecules (notably H2O, CH4, H2CO, CH3OH, and NH3) and perhaps even more complex organic molecules. The hallmark of this era is the super-deuteration phenomenon, i. e. the abnormal enhancement of molecules containing one or more D atoms instead of H atoms, by up to 13 orders of magnitude with respect to the cosmic elemental D/H ratio (~10−5). The frozen molecules are released into the gas upon warming by the forming star and undergo reactions which further increase the molecular complexity, leading to several complex organic molecules. Products of this efficient chemical factory are observed in the hot corinos, which are warm (~100 K), dense (~107–108 cm−3) solar-system-sized regions at the centre of the collapsing envelopes of solar type protostars. In this contribution, I review what is known about the organic molecules in protostellar environments, with emphasis on the hot corinos, and how possibly the organic molecules formed at this stage may constitute an heritage for the forming planetary system.
Dissertations / Theses on the topic "Complex organic molecules"
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Saywell, Alexander. "2D organisation of complex organic molecules." Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/14588/.
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The self-assembly of two-dimensional molecular systems is of significant interest, offering an insight into the fundamental interactions which drive the formation of complex supramolecular structures. A careful choice of the molecular 'building blocks' for such self-assembled systems potentially allows the design and production of nanoscale architectures with pre-determined geometries and specific chemical functionalities. Within this thesis the two-dimensional structures formed by the self-assembly of complex organic molecules, deposited on an Au(111) surface held in an ultrahigh vacuum (URV) environment, are studied using a combination of scanning tunnelling microscopy (STM), photoelectron spectroscopy (PES), molecular dynamics (MD), and density functional theory (DFT) techniques. A UHV electrospray deposition (URV-ESD) technique is employed to facilitate the introduction of thermally labile molecules into the URV environment. Bi-molecular networks, formed from perylene tetracarboxylic diimide (PTCDI) and melamine, have previously been observed to assemble on the Au(111) surface. Several more complex phases are reported here, as characterised by S'I'M, with the balance between isotropic and anisotropic interactions giving rise to a variety of structures. Chemical functionality may be added to these networks by incorporating functionalised derivatives of PTCDI. Alternative structures produced by altering the shape of the molecular 'building blocks' are also discussed. The URV-ESD technique is demonstrated here to be compatible with the deposition of the fullerene C60,the single molecule magnet Mn12012(02CCR3h6(H20)4 (Mn12(acetate)16), and porphyrin based oligomers (P4 and P6) and polymers (Pn). The URV-ESD of C60on the clean AU(ll1) surface, and on a surface prepatterned with a PTCDI/melamine network, results in similar structures to those previously observed to be produced by sublimation. Mn12(acetate)16 and the porphyrin oligomers and polymers represent complex molecules which are thermally labile and possess, respectively, novel magnetic and electronic properties. Mn12(acetate) 16is observed to form filamentary aggregates due to the anisotropic nature of the molecule-molecule and molecule-substrate interactions, while P4, P6 and Pn form highly ordered close-packed domains driven by the interdigitation of the alkyl chains attached to the porphyrin cores. The findings presented within this thesis demonstrate that self-assembled molecular structures can be understood in terms of intermolecular interactions, and that for systems containing complex molecules the molecule-molecule interaction potential can lead to the formation of novel structures.
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Al-Edhari, Ali Jaber. "Complex organic molecules in solar-type star forming regions." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY048/document.
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Le but de la présente thèse est l'étude de la compléxité moléculaire dans les régions de formation stellaires. Cette thèse s'axe sur deux classes de molécule aux caractéristiques prébiotiques : les molécules organiques complexes et les cyanopolyynes.Dans ce contexte, j'ai analysé des données d'un seul échantillon de relevés spec- traux en exploitant des codes de transfert radiatif à l'équilibre thermodynamique local (LTE) et/ou non-LTE pour deux sources : une proto-étoile de type solaire dans un environnement calme (IRAS 16293-2422) et un proto-ama constitué de proto-étoile de type solaire (OMC2-FIR4).L'objectif est de trouver des similar- ités et des différences entre ces deux cas.J'ai utilisé des données issu de deux relevés spectraux : TIMASSS (The IRAS16293-2422 Millimeter And Submilimeter Spectral Survey) réalisés en 2011 (Caux et al. 2011), et ASAI(Astrochemical Surveys At IRAM) réalisés pen- dant la période 2013-2015 (eg Lopez-Sepulcre et al.2015). J'ai extrais les lignes (identification et intensité intégrée) en utilisant le paquet disponible publique- ment : CASSIS (Centre d'Analyse Scientifique de Spectres Infrarouges et Sub- millimetrique). Pour finir, j'ai utilisé le paquet GRAPES (GRenoble Analysis of Protostellar Envelope Spectral) afin de modéliser la distribution spectrale énergétique de ligne (SLED) des molécules détectées, mais aussi afin d'estimer leurs abondances à travers l'envelope de IRAS16293 et du coeur chaud OMC2- FIR4.Les principaux résultats de la thèse sont :1. Le premier recensement complet des molecules organiques complexes (COMs) dans IRAS162932. La première détéction de COMs dans l'enveloppe froide d'une proto-étoile de type solaire (IRAS16293-2422) supportant l'idée qu'un méchanisme de formation, relativement efficace pour les COMs détectées, doit exister en phase gazeuse froide.3. La découverte d'une fine corrélation entre le diméthyle-éther (DME) et le méthyle-formate (MF) suggère une relation mère fille entre ces deux espèces.4. La detection de formamide, espèce avec un très fort potentiel prébiotique, dans plusieurs protoétoiles incluant IRAS16293-2422 et OMC2-FIR4.5. Le recensement complet des cyanopolyynes dans IRAS16293 et OMC2- FIR4 avec la détection de HC3N, HC5N, DC3N et pour OMC2-FIR4: le C13 isotopologue du HC3N cyanopolyynes.Ces résultats sont le sujet principal de deux publications (Jaber et al.2014, ApJ; Lopez-Sepulcre, Jaber et al.2015,MNRAS), un article accepté (Jaber et al., A & A) et un article à soumettre (Jaber et al. A & A)The present PhD thesis goal is the study of the molecular complexity in solar type star forming regions. It specifically focuses on two classes of molecules with a pre-biotic value, the complex organic molecules and the cyanopolyynes.At this scope, I analyzed data from single-dish spectral surveys by means of non-LTE or/and non-LTE radiative transfer codes in two sources, a solar type protostar in an isolated and quiet environment (IRAS16293-2422) and a proto-cluster of solar type protostars (OMC2-FIR4). The goal is to find similarities and differences between these two cases.I used data from two spectra surveys: TIMASSS (The IRAS16293-2422 Millimeter And Submillimeter Spectral Survey), which has been carried out in 2011 (Caux et al. 2011), and ASAI (Astrochemical Surveys At IRAM), which has been carried out in 2013-2015 (e.g. Lopez-Sepulcre et al. 2015).I extracted the lines (identification and integrated intensity) by means of the publicly available package CASSIS (Centre dAnalyse Scientifique de Spectres Infrarouges et Submillimtriques).Finally, I used the package GRAPES (GRenoble Analysis of Protostellar Envelope Spectra) to model the Spectral Line Energy Distribution (SLED) of the detected molecules, and to estimate their abundance across the envelope and hot corino of IRAS16293-2422 and OMC2-FIR4, respectively.The major results of the thesis are:1) The first full census of complex organic molecules (COMs) in IRAS16293-2422;2) The first detection of COMs in the cold envelope of a solar type protostar (IRAS16293-2422), supporting the idea that a relatively efficient formation mechanism for the detected COMs must exist in the cold gas phase;3) The discovery of a tight correlation between the dimethyl ether (DME) and methyl format (MF), suggesting a mother-daughter relationship;4) The detection of formamide, a species with a very high pre-biotic value, in several protostars, included IRAS16293-2422 and OMC2-FIR4;5) The full census of the cyanopolyynes in IRAS16293-2422 and OMC2-FIR4, with the detection of HC3N and HC5N, DC3N and, for OMC2-FIR4, the 13C isotopologue of HC3N cyanopolyynes.These results are the focus of two published articles (Jaber et al. 2014, ApJ; Lopez-Sepulcre, Jaber et al. 2015, MNRAS), one accepted article (Jaber et al., A&A) and a final article to be submitted (Jaber et al., A&A)
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Sadownik, Jan. "Evolving complex systems from simple molecules." Thesis, St Andrews, 2009. http://hdl.handle.net/10023/857.
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Silva, Bermudez Phaedra Suriel. "Adsorption of complex organic molecules on metal single crystal surfaces." Thesis, University of Liverpool, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426136.
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Clay, Matthew D. "Synthetic approaches to complex organic molecules: Desogestrel, acetylenic allenophanes, and Buckminsterfullerene." Thesis, University of Ottawa (Canada), 2006. http://hdl.handle.net/10393/29344.
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This thesis is composed of three sections and describes our work towards the synthesis of three molecules: Desogestrel, the first acetylenic allenophane, and Buckminsterfullerene.
Section A details a tether-controlled diene-transmissive intramolecular Diels-Alder reaction approach to the oral contraceptive progestin Desogestrel. Using our indium-mediated gamma-pentadienylation chemistry as a key step, we synthesized tetraenes 92 and 68. Unfortunately, the intramolecular Diels-Alder reaction of these tetraenes resulted in formation of three isomers, bicyclo[4.3.0]nonenes 96 and 97, and the unusual bicyclo[3.3.1]nonene 99. Attempts to improve the selectivity were unsuccessful and precluded further pursuit of the synthesis.
Section B of this thesis describes our design and asymmetric synthesis of the first acetylenic allenophane (308). This molecule represented a new class of cyclophane, and illustrative of the current interest in this type of molecule, several additional examples have since been reported, as well as an independent highlight in Angewandte Chemie. To complete our asymmetric synthesis, we developed a novel method of synthesizing tertiary propargyl alcohols (e.g., 299) in very good yield and enantioselectivity using a Sharpless asymmetric epoxidation as a key step. In contrast to the few procedures available for the asymmetric synthesis of tertiary propargyl alcohols, our protocol could be completed in roughly half the time, did not require the rigorous exclusion of oxygen or moisture, and did not require particularly specialized equipment.
Section C describes our work towards a controlled laboratory synthesis of Buckminsterfullerene (C60) using hexakis[(Z)-enynyl]benzenes. We have developed several approaches to these molecules using trisubstituted benzene test substrates and have used these methods to construct hexasubstituted benzenes 417 and 418 from bromoaldehyde 399 . We are presently attempting to convert 418 to our cyclophane precursor to C60.
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Vazart, Fanny. "Gas-phase formation of Complex Organic Models molecules in interstellar medium: computational investigations." Doctoral thesis, Scuola Normale Superiore, 2017. http://hdl.handle.net/11384/85813.
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[excerpt form the abstract:] In the field of astro- and prebiotic chemistry, the building blocks of life, which are molecules composed of more than 6 atoms, are called Complex Organic Molecules (COMs). Their appearances on the early inorganic Earth is therefore one of the major issues faced by researchers interested in the origin of life. In this thesis, split into three parts, the main purpose is to show how different COMs are formed in interstellar medium (ISM), using computational chemistry.
The first part focuses mainly on preliminary studies aiming at evaluating the appropriate level of theory to use to perform studies of formation reactions. First, a comprehensive benchmark of C≡N stretching vibrations computed at harmonic and anharmonic levels is reported with the goal of proposing and validating a reliable computational strategy to get accurate results for this puzzling vibrational mode, involved in biological molcules, without any ad hoc scaling factor.
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Repiscak, Peter. "Computational chemistry for complex systems : open-shell molecules to conjugated organic materials." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3348.
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This thesis focuses on two different, but equally challenging, areas of computational chemistry: transition metal organic molecule interactions and parameterisation of organic conjugated polymers for molecular dynamics simulations. The metal-binding properties are important for understanding of biomolecular action of type 2 diabetes drug and development of novel protocols for redox calculations of copper systems. In this area the challenge is mainly related to the complex electronic structure of the open-shell transition metals. The main challenges for the parameterisation of conjugated polymers are due to the size of the studied systems, their conjugated nature and inclusion of environment. Metal-binding properties as well as electronic structures of copper complexes of type 2 diabetes drug metformin (Metf) and other similar, but often inactive, compounds were examined using DFT method. It was found that for neutral compounds it is not possible to explain the differences in their biological effects solely by examining the copper-binding properties. Further, the proposed mechanism potentially explaining the difference in the biomolecular mode of action involves a possible deprotonation of biguanide and Metf compounds under higher mitochondrial pH which would lead to formation of more stable copper complexes and potentially affecting the mitochondrial copper homeostasis. In addition, redox properties of copper-biguanide complexes could interfere with the sensitive redox chemistry or interact with important metalloproteins in the mitochondria. Understanding the copper-binding properties is also important for a systematic development and testing of computational protocols for calculations of reduction potentials of copper complexes. Copper macrocyclic complexes previously used as model systems for redox-active metalloenzymes and for which experimentally determined redox potentials are available were used as model systems. First adequacy of using single reference methods such as DFT was examined for these systems and then various DFT functionals and basis sets were tested in order to develop accurate redox potential protocol. It was shown that good relative cor-relations were obtained for several functionals while the best absolute agreement was obtained with either the M06/cc-pVTZ functional with the SMD or either M06L or TPSSTPSS functional with cc-pVTZ basis set and the PCM solvation model. Organic conjugated polymers have a great potential due to their application in organic optoelectronics. Various wavefunction and DFT methods are utilized in order to systematically develop parameterisation scheme that can be used to derive selected force-field parameters such as torsional potentials between monomer units that are critical for these systems and partial charges. Moreover, critical points of such a parameterisation are addressed in order to obtain accurate MD simulations that could provide valuable insight into material morphology and conformation that affect their optical properties and conductivity. It was shown that a two step approach of geometry optimisation with CAM-B3LYP/631G* and single point (SP) energy scan with CAM-B3LYP/cc-pVTZ is able to yield accurate dihedral potentials in agreement with the potentials calculated using higher level methods such as MP2 and CBS limit CCSD(T). Further, investigating partial charge distribution for increasing backbone length of fluorene and thiophene it has been found that it is possible to obtain a three residue model of converged charge distributions using the RESP scheme. The three partial charge residues can be then used to build and simulate much longer polymers without the need to re-parametrize charge distributions. In the case of side-chains, it was found that it is not possible to obtain converged charge sets for sidechain lengths of up to 10 carbons due to the strong asymmetry between the side-chain ends. Initial validation of derived force-field parameters performed by simulations of 32mers of fluorene with octyl side-chains (PF8) and thiophene with hexyl side-chains (P3HT) in chloroform and calculation of persistence lengths and end-to-end lengths showed close correspondence to experimentally obtained values.
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Halfen, DeWayne Terrence. "Studies in Laboratory Spectroscopy and Radio Astronomy: From Simple Hydrides to Complex Organic Molecules." Diss., The University of Arizona, 2006. http://hdl.handle.net/10150/195962.
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There are two main objectives for this thesis. First, laboratory rotational spectra of metal-containing molecules were measured using the millimeter-wave spectrometers of the Ziurys group. Second, radio astronomical observations were performed on a number of the molecules measured in the laboratory, along with several organic species. The laboratory work is essential to the discovery of new molecules in the interstellar medium, and the understanding of the chemical composition of the universe. Identification of these species can only occur after their pure rotational spectra have been measured. Therefore, an investigation of the rotational spectra of several classes of molecules was performed including metal-bearing hydrides, chlorides, carbon-containing species, and molecular ions. The experimental measurements were aided by necessary improvements in the operation of the spectrometers. Many of these species had not been observed by any spectroscopic technique, including CaC, CuCH₃, FeCO⁺ and VCl⁺. Several of these molecules exhibited unusual interactions that complicated the analysis of their spectra, such as VCl, TiCl⁺, VCl⁺, and FeCO⁺. Synthesis of these species required exotic production techniques, including the use of Broida ovens and AC and DC discharges. Astronomical observations of several of the molecules studied in the laboratory were conducted, and upper limits to the abundances obtained. Additional searches for more of the species studied are planned. A region in the Galactic center with a complex chemical composition called Sgr B2(N) was recognized through observations of N₂O. Several organic species were then searched for in this source. The detection of the simple sugar glycolaldehyde was confirmed by observing all of the favorable transitions of this molecule in Sgr B2(N). A standard set of criteria for identifying complex organic molecules was drawn up as a result of this study. This investigation led to an attempt to confirm a larger sugar, dihydroxyacetone. Unfortunately the detection of this species was proven false, and a limit could be placed on the chemical complexity of this source.
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Rahnejat, K. A. "Capturing complex reaction pathways step by step : organic molecules on the Si(001) surface." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1473368/.
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Experts expect that inherent limitations in semiconductor electronics will become apparent within the next couple of decades. Consequently, the construction of novel electronic-devices that surpass existing technologies in both miniaturisation and intrinsic functionality is becoming increasingly important. The assembly of nanoscale circuitries comprised of individual, synthetically-tailored molecules designed to substitute conventional electronic-components is a popular approach to tackling this challenge. The incorporation of functional molecules with existing silicon-based electronics is the most credible route towards realising this goal in the near-future. To this end, we present a scanning tunnelling microscopy (STM) study of acetophenone—an archetypal, small, aromatic molecule—adsorbed onto the Si(001) surface. An elevated imaging bias is used to induce sequential structural-transitions in hundreds of adsorbates simultaneously. Specifically developed analytical-software was used to catalogue and analyse the transition sequences that were recorded. These transitions described long, complex surface-bound reaction-pathways in a step-by-step manner. Density functional theory (DFT) analysis reveals that acetophenone adsorbates adopt a remarkable 24 distinct adsorbate structures. Moreover, the captured reaction-pathways are up to six discreet steps in length and belong to one of three separate branches determined upon adsorption. These transitions are governed by predictable pivoting motions about a strong O–Si bond formed with the substrate. Our fundamental studies have informed the direct manipulation of individual adsorbates using precisely targeted voltage-pulses affording the control of specific transitions. In addition, we explore changes in the adsorption behaviour of these molecules after minor chemical modification through substitution of function groups. Finally, we construct and study 2D systems of overlapping wavefunctions by manufacturing dangling bonds (DB) on Si(001):H.
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Kong, Caleb J. "Engineering High Reaction Economy or, An Intensification/Scoring Program for the Preparation of Simple and Complex Molecules." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/6023.
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Success of newly discovered chemistry in academia is often scored in terms of its novelty and level of scholarship. In industrial settings, cost, safety and quality are often times the ruler by which new processes are measured. Our group has identified that there is a gap between these two measures of success and has sought to develop principles in order formalize an approach to synthetic strategy and developing ready-to-implement manufacturing processes for molecules, simple and complex.
Some of these principles include (1) the development and application of new chemical methods and reactor technologies (2) recognition of globally amenable chemical environments for each chemical step to consolidate unit operations and obviate the need for purification (3) vertical integration of starting materials to generate complexity from the most elementary building blocks in a chemical supply space and (4) the development of new materials that allow for recovery and reuse. These principles are iteratively scored and redeveloped through various metrics that our group has identified as effective tools in maximizing efficiency such as cost of goods (CoG), process mass intensity (PMI) and volume-time output (VTO). The intended benefits of this approach is that these processes become not only cost effective but sustainable and impactful in the manufacturing landscape and increase access of these products to consumers.
Books on the topic "Complex organic molecules"
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Transition metals in the synthesis of complex organic molecules. 2nd ed. Sausalito, Calif: University Science Books, 1999.
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G, Söderberg Björn C., ed. Transition metals in the synthesis of complex organic molecules. 3rd ed. Sausalito, Calif: University Science Books, 2009.
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Transition metals in the synthesis of complex organic molecules. Mill Valley, Calif: University Science Books, 1994.
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Modern tools for the synthesis of complex bioactive molecules. Hoboken, N.J: Wiley, 2012.
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Vicario, Jose L. Organocatalytic enantioselective conjugate addition reactions: A powerful tool for the stereocontrolled synthesis of complex molecules. Cambridge: Royal Society of Chemistry, 2010.
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Steinhoff, Gustav. Cell adhesion molecules in organ transplantation. 2nd ed. Austin, Tex: Landes Bioscience, 1998.
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Steinhoff, Gustav. Cell adhesion molecules in human organ transplants. Austin: R.G. Landes, 1993.
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Nino, Russo, Salahub Dennis R. 1946-, Witko Malgorzata, and North Atlantic Treaty Organization. Scientific Affairs Division., eds. Metal-ligand interactions: Molecular-, nano-, micro-, and macro-systems in complex environments. Dordrecht: Kluwer Academic Publishers, 2003.
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service), SpringerLink (Online, ed. Assessing the Functional Structure of Molecular Transporters by EPR Spectroscopy. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.
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Symposium, COSPAR Scientific Commission F. F3 1. Life sciences: new insights into complex organics in space: Proceedings of the F3.1 Symposium of COSPAR Scientific Commission F which was held during the thirty-second COSPAR Scientific Assembly, Nagoya, Japan, 12-19 July, 1998. Oxford: Pergamon [for the] Committee on Space Research, 1999.
Find full textBook chapters on the topic "Complex organic molecules"
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Kobayashi, Kensei. "Complex Organic Molecules." In Encyclopedia of Astrobiology, 528. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_337.
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Kobayashi, K. "Complex Organic Molecules." In Encyclopedia of Astrobiology, 352. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_337.
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Kobayashi, Kensei. "Complex Organic Molecules." In Encyclopedia of Astrobiology, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27833-4_337-5.
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Ohishi, Masatoshi. "Prebiotic Complex Organic Molecules in Space." In Astrobiology, 11–21. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-3639-3_2.
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Ashida, Michio. "Epitaxial Growth of Octacyanometalphthalocyanine-Metal Complex Crystals." In Electron Crystallography of Organic Molecules, 227–40. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3278-7_18.
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Šunjić, Vitomir, and Vesna Petrović Peroković. "Retrosynthetic Considerations and Syntheses of Complex, Biologically Active Molecules." In Organic Chemistry from Retrosynthesis to Asymmetric Synthesis, 189–211. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-29926-6_9.
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Kloprogge, Jacob. "Interactions of the Kaolin Minerals with Complex Organic Molecules." In Spectroscopic Methods in the Study of Kaolin Minerals and Their Modifications, 321–415. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-02373-7_7.
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Rodriguez, Raphaël. "Target-Oriented and Diversity-Oriented Organic Synthesis." In Modern Tools for the Synthesis of Complex Bioactive Molecules, 513–18. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118342886.ch15.
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Greenberg, J. Mayo, and Willem Schutte. "Infrared Spectral Identification of Complex Organic Molecules in Interstellar Grains." In The Search for Extraterrestrial Life: Recent Developments, 145–50. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5462-5_21.
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Hudlicky, T., A. Fleming, T. Lovelace, G. Seoane, K. Gadamasetti, and G. Sinai-Zingde. "[2+3] Carbo- and Hetero-Cyclic Annulation in the Design of Complex Molecules.1." In Strain and Its Implications in Organic Chemistry, 109–15. Dordrecht: Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-0929-8_7.
Full textConference papers on the topic "Complex organic molecules"
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Yuzhakov, Victor I., K. G. Yevsyukhina, and Svetlana V. Patsayeva. "Laser-induced saturation of fluorescence for complex organic molecules." In ALT '97 International Conference on Laser Surface Processing, edited by Vladimir I. Pustovoy. SPIE, 1998. http://dx.doi.org/10.1117/12.308644.
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Moulin, Christophe, and Alain D. Petit. "Selective laser photolysis of organic molecules in complex matrices." In Photonics West '95, edited by Randy D. Curry. SPIE, 1995. http://dx.doi.org/10.1117/12.205022.
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Codella, Claudio, L. Podio, F. Fontani, I. Jimenez-Serra, P. Caselli, M. E. Palumbo, A. Lopez-Sepulcre, et al. "Complex organic molecules in protostellar environments in the SKA era." In Advancing Astrophysics with the Square Kilometre Array. Trieste, Italy: Sissa Medialab, 2015. http://dx.doi.org/10.22323/1.215.0123.
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Knuth, Kevin H., Man Kit Tse, Joshua Choinsky, Haley A. Maunu, and Duane F. Carbon. "Bayesian Source Separation Applied to Identifying Complex Organic Molecules in Space." In 2007 IEEE/SP 14th Workshop on Statistical Signal Processing. IEEE, 2007. http://dx.doi.org/10.1109/ssp.2007.4301277.
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Kiskin, M. Yu, A. I. Vasyunin, and V. V. Akimkin. "Modeling the formation of complex organic molecules in a protoplanetary disk." In ASTRONOMY AT THE EPOCH OF MULTIMESSENGER STUDIES. Proceedings of the VAK-2021 conference, Aug 23–28, 2021. Crossref, 2022. http://dx.doi.org/10.51194/vak2021.2022.1.1.050.
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Sarkas, Harry W., Charles D. Merritt, and Zakya H. Kafafi. "Preparation, Optical Spectroscopy, and Fluorescence of Molecular Organic Composites for Light-Emitting Diodes." In Organic Thin Films for Photonic Applications. Washington, D.C.: Optica Publishing Group, 1995. http://dx.doi.org/10.1364/otfa.1995.md.35.
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Electroluminescence from small organic molecules has been known for some time. Thirty years ago, Helfrich and Schneider reported blue-violet electroluminescence in anthracene with an external quantum efficiency as high as 8%.1 This quantum efficiency is much better than that for the best polymer-based light-emitting diode (LED) reported to date.2 In spite of the superior quantum efficiency of molecular-based electroluminescent devices, no major progress was achieved until fairly recently when Tang and VanSlyke reported the first low-voltage organic LED with an external quantum efficiency of 1% (number of photons per electron).3 The emitting layer in this device consists of a thin layer of the metal complex, tris (8-hydroxyquinolinato) aluminum (AlQ3). Later, Littman and Martie showed an enhancement in the electroluminescence quantum efficiency of AlQ3 by doping it with the highly fluorescent laser dyes, Coumarin 540, Coumarin 343, and DCM.4 The paper focuses on a new class of organic composites consisting of highly fluorescent guest molecules dispersed in AlQ3. The electronic and optical properties of organic nanostructures based on these materials are studied, as functions of the luminescent center concentration, via optical and fluorescence spectroscopies. Photoluminescence quantum yields are measured and used to probe the efficiency of energy transfer between host and guest molecules.
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Cruz-Diaz, Gustavo, Susanna Widicus Weaver, Stefanie Milam, Perry Gerakines, Catherine Walker, Collette Sarver, and Will Thompson. "THE SEARCH FOR COMPLEX ORGANIC MOLECULES DESORBING FROM INTERSTELLAR ICE ANALOGS: PRESENTING SubLIME2." In 2022 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2022. http://dx.doi.org/10.15278/isms.2022.fg03.
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Fukasawa, K., T. Takahashi, T. Matsunami, H. Nakayama, and K. Ishii. "In situ wide angle X-ray diffraction of vapor-deposited glasses of small organic molecules." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794585.
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Wehres, Nadine, Susanna Widicus Weaver, Eric Herbst, D. Lis, Trevor Cross, Brian Hays, Jacob Laas, et al. "DETECTION, IDENTIFICATION AND CORRELATION OF COMPLEX ORGANIC MOLECULES IN 32 INTERSTELLAR CLOUDS USING SUBMM OBSERVATIONS." In 69th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2014. http://dx.doi.org/10.15278/isms.2014.rf10.
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Terwilliger, Thomas C., and Joel Berendzen. "Protein Crystallography: From X-ray diffraction spots to a three-dimensional image." In Signal Recovery and Synthesis. Washington, D.C.: Optica Publishing Group, 1998. http://dx.doi.org/10.1364/srs.1998.swa.1.
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Proteins are remarkable molecular machines that are essential for life. They can do many things ranging from the precise control of blood clotting to synthesizing complex organic compounds. Pictures of protein molecules are in high demand in biotechnology because they are important for applications such as drug discovery and for engineering enzymes for commercial use.
Reports on the topic "Complex organic molecules"
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Barney, Ellison G. Interfacial Oxidation of Complex Organic Molecules. Office of Scientific and Technical Information (OSTI), September 2013. http://dx.doi.org/10.2172/1092424.
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Phillips, Donald A., Yitzhak Spiegel, and Howard Ferris. Optimizing nematode management by defining natural chemical bases of behavior. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7587234.bard.
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This project was based on the hypothesis that nematodes interacting with plants as either parasites or beneficial saprophytes are attracted to their host by natural products. This concept was supported by numerous observations that parasitic nematodes are attracted to root exudates. Our overall goal was to identify nematode sensory compounds from root exudates and to use that information for reducing nematicide applications. We applied skills of the investigators to achieve three specific objectives: 1) Identify nematode behavioral cues (e.g., attractants or repellents) in root exudates; 2) Identify new natural nematicidal compounds; and 3) Combine a natural attractant and a nematicide into a nematode trap. Because saprophytic nematodes benefit plants by mineralizing organic matter, we sought compounds attractive primarily to parasitic nematodes. The project was constructed on several complementary foundations. First, data from Dr. Spiegel’s lab showed that under aseptic conditions Ditylenchus dipsaci, a parasite on onion, is attracted to certain fractions of onion root exudates. Second, PI Phillips had a sizeable collection of natural plant products he had identified from previous work on Rhizobium-legume interactions, which could be tested “off the shelf”. Third, Dr. Ferris had access to aseptic and natural populations of various saprophytic and parasitic nematodes. The project focused on five nematode species: D.dipsaci, Heterodera avenae, and Tylenchulussemipenetransat ARO, and Meloidogyne javanicand Caenorhabditis elegans at UCD. Ten pure plant compounds, mostly flavonoids, were tested on the various nematode species using six different assay systems. Results obtained with assorted test systems and by various scientists in the same test systems were essentially irreproducible. Many convincing, Many convincing, i.e. statistically significant, results in one system or with one investigator could not be repeated with other assays or different people. A recent report from others found that these compounds, plus another 30, were inactive as attractants in three additional parasitic nematode species (Wuyts et al. Nematology 8:89- 101, 2006). Assays designed to test the hypothesis that several compounds together are required to attract nematodes have thus far failed to find a reproducibly active combination. In contrast to results using pure plant compounds, complex unfractionated exudates from aseptic onion root reproducibly attracted D. dipsaci in both the ARO and UCD labs. Onion root exudate collection, separation into HPLC fractions, assays using D. dipsaci and MS-MS experiments proceeded collaboratively between ARO and UCD without any definitive identification of an active compound. The final active fraction contained two major molecules and traces of several other compounds. In the end, analytical studies were limited by the amount of onion root exudate and the complexity of the purification process. These tests showed that aseptic plant roots release attractant molecules, but whether nematodes influence that release, as insects trigger release of attractants from plants, is unknown. Related experiments showed that the saprophyte C. elegans stimulates its prey, Pseudomonas bacteria, to increase production of 2, 4-diacetylphloroglucinol (DAPG) a compound that promotes amino acid exudation by plant roots. It is thus possible that saprophytic nematodes are attracted primarily to their bacterial or fungal prey and secondarily to effects of those microorganisms on root exudation. These observations offer promising avenues for understanding root-zone interactions, but no direct routes to controlling nematodes in agriculture were evident. Extracts from two plant sources, Chrysanthemum coronarium and Sequoia sempervirens, showed nematicidal activity at ARO and UCD, respectively. Attempts to purify an active compound from S. sempervirens failed, but preliminary results from C. coronarium are judged to form a potential basis for further work at ARO. These results highlight the problems of studying complex movement patterns in sentient organisms like nematodes and the issues associated with natural product isolation from complex mixtures. Those two difficulties combined with complications now associated with obtaining US visas, slowed and ultimately limited progress on this project. As a result, US investigators expended only 65% of the $207,400 originally planned for this project. The Israeli side of the project advanced more directly toward its scientific goals and lists its expenditures in the customary financial report.
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Meir, Shimon, Michael S. Reid, Cai-Zhong Jiang, Amnon Lers, and Sonia Philosoph-Hadas. Molecular Studies of Postharvest Leaf and Flower Senescence. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7592657.bard.
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Original objectives: To understand the regulation of abscission by exploring the nature of changes of auxin-related gene expression in tomato (Lycopersicon esculatumMill) abscission zones (AZs) following organ removal, and by analyzing the function of these genes. Our specific goals were: 1) To complete the microarray analyses in tomato flower and leaf AZs, for identifying genes whose expression changes early in response to auxin depletion; 2) To examine, using virus-induced gene silencing (VIGS), the effect of silencing target genes on ethylene sensitivity and abscission competence of the leaf and flower AZs; 3) To isolate and characterize promoters from AZ-specific genes to be used in functional analysis; 4) To generate stable transgenic tomato plants with selected genes silenced with RNAi, under the control of an AZ-specific promoter, for further characterization of their abscission phenotypes. Background: Abscission, the separation of organs from the parent plant, results in postharvest quality loss in many ornamentals and other fresh produce. The process is initiated by changes in the auxin gradient across the AZ, and is triggered by ethylene. Although changes in gene expression have been correlated with the ethylene-mediated execution of abscission, there is almost no information on the initiation of the abscission process, as the AZ becomes sensitized to ethylene. The present project was focused on elucidating these early molecular regulatory events, in order to gain a better control of the abscission process for agricultural manipulations. Major conclusions, solutions, achievements: Microarray analyses, using the Affymetrix Tomato GeneChip®, revealed changes in expression, occurring early in abscission, of many genes with possible regulatory functions. These included a range of auxin- and ethylene-related transcription factors (TFs), other TFs that are transiently induced just after flower removal, and a set of novel AZ-specific genes. We also identified four different defense-related genes, including: Cysteine-type endopeptidase, α- DOX1, WIN2, and SDF2, that are newly-associated with the late stage of the abscission process. This supports the activation of different defense responses and strategies at the late abscission stages, which may enable efficient protection of the exposed tissue toward different environmental stresses. To facilitate functional studies we implemented an efficient VIGS system in tomato, and isolated two abscission-specific promoters (pTAPG1 and pTAPG4) for gene silencing in stable transformation. Using the VIGS system we could demonstrate the importance of TAPGs in abscission of tomato leaf petioles, and evaluated the importance of more than 45 genes in abscission. Among them we identified few critical genes involved in leaf and flower abscission. These included: PTRP-F1, PRP, TKN4, KNOTTED-like homeobox TF, KD1, and KNOX-like homeodomain protein genes, the silencing of which caused a striking retardation of pedicel abscission, and ERF1, ERF4, Clavata-like3 protein, Sucrose transporter protein, and IAA10 genes, the silencing of which delayed petiole abscission. The importance of PRPand KD1 genes in abscission was confirmed also by antisense–silencing using pTAPG4. Experiments testing the effects of RNAi silencing of few other genes are still in progress, The analysis of the microarray results of flower and leaf AZs allowed us to establish a clear sequence of events occurring during acquisition of tissue sensitivity to ethylene, and to confirm our hypothesis that acquisition of ethylene sensitivity in the AZ is associated with altered expression of auxin-regulated genes in both AZs. Implication, both scientific and agricultural: Our studies had provided new insights into the regulation of the abscission process, and shaded light on the molecular mechanisms that drive the acquisition of abscission competence in the AZ. We pointed out some critical genes involved in regulation of abscission, and further expanded our knowledge of auxin-ethylene cross talk during the abscission process. This permits the development of novel techniques for manipulating abscission, and thereby improving the postharvest performance of ornamentals and other crops.
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Shenker, Moshe, Paul R. Bloom, Abraham Shaviv, Adina Paytan, Barbara J. Cade-Menun, Yona Chen, and Jorge Tarchitzky. Fate of Phosphorus Originated from Treated Wastewater and Biosolids in Soils: Speciation, Transport, and Accumulation. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697103.bard.
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Beneficial use of reclaimed wastewater (RW) and biosolids (BS) in soils is accompanied by large input of sewage-originated P. Prolonged application may result in P accumulation up to levelsBeneficial use of reclaimed wastewater (RW) and biosolids (BS) in soils is accompanied by large input of sewage-originated P. Prolonged application may result in P accumulation up to levels that impair plant nutrition, increase P loss, and promote eutrophication in downstream waters. This study aims to shed light on the RW- and BS-P forms in soils and to follow the processes that determine P reactivity, solubility, availability, and loss in RW and BS treated soils. The Technion group used sequential P extraction combined with measuring stable oxygen isotopic composition in phosphate (δ18OP) and with 31P-NMR studies to probe P speciation and transformations in soils irrigated with RW or fresh water (FW). The application of the δ18OP method to probe inorganic P (Pi) speciation and transformations in soils was developed through collaboration between the Technion and the UCSC groups. The method was used to trace Pi in water-, NaHCO3-, NaOH-, and HCl- P fractions in a calcareous clay soil (Acre, Israel) irrigated with RW or FW. The δ18OP signature changes during a month of incubation indicated biogeochemical processes. The water soluble Pi (WSPi) was affected by enzymatic activity yielding isotopic equilibrium with the water molecules in the soil solution. Further it interacted rapidly with the NaHCO3-Pi. The more stable Pi pools also exhibited isotopic alterations in the first two weeks after P application, likely related to microbial activity. Isotopic depletion which could result from organic P (PO) mineralization was followed by enrichment which may result from biologic discrimination in the uptake. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with RW. Specific P compounds were identified by the Technion group, using solution-state 31P-NMR in wastewater and in soil P extracts from Acre soils irrigated by RW and FW. Few identified PO compounds (e.g., D-glucose-6-phosphate) indicated coupled transformations of P and C in the wastewater. The RW soil retained higher P content, mainly in the labile fractions, but lower labile PO, than the FW soil; this and the fact that P species in the various soil extracts of the RW soil appear independent of P species in the RW are attributed to enhanced biological activity and P recycling in the RW soil. Consistent with that, both soils retained very similar P species in the soil pools. The HUJ group tested P stabilization to maximize the environmental safe application rates and the agronomic beneficial use of BS. Sequential P extraction indicated that the most reactive BS-P forms: WSP, membrane-P, and NaHCO3-P, were effectively stabilized by ferrous sulfate (FeSul), calcium oxide (CaO), or aluminum sulfate (alum). After applying the stabilized BS, or fresh BS (FBS), FBS compost (BSC), or P fertilizer (KH2PO4) to an alluvial soil, P availability was probed during 100 days of incubation. A plant-based bioassay indicated that P availability followed the order KH2PO4 >> alum-BS > BSC ≥ FBS > CaO-BS >> FeSul-BS. The WSPi concentration in soil increased following FBS or BSC application, and P mineralization further increased it during incubation. In contrast, the chemically stabilized BS reduced WSPi concentrations relative to the untreated soil. It was concluded that the chemically stabilized BS effectively controlled WSPi in the soil while still supplying P to support plant growth. Using the sequential extraction procedure the persistence of P availability in BS treated soils was shown to be of a long-term nature. 15 years after the last BS application to MN soils that were annually amended for 20 years by heavy rates of BS, about 25% of the added BS-P was found in the labile fractions. The UMN group further probed soil-P speciation in these soils by bulk and micro X-ray absorption near edge structure (XANES). This newly developed method was shown to be a powerful tool for P speciation in soils. In a control soil (no BS added), 54% of the total P was PO and it was mostly identified as phytic acid; 15% was identified as brushite and 26% as strengite. A corn crop BS amended soil included mostly P-Fe-peat complex, variscite and Al-P-peat complex but no Ca-P while in a BS-grass soil octacalcium phosphate was identified and o-phosphorylethanolamine or phytic acid was shown to dominate the PO fraction that impair plant nutrition, increase P loss, and promote eutrophication in downstream waters. This study aims to shed light on the RW- and BS-P forms in soils and to follow the processes that determine P reactivity, solubility, availability, and loss in RW and BS treated soils. The Technion group used sequential P extraction combined with measuring stable oxygen isotopic composition in phosphate (δ18OP) and with 31P-NMR studies to probe P speciation and transformations in soils irrigated with RW or fresh water (FW). The application of the δ18OP method to probe inorganic P (Pi) speciation and transformations in soils was developed through collaboration between the Technion and the UCSC groups. The method was used to trace Pi in water-, NaHCO3-, NaOH-, and HCl- P fractions in a calcareous clay soil (Acre, Israel) irrigated with RW or FW. The δ18OP signature changes during a month of incubation indicated biogeochemical processes. The water soluble Pi (WSPi) was affected by enzymatic activity yielding isotopic equilibrium with the water molecules in the soil solution. Further it interacted rapidly with the NaHCO3-Pi. The more stable Pi pools also exhibited isotopic alterations in the first two weeks after P application, likely related to microbial activity. Isotopic depletion which could result from organic P (PO) mineralization was followed by enrichment which may result from biologic discrimination in the uptake. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with RW. Specific P compounds were identified by the Technion group, using solution-state 31P-NMR in wastewater and in soil P extracts from Acre soils irrigated by RW and FW. Few identified PO compounds (e.g., D-glucose-6-phosphate) indicated coupled transformations of P and C in the wastewater. The RW soil retained higher P content, mainly in the labile fractions, but lower labile PO, than the FW soil; this and the fact that P species in the various soil extracts of the RW soil appear independent of P species in the RW are attributed to enhanced biological activity and P recycling in the RW soil. Consistent with that, both soils retained very similar P species in the soil pools. The HUJ group tested P stabilization to maximize the environmental safe application rates and the agronomic beneficial use of BS. Sequential P extraction indicated that the most reactive BS-P forms: WSP, membrane-P, and NaHCO3-P, were effectively stabilized by ferrous sulfate (FeSul), calcium oxide (CaO), or aluminum sulfate (alum). After applying the stabilized BS, or fresh BS (FBS), FBS compost (BSC), or P fertilizer (KH2PO4) to an alluvial soil, P availability was probed during 100 days of incubation. A plant-based bioassay indicated that P availability followed the order KH2PO4 >> alum-BS > BSC ≥ FBS > CaO-BS >> FeSul-BS. The WSPi concentration in soil increased following FBS or BSC application, and P mineralization further increased it during incubation. In contrast, the chemically stabilized BS reduced WSPi concentrations relative to the untreated soil. It was concluded that the chemically stabilized BS effectively controlled WSPi in the soil while still supplying P to support plant growth. Using the sequential extraction procedure the persistence of P availability in BS treated soils was shown to be of a long-term nature. 15 years after the last BS application to MN soils that were annually amended for 20 years by heavy rates of BS, about 25% of the added BS-P was found in the labile fractions. The UMN group further probed soil-P speciation in these soils by bulk and micro X-ray absorption near edge structure (XANES). This newly developed method was shown to be a powerful tool for P speciation in soils. In a control soil (no BS added), 54% of the total P was PO and it was mostly identified as phytic acid; 15% was identified as brushite and 26% as strengite. A corn crop BS amended soil included mostly P-Fe-peat complex, variscite and Al-P-peat complex but no Ca-P while in a BS-grass soil octacalcium phosphate was identified and o-phosphorylethanolamine or phytic acid was shown to dominate the PO fraction.
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Ori, Naomi, and Mark Estelle. Role of GOBLET and Auxin in Controlling Organ Development and Patterning. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697122.bard.
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The size and shape of plant leaves are extremely diverse within and among species, and are also sensitive to growth conditions. Compound leaves, such as those of tomato, maintain morphogenetic activity during early stages of their development, enabling them to elaborate lateral appendages such as leaflets. The aim of the research project was to understand the interaction between the plant hormone auxin, the putative auxin response inhibitor ENTIRE (E, SlIAA9) and the NAM/CUC transcription factor GOBLET (GOB) in compound-leaf development in tomato (Solanum lycopersicum). The specific aims of the project were: 1. Investigation of the role of GOB in compound-leaf development. 2. Characterization of E function in auxin signaling. 3. Characterization of the role of auxin in compound-leaf development. 4. Investigation of the genetic and molecular interaction between E and GOB. 5. Investigate the role of these factors in fruit development. There were no major changes in these objectives. GOB was shown to mark and promote the boundaries between the leaf and initiating leaflets. Its accurate distribution was found to be required for proper leaflet initiation and separation. E was found to interact with the TIR1 and AFB6 proteins in an auxin-dependant manner, indicating that these are functional auxin receptors that mediate E degradation in the presence of auxin. This was further supported by the stabilization of E by a mutation in domain II of the protein, which is thought to mediate its auxin-dependant degradation. Over expression of this stabilized form in tomato leaves and characterization of the e mutant phenotype and the E expression domain indicated that E acts between initiating leaflets to inhibit auxin response and lamina growth. Generation and analysis of tomato plants expressing the auxin response reporter DR5::VENUS, and analysis of the effect of auxin microapplication or overexpression of an auxin biosynthesis gene, indicated that auxin marks the sites of leaflet initiation and promotes lamina growth. Investigation of the molecular and genetic interaction between auxin, GOB and E revealed a complex network of mutual regulation that is utilized to precisely pattern the leaf margin in a manner that enables the combination of tight control and flexibility. E, auxin and GOB were shown to affect fruit development and fruit set, and in an extension of the project are currently utilized to identify new players that affect these processes. The research project yielded enhanced understanding of the mechanisms of compound leaf patterning and provided tools that will enable the manipulation of leaf shape and fruit set.
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Chefetz, Benny, Baoshan Xing, Leor Eshed-Williams, Tamara Polubesova, and Jason Unrine. DOM affected behavior of manufactured nanoparticles in soil-plant system. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604286.bard.
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The overall goal of this project was to elucidate the role of dissolved organic matter (DOM) in soil retention, bioavailability and plant uptake of silver and cerium oxide NPs. The environmental risks of manufactured nanoparticles (NPs) are attracting increasing attention from both industrial and scientific communities. These NPs have shown to be taken-up, translocated and bio- accumulated in plant edible parts. However, very little is known about the behavior of NPs in soil-plant system as affected by dissolved organic matter (DOM). Thus DOM effect on NPs behavior is critical to assessing the environmental fate and risks related to NP exposure. Carbon-based nanomaterials embedded with metal NPs demonstrate a great potential to serve as catalyst and disinfectors. Hence, synthesis of novel carbon-based nanocomposites and testing them in the environmentally relevant conditions (particularly in the DOM presence) is important for their implementation in water purification. Sorption of DOM on Ag-Ag₂S NPs, CeO₂ NPs and synthesized Ag-Fe₃O₄-carbon nanotubebifunctional composite has been studied. High DOM concentration (50mg/L) decreased the adsorptive and catalytic efficiencies of all synthesized NPs. Recyclable Ag-Fe₃O₄-carbon nanotube composite exhibited excellent catalytic and anti-bacterial action, providing complete reduction of common pollutants and inactivating gram-negative and gram-positive bacteria at environmentally relevant DOM concentrations (5-10 mg/L). Our composite material may be suitable for water purification ranging from natural to the industrial waste effluents. We also examined the role of maize (Zeamays L.)-derived root exudates (a form of DOM) and their components on the aggregation and dissolution of CuONPs in the rhizosphere. Root exudates (RE) significantly inhibited the aggregation of CuONPs regardless of ionic strength and electrolyte type. With RE, the critical coagulation concentration of CuONPs in NaCl shifted from 30 to 125 mM and the value in CaCl₂ shifted from 4 to 20 mM. This inhibition was correlated with molecular weight (MW) of RE fractions. Higher MW fraction (> 10 kDa) reduced the aggregation most. RE also significantly promoted the dissolution of CuONPs and lower MW fraction (< 3 kDa) RE mainly contributed to this process. Also, Cu accumulation in plant root tissues was significantly enhanced by RE. This study provides useful insights into the interactions between RE and CuONPs, which is of significance for the safe use of CuONPs-based antimicrobial products in agricultural production. Wheat root exudates (RE) had high reducing ability to convert Ag+ to nAg under light exposure. Photo-induced reduction of Ag+ to nAg in pristine RE was mainly attributed to the 0-3 kDa fraction. Quantification of the silver species change over time suggested that Cl⁻ played an important role in photoconversion of Ag+ to nAg through the formation and redox cycling of photoreactiveAgCl. Potential electron donors for the photoreduction of Ag+ were identified to be reducing sugars and organic acids of low MW. Meanwhile, the stabilization of the formed particles was controlled by both low (0-3 kDa) and high (>3 kDa) MW molecules. This work provides new information for the formation mechanism of metal nanoparticles mediated by RE, which may further our understanding of the biogeochemical cycling and toxicity of heavy metal ions in agricultural and environmental systems. Copper sulfide nanoparticles (CuSNPs) at 1:1 and 1:4 ratios of Cu and S were synthesized, and their respective antifungal efficacy was evaluated against the pathogenic activity of Gibberellafujikuroi(Bakanae disease) in rice (Oryza sativa). In a 2-d in vitro study, CuS decreased G. fujikuroiColony- Forming Units (CFU) compared to controls. In a greenhouse study, treating with CuSNPs at 50 mg/L at the seed stage significantly decreased disease incidence on rice while the commercial Cu-based pesticide Kocide 3000 had no impact on disease. Foliar-applied CuONPs and CuS (1:1) NPs decreased disease incidence by 30.0 and 32.5%, respectively, which outperformed CuS (1:4) NPs (15%) and Kocide 3000 (12.5%). CuS (1:4) NPs also modulated the shoot salicylic acid (SA) and Jasmonic acid (JA) production to enhance the plant defense mechanisms against G. fujikuroiinfection. These results are useful for improving the delivery efficiency of agrichemicals via nano-enabled strategies while minimizing their environmental impact, and advance our understanding of the defense mechanisms triggered by the NPs presence in plants.
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Wolf, Shmuel, and William J. Lucas. Involvement of the TMV-MP in the Control of Carbon Metabolism and Partitioning in Transgenic Plants. United States Department of Agriculture, October 1999. http://dx.doi.org/10.32747/1999.7570560.bard.
Full textAbstract:
The function of the 30-kilodalton movement protein (MP) of tobacco mosaic virus (TMV) is to facilitate cell-to-cell movement of viral progeny in infected plants. Our earlier findings have indicated that this protein has a direct effect on plasmodesmal function. In addition, these studies demonstrated that constitutive expression of the TMV MP gene (under the control of the CaMV 35S promoter) in transgenic tobacco plants significantly affects carbon metabolism in source leaves and alters the biomass distribution between the various plant organs. The long-term goal of the proposed research was to better understand the factors controlling carbon translocation in plants. The specific objectives were: A) To introduce into tobacco and potato plants a virally-encoded (TMV-MP) gene that affects plasmodesmal functioning and photosynthate partitioning under tissue-specific promoters. B) To introduce into tobacco and potato plants the TMV-MP gene under the control of promoters which are tightly repressed by the Tn10-encoded Tet repressor, to enable the expression of the protein by external application of tetracycline. C) To explore the mechanism by which the TMV-MP interacts with the endogenous control o~ carbon allocation. Data obtained in our previous project together with the results of this current study established that the TMV-MP has pleiotropic effects when expressed in transgenic tobacco plants. In addition to its ability to increase the plasmodesmal size exclusion limit, it alters carbohydrate metabolism in source leaves and dry matter partitioning between the various plant organs, Expression of the TMV-MP in various tissues of transgenic potato plants indicated that sugars and starch levels in source leaves are reduced below those of control plants when the TMV-MP is expressed in green tissue only. However, when the TMV-MP was expressed predominantly in PP and CC, sugar and starch levels were raised above those of control plants. Perhaps the most significant result obtained from experiments performed on transgenic potato plants was the discovery that the influence of the TMV-MP on carbohydrate allocation within source leaves was under developmental control and was exerted only during tuber development. The complexity of the mode by which the TMV-MP exerts its effect on the process of carbohydrate allocation was further demonstrated when transgenic tobacco plants were subjected to environmental stresses such as drought stress and nutrients deficiencies, Collectively, these studies indicated that the influence of the TMV-MP on carbon allocation L the result of protein-protein interaction within the source tissue. Based on these results, together with the findings that plasmodesmata potentiate the cell-to-cell trafficking of viral and endogenous proteins and nucleoproteins complexes, we developed the theme that at the whole plant level, the phloem serves as an information superhighway. Such a long-distance communication system may utilize a new class of signaling molecules (proteins and/or RNA) to co-ordinate photosynthesis and carbon/nitrogen metabolism in source leaves with the complex growth requirements of the plant under the prevailing environmental conditions. The discovery that expression of viral MP in plants can induce precise changes in carbon metabolism and photoassimilate allocation, now provide a conceptual foundation for future studies aimed at elucidating the communication network responsible for integrating photosynthetic productivity with resource allocation at the whole-plant level. Such information will surely provide an understanding of how plants coordinate the essential physiological functions performed by distantly-separated organs. Identification of the proteins involved in mediating and controlling cell-to-cell transport, especially at the companion cell-sieve element boundary, will provide an important first step towards achieving this goal.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.
Full textAbstract:
The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Tucker, Mark L., Shimon Meir, Amnon Lers, Sonia Philosoph-Hadas, and Cai-Zhong Jiang. Elucidation of signaling pathways that regulate ethylene-induced leaf and flower abscission of agriculturally important plants. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597929.bard.
Full textAbstract:
The Problem: Abscission is a highly regulated process, occurring as a natural terminal stage of development, in which various organs are separated from the parent plant. In most plant species, the process is initiated by a decrease in active auxin in the abscission zone (AZ) and an increase in ethylene, and may be accelerated by postharvest or environmental stresses. Another potential key regulator in abscission is IDA (Inflorescence Deficient in Abscission), which was identified as an essential peptide signal for floral organ abscission in Arabidopsis. However, information is still lacking regarding the molecular mechanisms integrating all these regulators. In our previous BARD funded research we made substantial progress towards understanding these molecular events in tomato, and the study is still in progress. We established a powerful platform for analysis of genes for regulatory proteins expressed in AZ. We identified changes in gene expression for several transcription factors (TFs) directly linked to ethylene and auxin signaling and several additional regulatory proteins not so obviously linked to these hormones. Moreover, we demonstrated using a virus-induced gene silencing (VIGS) assay that several play a functional role in the onset of abscission. Based on these results we have selected 14 genes for further analysis in stably transformed tomato plants. All 14 genes were suppressed by RNA interference (RNAi) using a constitutive promoter, and 5 of them were also suppressed using an abscission-specific promoter. Transformations are currently at different stages of progress including some lines that already display an abscission phenotype. Objectives: We propose here to (1) complete the functional analysis of the stably transformed tomato plants with T2 lines and perform transcriptome analysis using custom abscission-specific microarrays; (2) conduct an indepth analysis of the role of IDA signaling in tomato leaf and flower abscission; (3) perform transcriptome and proteome analyses to extend the earlier gene expression studies to identify transcripts and proteins that are highly specific to the separation layer (i.e., target cells for cell separation) prior to the onset of abscission; (4) extend and compliment the work in tomato using a winnowed set of genes in soybean. Methodology: Next Generation Sequencing (NGS) of mRNA will be used to further increase the list of abscission-associated genes, and for preparation of a custom tomato abscission microarray to test altered gene expression in transgenic plants. Tandem mass spectrometry (LC-MS/MS) of protein extracts from leaf petiole, flower pedicel and their AZ tissues will be used to identify the proteome of the AZ before and during abscission. AZ-specific gene promoters will be used in stably transformed tomato plants to reduce non-target phenotypes. The bean pod mottle virus (BPMV) plasmid vectors will be used for VIGS analysis in soybean. Expected Contribution: Our study will provide new insights into the regulation of ethylene-induced abscission by further revealing the role of key regulators in the process. This will permit development of novel techniques for manipulating leaf and flower abscission, thereby improving the postharvest performance of agriculturally important crops.
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Savaldi-Goldstein, Sigal, and Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7699849.bard.
Full textAbstract:
Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is apparent that hormones are acting in selected cells of the plant body to regulate organ growth, and furthermore, that local cell-cell communication is an important mechanism. In this proposal our goals were to identify the global profile of translated genes in response to BR stimulation and depletion in specific tissues in Arabidopsis; determine the spatio-temporal dependency of BR response on auxin transport and signaling and construct an interactive public website that will provide an integrated analysis of the data set. Our technology incorporated cell-specific polysome isolation and sequencing using the Solexa technology. In the first aim, we generated and confirmed the specificity of novel transgenic lines expressing tagged ribosomal protein in various cell types in the Arabidopsis primary root. We next crossed these lines to lines with targeted expression of BRI1 in the bri1 background. All lines were treated with BRs for two time points. The RNA-seq of their corresponding immunopurified polysomal RNA is nearly completed and the bioinformatic analysis of the data set will be completed this year. Followed, we will construct an interactive public website (our third aim). In the second aim we started revealing how spatio-temporalBR activity impinges on auxin transport in the Arabidopsis primary root. We discovered the unexpected role of BRs in controlling the expression of specific auxin efflux carriers, post-transcriptionally (Hacham et al, 2012). We also showed that this regulation depends on the specific expression of BRI1 in the epidermis. This complex and long term effect of BRs on auxin transport led us to focus on high resolution analysis of the BR signaling per se. Taking together, our ongoing collaboration and synergistic expertise (hormone action and plant development (IL) and whole-genome scale data analysis (US)) enabled the establishment of a powerful system that will tell us how distinct cell types respond to local and systemic BR signal. BR research is of special agriculture importance since BR application and BR genetic modification have been shown to significantly increase crop yield and to play an important role in plant thermotolerance. Hence, our integrated dataset is valuable for improving crop traits without unwanted impairment of unrelated pathways, for example, establishing semi-dwarf stature to allow increased yield in high planting density, inducing erect leaves for better light capture and consequent biomass increase and plant resistance to abiotic stresses.