Дисертації: "Prebiotic molecules"

1

Widicus, Weaver Susanna Leigh Beauchamp Jesse L. "Rotational spectroscopy and observational astronomy of prebiotic molecules /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-05162005-153745.

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2

Laporte, Sara. "The Electric Field at an Oxide Surface - Impact on Reactivity of Prebiotic Molecules." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066314/document.

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Les surfaces minérales auraient eu un rôle important dans la chimie prébiotique, grace à leurs propriétés catalytiques, tel que le champ électrique de surface. Dans ce travail, le champ électrique à la surface de MgO et à l'interface MgO/eau est étudié en utilisant la dynamique moléculaire ab-initio. Ce champ est local et intense, de l'ordre de V/Å, même lorque la surface est recouverte d'eau. Une réaction prébiotique modèle est ensuite étudiée, à la surface de MgO : une molécule de monoxide de carbone et une molécule d'eau, donnant une molécule d'acide formique. En utilisant la métadynamique, et sans connaissance des états de transition en amont, des chemins de réaction sont trouvés et leurs profils d 'énergie libre sont calculés à 5 kcal/mol près, avec l'aide d'un échantillonage dans l'espace des configurations par « umbrella sampling ». La présence de la surface minérale stabilise l'acide formique d'au moins 15 kcal/mol par-rapport au cas en solution sans surface. La même réaction a aussi été étudiée sous un champ électrique homogène de 0,3 V/Å, afin de comparer l'effet de ce champ à l'effet du champ de surface sur le paysage d'énergie libre. Le champ homogène stabilise aussi le produit, et l'acide formique se trouve orienté dans la direction du champ électrique de surface ainsi que dans le champ électrique homogène. Ce travail montre que les conditions proche d'une surface minérale, même sans adsorption directe, peut modifier considerablement le paysage d'énergie libre de réactions chimiques, ce qui pourrait avoir de l'importance en chimie prébiotique
Mineral surfaces are thought to be of importance to prebiotic chemistry due to their catalytic properties, which include a strong electric field at the interface. In this work the electric field at the surface of MgO and at the interface of MgO and water is studied through ab-initio molecular dynamics. The spontaneous electric field from the surface is found to be local and intense, on the order of V/Å, even when completely covered with water. A model prebiotic reaction is then studied on the model MgO surface : carbon monoxide and water yielding formic acid. Using metadynamics, reaction pathways were found with no a priori knowledge of the transition states, and umbrella sampling was then used to compute free energy landscapes to about 5 kcal/mol accuracy. The presence of the mineral surface was found to stabilise formic acid by at least 15 kcal/mol compared to the bulk case. The reaction was also studied in solution with an applied electric field of 0.3 V/Å, in order to estimate to impact of the surface electric field on the free energy landscape. The field is also found to stabilise the product, and formic acid is found to have a preferred orientation in the direction of both the applied electric field and the surface electric field. This work shows that near surface conditions (without direct adsorption) can significantly alter the free energy landscapes of chemical reactions, in a way which could be of importance for prebiotic chemistry

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3

Neish, Catherine Dorothy. "Formation of Prebiotic Molecules in Liquid Water Environments on the Surface of Titan." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194180.

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Saturn’s moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen-methane atmosphere produce a wide variety of carbon, hydrogen, and nitrogen containing organic molecules. If these molecules are exposed to liquid water, they may react further to produce oxygen-containing species, a key step in the formation of terrestrial biomolecules. On average, Titan's surface is too cold for liquid water. However, models indicate that melting caused by impacts and/or cryovolcanism may lead to its episodic availability. One possible cryovolcanic dome, Ganesa Macula, was identified in early observations by the Cassini spacecraft. In this work, I estimate the height and morphology of this feature using a synthetic aperture radar (SAR) image. I then use a thermal conduction code to calculate the freezing timescale for an initially liquid dome, yielding freezing timescales of ~10² - 10⁵ years. To determine how far aqueous organic chemistry can proceed in liquid water environments on Titan, I measure the rate coefficients of Titan analogue organic molecules ("tholins") with low temperature aqueous solutions to produce oxygenated species. These reactions display first-order kinetics with half-lives between 0.4 and 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis in aqueous solutions is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years to freeze. The fast incorporation of oxygen, along with new chemistry made available by the introduction of ammonia, may lead to the formation of molecules of prebiotic interest in these transient liquid water environments. This chemistry makes impact craters and cryovolcanoes important targets for future missions to Titan.

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4

Dioses, Castro Silvio, and Richard Korswagen. "Over the possible role of metal atom clusters in cosmochemistry and in the origin of life." Revista de Química, 2013. http://repositorio.pucp.edu.pe/index/handle/123456789/100714.

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We present here the hypothesis of a possible relationship between metal atom clusters and the formation of organic molecules in the interstellar medium and on small bodies as a possible pathway to the origin of such molecules. Two distinct stages are díscussed: a) the possible formation and presence of atom clusters in space and on the primitive Earth, and b) the synthesis of interstellar and terrestrial prebiotic organic molecules, a process in which metalclusters could be the active catalysts. The confirmatíon of these suggestions might be very important in arder to explain the presence of extra-terrestrial organic molecules in the interstellar medium, small bodies and planetary systems, and therefore would have great relevance in cosmochemistry and in the current theories about the origins of life.

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5

Morasch, Matthias [Verfasser], and Dieter [Akademischer Betreuer] Braun. "Accumulation, gelation, and crystallization of prebiotic molecules in a thermal gradient and deep UV Circular dichroism / Matthias Morasch ; Betreuer: Dieter Braun." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1210424290/34.

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6

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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7

Bean, Heather D. "Prebiotic synthesis of nucleic acids." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/28259.

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Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2008.
Committee Chair: Hud, Nicholas V.; Committee Member: Fox, Ronald F.; Committee Member: Lynn, David G.; Committee Member: Powers, James C.; Committee Member: Wartell, Roger M.; Committee Member: Williams, Loren D.

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8

Aylward, Nigel Nunn. "Studies of electronic and structural properties of molecular clusters of prebiotic importance." Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16328/1/Nigel_Aylward_Thesis.pdf.

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This thesis applies the ab initio techniques of computational chemistry to studies of molecular clusters containing covalent (strong) or van der Waals (weak) bonds formed in chemistry and biochemistry in the temperature range 10-300 K. Van derWaals complexes with an enthalpy of formation from reactants of less than 25 kJ mol-1 and covalent clusters are described in this thesis. The first group of van der Waals complexes involved the molecule carbon monoxide that possesses a small permanent dipole that could lead to dipole - induced dipole interaction and dipole - dipole interaction with another reactant in addition to dispersion. The substrates investigated were methanimine and cyanogen where endergonic unstable molecules were formed, and the clustering of carbon monoxideon a porphin surface leading to the formation of carbon - carbon fragments. TheFaraday effect was invoked to suggest that this was the original method by which thechirality of the D-sugars was selected. Coordination of imino-compounds on thesame surface involving induction and electrostatic interactions could lead to the preferential formation of L-aziridones, hydrolysable to L-amino-acids.The preferred formation of D-ribose, and the more stable D-2-deoxyribose, andnucleotides polymerisable to deoxyribonucleic acids was described. The second group of van der Waals complexes involved the polymerisation of acetylene molecules, to di- and tri-acetylene complexes where the exchange interaction involved the quadrupole moment of the acetylene radical reacting with acetylene or diacetylene. The reaction of carbon monoxide was extended to include its interaction with diacetylene. The entire potential energy surface for the interaction with diacetylene was investigated. The reaction was shown to be endergonic to produce a reactive species, here postulated to rearrange with a reasonable activation energy toform an aldehyde. The energetics of the formation of diacetylene, triacetylene andhigher polymers was briefly investigated. The reactivity of the acetylene polymeraldehydes with other substrates was briefly investigated. This work has apparently laid a firm basis both, qualitative and quantitative, tounderstand some of the weakest interactions in nature involving the simplest ofreactions that have been important in atmospheric chemistry.

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9

Aylward, Nigel Nunn. "Studies of electronic and structural properties of molecular clusters of prebiotic importance." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16328/.

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This thesis applies the ab initio techniques of computational chemistry to studies of molecular clusters containing covalent (strong) or van der Waals (weak) bonds formed in chemistry and biochemistry in the temperature range 10-300 K. Van derWaals complexes with an enthalpy of formation from reactants of less than 25 kJ mol-1 and covalent clusters are described in this thesis. The first group of van der Waals complexes involved the molecule carbon monoxide that possesses a small permanent dipole that could lead to dipole - induced dipole interaction and dipole - dipole interaction with another reactant in addition to dispersion. The substrates investigated were methanimine and cyanogen where endergonic unstable molecules were formed, and the clustering of carbon monoxideon a porphin surface leading to the formation of carbon - carbon fragments. TheFaraday effect was invoked to suggest that this was the original method by which thechirality of the D-sugars was selected. Coordination of imino-compounds on thesame surface involving induction and electrostatic interactions could lead to the preferential formation of L-aziridones, hydrolysable to L-amino-acids.The preferred formation of D-ribose, and the more stable D-2-deoxyribose, andnucleotides polymerisable to deoxyribonucleic acids was described. The second group of van der Waals complexes involved the polymerisation of acetylene molecules, to di- and tri-acetylene complexes where the exchange interaction involved the quadrupole moment of the acetylene radical reacting with acetylene or diacetylene. The reaction of carbon monoxide was extended to include its interaction with diacetylene. The entire potential energy surface for the interaction with diacetylene was investigated. The reaction was shown to be endergonic to produce a reactive species, here postulated to rearrange with a reasonable activation energy toform an aldehyde. The energetics of the formation of diacetylene, triacetylene andhigher polymers was briefly investigated. The reactivity of the acetylene polymeraldehydes with other substrates was briefly investigated. This work has apparently laid a firm basis both, qualitative and quantitative, tounderstand some of the weakest interactions in nature involving the simplest ofreactions that have been important in atmospheric chemistry.

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10

Hoffman, Jessie Baldwin. "PCB DISRUPTION OF GUT AND HOST HEALTH: IMPLICATIONS OF PREBIOTIC NUTRITIONAL INTERVENTION." UKnowledge, 2018. https://uknowledge.uky.edu/pharmacol_etds/25.

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Exposure to environmental pollutants poses numerous risk factors for human health, including increasing incidence of cardiovascular disease and diabetes. Persistent organic pollutants, such as polychlorinated biphenyls (PCBs) have been strongly linked to the development of these chronic inflammatory diseases and the primary route of exposure is through consumption of contaminated food products. Thus, the gastrointestinal tract is susceptible to the greatest levels of these pollutants and is an important facet to study. The first two hypotheses of this dissertation tested that exposure to PCBs disrupts gut microbiota directly (in vitro) and within a whole body system. PCB exposure disrupted microbial metabolism and production of metabolites (i.e. short chain fatty acids) in vitro. These disruptions in microbial populations were consistent in our mouse model of cardiometabolic disease, where we observed reductions in microbial diversity, an increase in the putative pro-inflammatory ratio of Firmicutes to Bacteroidetes, and reductions in beneficial microbial populations in exposed mice. Furthermore, observed greater inflammation was observed both within the intestines and peripherally in PCB exposed mice as well as disruptions in circulating markers associated with glucose homeostasis. Nutritional interventions high in prebiotic dietary fiber such as inulin may be able to attenuate the toxic effects of pollutant exposure. To test the hypothesis that consumption of the prebiotic inulin can decrease PCB-induced disruption in gut microbial and metabolic homeostasis, LDLr-\- mice were fed a diet containing inulin and exposed to PCB 126. Mice fed an inulin-containing diet and exposed to PCBs exhibited improved glucose tolerance, lower hepatic inflammation and steatosis, and distinct differences in gut microbial populations. Overall, these data suggests that nutritional intervention, specifically prebiotic consumption, may reduce pollutant-induced disease risk.

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11

Bottinelli, Sandrine. "Hot corinos : molécules pré-biotiques autour des protoétoiles de type solaire." Grenoble 1, 2006. http://www.theses.fr/2006GRE10127.

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L'un des buts majeurs de l'astrophysique moderne est de comprendre la formation du Système Solaire. Puisque les protoétoiles de faible masse sont des soleils en formation, l'étude de ces objets est un des meilleurs moyens d'étudier le processus de formation du Soleil et de son système planétaire. Dans ma thèse, je me suis concentrée sur la chimie des premières phases d'évolution des protoétoiles de faible masse en étudiant les molécules organiques complexes dans des sources de Classe 0, qui représentent les phases les plus jeunes connues. De telles molécules ont été découvertes dans IRAS16293-2422, le prototype des sources de Classe 0, démontrant l'existence des ``hot corinos'', des régions où les manteaux des grains subliment. Certaines de ces molécules ont aussi été observées dans des comètes de notre Système Solaire, soulevant la question de savoir si (et auquel cas, comment) la chimie des Classes 0 affecte la composition chimique de la matière du disque protoplanétaire incorporée dans les comètes et autres corps planétaires. Cependant, il est d'abord nécessaire de déterminer si les hot corinos sont omniprésents dans les protoétoiles de faible masse, ou si IRAS16293-2422 est une exception. Ceci était le premier but de ma thèse. L'approche consistait principalement à observer trois sources de Classe 0 pour chercher des molécules organiques complexes. J'ai ainsi découvert et/ou confirmé trois hot corinos de plus. Le second but était de contraindre la taille de la région d'émission des molécules complexes au moyen d'observations interférométriques des deux hot corinos les plus brillants : cette émission est compacte (<150 AU), avec, dans l'un des cas, une composante étendue provenant de l'enveloppe externe. Le troisième but avait pour lieu de confronter les voies de formation possibles des molécules complexes avec les résultats de mes observations pour essayer de distinguer si ces molécules se forment en phase gazeuse ou à la surface des grains. Bien que mes données ne puissent éliminer aucun des deux cas, elles semblent favoriser le second type de formation. De plus, la comparaison entre hot corinos et leurs homologues massifs, les hot cores (qui montre que les molécules complexes sont relativement plus abondantes dans les hot corinos), soutient également la formation à la surface des grains
One of the major goals of modern astrophysics is to understand the formation of our Solar System. Since low-mass protostars are suns in the making, the study of these objects and their environment provides one of the best ways to investigate the Sun's formation process and to peek in the past history of our Solar System. In my thesis, I focused on the chemistry occuring in Class 0 sources (the earliest known phases in the evolutionary scenario of low-mass protostars) by studying complex organic molecules in their envelopes. Such molecules have been discovered in IRAS16293--2422, the prototype of Class 0 sources, proving the existence of hot corinos, the inner regions of the protostellar envelope where the icy grain mantles sublimate. Some of these molecules have also been observed in comets in our Solar System, raising the question of whether (and if so, how) the chemistry of Class 0 objects affects the chemical composition of the protoplanetary disk material from which comets and other planetary bodies form. However, it is first necessary to determine whether hot corinos are ubiquitous in low-mass protostars or if IRAS16293-2422 is an exception. This was the first goal of my thesis. The approach consisted mainly in observing three Class 0 sources to search for complex organic molecules. I thereby discovered and/or confirmed three more hot corinos. The second goal was then to constrain the size of emission of complex molecules. For this, I carried out interferometric observations of the two brightest hot corinos: this emission is compact (<150 AU) with, in one of the sources, an extended component originating from the cooler, less dense outer envelope. The third goal consisted in confronting the possible formation pathways with the results of my observations to try and discriminate whether complex organic molecules form via gas-phase or grain-surface reactions. Although it was not possible to arrive at a definite answer, my data seem to favor the later formation route. Moreover, the comparison of hot corinos and their high-mass analogs, the hot cores (showing that complex molecules are relatively more abundant in hot corinos), also support grain-surface synthesis of these molecules

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12

Dawley, Margaret Michele. "Radiation and thermal processing of ices and surfaces relevant to prebiotic chemistry in the solar system and interstellar regions." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/51767.

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This dissertation has investigated the adsorption, thermal behavior, and radiation (both photon and electron) processing of prebiotically-relevant ices and surfaces. A custom ultra-high vacuum (UHV) chamber has been built that is coupled with a Fourier Transform-Infrared (FT IR) spectrometer and a Temperature Programmed Desorption (TPD) system that utilizes Quadrupole Mass Spectrometry (QMS) to study selected organic:surface systems. Formamide (HCONH₂) has been studied in two related but distinct studies relevant to primitive Earth and interstellar chemistry. First, in collaboration with a theory group, formamide’s interaction with kaolinite (Al6Si6O36H30), a clay mineral relevant to early Earth chemistry, has been studied experimentally and theoretically. Experimental infrared results are compared with calculated infrared frequencies obtained by our collaborators. TPD analysis is compared with the calculated values of adsorption energy, and the optimal kaolinite termination site for adsorption is reported. Second, the first thermal and radiation damage study of pure formamide and HCONH₂:H₂O mixed ices on an interstellar icy grain analog (SiO₂) is reported. A discussion of the pure formamide ice phases identified with FT-IR upon warm-up, as well as the TPD binding energies of HCONH₂ on SiO₂, is presented. The observed Lyman-alpha photochemical products and proposed formation mechanisms from pure formamide ice is reported and discussed. In addition, results of Lyman alpha processing of mixed HCONH₂:H₂O ices are provided. Low-energy electron irradiation of pure HCONH₂ and HCONH₂:H₂O mixed ices has also been reported for the first time. A third investigation has studied acetylene (C₂D₂) and acetonitrile (CH₃CN) interactions and radiation stability in mixed low-temperature ices to simulate possible prebiotic reactions that may occur on Saturn’s moon, Titan. This investigation contributes to understanding the possible consumption, trapping, and degradation of these species on the surface of Titan.

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13

Laos, Roberto, and Steven Benner. "The first self-replicating molecule and the origin of life." Revista de Química, 2014. http://repositorio.pucp.edu.pe/index/handle/123456789/99479.

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El origen de la vida en la Tierra es una de las preguntas más difíciles presentadas a la ciencia. En los últimos 60 años, ha habido un progreso considerable en entender cómo moléculas relativamente sencillas, que son relevantes para la vida, pueden ser generadas espontáneamente o pueden llegar a la Tierra desde el espacio. Además, los análisis de la evolución de la historia de ácidos nucleicos, los cuales almacenan la información genética, apuntan a un ancestro común universal ya extinto. Los estudios del origen de la vida ofrecen muchas pistas que apuntan hacia un origen común, quizás no solo en el Tierra sino también en algún otro punto del sistema solar. Debido al largo tiempo transcurrido desde que la Tierra empezó a albergar vida, las pistas más antiguas de los primeros organismos se han perdido. Es muy poco probable encontrar exactamente cómo fue este primer organismo. Sin embargo, en los últimos años la biología sintética ha logrado progresar mucho en la modificación de biomoléculas, en particular, los ácidos nucleicos. Es posible que pronto podamos construir y comprender un sistema minimalista en el cual las moléculas puedan copiarse a sí mismas dentro de una célula rudimentaria. El estudio de un sistema así podría permitirnos develar el origen de los primeros organismos.
The origin of life on Earth is one of the most challenging questions in science. In the last 60 years, considerable progress has been made in understanding how simple molecules relevant to life can be generated spontaneously or are known to arrive to Earth from space. Additionally, analysis of the evolution history of nucleic acids, which are the repository of genetic information, points to a now extinct, universal common ancestor for all life on Earth. The studies of the origin of life offer many clues towards a common origin, perhaps not just on Earth but somewhere else in the solar system. However due to the length of time that the Earth has harbored life, the oldest clues of the first organisms are mostly gone. It is unlikely to find exactly what this first organism was like. Nevertheless, in the last few years, synthetic biology has made remarkable progress at modifying biomolecules, particularly nucleic acids. It is possible that soon we will be able to construct and understand a minimalistic system in which molecules can copy themselves in a protocell. The study of such systems could shed light into the origin of the first organisms.

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14

Stiverson, Jill A. "Impact of Buffering Capacity and Low Dose Galacto-Oligosaccharide on in-vitro Infant Fecal Cultures." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1301024698.

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15

Widicus, Weaver Susanna Leigh. "Rotational Spectroscopy and Observational Astronomy of Prebiotic Molecules." Thesis, 2005. https://thesis.library.caltech.edu/1835/12/Chapter1.pdf.

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It is now widely believed that prebiotic molecules were delivered to the early Earth by planetesimals and their associated interplanetary dust particles. Yet the formation pathways for these molecules are not clear. Amino acids and sugars have been found in carbonaceous chondrites, but only much simpler species have been detected in the interstellar medium (ISM). Prebiotic organics could have formed in the ISM and been directly incorporated into planetesimals, or simpler species could have formed in the ISM and then been incorporated into planetesimals, undergone further processing, and been delivered to Earth. Limits on interstellar chemistry must therefore be established through observational astronomy before potential prebiotic formation pathways can be assessed. These observations require laboratory spectroscopic investigation of the species of interest.

This thesis is an interdisciplinary study involving laboratory rotational spectroscopy and astronomical observations of several key prebiotic molecules. The laboratory work has focused on obtaining the rotational spectra of the simplest three-carbon ketose sugar, 1,3-dihydroxyacetone, and its structural isomers methyl glycolate and dimethyl carbonate, as well as aminoethanol, the predicted interstellar precursor to alanine. The pure rotational spectral analysis of the low-lying torsional states of the simplest alpha-hydroxy aldehyde, glycolaldehyde, has also been completed. The original Balle-Flygare Fourier transform microwave spectrometer was used to obtain the microwave spectra, while both the Jet Propulsion Laboratory and Caltech direct absorption flow cell spectrometers were used for additional direct absorption millimeter and submillimeter studies.

The results of these laboratory experiments were used to guide observational searches with the Caltech Submillimeter Observatory, the Owens Valley Millimeter Array, and the Green Bank Telescope toward the hot core sources Sgr B2(N-LMH), Orion Hot Core/Compact Ridge, and W51 e1/e2. Evidence has been found for the presence of dihydroxyacetone and methyl glycolate in Sgr B2(N-LMH).

These results have important implications for interstellar grain surface chemistry, and proposed additions to grain surface chemical models are also discussed. Reactions involving surface radicals and molecules containing carbonyl groups can efficiently compete with the simple grain surface reactions included in previous models. Such aldehyde abstraction reactions should be considered as pathways to complex carbonyl-containing species on interstellar grain surfaces.

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16

Blair, Samantha Kaj. "The search for prebiotic organic molecules in the outer Galaxy." 2008. http://purl.galileo.usg.edu/uga%5Fetd/blair%5Fsamantha%5Fk%5F200812%5Fphd.

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17

Corazzi, Maria Angela. "Laboratory studies on photoprocessing and desorption of prebiotic molecules in space." Doctoral thesis, 2022. http://hdl.handle.net/2158/1264298.

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This Ph.D. project was developed within the research projects of astrobiology “Space life- OPPS” and “Reservoirs for Planetary Atmospheres”. The project was focused on laboratory studies on photoprocessing and thermal desorption of formamide (HCONH2), acetonitrile (CH3CN), and acetaldehyde (CH3COH) in simulated space conditions. The analytical techniques used were Fourier Transformed Infrared Spectroscopy (FTIR), Temperature Programmed Desorption (TPD) analysis, and mass spectroscopy.

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18

Lin, Ching-Chan, and 林經展. "Theoretical Study on new Noble Gas Anions, Prebiotic Synthesis of Ribose, and the OSO and SOO molecules." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/zs56ym.

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碩士
國立中正大學
化學暨生物化學研究所
103
This thesis consists of five chapters. In chapters 1 and 2, we studied the stability of some metal-containing noble-gas anions. In chapter 3, we studied the stability of transition metal-containing noble-gas anions. In chapter 4, we studied the prebiotic synthesis of glyceraldehyde and dihydroacetone by formose reaction in neutral environment. In addition to the gas-phase study, we also model the solvation effects with two different approaches, micro-solvation and polarizable continuum model (PCM). In chapter 5, we studied the stability of various OSO isomers and their isomerization and dissociation reactions. In Chapter 1, we calculated the geometry and stability of a series of noble-gas anions X−NgO ( X = OBO, OAlO, NCO, OCN, NC, OAg, and etc) by ab initio methods . The anions can induce theformation of the NgO bond by polarization. We found that the stability of X−NgO depended strongly on the electron affinity of the neutral species X. Usually the X with higher electron affinity can form more stable X−NgO anions. The calculated results showed that the OMO−NgO ( Ng=Ar , Kr, Xe ; M=Al , B) anions which has high dissociation energy may be experimentally detectable in low-temperature conditions. In Chapter 2, we have calculated the molecular geometries, bond energies, and charge distribution of the metal-containing noble-gas anions OMO−(NgO )n ( Ng= Ar, Kr, and Xe ; M=Al , B；n =1~2 ). The geometries of these anions were found to be highly symmetric. The calculated results revealed that the OMO−( NgO )n ( Ng= Ar, Kr, and Xe ; M=Al , B；n =1~2 ) anions may be experimentally detectable at low-temperature. We also calculated the OArOMOKr−, OArOMOXe−, and OKrOMOXe− (M=Al , B) anions which has high dissociation energy may be experimentally detectable in low-temperature conditions. In Chapter 3, we have calculated the molecular geometries and the stability of the transition metal-containing noble-gas anions OMOO−ArO (M = Ti, V, Co, Cu). The stable noble-gas anions previously studied were all in singlet states. It is expected that the stable noble-gas anions could exist in different spin states by including 3d transition metal elements. The calculated results showed that the stable anion OVOO−ArO was in singlet state and the stable anion OCoOO−ArO was in the triplet state. We also used various DFT methods to calculate electron affinities of OMOO− (M = Ti, V, Co, Cu) and compared them to experimental results. In Chapter 4, we studied the the prebiotic synthesis of glyceraldehyde and dihydroacetone, which are precursors of ribose, by formose reaction. The possible reaction pathways of synthesis for glyceraldehyde and dihydroacetone from formaldehyde were calculated in the gas phase, in bulk solvent, and with microsolvation by H2O or NH3 molecules. We found that if a reaction step involves a proton transfer, the energy barrier could be significantly reduced by approximately 20 ~ 30 kcal/mol with microsolvation by H2O or NH3. The polarized continuum solvation model (PCM) could sometimes further lower the barrier by 3~5 kcal/mol. So the formose reaction can occurs more readily in comparison with the reactions in the gas phase. In chapter 5, we studied the molecules OSO and SOO which are isoelectronic to the ozone. The high level methods, CASPT2, MRCISD+Q, were used to calculate the relative energies of the cyclic and the open forms of OSO. The first singlet excited state (1A" state) and the ground state (1A' state) potential energy surfaces were calculated. The result showed that when the ground state open-OSO was excited by radiation, it would become open-SOO through the cross section of 1A' and 1A" potential energy surfaces because of the near-degeneracy of ground and excited transition states. However, the reaction open-OSO → cyclic-SOO would not likely to occur through the intersection of the potential energy surfaces. The dissociation energies of reactions open-OSO → SO + O and S + O2 are 149.6 kcal/mol and 145.2 kcal/mol.

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19

Peng, Chia-Yu, and 彭家瑜. "Development of Multi-Coefficient Density Functional Theory and Theoretical Study on Noble Gas Molecules, Excited-State Proton Transfer Reactions, and Prebiotic Synthesis of Alpha-amino Acids." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/02494196428647060097.

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Анотація:

博士
國立中正大學
化學暨生物化學研究所
104
This thesis consists of five chapters. In chapter 1, we developed and tested several new efficient DFT methods. In chapter 2, we performed high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC. In chapter 3, we studied the mechanisms and reaction paths of the prebiotic strecker synthesis of alanine catalyzed by water and chiral molecules in the neutral environment. In chapter 4, we studied the kinetic stability of the cyclic-O3, cyclic-S3, and cyclic-Se3. In the last chapter, we cooperated with the experimental scientists and carried out the theoretical investigation on the excited state proton transfer of 1,8-dihydroxy-2-naphthaldehyde (DHNA). In chapter 1, we developed and tested several new efficient multi-coefficient density functional theory (MC-DFT) methods based on the DSD-BLYP functional and by including SCS-MP2 and MP4 correction energies on the performance of thermochemical kinetics against the database of 211 accurate energies. When the MP4 correlation energies were included, the new method gave an astonishingly small MUEs of 0.72 kcal/mol and cost only 78% of the DSD-BLYP/aug-cc- pVTZ method (with MUE = 1.36 kcal/mol). In chapter 2, we made high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC-. The results showed that FNgCC- (Ng = Ar, Kr, Xe) are kinetically stable anions in the gas phase with the three-body dissociation energies of 17-64 kcal/mol and two body-dissociation (FNgCC- -> FCC- + Ng) barriers of 21-43 kcal/mol; moreover, the S-T gaps of all the FNgCC- were over 81 kcal/mol. These results suggested that the future experimental identification of the FNgCC- anions is expected under cryogenic conditions. In chapter 3, the mechanisms and reaction paths of the prebiotic strecker synthesis of alanine catalyzed by water and chiral molecules in the neutral environment have been studied. In this three-step reaction, the energy barriers were calculated to be over 33 kcal/mol in the uncatalyzed condition; the reaction catalyzed by water, however, could significantly reduce the barriers by 17-27 kcal/mol. When the reactions were catalyzed by the chiral molecules (R-form or S-form) CH3CHCl(OH) and CH3CH2CHCl(OH), the differences of barriers between two chiral products (D- and L-Alanine) were calculated to be 0.6 and 0.9 kcal/mol; of the rates in 300 K, 2 and 4.5 times. This result suggested that the chiral catalysts in prebiotic conditions could produce different numbers of the two different chiral (D- and L-) amino acids, which was might be a plausible reason for the dominance of L-amino acids in nature nowadays. In chapter 4, high-level electronic structure calculations have been carried out on the kinetic stability of the cyclic-O3, cyclic-S3, and cyclic-Se3. In this study, the rate constant and tunneling effect for the isomerization reaction of cyclic-S3 was also calculated by using the VTST/MT and compared to our previous study about cyclic-O3. From our high-level calculations, the energy barriers of the isomerization reactions for O3, S3, and Se3 were predicted to be 21.1, 25.8, and 22.9 kcal/mol, respectively. The half-life of the cyclic-S3 estimated by VTST/MT was ~12.7 hours at 300 K and ∼106 years at 200 K. Since the Se3 systems were expected to show much less tunneling effects, both cyclic S3 and Se3 were expected to be kinetically stable. In chapter 5, we studied the proton transfer reactions of 1,8- dihydroxy-2-naphthaldehyde (DHNA) on both ground state (S0) and 1st singlet excited state (S1) and estimated the wavelenths of vertical S0 -> S1 excitation and S1 -> S0 emissions. On the ground-state (S0), the normal form (N) was lower in energies than tautomer A (TA) by 1.5 kcal/mol and the barrier of N -> TA was 2.6 kcal/mol, which suggested there were equilibrium between the N and TA species in S0. The calculated S1 barriers of N* -> TA* and TA* -> TB* were 0.3 and 2.1 kcal/mol, respectively, which suggested there existed a low energy path for N* to produced TA* and TB* by single and double proton transfer reactions. A comprehensive 2-D PES plot proved that the sequential, two-step proton motion is along the minimum energetic pathway, consistent with the experimental results.

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20

Capela, Paul. "Use Of Cryoprotectants, Prebiotics And Microencapsulation of Bacterial Cells in Improving the Viability of Probiotic Organisms in Freeze-Dried Yoghurt." 2006. http://eprints.vu.edu.au/580/1/Template.pdf.

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The main aim of this study was to improve the viability of probiotic organisms within freeze-dried yoghurt during processing and storage. Initially, probiotic organisms including Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus rhamnosus and Bifidobacterium spp. were incorporated in reconstituted skim milk and freeze-dried in order to select the most robust strains for use in further experiments The viability of B. infantis 17930 and L. rhamnosus GG was reduced by 0.07 log, while that of L. casei 1520 and B. longum 1941 was reduced by 0.28 and 0.39 log, respectively. The probiotic organisms selected for further experiments were L. acidophilus 33200, L. casei 279, L. rhamnosus GG and B. longum 536. The effectiveness of adding cryoprotectants and prebiotics in improving the viability of the selected probiotic organisms was investigated. There was a 7% improvement in the viability of L. casei 1520 when cryoprotectant 'UnipectineTM RS 150' was added at 2.5% (w/v). The addition of the prebiotic 'Raftilose P95 at 1.5% (w/v) to yoghurt improved the viability of the combined selected probiotic organisms by 1.42 log during four weeks of storage at 4°C. Microencapsulation of probiotic organisms was assessed to determine whether further improvements in viability were possible. Microencapsulation with calciumalginate using the emulsion technique was found to improve the viability of the combined selected probiotic organisms by 0.31 log in freeze-dried yoghurt stored at 21C. Further studies were carried out to compare the extrusion technique with the emulsion technique. It was found that the viability of the probiotic organism was 1.0 log10 CFU/g higher using the emulsion technique after freeze-drying. Coating with poly-L-lysine or chitosan further improved the survival of the probiotic organisms by 0.03 and 0.07 log10 cfu/g in yoghurt during 4 weeks of storage at 4ºC. The survival of probiotic organisms in yoghurt stored at 4ºC was highest (8.69 log10 cfu/g) in beads coated with chitosan. In freeze-dried yoghurt, coating with poly-L-lysine or chitosan improved survival of probiotic organisms by 0.2 and 0.4 log10 cfu/g in freezedried yoghurt during 16 weeks of storage at 21C. The survival of probiotic organisms in freeze-dried yoghurt stored at 4ºC was highest (8.47 log10 cfu/g) in beads coated with chitosan. Although microencapsulation was effective in improving the viability of probiotic organisms in freeze-dried yoghurt, the calcium-alginate beads were too large and influenced the texture of the yoghurt. Consequently, further work was carried out to identify an effective technique for reducing bead-size during microencapsulation of probiotic organisms. The diameters of calcium-alginate beads were reduced by forming emulsions using homogenisation with Ultra-Turrax benchtop homogeniser, Avestin Inc. Piston homogeniser and Silverson mixer. The smallest beads were formed using the Ultra-Turrax benchtop homogeniser with a modal diameter of 56 Î¼m. The counts of L. casei 279 after microencapsulation using the Ultra-Turrax benchtop homogeniser at 8000 rpm for 2 min were not adversely affected as the population was 8.8 log10 cfu/g. However, the count of microencapsulated B. longum 536 using the Silverson mixer was 6.3 log10 cfu/g. Overall, small beads containing viable probiotic organisms were created when an emulsion formed by homogenisation during microencapsulation. It is recommended that probiotic organisms present in freeze-dried yoghurt should be microencapsulated to improve their viability. The emulsion technique should be used and the emulsion. The sodium alginate/probiotic and oil mixture should be homogenised using the Ultra-Turrax Benchtop mixer at 8000 rpm for 2 minutes to effectively reduce bead size. Ideally, calcium-alginate beads should be coated in chitosan to provide maximum protection. Cryoprotectants should also be added to the yoghurt to provide probiotic organisms with additional protection during freeze-drying.

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21

Rasmussen, Steen, Liaohai Chen, Bärbel M. R. Stadler, and Peter F. Stadler. "Proto-Organism Kinetics." 2004. https://ul.qucosa.de/id/qucosa%3A31957.

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A synthetic proto-organism could be self-assembled by integrating a lipid proto-container with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and nutrients by means of either redox or photo-chemical reactions, evolve its proto-genome by means of template directed replication, and ultimately die. The evolutionary dynamics of the proto-organism depends crucially on the chemical kinetics of its sub-systems and on their interplay. In this work the template replication kinetics is investigated and it is found that the product inhibition inherent in the ligation-like replication process allows for coexistence of unrelated self-replicating proto-genes in the lipid surface layer. The combined catalytic effects from the proto-genes on the metabolic production rates determine the fate of the strain protocell.

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22

Capela, Paul. "Use Of Cryoprotectants, Prebiotics And Microencapsulation of Bacterial Cells in Improving the Viability of Probiotic Organisms in Freeze-Dried Yoghurt." Thesis, 2006. https://vuir.vu.edu.au/580/.

Повний текст джерела

Анотація:

The main aim of this study was to improve the viability of probiotic organisms within freeze-dried yoghurt during processing and storage. Initially, probiotic organisms including Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus rhamnosus and Bifidobacterium spp. were incorporated in reconstituted skim milk and freeze-dried in order to select the most robust strains for use in further experiments The viability of B. infantis 17930 and L. rhamnosus GG was reduced by 0.07 log, while that of L. casei 1520 and B. longum 1941 was reduced by 0.28 and 0.39 log, respectively. The probiotic organisms selected for further experiments were L. acidophilus 33200, L. casei 279, L. rhamnosus GG and B. longum 536. The effectiveness of adding cryoprotectants and prebiotics in improving the viability of the selected probiotic organisms was investigated. There was a 7% improvement in the viability of L. casei 1520 when cryoprotectant 'UnipectineTM RS 150' was added at 2.5% (w/v). The addition of the prebiotic 'Raftilose P95 at 1.5% (w/v) to yoghurt improved the viability of the combined selected probiotic organisms by 1.42 log during four weeks of storage at 4°C. Microencapsulation of probiotic organisms was assessed to determine whether further improvements in viability were possible. Microencapsulation with calciumalginate using the emulsion technique was found to improve the viability of the combined selected probiotic organisms by 0.31 log in freeze-dried yoghurt stored at 21C. Further studies were carried out to compare the extrusion technique with the emulsion technique. It was found that the viability of the probiotic organism was 1.0 log10 CFU/g higher using the emulsion technique after freeze-drying. Coating with poly-L-lysine or chitosan further improved the survival of the probiotic organisms by 0.03 and 0.07 log10 cfu/g in yoghurt during 4 weeks of storage at 4ºC. The survival of probiotic organisms in yoghurt stored at 4ºC was highest (8.69 log10 cfu/g) in beads coated with chitosan. In freeze-dried yoghurt, coating with poly-L-lysine or chitosan improved survival of probiotic organisms by 0.2 and 0.4 log10 cfu/g in freezedried yoghurt during 16 weeks of storage at 21C. The survival of probiotic organisms in freeze-dried yoghurt stored at 4ºC was highest (8.47 log10 cfu/g) in beads coated with chitosan. Although microencapsulation was effective in improving the viability of probiotic organisms in freeze-dried yoghurt, the calcium-alginate beads were too large and influenced the texture of the yoghurt. Consequently, further work was carried out to identify an effective technique for reducing bead-size during microencapsulation of probiotic organisms. The diameters of calcium-alginate beads were reduced by forming emulsions using homogenisation with Ultra-Turrax benchtop homogeniser, Avestin Inc. Piston homogeniser and Silverson mixer. The smallest beads were formed using the Ultra-Turrax benchtop homogeniser with a modal diameter of 56 Î¼m. The counts of L. casei 279 after microencapsulation using the Ultra-Turrax benchtop homogeniser at 8000 rpm for 2 min were not adversely affected as the population was 8.8 log10 cfu/g. However, the count of microencapsulated B. longum 536 using the Silverson mixer was 6.3 log10 cfu/g. Overall, small beads containing viable probiotic organisms were created when an emulsion formed by homogenisation during microencapsulation. It is recommended that probiotic organisms present in freeze-dried yoghurt should be microencapsulated to improve their viability. The emulsion technique should be used and the emulsion. The sodium alginate/probiotic and oil mixture should be homogenised using the Ultra-Turrax Benchtop mixer at 8000 rpm for 2 minutes to effectively reduce bead size. Ideally, calcium-alginate beads should be coated in chitosan to provide maximum protection. Cryoprotectants should also be added to the yoghurt to provide probiotic organisms with additional protection during freeze-drying.

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23

Huynh, Bao Lam. "Genetic characterization and QTL mapping for grain fructan in wheat (Triticum aestivum L.)." 2009. http://hdl.handle.net/2440/52594.

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Анотація:

Fructans are polysaccharides that are made up mainly of fructose. They are non-digestible carbohydrates and act as prebiotics to selectively promote the growth of colonic bifidobacteria, thereby improving human gut health. Fructans are present in the grain of wheat (Triticum aestivum L.), a staple food crop. Until now, there has been no research on genetic improvement of the concentration of fructans in wheat grain, partly because it has been difficult to accurately measure. One aim of this research project was to develop a simple and effective method to measure the fructan concentration in wheat grain. This was achieved by modifying a method that involves extraction of fructans from wheat grain followed by enzymatic hydrolysis to break down fructans into monosaccharides and quantification by anion-exchange liquid chromatography coupled with pulsed amperometric detection. The modified procedure is reliable and allows the handling of large numbers of flour samples at a relatively low cost, and can therefore be useful for assessing large numbers of wheat breeding lines. Using this method, grain samples taken from a diverse set of 117 wheat cultivars and breeding lines, including parents of mapping populations, were analysed for grain fructan concentration. There was significant genotypic variation among these materials, with grain fructan concentration ranging from 0.3 to 2.3% of grain dry weight. There was no evidence of strong genotype-byenvironment interaction; the fructan concentrations of the same genotypes were positively correlated over different environments in Australia. Genetic mapping was carried out to detect and map loci affecting grain fructan concentration in wheat using a doubled haploid population derived from a cross between Berkut (high fructan) and Krichauff (low fructan). Grain samples were obtained from two field sites in South Australia and one in Kazakhstan. Fructan concentration varied widely within the population (0.6-2.6% of grain dry weight), with heritability estimated as h² = 0.71. A linkage map of 528 molecular markers covering 21 wheat chromosomes was used for locating quantitative trait loci (QTL). Genetic mapping identified two major QTLs on chromosomes 6D and 7A, with the (high fructan concentration) alleles contributed from Berkut, contributing to a 30-40% increase in wheat grain fructan compared to the Krichauff alleles. Effects of these chromosome regions were validated in additional environments and in another mapping population, Sokoll/Krichauff, with the favourable alleles contributed from Sokoll. The major QTL on chromosome 7A was in the same region with a reported fructosyltransferase orthologue (AB029888), while the major QTL on chromosome 6D seemed to be co-located with a reported gene encoding for a fructan-degrading enzyme 1-exohydrolase (1-FEHw2). It is concluded that grain fructan concentration of wheat can be improved by breeding and that molecular markers could be used to select effectively for favourable alleles in two regions of the wheat genome.
Thesis (Ph.D.) - University of Adelaide, School of Agriculture, Food and Wine, 2009

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24

Huynh, Bao Lam. "Genetic characterization and QTL mapping for grain fructan in wheat (Triticum aestivum L.)." Thesis, 2009. http://hdl.handle.net/2440/52594.

Повний текст джерела

Анотація:

Fructans are polysaccharides that are made up mainly of fructose. They are non-digestible carbohydrates and act as prebiotics to selectively promote the growth of colonic bifidobacteria, thereby improving human gut health. Fructans are present in the grain of wheat (Triticum aestivum L.), a staple food crop. Until now, there has been no research on genetic improvement of the concentration of fructans in wheat grain, partly because it has been difficult to accurately measure. One aim of this research project was to develop a simple and effective method to measure the fructan concentration in wheat grain. This was achieved by modifying a method that involves extraction of fructans from wheat grain followed by enzymatic hydrolysis to break down fructans into monosaccharides and quantification by anion-exchange liquid chromatography coupled with pulsed amperometric detection. The modified procedure is reliable and allows the handling of large numbers of flour samples at a relatively low cost, and can therefore be useful for assessing large numbers of wheat breeding lines. Using this method, grain samples taken from a diverse set of 117 wheat cultivars and breeding lines, including parents of mapping populations, were analysed for grain fructan concentration. There was significant genotypic variation among these materials, with grain fructan concentration ranging from 0.3 to 2.3% of grain dry weight. There was no evidence of strong genotype-byenvironment interaction; the fructan concentrations of the same genotypes were positively correlated over different environments in Australia. Genetic mapping was carried out to detect and map loci affecting grain fructan concentration in wheat using a doubled haploid population derived from a cross between Berkut (high fructan) and Krichauff (low fructan). Grain samples were obtained from two field sites in South Australia and one in Kazakhstan. Fructan concentration varied widely within the population (0.6-2.6% of grain dry weight), with heritability estimated as h² = 0.71. A linkage map of 528 molecular markers covering 21 wheat chromosomes was used for locating quantitative trait loci (QTL). Genetic mapping identified two major QTLs on chromosomes 6D and 7A, with the (high fructan concentration) alleles contributed from Berkut, contributing to a 30-40% increase in wheat grain fructan compared to the Krichauff alleles. Effects of these chromosome regions were validated in additional environments and in another mapping population, Sokoll/Krichauff, with the favourable alleles contributed from Sokoll. The major QTL on chromosome 7A was in the same region with a reported fructosyltransferase orthologue (AB029888), while the major QTL on chromosome 6D seemed to be co-located with a reported gene encoding for a fructan-degrading enzyme 1-exohydrolase (1-FEHw2). It is concluded that grain fructan concentration of wheat can be improved by breeding and that molecular markers could be used to select effectively for favourable alleles in two regions of the wheat genome.
Thesis (Ph.D.) - University of Adelaide, School of Agriculture, Food and Wine, 2009

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