Chapter 1 Introduction to Organic Chemistry 1.1
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Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
This Ubiquitous Carbon…
Engineering Physics Department Presents Dr. Cristian Contescu Senior Research Staff, Materials Science and Technology Division Oak Ridge National Laboratory This ubiquitous carbon… Abstract: After Stone Age, Bronze Age, and Iron Age, and after the Silicon Age of the informational revolution, the technologies of 21st century are marked by the ubiquitous presence of various forms of carbon allotropes. For a very long time, diamond and graphite were the only known carbon allotropes, but that has changed with the serendipitous discovery of fullerenes, carbon nanotubes, and graphene. Every ten or fifteen years scientists unveil new forms of carbons with new and perplexing properties, while computations suggest that the carbon’s family still has members unknown to us today. At a dramatically accelerated pace, new carbon forms find their place at the leading edge of scientific and technological innovations. At the same time traditional forms of carbon are being used in new and exciting applications that make our life safer, healthier, and more enjoyable. The 21st century may soon be recognized as the Age of Carbon forms. This educational talk will show how carbon, the fourth most abundant element in the Galaxy and the basis of life on Earth, was the engine of most important technological developments throughout the history of civilization. It will emphasize the ability of carbon atoms to generate a variety of mutual combinations and with many other chemical elements. These properties have placed carbon at the core of numerous inventions that define our civilization, while emerging new technologies open a rich path for value-added products in today’s market. -
Properties of Carbon the Atomic Element Carbon Has Very Diverse
Properties of Carbon The atomic element carbon has very diverse physical and chemical properties due to the nature of its bonding and atomic arrangement. fig. 1 Allotropes of Carbon Some allotropes of carbon: (a) diamond, (b) graphite, (c) lonsdaleite, (d–f) fullerenes (C60, C540, C70), (g) amorphous carbon, and (h) carbon nanotube. Carbon has several allotropes, or different forms in which it can exist. These allotropes include graphite and diamond, whose properties span a range of extremes. Despite carbon's ability to make 4 bonds and its presence in many compounds, it is highly unreactive under normal conditions. Carbon exists in 2 main isotopes: 12C and 13C. There are many other known isotopes, but they tend to be short-lived and have extremely short half-lives. Allotropes The different forms of a chemical element. Cabon is the chemical element with the symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds. Carbon has 6 protons and 6 Source URL: https://www.boundless.com/chemistry/nonmetallic-elements/carbon/properties-carbon/ Saylor URL: http://www.saylor.org/courses/chem102#6.1 Attributed to: Boundless www.saylor.org Page 1 of 2 neutrons, and has a standard atomic weight of 12.0107 amu. Its electron configuration is denoted as 1s22s22p2. It is a solid, and sublimes at 3,642 °C. It's oxidation state ranges from 4 to -4, and it has an electronegativity rating of 2.55 on the Pauling scale. Carbon has several allotropes, or different forms in which it exists. -
Chemistry 0310 - Organic Chemistry 1 Chapter 3
Dr. Peter Wipf Chemistry 0310 - Organic Chemistry 1 Chapter 3. Reactions of Alkanes The heterolysis of covalent bonds yields anions and cations, whereas the homolysis creates radicals. Radicals are species with unpaired electrons that react mostly as electrophiles, seeking a single electron to complete their octet. Free radicals are important reaction intermediates and are formed in initiation reactions under conditions that cause the homolytic cleavage of bonds. In propagation steps, radicals abstract hydrogen or halogen atoms to create new radicals. Combinations of radicals are rare due to the low concentration of these reactive intermediates and result in termination of the radical chain. !CHAIN REACTION SUMMARY reactant product initiation PhCH3 HCl Cl 2 h DH = -16 kcal/mol chain-carrying intermediates n o r D (low concentrations) PhCH2 . Cl . propagation PhCH2 . or Cl . PhCH . 2 DH = -15 kcal/mol or Cl . PhCH2Cl or PhCH CH Ph PhCH2Cl Cl2 2 2 PhCH2Cl or Cl2 termination product reactant termination Alkanes are converted to alkyl halides by free radical halogenation reactions. The relative stability of radicals is increased by conjugation and hyperconjugation: R H H H . CH2 > R C . > R C . > H C . > H C . R R R H Oxygen is a diradical. In the presence of free-radical initiators such as metal salts, organic compounds and oxygen react to give hydroperoxides. These autoxidation reactions are responsible for the degradation reactions of oils, fatty acids, and other biological substances when exposed to air. Antioxidants such as hindered phenols are important food additives. Vitamins E and C are biological antioxidants. Radical chain reactions of chlorinated fluorocarbons in the stratosphere are responsible for the "ozone hole". -
Sp Carbon Chain Interaction with Silver Nanoparticles Probed by Surface Enhanced Raman Scattering
sp carbon chain interaction with silver nanoparticles probed by Surface Enhanced Raman Scattering A. Lucotti1, C. S. Casari2, M. Tommasini1, A. Li Bassi2, D. Fazzi1, V. Russo2, M. Del Zoppo1, C. Castiglioni1, F. Cataldo3, C. E. Bottani2, G. Zerbi1 1 Dipartimento di Chimica, Materiali e Ingegneria Chimica ‘G. Natta’ and NEMAS - Center for NanoEngineered MAterials and Surfaces, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy 2 Dipartimento di Energia and NEMAS - Center for NanoEngineered MAterials and Surfaces, Politecnico di Milano, via Ponzio 34/3, I-20133 Milano, Italy 3 Actinium Chemical Research srl, via Casilina 1626/A, 00133 Roma, Italy and INAF – Osservatorio Astrofisico di Catania, Via S. Sofia 78, 95123 Catania, Italy Abstract Surface Enhanced Raman Spectroscopy (SERS) is exploited here to investigate the interaction of isolated sp carbon chains (polyynes) in a methanol solution with silver nanoparticles. Hydrogen-terminated polyynes show a strong interaction with silver colloids used as the SERS active medium revealing a chemical SERS effect. SERS spectra after mixing polyynes with silver colloids show a noticeable time evolution. Experimental results, supported by density functional theory (DFT) calculations of the Raman modes, allow us to investigate the behaviour and stability of polyynes of different lengths and the overall sp conversion towards sp2 phase. 1 2 1. Introduction Linear carbon chains with sp hybridization represent one of the simplest one dimensional systems and have therefore attracted a great interest for many years [1, 2]. sp chains can display two types of carbon-carbon bonding: polyynes, chains with single-triple alternating bonds (…-C≡C- C≡C-…) and polycumulenes, chains with all double bonds (…=C=C=C=…). -
Agricultural Soil Carbon Credits: Making Sense of Protocols for Carbon Sequestration and Net Greenhouse Gas Removals
Agricultural Soil Carbon Credits: Making sense of protocols for carbon sequestration and net greenhouse gas removals NATURAL CLIMATE SOLUTIONS About this report This synthesis is for federal and state We contacted each carbon registry and policymakers looking to shape public marketplace to ensure that details investments in climate mitigation presented in this report and through agricultural soil carbon credits, accompanying appendix are accurate. protocol developers, project developers This report does not address carbon and aggregators, buyers of credits and accounting outside of published others interested in learning about the protocols meant to generate verified landscape of soil carbon and net carbon credits. greenhouse gas measurement, reporting While not a focus of the report, we and verification protocols. We use the remain concerned that any end-use of term MRV broadly to encompass the carbon credits as an offset, without range of quantification activities, robust local pollution regulations, will structural considerations and perpetuate the historic and ongoing requirements intended to ensure the negative impacts of carbon trading on integrity of quantified credits. disadvantaged communities and Black, This report is based on careful review Indigenous and other communities of and synthesis of publicly available soil color. Carbon markets have enormous organic carbon MRV protocols published potential to incentivize and reward by nonprofit carbon registries and by climate progress, but markets must be private carbon crediting marketplaces. paired with a strong regulatory backing. Acknowledgements This report was supported through a gift Conservation Cropping Protocol; Miguel to Environmental Defense Fund from the Taboada who provided feedback on the High Meadows Foundation for post- FAO GSOC protocol; Radhika Moolgavkar doctoral fellowships and through the at Nori; Robin Rather, Jim Blackburn, Bezos Earth Fund. -
INFORMATION to USERS the Most Advanced Technology Has Been
INFORMATION TO USERS The most advanced technology has been used to photo graph and reproduce this manuscript from the microfilm master. UMI films the original text directly from the copy submitted. Thus, some dissertation copies are in typewriter face, while others may be from a computer printer. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyrighted material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are re produced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each oversize page is available as one exposure on a standard 35 mm slide or as a 17" x 23" black and white photographic print for an additional charge. Photographs included in the original manuscript have been reproduced xerographically in this copy. 35 mm slides or 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. Accessing the World'sUMI Information since 1938 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA Order Number 8820378 Stereochemical studies in anaerobic metabolism Zydowsky, Lynne Douthit, Ph.D. The Ohio State University, 1988 UMI 300 N. Zeeb Rd. Ann Aibor, M I 48106 PLEASE NOTE: In all cases this material has been filmed in the best possible way from the available copy. Problems encountered with this document have been identified here with a check mark V . -
Constraint Closure Drove Major Transitions in the Origins of Life
entropy Article Constraint Closure Drove Major Transitions in the Origins of Life Niles E. Lehman 1 and Stuart. A. Kauffman 2,* 1 Edac Research, 1879 Camino Cruz Blanca, Santa Fe, NM 87505, USA; [email protected] 2 Institute for Systems Biology, Seattle, WA 98109, USA * Correspondence: [email protected] Abstract: Life is an epiphenomenon for which origins are of tremendous interest to explain. We provide a framework for doing so based on the thermodynamic concept of work cycles. These cycles can create their own closure events, and thereby provide a mechanism for engendering novelty. We note that three significant such events led to life as we know it on Earth: (1) the advent of collective autocatalytic sets (CASs) of small molecules; (2) the advent of CASs of reproducing informational polymers; and (3) the advent of CASs of polymerase replicases. Each step could occur only when the boundary conditions of the system fostered constraints that fundamentally changed the phase space. With the realization that these successive events are required for innovative forms of life, we may now be able to focus more clearly on the question of life’s abundance in the universe. Keywords: origins of life; constraint closure; RNA world; novelty; autocatalytic sets 1. Introduction The plausibility of life in the universe is a hotly debated topic. As of today, life is only known to exist on Earth. Thus, it may have been a singular event, an infrequent event, or a common event, albeit one that has thus far evaded our detection outside our own planet. Herein, we will not attempt to argue for any particular frequency of life. -
Basic Concepts of Chemical Bonding
Basic Concepts of Chemical Bonding Cover 8.1 to 8.7 EXCEPT 1. Omit Energetics of Ionic Bond Formation Omit Born-Haber Cycle 2. Omit Dipole Moments ELEMENTS & COMPOUNDS • Why do elements react to form compounds ? • What are the forces that hold atoms together in molecules ? and ions in ionic compounds ? Electron configuration predict reactivity Element Electron configurations Mg (12e) 1S 2 2S 2 2P 6 3S 2 Reactive Mg 2+ (10e) [Ne] Stable Cl(17e) 1S 2 2S 2 2P 6 3S 2 3P 5 Reactive Cl - (18e) [Ar] Stable CHEMICAL BONDSBONDS attractive force holding atoms together Single Bond : involves an electron pair e.g. H 2 Double Bond : involves two electron pairs e.g. O 2 Triple Bond : involves three electron pairs e.g. N 2 TYPES OF CHEMICAL BONDSBONDS Ionic Polar Covalent Two Extremes Covalent The Two Extremes IONIC BOND results from the transfer of electrons from a metal to a nonmetal. COVALENT BOND results from the sharing of electrons between the atoms. Usually found between nonmetals. The POLAR COVALENT bond is In-between • the IONIC BOND [ transfer of electrons ] and • the COVALENT BOND [ shared electrons] The pair of electrons in a polar covalent bond are not shared equally . DISCRIPTION OF ELECTRONS 1. How Many Electrons ? 2. Electron Configuration 3. Orbital Diagram 4. Quantum Numbers 5. LEWISLEWIS SYMBOLSSYMBOLS LEWISLEWIS SYMBOLSSYMBOLS 1. Electrons are represented as DOTS 2. Only VALENCE electrons are used Atomic Hydrogen is H • Atomic Lithium is Li • Atomic Sodium is Na • All of Group 1 has only one dot The Octet Rule Atoms gain, lose, or share electrons until they are surrounded by 8 valence electrons (s2 p6 ) All noble gases [EXCEPT HE] have s2 p6 configuration. -
Organic Chemistry PEIMS Code: N1120027 Abbreviation: ORGCHEM Number of Credits That May Be Earned: 1/2-1
Course: Organic Chemistry PEIMS Code: N1120027 Abbreviation: ORGCHEM Number of credits that may be earned: 1/2-1 Brief description of the course (150 words or less): Organic chemistry is an introductory course that is designed for the student who intends to continue future study in the sciences. The student will learn the concepts and applications of organic chemistry. Topics covered include aliphatic and aromatic compounds, alcohols, aldehydes, ketones, acids, ethers, amines, spectra, and stereochemistry. A brief introduction into biochemistry is also provided. The laboratory experiments will familiarize the student with the important laboratory techniques, specifically spectroscopy. Traditional high school chemistry courses focus on the inorganic aspects of chemistry whereas organic chemistry introduces the student to organic compounds and their properties, mechanisms of formations, and introduces the student to laboratory techniques beyond the traditional high school chemistry curriculum. Essential Knowledge and Skills of the course: (a) General requirements. This course is recommended for students in Grades 11-12. The recommended prerequisite for this course is AP Chemistry. (b) Introduction. Organic chemistry is designed to introduce students to the fundamental concepts of organic chemistry and key experimental evidence and data, which support these concepts. Students will learn to apply these data and concepts to chemical problem solving. Additionally, students will learn that organic chemistry is still evolving by reading about current breakthroughs in the field. Finally, students will gain appreciation for role that organic chemistry plays in modern technological developments in diverse fields, ranging from biology to materials science. (c) Knowledge and skills. (1) The student will be able to write both common an IUPAC names for the hydrocarbon. -
HISTORICAL ASPECTS of ORGANIC CHEMISTRY TEACHING (On the Example of Chemistry Direction of Higher Educational Institutions)
Journal of Critical Reviews ISSN- 2394-5125 Vol 7, Issue 13, 2020 CONCEPTUAL - HISTORICAL ASPECTS OF ORGANIC CHEMISTRY TEACHING (on the example of chemistry direction of Higher educational institutions) Rajabov Khudayor Madrimovich Uzbekistan, Khorasm region, Rajabov Khudayor Madrimovich, Doctor of philosophy (PhD) on pedagogical sciences, Urganch State University E-mail: [email protected] Received: 16.04.2020 Revised: 18.05.2020 Accepted: 13.06.2020 Abstract. The article reveals the historical approach on the teaching of organic chemistry in pedagogical universities. The development of modern trends and general competencies of students on the basis of historical approach, the creation of educational motivation, the focus on independent research and training of creative specialists are the most important directions. In this regard, it is important to improve the technology for organizing the educational process on the basis of historical principles in the system of training future chemistry teachers, to improve the mechanisms on the methodological support, to fulfill the system of competencies and cyclic diagnostics. Keywords: historical approach, organic chemistry, conceptual - historical aspects, professional competence, principle of historicism, methodology, self-improvement, innovation, non-historical, positive attitude, extracurricular activities. © 2020 by Advance Scientific Research. This is an open-access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) DOI: http://dx.doi.org/10.31838/jcr.07.13.129 -
Ocw-5.112-Lec24 the Following Content Is Provided by MIT Opencourseware Under a Creative Commons License
MITOCW | ocw-5.112-lec24 The following content is provided by MIT OpenCourseWare under a Creative Commons license. Additional information about our license and MIT OpenCourseWare in general is available at ocw.mit.edu. Today I would like to start by discussing a timeline. And you will see in a moment what this timeline has to do with. It is obviously only a partial timeline. But let's start here in 1916, as we have done this semester, by talking about the Lewis theory of electronic structure. And his electron pair theory is something we are going to come back to a couple of times during lecture today. Let's move on to 1954. 1954 was an important year in electronic structure theory, because in that year there was awarded, to Linus Pauling, the Nobel Prize in chemistry. Let me write down Pauling here. And if you are interested in knowing something about what Pauling was awarded the Nobel Prize in chemistry for, I will show you over here on the side boards. What you are going to see here, if you read this citation for Linus Carl Pauling in 1954 for the Nobel Prize in chemistry, his prize was awarded principally for his contributions to our understanding of the nature of the chemical bond. If you think back to the elegant title of the paper by Lewis that we started out our discussion of acid-base theory with, it was a paper entitled "The Atom and the Molecule." And now we have gotten to Pauling, in 1954, who is being awarded a Nobel Prize in chemistry for the nature of the chemical bond.