Achievements and Trends in Developments of Stereochemistry
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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. -
Chapter 3 • Ratio: Cnh2n+2
Organic Chemistry, 5th Edition Alkane Formulas L. G. Wade, Jr. • All C-C single bonds • Saturated with hydrogens Chapter 3 • Ratio: CnH2n+2 Structure and Stereochemistry • Alkane homologs: CH3(CH2)nCH3 of Alkanes • Same ratio for branched alkanes H H H H H H CH H C C C C H H H H C CCH Jo Blackburn H H H H H H Richland College, Dallas, TX H => Butane, C4H10 Dallas County Community College District Chapter 3Isobutane, C H 2 © 2003, Prentice Hall 4 10 Common Names Pentanes H H H H H H H CH • Isobutane, “isomer of butane” H C C C C C H H H • Isopentane, isohexane, etc., methyl H H H H H H H C CCC H branch on next-to-last carbon in chain. H H H H • Neopentane, most highly branched n-pentane, C5H12 isopentane, C5H12 • Five possible isomers of hexane, CH3 18 isomers of octane and 75 for H3C C CH3 decane! CH3 => => neopentane, C5H12 Chapter 3 3 Chapter 3 4 Longest Chain IUPAC Names • The number of carbons in the longest • Find the longest continuous carbon chain determines the base name: chain. ethane, hexane. (Listed in Table 3.2, • Number the carbons, starting closest to page 81.) the first branch. • If there are two possible chains with the • Name the groups attached to the chain, same number of carbons, use the chain using the carbon number as the locator. with the most substituents. • Alphabetize substituents. H3C CH CH CH • Use di-, tri-, etc., for multiples of same 2 3 CH3 substituent. -
Chemistry Courses 2005-2006
Chemistry Courses 2005-2006 Autumn 2005 Chem 11101 General Chemistry I, Variant A Lee Chem 11102 General Chemistry I, Variant B Norris Chem 12200 Honors General Chemistry I Levy Chem 22000 Organic Chemistry I Yu Chem 22300 Intermediate Organic Chemistry Mrksich Chem 26100 Quantum Mechanics Mazziotti Chem 30100 Advanced Inorganic Chemistry Hopkins Chem 30900 Bioinorganic Chemistry He Chem 32100 Physical Organic Chemistry I Ismagilov Chem 32200 Organic Synthesis and Structure Rawal Chem 32600 Protein Fundamentals Piccirilli Chem 36100 Wave Mechanics & Spectroscopy Butler Chem 36400 Chemical Thermodynamics Dinner Winter 2006 Chem 11201 General Chemistry II, Variant A Scherer Chem 11202 General Chemistry II, Variant B Butler Chem 12300 Honors General Chemistry II Dinner Chem 20100 Inorganic Chemistry I Hillhouse Chem 22100 Organic Chemistry II Rawal Chem 23100 Honors Organic Chemistry II Kozmin Chem 26200 Thermodynamics Norris Chem 26700 Experimental Physical Chemistry Levy Chem 30200 Synthesis & Physical Methods in Inorganic Chemistry Jordan Chem 30400 Organometallic Chemistry Bosnich Chem 32300 Tactics of Organic Synthesis Yamamoto Chem 32400 Physical Organic Chemistry II Mrksich Chem 36200 Quantum Mechanics Freed Chem 36300 Statistical Mechanics Mazziotti Chem 38700 Biophysical Chemistry Lee Spring 2006 Chem 11301 General Chemistry III, Variant A Kozmin Chem 11302 General Chemistry III, Variant B Guyot-Sionnest Chem 20200 Inorganic Chemistry II Jordan Chem 22200 Organic Chemistry III Kent Chem 23200 Honors Organic Chemistry III Yamamoto Chem 22700 Advanced Organic / Inorganic Laboratory (8 students) He Chem 26300 Chemical Kinetics and Dynamics Sibner Chem 26800 Computational Chemistry & Biology Freed Chem 30600 Chemistry of the Elements Hillhouse Chem 31100 Supramolecular Chemistry Bosnich Chem 32500 Bioorganic Chemistry Piccirilli Chem 32900 Polymer Chemistry Yu Chem 33000 Complex Systems Ismagilov Chem 36500 Chemical Dynamics Scherer Chem 36800 Advanced Computational Chemistry & Biology Freed . -
Stereochemistry of Alkanes and Cycloalkanes
STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES CONFORMATIONAL ISOMERS 1 CONFORMATIONAL ISOMERS • Stereochemistry concerned with the 3-D aspects of molecules • Rotation is possible around C-C bonds in open- chain molecules • A conformation is one of the many possible arrangements of atoms caused by rotation about a single bond, and a specific conformation is called a conformer (conformational isomer). 2 SOME VOCABULARY • A staggered conformation is the conformation in which all groups on two adjacent carbons are as far from each other as possible. • An eclipsed conformation is the conformation in which all groups on two adjacent carbons are as close to each other as possible. • Dihedral angle is angle between the substituents on two adjacent carbons; changes with rotation around the C-C bond 3 MORE VOCABULARY • Angle strain is the strain caused by the deformation of a bond angle from its normal value. • Steric strain is the repulsive interaction caused by atoms attempting to occupy the same space. • Torsional strain is the repulsive interaction between two bonds as they rotate past each other. Torsional strain is responsible for the barrier to rotation around the C-C bond. The eclipsed from higher in energy than the staggered form. 4 CONFORMATION OF ETHANE • Conformation- Different arrangement of atoms resulting from bond rotation • Conformations can be represented in 2 ways: 5 TORSIONAL STRAIN • We do not observe perfectly free rotation • There is a barrier to rotation, and some conformers are more stable than others • Staggered- most stable: -
Curriculum of Department of Pharmacy (6-Year Program)
Curriculum of Department of Pharmacy (6-year program) 1st year 2nd year 3rd year 4th year 5th year 6th year Basic Subjects for Pharmacy Student; Lectures and Practices of Basic Specialized Lectures and Practices Drug Therapy and its Related Practical Training and Beginning of Research for Graduation and SGL and more Sciences Research for Graduation Advanced Lectures Fundamental Education Professional Education Ⅰ Professional Education Ⅱ ■Humanism ■Humanism ■Preparatory Pharmacy Education ■Professional Pharmacy Education ■Practical Training ■Advanced Education Introduction to Humanism I Introduction to Humanism Ⅱ English for Pharmacy Oriental Medicine Preparation for Practical Training Research for Graduation Pharmacotherapeutics Practical Training in Hospital Advanced Clinical Training ■Preparatory Pharmacy Education ■Professional Pharmacy Education Drug Information Science Practical Training in Community Phrarmacy General Pharmacy Practice II ■Introduction of Pharmacy Basic English and English for Pharmacy Clinical Chemistry Drug Development and Production Japanese Traditional Medicine Invitation to Pharmacy Basic Statistics Synthesis of Target Molecules Pharmacy and Society ■Advanced Education Clinical Pharmacokinetics Early Exposure to Pharmacy Practical Trainings for Pharmacy Bioorganic Chemistry General Pharmacy Practice Research for Graduation Clinical Drug Evaluation Students Pharmaceutical Health Care Training Medical Economy Natural Products Chemistry ■Practical Training Education Drug Safty Evaluation and Pharmacoepidemiology -
Safe Hydroformylation of Aliphatic Alkene in a Flow Reactor
International Journal of Organic Chemistry, 2018, 8, 135-141 http://www.scirp.org/journal/ijoc ISSN Online: 2161-4695 ISSN Print: 2161-4687 Safe Hydroformylation of Aliphatic Alkene in a Flow Reactor Hisashi Masui, Eiki Honda, Sakura Niitsu, Mitsuru Shoji, Takashi Takahashi* Department of Pharmaceutical Sciences, Yokohama University of Pharmacy, Yokohama, Japan How to cite this paper: Masui, H., Honda, Abstract E., Niitsu, S., Shoji, M. and Takahashi, T. (2018) Safe Hydroformylation of Aliphatic Despite hydroformylation being a very efficient method for the transforma- Alkene in a Flow Reactor. International tion of alkenes, it is not commonly employed in laboratories owing to the Journal of Organic Chemistry, 8, 135-141. flammable/toxic nature of hydrogen and carbon monoxide gases and the ne- https://doi.org/10.4236/ijoc.2018.81009 cessity of high-pressure equipment in a batch system. Flow chemistry often Received: November 30, 2017 raises the safety profiles against high-pressure and toxic gases because the Accepted: March 6, 2018 diameter of the flow reactor is small. Herein, we show that aliphatic alkenes Published: March 9, 2018 can be safely hydroformylated in a flow reactor. In our flow method, although Copyright © 2018 by authors and the target hydroformylated product was obtained in a low yield (19%), toxic Scientific Research Publishing Inc. gases were safely treated using a flow reactor. Better yields could possibly be This work is licensed under the Creative achieved by recycling of the unreacted alkene. Commons Attribution International License (CC BY 4.0). http://creativecommons.org/licenses/by/4.0/ Keywords Open Access Hydroformylation, Flow Synthesis, Alkene, Carbon Monoxide, Aldehyde 1. -
Recreating Ancient Metabolic Pathways Before Enzymes Kamila B
Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran To cite this version: Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran. Recreating ancient metabolic path- ways before enzymes. Bioorganic and Medicinal Chemistry, Elsevier, 2019, 27 (12), pp.2292-2297. 10.1016/j.bmc.2019.03.012. hal-02516541 HAL Id: hal-02516541 https://hal.archives-ouvertes.fr/hal-02516541 Submitted on 23 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Graphical Abstract To create your abstract, type over the instructions in the template box below. Fonts or abstract dimensions should not be changed or altered. Recreating ancient metabolic pathways Leave this area blank for abstract info. before enzymes Kamila B. Muchowskaa* , Elodie Chevallot-Berouxa, and Joseph Morana* University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France Bioorganic & Medicinal Chemistry journal homepage: www.elsevier.com Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska,a* Elodie Chevallot-Beroux,a and Joseph Morana* a University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France. ARTICLE INFO ABSTRACT Article history: The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction Received networks. -
Catalytic Systems Based on Cp2zrx2 (X = Cl, H), Organoaluminum
catalysts Article Catalytic Systems Based on Cp2ZrX2 (X = Cl, H), Organoaluminum Compounds and Perfluorophenylboranes: Role of Zr,Zr- and Zr,Al-Hydride Intermediates in Alkene Dimerization and Oligomerization Lyudmila V. Parfenova 1,* , Pavel V. Kovyazin 1, Almira Kh. Bikmeeva 1 and Eldar R. Palatov 2 1 Institute of Petrochemistry and Catalysis of Russian Academy of Sciences, Prospekt Oktyabrya, 141, 450075 Ufa, Russia; [email protected] (P.V.K.); [email protected] (A.K.B.) 2 Bashkir State University, st. Zaki Validi, 32, 450076 Ufa, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-347-284-3527 i i Abstract: The activity and chemoselectivity of the Cp2ZrCl2-XAlBu 2 (X = H, Bu ) and [Cp2ZrH2]2- ClAlEt2 catalytic systems activated by (Ph3C)[B(C6F5)4] or B(C6F5)3 were studied in reactions with 1-hexene. The activation of the systems by B(C6F5)3 resulted in the selective formation of head- to-tail alkene dimers in up to 93% yields. NMR studies of the reactions of Zr complexes with organoaluminum compounds (OACs) and boron activators showed the formation of Zr,Zr- and Zr,Al-hydride intermediates, for which diffusion coefficients, hydrodynamic radii, and volumes were estimated using the diffusion ordered spectroscopy DOSY. Bis-zirconium hydride clusters of type x[Cp ZrH ·Cp ZrHCl·ClAlR ]·yRnAl(C F ) − were found to be the key intermediates of alkene 2 2 2 2 6 5 3 n dimerization, whereas cationic Zr,Al-hydrides led to the formation of oligomers. Citation: Parfenova, L.V.; Kovyazin, P.V.; Bikmeeva, A.K.; Palatov, E.R. -
Petrochemistry and Chemical Engineering November 18-20, 2013 Hilton San Antonio Airport, TX, USA
Gordadze G. N et al., J Pet Environ Biotechnol 2013, 4:6 http://dx.doi.org/10.4172/2157-7463.S1.002 World Congress on Petrochemistry and Chemical Engineering November 18-20, 2013 Hilton San Antonio Airport, TX, USA Formation of n-alkanes by bacteria Arthrobacter sp. RV and Pseudomonas aeruginosa RM Gordadze G. N and Stroeva A.R Gubkin Russian State University of Oil and Gas, Russia rocesses of petroleum hydrocarbons (HC) formation in literature have been discussing for 200 years. At present time there Pare two main theories of oil formation: organic (sedimentary-migration) and inorganic (abiotic). It is believed that n-alkanes formed from n-saturated fatty acids by decarboxylation. It is known that in the original organic matter (OM) fatty acids with an even number of carbon atoms in the molecule are prevail. In case sapropelic OM, low molecular weight acids (n-C16, n-C18 and n-C20) are mainly produced and if OM is humus higher molecular (n-C26, n-C28 and n-C30) are produced. It is important to note there are high molecular n-alkanes C23, C25, C27, C29, C31 and C33 in soil OM. Bacterial synthesis of n-alkanes could be accounted by decarboxylation with relatively high temperatures. However, this phenomenon doesn’t support by experiment. In this work we studied, if n-alkanes with an odd number of carbon atoms in the molecule formed by bacteria. The objects of study were the hydrocarbon aerobic bacteria Arthrobacter sp. RV and the bacteria Pseudomonas aeruginosa RM, that are able to both aerobic and anaerobic growth in the process of denitrification. -
Chapter 4: Stereochemistry Introduction to Stereochemistry
Chapter 4: Stereochemistry Introduction To Stereochemistry Consider two of the compounds we produced while finding all the isomers of C7H16: CH3 CH3 2-methylhexane 3-methylhexane Me Me Me C Me H Bu Bu Me Me 2-methylhexane H H mirror Me rotate Bu Me H 2-methylhexame is superimposable with its mirror image Introduction To Stereochemistry Consider two of the compounds we produced while finding all the isomers of C7H16: CH3 CH3 2-methylhexane 3-methylhexane H C Et Et Me Pr Pr 3-methylhexane Me Me H H mirror Et rotate H Me Pr 2-methylhexame is superimposable with its mirror image Introduction To Stereochemistry Consider two of the compounds we produced while finding all the isomers of C7H16: CH3 CH3 2-methylhexane 3-methylhexane .Compounds that are not superimposable with their mirror image are called chiral (in Greek, chiral means "handed") 3-methylhexane is a chiral molecule. .Compounds that are superimposable with their mirror image are called achiral. 2-methylhexane is an achiral molecule. .An atom (usually carbon) with 4 different substituents is called a stereogenic center or stereocenter. Enantiomers Et Et Pr Pr Me CH3 Me H H 3-methylhexane mirror enantiomers Et Et Pr Pr Me Me Me H H Me H H Two compounds that are non-superimposable mirror images (the two "hands") are called enantiomers. Introduction To Stereochemistry Structural (constitutional) Isomers - Compounds of the same molecular formula with different connectivity (structure, constitution) 2-methylpentane 3-methylpentane Conformational Isomers - Compounds of the same structure that differ in rotation around one or more single bonds Me Me H H H Me H H H H Me H Configurational Isomers or Stereoisomers - Compounds of the same structure that differ in one or more aspects of stereochemistry (how groups are oriented in space - enantiomers or diastereomers) We need a a way to describe the stereochemistry! Me H H Me 3-methylhexane 3-methylhexane The CIP System Revisited 1. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
Petrochemistry April 25-27, 2018 Rome, Italy
J-M. Basset et al., Int J Petrochem Res. 2018 http://dx.doi.org/10.18689/2638-1974.a2.002 2nd International Conference on Petrochemistry April 25-27, 2018 Rome, Italy Predictive Heterogeneous Catalysis by Design: Well-Defined Single-Site Catalysts J-M. Basset1*, M. K. Samantaray1, S. Barman1, S. Kavitake1, N. Morlanes1, L Cavallo1, A. Hamieh1, R. Dey1, Abou Hamad1, J. Pelletier1, S. Ould-Chikh1, A. Bendjeriou-Sedjerari1, Eva B. Pump1, N. Merle2, F. Le Quemener2, K. C. Szeto2, A. De Mallmann2, Laurent Delevoye3, R. Gauvin3 and Mostafa Taoufik3 1KAUST Catalysis Center, King Abdullah University of Science and Technology, Saudi Arabia 2Laboratoire de Chimie, Catalyse, Polymères et Procédés, France 3Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, Unité de Catalyse et Chimie du Solide, France redictive catalysis” or “catalysis by design” in heterogeneous catalysis has recently benefited from using “surface “Porganometallic fragments” (SOMF) or Surface Coordination fragments (SCF) to enter any presumed catalytic cycle. These conceptual tools in which one or several fragments of the molecule are linked to metal grafted on the surface (M-H, M-R, M=CR2, M≡CR, M=O, M=NR) became the logical continuation of the abundant work published in the field of Surface Organometallic Chemistry (SOMC). To note, SOMC has produced new catalytic reactions (e.g. Ziegler Natta depolymerisation, alkane metathesis, non-oxidative methane coupling etc…) and had improved the activity or selectivity or life time of known ones. The catalytic mechanisms employs the concepts of molecular chemistry (organic, organometallic, coordination chemistry) to explain how bonds can be broken and reformed. In this context, the reactivity of “surface organometallic fragments” (SOMF) or Surface Coordination fragments (SCF) is pivotal to the outcome of the catalysis.