The Stereochemistry of the Catalytic Hydrogenation Of
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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. -
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: -
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. -
Cycloalkanes, Cycloalkenes, and Cycloalkynes
CYCLOALKANES, CYCLOALKENES, AND CYCLOALKYNES any important hydrocarbons, known as cycloalkanes, contain rings of carbon atoms linked together by single bonds. The simple cycloalkanes of formula (CH,), make up a particularly important homologous series in which the chemical properties change in a much more dramatic way with increasing n than do those of the acyclic hydrocarbons CH,(CH,),,-,H. The cyclo- alkanes with small rings (n = 3-6) are of special interest in exhibiting chemical properties intermediate between those of alkanes and alkenes. In this chapter we will show how this behavior can be explained in terms of angle strain and steric hindrance, concepts that have been introduced previously and will be used with increasing frequency as we proceed further. We also discuss the conformations of cycloalkanes, especially cyclo- hexane, in detail because of their importance to the chemistry of many kinds of naturally occurring organic compounds. Some attention also will be paid to polycyclic compounds, substances with more than one ring, and to cyclo- alkenes and cycloalkynes. 12-1 NOMENCLATURE AND PHYSICAL PROPERTIES OF CYCLOALKANES The IUPAC system for naming cycloalkanes and cycloalkenes was presented in some detail in Sections 3-2 and 3-3, and you may wish to review that ma- terial before proceeding further. Additional procedures are required for naming 446 12 Cycloalkanes, Cycloalkenes, and Cycloalkynes Table 12-1 Physical Properties of Alkanes and Cycloalkanes Density, Compounds Bp, "C Mp, "C diO,g ml-' propane cyclopropane butane cyclobutane pentane cyclopentane hexane cyclohexane heptane cycloheptane octane cyclooctane nonane cyclononane "At -40". bUnder pressure. polycyclic compounds, which have rings with common carbons, and these will be discussed later in this chapter. -
Studies on Photochemical Reactions of Simple Alkenes
Title STUDIES ON PHOTOCHEMICAL REACTIONS OF SIMPLE ALKENES Author(s) 井上, 佳久 Citation Issue Date Text Version ETD URL http://hdl.handle.net/11094/1547 DOI rights Note Osaka University Knowledge Archive : OUKA https://ir.library.osaka-u.ac.jp/ Osaka University STUDIESON PHOTOCHEMICAL REACTIONS CF SIMPLE ALKENES YOSHIHISA INOUE OSAKA UNIVERSITY OSAKA, JAPAN JANUARY, 1977 ii Preface The work of thi's•theSis 'was performed under the guiqance of Professor Hiroshi Sakurai at the ZnstituteofScientific and lndustrial Research, Osaka University. I arn deeply grateÅíul to Professor Hiroshi Sakurai for his appro- priate guidance and continuOus encouragernent throughout this work since 1972. : am aiso grateful to Professor Yoshinobu Odaira-who initiated me into the organic photochemistry in 1971-1972. : arn indebted to Assistant Professor Setsuo Takamuku for his invaluable discussions throughout the work. Many thanks are given to Drs. Yoshiki Okarrtoto, Chyongjin Pac, Susumu Toki, and Yasuo Shige- mitsu for their helpful suggestions through the stimulating discussions with me. T would like to express my gratitude to Mr. Kazuyoshi Mori- tsugut Mr. Masahiro Kadohira, and Ms. Yoko Kunitomi for their collabo- rations in the course of experiment. Finally I wish to thank all the members of Sakurai Laboratory for their warm friendship. t- ..<2IZI Yoshihisa Inoue Suita, Osaka January, Z977 iii List of Papers The contents of this thesis are composed of the following papers. 1) Mercury Photosensitized Rbaction of Cycloheptene. Mechanism of Norcarane Formation Y. Tnoue, M. Kadohira, S. Takasnuku, and H. Sakurait Tetrahedron Lett., 459(1974). 2) Vapor-phase Photolysis of cis-- and trans-4i5-Diraethylcyclohexenes Y. rnoue, S. -
Revised Group Additivity Values for Enthalpies of Formation (At 298 K) of Carbon– Hydrogen and Carbon–Hydrogen–Oxygen Compounds
Revised Group Additivity Values for Enthalpies of Formation (at 298 K) of Carbon– Hydrogen and Carbon–Hydrogen–Oxygen Compounds Cite as: Journal of Physical and Chemical Reference Data 25, 1411 (1996); https://doi.org/10.1063/1.555988 Submitted: 17 January 1996 . Published Online: 15 October 2009 N. Cohen ARTICLES YOU MAY BE INTERESTED IN Additivity Rules for the Estimation of Molecular Properties. Thermodynamic Properties The Journal of Chemical Physics 29, 546 (1958); https://doi.org/10.1063/1.1744539 Critical Evaluation of Thermochemical Properties of C1–C4 Species: Updated Group- Contributions to Estimate Thermochemical Properties Journal of Physical and Chemical Reference Data 44, 013101 (2015); https:// doi.org/10.1063/1.4902535 Estimation of the Thermodynamic Properties of Hydrocarbons at 298.15 K Journal of Physical and Chemical Reference Data 17, 1637 (1988); https:// doi.org/10.1063/1.555814 Journal of Physical and Chemical Reference Data 25, 1411 (1996); https://doi.org/10.1063/1.555988 25, 1411 © 1996 American Institute of Physics for the National Institute of Standards and Technology. Revised Group Additivity Values for Enthalpies of Formation (at 298 K) of Carbon-Hydrogen and Carbon-Hydrogen-Oxygen Compounds N. Cohen Thermochemical Kinetics Research, 6507 SE 31st Avenue, Portland, Oregon 97202-8627 Received January 17, 1996; revised manuscript received September 4, 1996 A program has been undertaken for the evaluation and revision of group additivity values (GAVs) necessary for predicting, by means of Benson's group additivity method, thermochemical properties of organic molecules. This review reports on the portion of that program dealing with GAVs for enthalpies of formation at 298.15 K (hereinafter abbreviated as 298 K) for carbon-hydrogen and carbon-hydrogen-oxygen compounds. -
Open Ronald Aungst Thesis 2.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science STEREOSELECTIVE SYNTHESIS OF (Z)-2-ACYL-2-ENALS VIA RETROCYCLOADDITIONS OF 5-ACYL-4-ALKYL-4H-1,3-DIOXINS: APPLICATIONS IN NATURAL PRODUCT SYNTHESIS A Thesis in Chemistry By Ronald A. Aungst, Jr. © 2007 Ronald A. Aungst, Jr. Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2007 The thesis of Ronald A. Aungst, Jr., was reviewed and approved* by the following: Raymond L. Funk Professor of Chemistry Thesis Advisor Chair of Committee Steven M. Weinreb Russell and Mildred Marker Professor Of Natural Products Chemistry Kenneth S. Feldman Professor of Chemistry J. Martin Bollinger, Jr. Associate Professor of Biochemistry and Molecular Biology Associate Professor of Chemistry Ayusman Sen Professor of Chemistry Head of Chemistry *Signatures are on file in the Graduate School ABSTRACT Reported herein are several approaches for the synthesis of substituted acrolein derivatives via the retrocycloaddition of substituted 4H-1,3-dioxins. Upon thermal or Lewis acid mediated retro hetero Diels-Alder reactions of these substrates, an appropriately substituted acrolein derivative is generated (stereoselectively in most cases) which can be utilized as a substrate for a variety of cycloaddition reactions. These cycloadditions, including Diels-Alder, hetero Diels-Alder, and [4 + 3], have provided access to several ring systems with excellent control over regio- and stereoselectivity. A strategy for the stereocontrolled synthesis of (Z)-2-acylenals has been developed through utilization of a retrocycloaddition reaction of 5-acyl-4-alkyl-4H- 1,3-dioxins. This approach has provided concise synthetic routes to several natural products containing the 5-acyl-2H-3,4-dihydropyran substructure. -
Organic Chemistry by Robert C
(2/94)(6,7,9/95)(8,9/97)(12/99)(1/00) Neuman Chapter 4 Chapter 4 Stereochemistry from Organic Chemistry by Robert C. Neuman, Jr. Professor of Chemistry, emeritus University of California, Riverside [email protected] <http://web.chem.ucsb.edu/~neuman/orgchembyneuman/> Chapter Outline of the Book ************************************************************************************** I. Foundations 1. Organic Molecules and Chemical Bonding 2. Alkanes and Cycloalkanes 3. Haloalkanes, Alcohols, Ethers, and Amines 4. Stereochemistry 5. Organic Spectrometry II. Reactions, Mechanisms, Multiple Bonds 6. Organic Reactions *(Not yet Posted) 7. Reactions of Haloalkanes, Alcohols, and Amines. Nucleophilic Substitution 8. Alkenes and Alkynes 9. Formation of Alkenes and Alkynes. Elimination Reactions 10. Alkenes and Alkynes. Addition Reactions 11. Free Radical Addition and Substitution Reactions III. Conjugation, Electronic Effects, Carbonyl Groups 12. Conjugated and Aromatic Molecules 13. Carbonyl Compounds. Ketones, Aldehydes, and Carboxylic Acids 14. Substituent Effects 15. Carbonyl Compounds. Esters, Amides, and Related Molecules IV. Carbonyl and Pericyclic Reactions and Mechanisms 16. Carbonyl Compounds. Addition and Substitution Reactions 17. Oxidation and Reduction Reactions 18. Reactions of Enolate Ions and Enols 19. Cyclization and Pericyclic Reactions *(Not yet Posted) V. Bioorganic Compounds 20. Carbohydrates 21. Lipids 22. Peptides, Proteins, and α−Amino Acids 23. Nucleic Acids ************************************************************************************** -
Stereochemistry of Bruice's Organic Chemistry Before Embarking on Comprehending This Summary
Enantioselective synthesis It helps if you review the concepts in Chapter 5: Stereochemistry of Bruice's Organic Chemistry before embarking on comprehending this summary Most of the molecules on earth are chiral, such as amino acids and carbohydrates. Enantioselective synthesis is an important means by which enantiopure chiral molecules may be obtained for study and medicine. The study of enantioselective synthesis has evolved from issues of diastereoselectivity, through auxiliary-based methods for the synthesis of enantiomerically pure compounds (diastereoselectivity followed by separation and auxiliary cleavage), to asymmetric catalysis. In the latter technology, enantiomers are the products, and highly selective reactions allow preparation - in a single step - of chiral substances in high enantiomeric excess (ee) for many reaction types. Enantioselective synthesis, also known as asymmetric synthesis, is organic synthesis that introduces one or more new and desired elements of chirality. This methodology is important in the field of pharmaceuticals because the different enantiomers or diastereomers of a molecule often have different biological activity. See examples from Chapter 5 of Bruice's Organic Chemistry. Methodologies of Asymmetric Synthesis Chiral pool synthesis Chiral pool synthesis is the easiest approach: A chiral starting material is manipulated through successive reactions using achiral reagents that retain its chirality to obtain the desired target molecule. This is especially attractive for target molecules having the similar chirality to a relatively inexpensive naturally occurring building-block such as a sugar or amino acid. However, the number of possible reactions the molecule can undergo is restricted, and lengthy synthetic routes may be required. Also, this approach requires a stoichiometric amount of the enantiopure starting material, which may be rather expensive if not occurring in nature, whereas chiral catalysis requires only a catalytic amount of chiral material. -
NMR and Stereochemistry Chem 4010/5326: Organic Spectroscopic Analysis
NMR and Stereochemistry Chem 4010/5326: Organic Spectroscopic Analysis © 2015 Andrew Harned General flow for solving structures C10H20O Molecular weight/formula (MS) Exact Mass: 156.1514 Molecular Weight: 156.2652 Functional groups (IR, NMR) Carbon connectivities (substructures) (NMR) Positions of functional groups within framework (gross structure) (2D NMR, coupling constants) How can this Stereochemical issues be solved??? Relative Stereochemistry (Diastereomers) Can be determined with many of the tools we have already discussed, along with some new ones Bifulco, G.; Dambruoso, P.; Gomex-Paloma, L.; Riccio, R. Chem. Rev. 2007, 107, 3744. NMR Spectroscopy Strategies for determining relative stereochemistry Chemical Shifts – Diastereotopic protons will have different chemical shifts, this will only tell you that diastereomers are present, cannot necessarily tell which is which by inspection only by comparison to known structures – Spatial orientation may place certain protons in shielding/deshielding portions of functional groups Coupling Constants – In acyclic systems, usually cannot tell which is which by inspection – Often must convert to rigid/cyclic structure Both require some knowledge of 3D structure –> Make model(s) NMR Spectroscopy Proximity of Protons Nuclear Overhauser Effect (nOe) – Through space interactions between nuclei, whether or not they are directly coupled – Magnitude decreases as inverse of sixth power of distance – Strongly irradiate one, get larger # in excited state – The others then shift to lower state to compensate -
United States Patent (19) 11 Patent Number: 4,880,764 Imai Et Al
United States Patent (19) 11 Patent Number: 4,880,764 Imai et al. (45) Date of Patent: "k Nov. 14, 1989 54 DEHYDROGENATION CATALYST AND 3,931,054 1/1976 Lester .................................. 502/332 PROCESS 3,936,395 2/1976 Hayes ....... ... 252/466 4,003,852 1/1977 Hayes ....... ... 252/466 (75) Inventors: Tamotsu Imai, Mt. Prospect; Hayim 4,104,317 8/1978 Antos ....... ... 585/434 Abrevaya, Wilmette, both of Ill, Y 4,672,146 6/1987 Abrevaya. ... 585/660 4,716, 143 12/1987 Inai .......... ... 585/660 73 Assignee: UOP, Des Plaines, Ill. 4,786,625 1/1988 Imai et al. ... 585/660 Notice: The portion of the term of this patent 4,827,072 5/1989 Imai .......... ... 585/443 subsequent to Nov. 22, 2005 has been Primary Examiner-Asok Pal disclaimed. 57 ABSTRACT Appl. No.: 21 289,137 A novel catalytic composite and a process of its use is 22 Fied: Dec. 23, 1988 disclosed. The catalyst comprises a platinum group metal component, a first modifier component selected Related U.S. Application Data from Group IA and IIA elements of the Periodic Table, 60 Continuation-in-part of Ser. No. 221,977, Jul. 20, 1988, a second modifier components selected from the group Pat. No. 4,827,072, which is a division of Ser. No. of elements consisting of palladium, iridum, and os 31,882, Dec. 11, 1987, Pat. No. 4,786,625, which is a mium, and a third modifier component selected from continuation-in-part of Ser. No. 18,541, Feb. 25, 1987, the elements of Group IVA of the Peridoic Table of the Pat.