Principles 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. -
– with Novozymes Enzymes for Biocatalysis
Biocatalysis Pregabalin case study Smarter chemical synthesis – with Novozymes enzymes for biocatalysis The new biocatalytic route results in process improvements, reduced organic solvent usage and substantial reduction of waste streams in Pregabalin production. Introduction Biocatalysis is the application of enzymes to replace chemical Using Lipolase®, a commercially available lipase, rac-2- catalysts in synthetic processes. In recent past, the use of carboxyethyl-3-cyano-5-methylhexanoic acid ethyl ester biocatalysis has gained momentum in the chemical and (1) can be resolved to form (S)-2-carboxyethyl-3-cyano-5- pharmaceutical industries. Today, it’s an important tool for methylhexanoic acid (2). Compared to the first-generation medicinal, process and polymer chemists to develop efficient process, this new route substantially improves process and highly attractive organic synthetic processes on an efficiency by setting the stereocenter early in the synthesis and industrial scale. enabling the facile racemization and reuse of (R)-1. The biocatalytic process for Pregabalin has been developed It outperforms the first-generation manufacturing process also by Pfizer to boost efficiency in Pregabalin production using by delivering higher yields of Pregabalin and by resulting in Novozymes Lipolase®. substantial reductions of waste streams, corresponding to a 5-fold decrease in the E-Factor from 86 to 17. Development of the biocatalytic process for Pregabalin involves four stages: • Screening to identify a suitable enzyme • Performing optimization of the enzymatic reaction to optimize throughput and reduce enzyme loading • Exploring a chemical pathway to preserve the enantiopurity of the material already obtained and lead to Pregabalin, and • Developing a procedure for the racemization of (R)-1 Process improvements thanks to the biocatalytic route Pregabalin chemical synthesis H Knovenagel CN condensation cyanation KOH 0 Et02C CO2Et Et02C CO2Et Et02C CO2Et CNDE (1) CN NH2 1. -
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: -
A Reminder… Chirality: a Type of Stereoisomerism
A Reminder… Same molecular formula, isomers but not identical. constitutional isomers stereoisomers Different in the way their Same connectivity, but different atoms are connected. spatial arrangement. and trans-2-butene cis-2-butene are stereoisomers. Chirality: A Type of Stereoisomerism Any object that cannot be superimposed on its mirror image is chiral. Any object that can be superimposed on its mirror image is achiral. Chirality: A Type of Stereoisomerism Molecules can also be chiral or achiral. How do we know which? Example #1: Is this molecule chiral? 1. If a molecule can be superimposed on its mirror image, it is achiral. achiral. Mirror Plane of Symmetry = Achiral Example #1: Is this molecule chiral? 2. If you can find a mirror plane of symmetry in the molecule, in any achiral. conformation, it is achiral. Can subject unstable conformations to this test. ≡ achiral. Finding Chirality in Molecules Example #2: Is this molecule chiral? 1. If a molecule cannot be superimposed on its mirror image, it is chiral. chiral. The mirror image of a chiral molecule is called its enantiomer. Finding Chirality in Molecules Example #2: Is this molecule chiral? 2. If you cannot find a mirror plane of symmetry in the molecule, in any conformation, it is chiral. chiral. (Or maybe you haven’t looked hard enough.) Pharmacology of Enantiomers (+)-esomeprazole (-)-esomeprazole proton pump inhibitor inactive Prilosec: Mixture of both enantiomers. Patent to AstraZeneca expired 2002. Nexium: (+) enantiomer only. Process patent coverage to 2007. More examples at http://z.umn.edu/2301drugs. (+)-ibuprofen (-)-ibuprofen (+)-carvone (-)-carvone analgesic inactive (but is converted to spearmint oil caraway oil + enantiomer by an enzyme) Each enantiomer is recognized Advil (Wyeth) is a mixture of both enantiomers. -
Influence of Chirality on the Electromagnetic Wave Electrical and Computer Engineering
Influence of Chirality on the Electromagnetic Wave Propagation: Unbounded Media And Chirowaveguides Priyá Dilipa Gaunço Dessai Dissertation submitted to obtain the Master Degree in Electrical and Computer Engineering Jury President: Professor José Manuel Bioucas Dias Supervisor: Professor Carlos Manuel dos Reis Paiva Co- Supervisor: Professor António Luís da Silva Topa Member Professor Sérgio de Almeida Matos December 2011 Abstract When a chiral medium interacts with the polarization state of an electromag- netic plane wave and couples selectively with either the left or right circularly polarized component, we call this property the optical activity. Since the beginning of the 19th century, the study of complex materials has intensied, and the chiral and bi-isotropic (BI) media have generated one of the most interesting and challenging subjects in the electromagnetic research groups in terms of theoretical problems and potential applications. This dissertation addresses the theoretical interaction between waves and the chiral media. From the study of chiral structures it is possible to observe the eect of the polarization rotation, the propagation modes and the cuto frequencies. The reection and transmission coecients between a simple isotropic media (SIM) and chiral media are also analyzed, as well as the relation between the Brewster angle and the chiral parameter. The BI planar structures are also analyzed for a closed guide, the parallel-plate chirowaveguide, and for a semi-closed guide, the grounded chiroslab. From these structures -
Enantioselective Synthesis of the (1S,5R)-Enantiomer of Litseaverticillols a and B
Biosci. Biotechnol. Biochem., 70 (10), 2564–2566, 2006 Note Enantioselective Synthesis of the (1S,5R)-Enantiomer of Litseaverticillols A and B y Akira MORITA, Hiromasa KIYOTA, and Shigefumi KUWAHARA Laboratory of Applied Bioorganic Chemistry, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan Received May 8, 2006; Accepted May 31, 2006; Online Publication, October 7, 2006 [doi:10.1271/bbb.60253] An enantioselective synthesis of the (1S,5R)-enan- which have recently culminated in the first enantiose- tiomer of litseaverticillols A and B was accomplished in lective total synthesis of (1R,5S)-(À)-1 and (1R,5S)-(À)- line with our previously reported synthetic pathway for 2.4) In this note, we describe the synthesis of their their (1R,5S)-enantiomer. The use of ‘‘EtSCeCl2’’ pre- enantiomers directed toward an evaluation of the differ- pared from EtSLi and CeCl3, instead of previously ence in biological activity between the enantiomers of employed EtSLi itself, for the formation of thiol ester litseaverticillols A and B. intermediates prevented any undesirable epimerization Our synthesis of (1S,5R)-1 and (1S,5R)-2 basically occurring in the process. followed our previous synthesis of their corresponding enantiomers, (1R,5S)-1 and (1R,5S)-2, respectively,4) Key words: litseaverticillol; enantioselective synthesis; except that (R)-4-benzyloxazolidin-2-one was employed sesquiterpenoid; anti-HIV as the source of chirality, instead of its (S)-form used in the previous synthesis. Homogeranic -
Locally Enhanced and Tunable Optical Chirality in Helical Metamaterials
hv photonics Article Locally Enhanced and Tunable Optical Chirality in Helical Metamaterials Philipp Gutsche 1,*, Raquel Mäusle 1 and Sven Burger 1,2 1 Zuse Institute Berlin, Takustr. 7, 14195 Berlin, Germany; [email protected] (R.M.); [email protected] (S.B.) 2 JCMwave GmbH, Bolivarallee 22, 14050 Berlin, Germany * Correspondence: [email protected]; Tel.: +49-30-841-85-203 Received: 31 October 2016; Accepted: 18 November 2016; Published: 23 November 2016 Abstract: We report on a numerical study of optical chirality. Intertwined gold helices illuminated with plane waves concentrate right and left circularly polarized electromagnetic field energy to sub-wavelength regions. These spots of enhanced chirality can be smoothly shifted in position and magnitude by varying illumination parameters, allowing for the control of light-matter interactions on a nanometer scale. Keywords: metamaterials; optical chirality; computational nano-optics 1. Introduction Helical metamaterials strongly impact the optical response of incident circularly (CPL) and linearly polarized light. They serve as efficient circular polarizers [1] and are candidates for chiral near-field sources [2]. Both, advancement of fabrication techniques [3–5] and design which employs fundamental physical properties [6] have significantly increased the performance of these complex structures. Most experimental, numerical and theoretical studies focus on the far-field response of helical metamaterials. Nevertheless, near-field interaction of light and chiral matter is expected to be enhanced in chiral near-fields. Recently, the quantity of optical chirality has been introduced quantifying this phenomenon [7]. In the weak-coupling regime, the interplay of electromagnetic fields and chiral molecules, which are not superimposable with their mirror image, is directly proportional to this near-field measure [8]. -
Lecture 3: Stereochemistry and Drugs Key Objectives: 1
Lecture 3: Stereochemistry and drugs Key objectives: 1. Be able to explain the role of stereochemistry in drug action or metabolism 2. Be able to identify a chiral center (or centers) in a drug 3. Be able to explain the difference between enantiomers and diastereomers Value of chirality and stereochemistry: Chirality as expressed through stereoisomers increases the specificity of molecule recognition and signaling. Like a key in a lock, or a hand in a glove. Some useful definitions: Chirality (and chiral centers): An object (such as a molecule) that is asymmetric and therefore not superimposable on its own image. Chiral centers are the most common features within molecules that give rise to chirality. Stereoisomer: A molecule that possesses at least one chiral center (or center of chirality). Enantiomers: A type of stereoisomer that exists in mirror image forms. See Figure 1. Diastereomers: A type of stereoisomer that possesses more than one chiral center. Stereospecific: A term used to describe a stereochemical property that one isomer possesses but the other does not. For example, the stereospecific metabolism of the S-enantiomer of a compound by an enzyme but the R-enantiomer is not metabolized by that enzyme. Stereoselective: A term used to describe a stereochemical property that is shared by both stereoisomers, but the property is greater in one isomer than the other. For example, the stereoselective binding of the R-enantiomer for a receptor indicates that the S-enantiomer also binds but not as avidly as the R-enantiomer. Enantiomers Figure 1: For enantiomers, many times we use the example of our left and right hands to demonstrate their asymmetry. -
Diastereomers Diastereomers
Diastereomers Diastereomers: Stereoisomers that are not mirror images. enantiomer (R) (S) (S) (R) diastereomers diastereomer diastereomer enantiomer (R) (S) (R) (S) Diastereomers Diastereomers: Stereoisomers that are not mirror images. (R) enantiomer (S) (S) (R) diastereomer To draw the enantiomer of a molecule with chiral centers, invert stereochemistry at all chiral centers. (R) To draw a diastereomer of a molecule (R) with chiral centers, invert stereochemistry at only some chiral centers. Meso Compounds Meso: A molecule that contains chiral centers, but is achiral. 3 Are these molecules chiral? (R) (S) (These are diff eren t f rom th e 3 molecules I just showed; they have 2 -Cl’s, rather than 1 -Cl & 1 -OH. enantiomer (R) (S) (R) (S) These molecules are chiral mirror images of one another. (R,R) and (S,S) are not the same. Meso Compounds Meso: A molecule that contains chiral centers, but is achiral. 3 enantiomer ? (R) (S) (S) (R) no! 3 same molecule! enantiomer (R) (S) (R) (S) Meso Compounds Meso: A molecule that contains chiral centers, but is achiral. 3 enantiomer ? (R) (S) (S) (R) no! 3 same molecule! If a molecule • contains the same number of (R) and (S) stereocenters, and • those stereocenters have identical groups attached, then the molecule is achiral and meso. Meso Compounds Meso: A molecule that contains chiral centers, but is achiral. 3 same molecule (R) (S) (S) (R) 3 meso diastereomers meso diastereomer diastereomer enantiomer (R) (S) (R) (S) chiral chiral Properties of Enantiomers Most physical properties of enantiomers are identical. diethyl-(R,R)-tartrate diethyl-(S,S)-tartrate boiling point 280 °C 280 °C melting point 19 °C 19 °C density 1.204 g/mL 1.204 g/mL refractive index 1.447 1.447 i.e., chirality does not affect most physical properties. -
Enantiomers & Diastereomers
Chapter 5 Stereochemistry Chiral Molecules Ch. 5 - 1 1. Chirality & Stereochemistry An object is achiral (not chiral) if the object and its mirror image are identical Ch. 5 - 2 A chiral object is one that cannot be superposed on its mirror image Ch. 5 - 3 1A. The Biological Significance of Chirality Chiral molecules are molecules that cannot be superimposable with their mirror images O O ● One enantiomer NH causes birth defects, N O the other cures morning sickness O Thalidomide Ch. 5 - 4 HO NH HO OMe Tretoquinol OMe OMe ● One enantiomer is a bronchodilator, the other inhibits platelet aggregation Ch. 5 - 5 66% of all drugs in development are chiral, 51% are being studied as a single enantiomer Of the $475 billion in world-wide sales of formulated pharmaceutical products in 2008, $205 billion was attributable to single enantiomer drugs Ch. 5 - 6 2. Isomerisom: Constitutional Isomers & Stereoisomers 2A. Constitutional Isomers Isomers: different compounds that have the same molecular formula ● Constitutional isomers: isomers that have the same molecular formula but different connectivity – their atoms are connected in a different order Ch. 5 - 7 Examples Molecular Constitutional Formula Isomers C4H10 and Butane 2-Methylpropane Cl Cl C3H7Cl and 1-Chloropropane 2-Chloropropane Ch. 5 - 8 Examples Molecular Constitutional Formula Isomers CH O CH C H O OH and 3 3 2 6 Ethanol Methoxymethane O OCH and 3 C H O OH 4 8 2 O Butanoic acid Methyl propanoate Ch. 5 - 9 2B. Stereoisomers Stereoisomers are NOT constitutional isomers Stereoisomers have their atoms connected in the same sequence but they differ in the arrangement of their atoms in space. -
Chirality in Chemical Molecules
Chirality in Chemical Molecules. Molecules which are active in human physiology largely function as keys in locks. The active molecule is then called a ligand and the lock a receptor. The structures of both are highly specific to the degree that if one atom is positioned in a different position than that required by the receptor to be activated, then no stimulation of the receptor or only partial activation can take place. Again in a similar fashion if one tries to open the front door with a key that looks almost the same than the proper key for that lock, one will usually fail to get inside. A simple aspect like a lengthwise groove on the key which is on the left side instead of the right side, can mean that you can not open the lock if your key is the “chirally incorrect” one. The second aspect to understand is which molecules display chirality and which do not. The word chiral comes from the Greek which means “hand-like”. Our hands are mirror images of each other and as such are not identical. If they were, then we would not need a right hand and left hand glove. We can prove that they are not identical by trying to lay one hand on top of the other palms up. When we attempt to do this, we observe that the thumbs and fingers do not lie on top of one another. We say that they are non-super imposable upon one another. Since they are not the same and yet are mirror images of each other, they are said to exhibit chirality.