DOCSLIB.ORG

Download Article (PDF)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Download Article (PDF) DE GRUYTER Chemistry Teacher International. 2020; 20190006 Felix Lederle1,2 / Eike G. Hübner1,3 Organic chemistry lecture course and exercises based on true scale models 1 Clausthal University of Technology, Institute of Organic Chemistry, Leibnizstr. 6, DE-38678 Clausthal-Zellerfeld, Germany, E- mail: [email protected]. https://orcid.org/0000-0002-7369-7449, https://orcid.org/0000-0003-2104-9615. 2 Clausthal University of Technology, Institute of Technical Chemistry, Arnold-Sommerfeld-Str. 4, DE-38678 Clausthal- Zellerfeld, Germany. https://orcid.org/0000-0002-7369-7449. 3 Fraunhofer Heinrich-Hertz-Institute, Department Fiber Optical Sensor Systems, Am Stollen 19 H, DE-38640 Goslar, Germany, E-mail: [email protected]. https://orcid.org/0000-0003-2104-9615. Abstract: 3D models of chemical structures are an important tool for chemistry lectures and exercises. Usually, simplified models based on standard bond length and angles are used. These models allow for a visualized discussion of (stereo)chemical aspects, but they do not represent the true spatial conditions. 3D-printing technologies facilitate the production of scale models. Several protocols describe the process from X-ray structures, calculated geometries or virtual molecules to printable files. In contrast, only a few examples describe the integration of scaled models in lecture courses. True bond angles and scaled bond lengths allow for a detailed discussion of the geometry and parameters derived therefrom, for example double bond character, aromaticity and many more. Here, we report a complete organic chemistry/stereochemistry lecture course and exercise based on a set of 37 scale models made from poly(lactic acid) as sustainable material. All models have been derived from X-ray structures and quantum chemical calculations. Consequently, the models reflect the true structure as close as possible. A fixed scaling factor of 1 : 1.8·108 has been applied to all models. Hands-on measuring of bond angles and bond length leads to an interactive course. The course has been evaluated with a very positive feedback. Keywords: 3D-printing, hands-on learning, organic chemistry, scale models, stereochemistry DOI: 10.1515/cti-2019-0006 Introduction Visualization of 3D structures and spatial orientation has always been a major aspect of chemistry lectures (Oliver-Hoyo & Babilonia-Rosa, 2017). The typical representation in textbooks and on panels is a 2D projection of the 3D structure. For the understanding of complex geometries in the 3D space, molecular modelling kits with standardized sets of atoms and bonds are indispensable. Modern technologies allow for significantly im- proved representations of complex molecular structures. Recent examples are freely scalable and rotatable 3D models in software programs on tablets and smartphones (Chiu et al., 2018; Ping, Lok, Yeat, Cherynn, & Tan, 2018). Nevertheless, the combined haptic and visual feedback of a real 3D model is extremely helpful to discuss phenomena in the 3D world. Consequently, the technology of 3D-printing has been applied to generate true 3D models as scaled counterparts to the original molecular structure. These models can be handled as objects from molecular modelling kits, but have one significant advantage: They represent exactly scaled bond lengths from River Valley Technologies Ltd and bond angles instead of standardized atom distances. Furthermore, unlimited amounts of 3D-models can be reproduced from the template file. First protocols for the printing of crystal structures have been published in 2013 (Scalfani, 2013), rapidly followed by various publications explaining the concept from molecular co- ProofCheck ordinates to 3D-printed structures in detail (Chen, Lee, Flood, & Miljanić, 2014; Kitson et al., 2014; Scalfani & Vaid, 2014). Subsequent publications concentrate on optimization and simplification of the process (Jones & Spencer, 2018; Rossi, Benaglia, Brenna, Porta, & Orlandi, 2015; van Wieren, Tailor, Scalfani, & Merbouh, 2017), optimization of the 3D-print for unit cells (Rodenbough, Vanti, & Chan, 2015), biomolecules (Jones & Spencer, 2018; Meyer, 2015; Rossi et al., 2015; van Wieren et al., 2017), larger structures by connection of independently printed fragments (Paukstelis, 2018), reversibly interacting structures based on 3D-printed parts and velcro (Babilonia-Rosa, Kuo, & Oliver-Hoyo, 2018; Cooper & Oliver-Hoyo, 2016), and the 3D-print of components for a large structure modelling kit (Penny et al., 2017). Further work presents the application of 3D-printed ob- jects for the visualization of the structure of block-copolymers (Scalfani, Turner, Rupar, Jenkins, and Bara 2015), Eike G. Hübner is the corresponding author. © 2020 IUPAC & De Gruyter. Automatically generated rough PDF by This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. 1 Lederle and Hübner DE GRUYTER polyhedra for teaching of point groups (Casas & Estop, 2015), the Bohr atom model (Smiar & Mendez, 2016), VSEPR models generated with a 3D-printing pen (Dean, Ewan, & McIndoe, 2016), molecular orbitals (Carroll & Blauch, 2017; de Cataldo, Griffith, & Fogarty, 2018; Griffith, de Cataldo, & Fogarty, 2016; Robertson &Jor- gensen, 2015) (with inserted magnets to realize reversible interactions (Carroll & Blauch, 2018)), and potential energy surfaces (Blauch & Carroll, 2014; Kaliakin, Zaari, & Varganov, 2015; Lolur & Dawes, 2014; Teplukhin & Babikov, 2015) as well as reaction progress data (Higman, Situ, Blacklin, & Hein, 2017) based on spectroscopic results and periodic tables which represent periodic trends by tactile information (LeSuer, 2019). 3D-printed structures have been established in larger courses with a focus on the transfer of 2D to 3D structures allowing each student to print one unique model (Fourches & Feducia, 2019). In general, the feedback of students on 3D-printed structures is very positive (Fourches & Feducia, 2019; Frohock, Winterrowd, & Gallardo-Williams, 2018). As part of our work on 3D-printing in chemical laboratories (Lederle, Kaldun, Namyslo, & Hübner, 2016a; Lederle, Meyer, Brunotte, Kaldun, & Hübner, 2016b; Lederle, Meyer, Kaldun, Namyslo, & Hübner, 2017), we designed a set of 37 scaled structures for a lecture course and exercise (1 unit) in organic chemistry/stereo- chemistry for second/third year undergraduates. The course is intended for small groups of roughly to 20–30 students. The procedure for the generation of the scale models is based on the basic protocols given in literature (see Figure 1). In contrast to the protocols for the production of 3D models, which have been well established, the focus of our work was to fully integrate true scale models into the teaching concept. All structures discussed here have been 3D-printed on an affordable (€1000) fused deposition modeling printer and are attached asSTL files ready for reproduction. Poly(lactic acid) (PLA) has been chosen as sustainable printing material. Figure 1: General procedure for the 3D-printing process of all scaled molecular models discussed here. Experimental section Note: Various protocols are given in literature for the 3D-printing process of molecular models (Chen et al., 2014; Kitson et al., 2014; Scalfani, 2013; Scalfani & Vaid, 2014). The information given below is not a detailed description, but a summary of settings to allow for reproduction and extension towards further structures with the same appearance. All model numbers refer to the corresponding structure/STL file listed in the Supple- mentary material. PDB files containing the atom coordinates have been taken from the Cambridge Structural Database (Groom, Bruno, Lightfoot, & Ward, 2016) (CSD) or from quantum chemical calculations (see below). File format incon- sistencies have been corrected with Chem3D 14.0.0.17 (PerkinElmer Informatics). Ball and Stick models have been converted from the PDB files to 3D-printable STL files with Python Molecule Viewer (PMV) (Sanner, 1999) 1.5.6 with a stick radius of 0.12, a ball radius of 0 and a ball scale factor of 0.18. STL files have been scaled with a 8 from River Valley Technologies Ltd final factor of 1 : 1.8·10 with netfabb 5.2.1 (netfabb GmbH). Self-intersections have been removed with netfabb 5.2.1. 3D-Printing has been performed with BEEsoft 3.9.0 on a BEEthefirst 3D printer with black PLA from BeeVeryCreative, BEEVC – Electronic Systems Lda. All prints have been processed with a layer height of 50 μm and 40 % infill. In deviation from standard settings, a supportlinedistance of 1500 and supportXYdistance of 500 ProofCheck has been used for the implemented CURA slicer engine to realize prints of small spheres (hydrogen atoms). Supporting material has been removed by hand with knife and cutter. Atom coloring has been achieved with Revell email color (Revell GmbH). All density-functional theory (DFT)-calculations to obtain geometry optimized structures were carried out by using the Jaguar 9.1.013 software (Schrodinger, Inc) (Bochevarov et al., 2013) running on Linux 2.6.18–238.el5 SMP (x86_64) on five AMD Phenom II X6 1090T processor workstations (Beowulf-cluster) parallelized with OpenMPI. MM2 optimized structures were used as starting geometries. Complete geometry optimizations were carried out on the implemented LACVP* (Hay-Wadt effective core potential (ECP) basis on heavy atoms, N31G6* for all other atoms) basis set and with the PBE0 density functional. PDB files have been exported with Maestro 10.5.013, the graphical interface of Jaguar. Automatically
Load more

Recommended publications
  • Inorganic Chemistry for Dummies® Published by John Wiley & Sons, Inc
    Inorganic Chemistry Inorganic Chemistry by Michael L. Matson and Alvin W. Orbaek Inorganic Chemistry For Dummies® Published by John Wiley & Sons, Inc. 111 River St. Hoboken, NJ 07030-5774 www.wiley.com Copyright © 2013 by John Wiley & Sons, Inc., Hoboken, New Jersey Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permis- sion of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley. com/go/permissions. Trademarks: Wiley, the Wiley logo, For Dummies, the Dummies Man logo, A Reference for the Rest of Us!, The Dummies Way, Dummies Daily, The Fun and Easy Way, Dummies.com, Making Everything Easier, and related trade dress are trademarks or registered trademarks of John Wiley & Sons, Inc. and/or its affiliates in the United States and other countries, and may not be used without written permission. All other trade- marks are the property of their respective owners. John Wiley & Sons, Inc., is not associated with any product or vendor mentioned in this book.
    [Show full text]
  • 76 Chapt-24-Organic2
    The Chemistry of Alkanes Physical Properties of Alkanes as molecular size increases so does the boiling point of the alkane increased size increased dispersion forces Alkanes Boiling Point ˚C H Methane CH 4 H C H -161.6 H H H Ethane C2H6 H C C H -88.6 H H Propane C3H8 CH3 (CH2)1 CH3 -42.1 Butane C4H10 CH3 (CH2)2 CH3 -0.5 Pentane C5H12 CH3 (CH2)3 CH3 36.1 hexane C6H14 CH3 (CH2)4 CH3 68.7 Chemical Reactions and Alkanes because the C-C and C-H bonds are relatively strong , the alkanes are fairly unreactive their inertness makes them valuable as lubricating materials and as backbone material in the construction of other hydrocarbons Combustion of Alkanes At high temperatures alkanes combust ΔH˚ CH4 + O2 CO2 + 2H2O -890.4 kJ C4H10 + 13/2O2 4CO2 + 5H2O -3119 kJ these reactions are all highly exothermic Halogenation of Alkanes at temperatures above 100 ˚C CH4 + Cl2 CH3Cl + HCl chloromethane CH3Cl + Cl2 CH2Cl2 + HCl dichloromethane CH2Cl2 + Cl2 CHCl3 + HCl trichloromethane chloroform CHCl3 + Cl2 CCl4 + HCl tetrachloromethane Carbon tetrachloride Mechanism for Halogenation of Methane CH4 + Cl2 CH3Cl + HCl hν Cl2 • Cl + • Cl hν: energy required to break the Cl-Cl bond • Cl H H C H H • Cl is very reactive and able to attack the C-H bond Mechanism for Halogenation of Methane CH4 + Cl2 CH3Cl + HCl CH4 + • Cl • CH3 + HCl H Cl H • C H H Mechanism for Halogenation of Methane CH4 + Cl2 CH3Cl + HCl • CH3 + Cl2 CH3 Cl + • Cl Cl Cl H • Cl • C H H H Cl C H H Mechanism for Halogenation of Methane Cl2 • Cl + • Cl chlorine free radical CH4 + • Cl • CH3 + HCl
    [Show full text]
  • Standard Thermodynamic Properties of Chemical
    STANDARD THERMODYNAMIC PROPERTIES OF CHEMICAL SUBSTANCES ∆ ° –1 ∆ ° –1 ° –1 –1 –1 –1 Molecular fH /kJ mol fG /kJ mol S /J mol K Cp/J mol K formula Name Crys. Liq. Gas Crys. Liq. Gas Crys. Liq. Gas Crys. Liq. Gas Ac Actinium 0.0 406.0 366.0 56.5 188.1 27.2 20.8 Ag Silver 0.0 284.9 246.0 42.6 173.0 25.4 20.8 AgBr Silver(I) bromide -100.4 -96.9 107.1 52.4 AgBrO3 Silver(I) bromate -10.5 71.3 151.9 AgCl Silver(I) chloride -127.0 -109.8 96.3 50.8 AgClO3 Silver(I) chlorate -30.3 64.5 142.0 AgClO4 Silver(I) perchlorate -31.1 AgF Silver(I) fluoride -204.6 AgF2 Silver(II) fluoride -360.0 AgI Silver(I) iodide -61.8 -66.2 115.5 56.8 AgIO3 Silver(I) iodate -171.1 -93.7 149.4 102.9 AgNO3 Silver(I) nitrate -124.4 -33.4 140.9 93.1 Ag2 Disilver 410.0 358.8 257.1 37.0 Ag2CrO4 Silver(I) chromate -731.7 -641.8 217.6 142.3 Ag2O Silver(I) oxide -31.1 -11.2 121.3 65.9 Ag2O2 Silver(II) oxide -24.3 27.6 117.0 88.0 Ag2O3 Silver(III) oxide 33.9 121.4 100.0 Ag2O4S Silver(I) sulfate -715.9 -618.4 200.4 131.4 Ag2S Silver(I) sulfide (argentite) -32.6 -40.7 144.0 76.5 Al Aluminum 0.0 330.0 289.4 28.3 164.6 24.4 21.4 AlB3H12 Aluminum borohydride -16.3 13.0 145.0 147.0 289.1 379.2 194.6 AlBr Aluminum monobromide -4.0 -42.0 239.5 35.6 AlBr3 Aluminum tribromide -527.2 -425.1 180.2 100.6 AlCl Aluminum monochloride -47.7 -74.1 228.1 35.0 AlCl2 Aluminum dichloride -331.0 AlCl3 Aluminum trichloride -704.2 -583.2 -628.8 109.3 91.1 AlF Aluminum monofluoride -258.2 -283.7 215.0 31.9 AlF3 Aluminum trifluoride -1510.4 -1204.6 -1431.1 -1188.2 66.5 277.1 75.1 62.6 AlF4Na Sodium tetrafluoroaluminate
    [Show full text]
  • “Solid,” and Stereochemistry Refers to Chemistry in Three Dimensions
    CHAPTER 7 STEREOCHEMISTRY he Greek word stereos means “solid,” and stereochemistry refers to chemistry in three dimensions. The foundations of organic stereochemistry were laid by Jacobus Tvan’t Hoff* and Joseph Achille Le Bel in 1874. Independently of each other, van’t Hoff and Le Bel proposed that the four bonds to carbon were directed toward the cor- ners of a tetrahedron. One consequence of a tetrahedral arrangement of bonds to carbon is that two compounds may be different because the arrangement of their atoms in space is different. Isomers that have the same constitution but differ in the spatial arrangement of their atoms are called stereoisomers. We have already had considerable experience with certain types of stereoisomers—those involving cis and trans substitution patterns in alkenes and in cycloalkanes. Our major objectives in this chapter are to develop a feeling for molecules as three- dimensional objects and to become familiar with stereochemical principles, terms, and notation. A full understanding of organic and biological chemistry requires an awareness of the spatial requirements for interactions between molecules; this chapter provides the basis for that understanding. 7.1 MOLECULAR CHIRALITY: ENANTIOMERS Everything has a mirror image, but not all things are superposable on their mirror images. Mirror-image superposability characterizes many objects we use every day. Cups and saucers, forks and spoons, chairs and beds are all identical with their mirror images. Many other objects though—and this is the more interesting case—are not. Your left hand and your right hand, for example, are mirror images of each other but can’t be made to coin- cide point for point, palm to palm, knuckle to knuckle, in three dimensions.
    [Show full text]
  • 1 Three-Dimensional Structure of a Molecule
    Ch 1 Three dimentional structure of a molecule 1 Three-dimensional structure of a molecule Purpose In this chapter, you will learn that it is sometimes not sufficient to describe the structure of a molecule in a planar, two-dimensional way, which is usually used in textbooks, because the atoms that make up a molecule are arranged three-dimensionally in space. The three-dimensional structures of organic compounds significantly depend on the shapes and characteristics of the hybridized atomic orbitals of the carbon atom. Here you learn about sp3, sp2 and sp hybridized orbitals, which are involved deeply in the structure of molecules. Models are useful tools to conceptualize the shapes of molecules. The commercially available molecular models will be classified based on their features. Sometimes a compound may have two or more names. Similarly, several nomenclatures are used in discussing the stereochemistry of organic compounds. The nomenclature based on the sequence rule will be introduced because this method corresponds to the systematic nomenclature that is most widely used. New terms and concepts molecular formula rational formula structural formula dihedral angle (Compare with tortion angle in Ch. 2) carbon atomic orbital sp3 hybridization tetrahedral structure configurational isomer enantiomer (enantio isomer) Configuration (steric configuration) sp2 hybridization sp hybridization molecular model space filling model skeletal model ball and stick model free rotation restricted rotation sequence rule replica atom Goals of this chapter After you master this chapter successfully, you will be able to do the following: 1to understand that organic compounds are three-dimensional, and that you cannot properly draw these on a two-dimensional sheet of paper.
    [Show full text]
  • Status of Numerical Modeling of Halocarbon Impacts on Stratospheric Ozone
    THE STATUS OF NUMERICAL MODELING OF HALOCARBON IMPACTS ON STRATOSPHERIC OZONE Donald J. Wuebbles Department of Atmospheric Sciences University of Illinois, Urbana, IL 61801 Tel: 217-244-1568; Fax: 217-244-4393 [email protected] INTRODUCTION Numerical models of the chemistry and physics of the global atmosphere have played a key role in the scientific understanding of past, current and potential future effects of human-related emissions of halocarbons, including Halons, other brominated compounds and various replacement compounds on stratospheric ozone and climate change. As a result, these models have led directly to the Montreal Protocol and other national and international policy decisions regarding halocarbon controls due to their effects on stratospheric ozone. The purpose of this paper is to provide a perspective on atmospheric models, the role they have played in studies of the effects of Halons and other halocarbons on ozone, and to discuss what role models will likely play in future studies of stratospheric ozone THE COMPLEXITY OF STRATOSPHERIC OZONE It is important to recognize that the stratospheric ozone layer is a naturally occurring phenomenon that has great benefits to life on Earth. In fact, the formation of the ozone layer is generally believed to have played an important role in the development of life here on Earth. The accumulation of oxygen molecules in the atmosphere allowed for the production of ozone. Gradually the increasing levels of ozone led to the formation of the stratosphere, a region of the upper atmosphere where temperature increases with altitude largely as a result of the absorption of solar radiation by ozone.
    [Show full text]
  • Burske Norbert W 195708 Phd
    "In presenting the dissertation as a partial fulfillment of the requirements for an advanced degree from the Georgia Institute of Technology, I agree that the Library of the Institution shall make it available for inspection and circulation in accordance with its regulations governing materials of this type. I agree that permission to copy from, or to publish from, this dissertation may be granted by the professor under whose direction it was written, or, in his absence, by the dean of the Graduate Division when such copying or publication is solely for scholarly purposes and does not involve potential financial gain. It is understood that any copying from, or publication of, this dissertation which involves potential financial gain will not be allowed without written permission. n It THE KINETICS OF THE BASE-CATALYZED DEUTERIUM EXCHANGE OF SOME HALOFORMS IN AQUEOUS SOLUTION A THESIS Presented to the Faculty of the Graduate Division Georgia Institute of Technology In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Chemistry By Norbert William Burske June 1957 1< THE KINETICS OF THE BASE-CATALYZED DEUTERIUM EXCHANGE OF SOME HALOFORMS IN AQUEOUS SOLUTION Approved, J I ki Jack Hine I ,r Lod D. Frashier Erlft.Edg Grovenstein, Jr. Date Approved by Chairman, ii ACKNOWLEDGEMENT The author wishes to gratefully acknowledge his in- debtedness to Dr. J. Hine for invaluable guidance and without his aid this project would never have been completed. Also, the author is indebted to the Atomic Energy Commission and the Office of Ordnance Research, U. S. Army for sponsoring assistantships.
    [Show full text]
  • Process for the Production of 4-Chloroacetyl Chloride, 4
    (19) & (11) EP 2 518 043 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 31.10.2012 Bulletin 2012/44 C07C 51/58 (2006.01) C07C 67/14 (2006.01) C07C 231/02 (2006.01) C07C 59/21 (2006.01) (2006.01) (21) Application number: 11003510.2 C07C 69/63 (22) Date of filing: 29.04.2011 (84) Designated Contracting States: (71) Applicant: Lonza Ltd AL AT BE BG CH CY CZ DE DK EE ES FI FR GB 4052 Basel (CH) GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR (72) Inventor: The designation of the inventor has not Designated Extension States: yet been filed BA ME (54) Process for the production of 4- chloroacetyl chloride, 4-chloroacetic acid esters, amides and imides (57) The invention relates to process for the contin- acetoacetyl chloride. uous production of 4-chloroacetoacetyl chloride, com- prising the steps of The invention also relates to a process for the production (a) feeding diketene and chlorine into a thin film reactor of 4-chloroacetic acid ester, 4-chloroacetic acid amide or and 4-chloroacetic acid imide from 4- chloroacetoacetyl chlo- (b) reacting the diketene and chlorine to obtain 4- chloro- ride obtained according to the inventive process. EP 2 518 043 A1 Printed by Jouve, 75001 PARIS (FR) 1 EP 2 518 043 A1 2 Description reactors and equipment and more energy for cooling. When increasing the volume of the reactor, the yield [0001] The invention relates to processes for the pro- dropped "drastically" andthe selectivity was relatively low duction of 4-chloroacetoacetyl chloride, 4-chloroacetic (US 4,473,508, example 7).
    [Show full text]
  • This Table Gives the Standard State Chemical Thermodynamic Properties of About 2500 Individual Substances in the Crystalline, Liquid, and Gaseous States
    STANDARD THERMODYNAMIC PROPERTIES OF CHEMICAL SUBSTANCES This table gives the standard state chemical thermodynamic properties of about 2500 individual substances in the crystalline, liquid, and gaseous states. Substances are listed by molecular formula in a modified Hill order; all substances not containing carbon appear first, followed by those that contain carbon. The properties tabulated are: DfH° Standard molar enthalpy (heat) of formation at 298.15 K in kJ/mol DfG° Standard molar Gibbs energy of formation at 298.15 K in kJ/mol S° Standard molar entropy at 298.15 K in J/mol K Cp Molar heat capacity at constant pressure at 298.15 K in J/mol K The standard state pressure is 100 kPa (1 bar). The standard states are defined for different phases by: • The standard state of a pure gaseous substance is that of the substance as a (hypothetical) ideal gas at the standard state pressure. • The standard state of a pure liquid substance is that of the liquid under the standard state pressure. • The standard state of a pure crystalline substance is that of the crystalline substance under the standard state pressure. An entry of 0.0 for DfH° for an element indicates the reference state of that element. See References 1 and 2 for further information on reference states. A blank means no value is available. The data are derived from the sources listed in the references, from other papers appearing in the Journal of Physical and Chemical Reference Data, and from the primary research literature. We are indebted to M. V. Korobov for providing data on fullerene compounds.
    [Show full text]
  • Configuration of (+)-Glyceraldehyde.Pdf
    DOI: 10.1002/chem.201400296 Communication & Asymmetric Synthesis Coulomb Explosion Imaged Cryptochiral (R,R)-2,3- Dideuterooxirane: Unambiguous Access to the Absolute Configuration of (+)-Glyceraldehyde Kerstin Zawatzky,[a] Philipp Herwig,[b] Manfred Grieser,[b] Oded Heber,[c] Brandon Jordon- Thaden,[b] Claude Krantz,[b] Oldrˇich Novotny´,[b, d] Roland Repnow,[b] Volker Schurig,[e] Dirk Schwalm,[b] Zeev Vager,[c] Andreas Wolf,[b] Holger Kreckel,[b] and Oliver Trapp*[a] Abstract: The absolute configuration of (R,R)-2,3-dideu- terooxirane, which has been independently determined using Coulomb explosion imaging, has been unambigu- ously chemically correlated with the stereochemical key reference (+)-glyceraldehyde. This puts the absolute con- figuration of d(+)-glyceraldehyde on firm experimental Figure 1. Rational molecular design of (R,R)-2,3-dideuterooxirane derived grounds. from (+)-glyceraldehyde to determine the absolute configuration by Cou- lomb explosion imaging. More than 150 years after the discovery of molecular handed- image because the signal intensities only depend on the lattice ness by Louis Pasteur, the determination of absolute configura- planes, but not on the spatial orientation. In 1951 Bijvoet intro- tions is still a non-trivial problem.[1] The knowledge of the ab- duced anomalous single-crystal XRD to determine the absolute solute configuration is of central importance, when looking at configuration of rubidium sodium (+)-tartrate dihydrate crys- processes such as the lock-and-key relationship or structure- tals.[7,8] Here, the anomalous dispersion effect caused by specific targeting in drug development. The configurational a heavy atom in a crystal of an optically active compound is standard of chiral molecules is dextrorotatory (+)-glyceralde- used to determine its absolute configuration.
    [Show full text]
  • Molecular Model Building
    Molecular Model Building Name Date Class Period Introduction A group of atoms held together by covalent bonds is called a molecule. Although we represent molecules on paper as being two- dimensional for convenience, they are actually three-dimensional. By building molecular models, chemists come to understand the bonding, shapes, and polarity of even the most complex molecules. A molecule can be represented on paper by either a molecular or a structural formula. A molecular formula indicates the number and kind of each atom present in a molecule. Some familiar molecular formulas are shown below. NH3 CH4 The molecular formulas do not provide any information concerning the actual arrangement of atoms in a molecule. Such information is given by structural formulas such as the following. These structural formulas are two dimensional. The angles shown are not true to the shape of the molecule. Structural formulas can be made to convey more information by using the following symbolism. Using this symbolism, the structural formulas shown above can be redrawn in the following fashion. H H N H H C H H H Model Building Page 1 In this experiment, you will construct three-dimensional models to help you visualize the shapes of molecules. You will use ball-and-stick type models, in which colored plastic balls represent atoms and short plastic connectors represent the bonds. Double and triple bonds are represented by thin flexible connectors and thick in-flexible connectors serve as single bonds. The plastic balls have holes molded into them to accept the connectors. The number of holes in the ball represents the maximum number of bonds that a given atom can have.
    [Show full text]
  • Third Millennium Ideal Gas and Condensed Phase Thermochemical Database for Combustion with Updates from Active Thermochemical Tables
    ANL-05/20 TAE 960 Third Millennium Ideal Gas and Condensed Phase Thermochemical Database for Combustion with Updates from Active Thermochemical Tables Alexander Burcat Faculty of Aerospace Engineering, Technion – Israel Institute of Technology Branko Ruscic Chemistry Division, Argonne National Laboratory September 2005 Argonne National Laboratory is managed by The University of Chicago for the U. S. Department of Energy About Argonne National Laboratory Argonne is managed by The University of Chicago for the U.S. Department of Energy under contract W-31-109-Eng-38. The Laboratory’s main facility is outside Chicago, at 9700 South Cass Avenue, Argonne, Illinois 60439. For information about Argonne and its pioneering science and technology programs, see www.anl.gov. Availability of This Report This report is available, at no cost, at http://www.osti.gov/bridge. It is also available on paper to U.S. Department of Energy and its contractors, for a processing fee, from: U.S. Department of Energy Office of Scientific and Technical Information P.O. Box 62 Oak Ridge, TN 37831-0062 phone (865) 576-8401 fax (865) 576-5728 [email protected] Disclaimer This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor The University of Chicago, nor any of their employees or officers, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.
    [Show full text]