Quantification of Chirality: Attempting the Impossible*
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Chirality in the Plane
Chirality in the plane Christian G. B¨ohmer1 and Yongjo Lee2 and Patrizio Neff3 October 15, 2019 Abstract It is well-known that many three-dimensional chiral material models become non-chiral when reduced to two dimensions. Chiral properties of the two-dimensional model can then be restored by adding appropriate two-dimensional chiral terms. In this paper we show how to construct a three-dimensional chiral energy function which can achieve two-dimensional chirality induced already by a chiral three-dimensional model. The key ingredient to this approach is the consideration of a nonlinear chiral energy containing only rotational parts. After formulating an appropriate energy functional, we study the equations of motion and find explicit soliton solutions displaying two-dimensional chiral properties. Keywords: chiral materials, planar models, Cosserat continuum, isotropy, hemitropy, centro- symmetry AMS 2010 subject classification: 74J35, 74A35, 74J30, 74A30 1 Introduction 1.1 Background A group of geometric symmetries which keeps at least one point fixed is called a point group. A point group in d-dimensional Euclidean space is a subgroup of the orthogonal group O(d). Naturally this leads to the distinction of rotations and improper rotations. Centrosymmetry corresponds to a point group which contains an inversion centre as one of its symmetry elements. Chiral symmetry is one example of non-centrosymmetry which is characterised by the fact that a geometric figure cannot be mapped into its mirror image by an element of the Euclidean group, proper rotations SO(d) and translations. This non-superimposability (or chirality) to its mirror image is best illustrated by the left and right hands: there is no way to map the left hand onto the right by simply rotating the left hand in the plane. -
Chirality and Projective Linear Groups
DISCRETE MATHEMATICS Discrete Mathematics 131 (1994) 221-261 Chirality and projective linear groups Egon Schultea,l, Asia IviC Weissb**,’ “Depurtment qf Mathematics, Northeastern Uniwrsity, Boston, MA 02115, USA bDepartment qf Mathematics and Statistics, York University, North York, Ontario, M3JIP3, Camda Received 24 October 1991; revised 14 September 1992 Abstract In recent years the term ‘chiral’ has been used for geometric and combinatorial figures which are symmetrical by rotation but not by reflection. The correspondence of groups and polytopes is used to construct infinite series of chiral and regular polytopes whose facets or vertex-figures are chiral or regular toroidal maps. In particular, the groups PSL,(Z,) are used to construct chiral polytopes, while PSL,(Z,[I]) and PSL,(Z,[w]) are used to construct regular polytopes. 1. Introduction Abstract polytopes are combinatorial structures that generalize the classical poly- topes. We are particularly interested in those that possess a high degree of symmetry. In this section, we briefly outline some definitions and basic results from the theory of abstract polytopes. For details we refer to [9,22,25,27]. An (abstract) polytope 9 ofrank n, or an n-polytope, is a partially ordered set with a strictly monotone rank function rank( .) with range { - 1, 0, . , n}. The elements of 9 with rankj are called j-faces of 8. The maximal chains (totally ordered subsets) of .P are calledJags. We require that 6P have a smallest (- 1)-face F_ 1, a greatest n-face F,, and that each flag contains exactly n+2 faces. Furthermore, we require that .Y be strongly flag-connected and that .P have the following homogeneity property: when- ever F<G, rank(F)=j- 1 and rank(G)=j+l, then there are exactly two j-faces H with FcH-cG. -
Introduction to Organic Chemistry 2018 More
Introduction to Organic Chemistry 25 Introduction to Organic Chemistry Handout 2 - Stereochemistry OH O O OH enantiomers Me OH HO Me A B NH2 NH2 diastereomers diastereomers diastereomers OH O O OH Me OH HO Me C D NH2 enantiomers NH2 http://burton.chem.ox.ac.uk/teaching.html ◼ Organic Chemistry J. Clayden, N. Greeves, S. Warren ◼ Stereochemistry at a Glance J. Eames & J. M. Peach ◼ The majority of organic chemistry text books have good chapters on the topics covered by these lectures ◼ Eliel Stereochemistry of Organic Compounds (advanced reference text) Introduction to Organic Chemistry 26 ◼ representations of formulae in organic chemistry ◼ skeletal representations are far less cluttered and as a result are much clearer than drawing all carbon and hydrogen atoms explicitly, they also give a much better representation of the likely bond angles and hence hybridisation states of the carbon atoms ◼ skeletal representations allow functional groups (sites of reactivity) to be clearly seen ◼ guidelines for drawing skeletal structures i) draw chains of atoms as zig-zags ii) do not draw C atoms unless there is good reason to draw them iii) do not draw C-H bonds unless there is good reason to draw then iv) do not draw Hs attached to carbon atoms unless there is good reason to draw them v) make drawings realistic Introduction to Organic Chemistry 27 ◼ representing structures in three dimensions ◼ a wedged bond indicates the bond is projecting out in front of the plane of the paper ◼ a dashed bond indicates the bond is projecting behind the plane -
Chiral Icosahedral Hinge Elastegrity's Geometry of Motion
Chiral Icosahedral Hinge Elastegrity’s Geometry of Motion Eleftherios Pavlides, PhD AIA Roger Williams University1, Peter Fauci, Roger Williams University [email protected] 401 662 7521 Introduction Hinge Elastegrity, Definitions and Transformations Presented at G4G12 2a. 2 pairs 2b. 3 orthogonal H H 3.b 2 hypotenuse elastic of moving isosceles triangle faces hinges link each of 2 triangles for each of 8 irregular tetrahedra frame each tetrahedra 3c. isosceles leg elastic of 6 gates 3.a 4 free isosceles legss hinging pairs of right Fig.1 (left) edges per gate (6 gates) triangles forming 6-strut s 12 springs 24-cable Fig.2 Chiral Icosahedral nodal Hinge elastegrity rigid & Fig.3 Chiral Icosahedral tensegrity moving parts Hinge elastegrity rigid & hinges & gate edges The object that gave rise to the math in this paper is “hinge elastegrities”, a class of structures that originally arose from two Bauhaus exercises assigned at the Yale School of Architecture in the 1970’s and investigated in a series of art projects. The key new object obtained in 1982 involved cutting slits into folded pieces of paper and weaving them into 8 irregular tetrahedra, each with 3 isosceles right-triangle faces outlining an equilateral face fig.2b The 8 tetrahedra are suspended with 12 pairs of moving isosceles-right-triangles, congruent to the tetrahedral face right triangles fig.2a giving rise to an icosahedral shape (not necessarily regular) fig.2. Each pair of right triangles is attached to each other with an elastic hinge, along one of its isosceles legs fig.2a that act as springs. -
Teaching with SCIGRESS
Teaching with SCIGRESS Exercises on Molecular Modeling in Chemistry Crispin Wong and James Currie, eds. Pacific University Teaching with SCIGRES Molecular Modeling in Chemistry Crispin Wong and James Currie Editors Pacific University Forest Grove, Oregon 2 Copyright statement © 2001 - 2012 Fujitsu Limited. All rights reserved. This document may not be used, sold, transferred, copied or reproduced, in any manner or form, or in any medium, to any person other than with the prior written consent of Fujitsu Limited. Published by Fujitsu Limited. All possible care has been taken in the preparation of this publication. Fujitsu Limited does not accept liability for any inaccuracies that may be found. Fujitsu Limited reserves the right to make changes without notice both to this publication and to the product it describes. 3 Table of Contents Exercises 7 Part 1: General Chemistry Experiment 1 Calculating the Geometry of Molecules and Ions 16 Experiment 2 Kinetics of Substitution Reactions 29 Experiment 3 Sunscreen and Ultraviolet Absorption 38 Part 2: Organic Chemistry Experiment 4 Evaluations of Conformations of Menthone and Isomenthone 46 Experiment 5 The Evelyn Effect 52 Part 3: Physical Chemistry Experiment 6 Investigating the Resonance Stabilization of Benzene 63 Experiment 7 Investigation of the Rotational Barrier in N-N-dimethylacetamide 68 Part 4: Inorganic Chemistry Experiment 8 Polarities of Small Molecules 75 Experiment 9 Structures of Molecules Which Exceed the Octet Rule. 77 Experiment 10 Comparison of Gas Phase Acidities of Binary -
Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Names 2013
International Union of Pure and Applied Chemistry Division VIII Chemical Nomenclature and Structure Representation Division Nomenclature of Organic Chemistry. IUPAC Recommendations and Preferred Names 2013. Prepared for publication by Henri A. Favre and Warren H. Powell, Royal Society of Chemistry, ISBN 978-0-85404-182-4 Chapter P-9 SPECIFICATION OF CONFIGURATION AND CONFORMATION P-90 Introduction P-91 Stereoisomer graphical representation and naming P-92 The Cahn-Ingold-Prelog (CIP) priority system and the Sequence Rules P-93 Configuration specification P-94 Conformation and conformational stereodescriptors P-90 INTRODUCTION This Chapter is concerned only with the main principles for specification of configuration and conformation of organic compounds. The structure of an organic compound is systematically indicated by one or more affixes added to a name that does not itself prescribe stereochemical configuration or conformation; such affixes are generally called ‘stereodescriptors’. Thus, stereoisomers, such as enantiomers, have names that differ only in the stereodescriptors used. In contrast, ‘cis/trans’ isomers may have different names because of different stereodescriptors or names differing in the type of nomenclature. Also, certain retained names imply their own stereochemical description, for example, maleic acid, cholesterol, and other natural products described in Chapter P-10. In order to arrive at an unambiguous description of stereoisomers, Cahn, Ingold, and Prelog (refs. 34, 35) recommended an order of seniority for the ligands (atoms and groups) attached to carbon and other atoms, which is commonly called the ‘CIP priority system’. The priority is established by the application of ‘Sequence Rules’. These rules are discussed in P-92. Their application is then described for stereogenic units, mainly for the most usual compounds encountered in organic chemistry. -
Modular Chemical Descriptor Language (MCDL): Stereochemical Modules Andrei a Gakh1*, Michael N Burnett1, Sergei V Trepalin2, Alexander V Yarkov2
Gakh et al. Journal of Cheminformatics 2011, 3:5 http://www.jcheminf.com/content/3/1/5 METHODOLOGY Open Access Modular Chemical Descriptor Language (MCDL): Stereochemical modules Andrei A Gakh1*, Michael N Burnett1, Sergei V Trepalin2, Alexander V Yarkov2 Abstract Background: In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. Results: In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Conclusions: Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format. Background Java applet to be capable of restoring these coordinates In our previous paper we introduced the Modular Che- to draw a structure. As a result, the current applet algo- mical Descriptor Language (MCDL) for providing a lin- rithm that was developed to process MCDL descriptors ear representation of structural and other chemical can also be used for processing of other coordinate-less information [1]. All MCDL descriptors have two unique structure representations, such as SMILES [3,4] and modules that describe the composition and the connec- InChI [5]. -
Symmetry and Chirality in Discrete Structures
Symmetry and chirality in discrete structures Marston Conder University of Auckland, New Zealamd UW Math Day, Seattle, March 2013 Where is New Zealand? What is New Zealand famous for? • Great place to live (South Pacific) • Multi-cultural (European, Maori/Polynesian, Asian ...) • Beautiful scenery (beaches, volcanoes, lakes, mountains) • Kiwis (strange little birds), kiwi fruit (strange little fruit) • Dairy produce (milk, butter, cheese, etc.) • Film sites (Lord of the Rings, The Hobbit, Narnia, etc.) • Rugby football • Extreme sports (bungy-jumping, white-water rafting, etc.) What is symmetry? Symmetry can mean many different things, such as balance, uniform proportion, harmony, or congruence Generally, an object has symmetry if it can be transformed in way that leaves it looking the same as it did originally. Symmetry can be reflective: ... or rotational: ... or translational: ... or a combination of these types Examples of these kinds of symmetry abound in nature ... but have also been manufactured by human fascination and enterprise e.g. the Platonic solids (c. 360BC) or earlier ... the `Neolithic Scots' (c. 2000BC) ... as publicised by Atiyah and Sutcliffe (2003) ... but unfortunately a hoax! The claim that the Scots knew about these five regular solids over 1000 years before Plato was based on the above five `Scottish stones' at the Ashmolean Museum in Oxford | but one has 14 faces, and none of them is an icosahedron [See John Baez's website for the full story] Tilings at the Alhambra Palace { on its walls, floors, ceilings, and even some of the furniture { amazingly exhibit all of the 17 \wallpaper symmetries" (in two dimensions) [Rafael P´erezG´omezand Jos´eMara Montesinos, 1980s] Symmetry can induce strength and stability: .. -
On the Study of Chirality of Knots Through Polynomial Invariants
Treball final de grau GRAU DE MATEMÀTIQUES Facultat de Matemàtiques i Informàtica Universitat de Barcelona KNOT THEORY: On the study of chirality of knots through polynomial invariants Autor: Sergi Justiniano Claramunt Director: Dr. Javier José Gutiérrez Marín Realitzat a: Departament de Matemàtiques i Informàtica Barcelona, January 18, 2019 Contents Abstract ii Introduction iii 1 Mathematical bases 1 1.1 Definition of a knot . .1 1.2 Equivalence of knots . .4 1.3 Knot projections and diagrams . .6 1.4 Reidemeister moves . .8 1.5 Invariants . .9 1.6 Symmetries, properties and generation of knots . 11 1.7 Tangles and Conway notation . 12 2 Jones Polynomial 15 2.1 Introduction . 15 2.2 Rules of bracket polynomial . 16 2.3 Writhe and invariance of Jones polynomial . 18 2.4 Main theorems and applications . 22 3 HOMFLY and Kauffman polynomials on chirality detection 25 3.1 HOMFLY polynomial . 25 3.2 Kauffman polynomial . 28 3.3 Testing chirality . 31 4 Conclusions 33 Bibliography 35 i Abstract In this project we introduce the theory of knots and specialize in the compu- tation of the knot polynomials. After presenting the Jones polynomial, its two two-variable generalizations are also introduced: the Kauffman and HOMFLY polynomial. Then we study the ability of these polynomials on detecting chirality, obtaining a knot not detected chiral by the HOMFLY polynomial, but detected chiral by the Kauffman polynomial. Introduction The main idea of this project is to give a clear and short introduction to the theory of knots and in particular the utility of knot polynomials on detecting chirality of knots. -
IR-9 Coordination Compounds (Draft March 2004)
1 IR-9 Coordination Compounds (Draft March 2004) CONTENTS IR-9.1 Introduction IR-9.1.1 General IR-9.1.2 Definitions IR-9.1.2.1 Background IR-9.1.2.2 Coordination compounds and the coordination entity IR-9.1.2.3 Central atom IR-9.1.2.4 Ligands IR-9.1.2.5 Coordination polyhedron IR-9.1.2.6 Coordination number IR-9.1.2.7 Chelation IR-9.1.2.8 Oxidation state IR-9.1.2.9 Coordination nomenclature: an additive nomenclature IR-9.1.2.10 Bridging ligands IR-9.1.2.11 Metal-metal bonds IR-9.2 Describing the constitution of coordination compounds IR-9.2.1 General IR-9.2.2 Naming coordination compounds IR-9.2.2.1 Sequences of ligands and central atoms within names IR-9.2.2.2 Number of ligands in a coordination entity IR-9.2.2.3 Representing ligands in names IR-9.2.2.4 Charge numbers, oxidation numbers, and ionic proportions IR-9.2.3 Formulae of coordination compounds IR-9.2.3.1 Sequence of symbols within the coordination formula IR-9.2.3.2 Use of enclosing marks IR-9.2.3.3 Ionic charges and oxidation numbers IR-9.2.3.4 Use of abbreviations IR-9.2.4 Specifying donor atoms IR-9.2.4.1 General IUPAC ProvisionalIR-9.2.4.2 The kappa convention Recommendations IR-9.2.4.3 Comparison of the eta and kappa nomenclatures Page 1 of 69 DRAFT 2 April 2004 2 IR-9.2.4.4 Donor atom symbol to indicate points of ligation IR-9.2.5 Polynuclear complexes IR-9.2.5.1 General IR-9.2.5.2 Bridging ligands IR-9.2.5.3 Metal-metal bonding IR-9.2.5.4 Symmetrical dinuclear entities IR-9.2.5.5 Unsymmetrical dinuclear entities IR-9.2.5.6 Trinuclear and larger structures IR-9.2.5.7 Polynuclear -
Chirality: the Handedness of Molecules
06 Chirality: The Handedness of Molecules Tartaric acid is found in grapes and other fruits, both free and as its salts (see Section 6.4B). Inset: A model of tartaric acid. (© fatihhoca/iStockphoto) KEY QUESTIONS 6.1 What Are Stereoisomers? 6.9 What Is the Significance of Chirality in the 6.2 What Are Enantiomers? Biological World? 6.3 How Do We Designate the Configuration of a 6.10 How Can Enantiomers Be Resolved? Stereocenter? HOW TO 6.4 What Is the 2n Rule? 6.1 How to Draw Enantiomers 6.5 How Do We Describe the Chirality of 6.2 How to Determine the R & S Configuration Cyclic Molecules with Two Stereocenters? without Rotating the Molecule 6.6 How Do We Describe the Chirality 6.3 How to Determine Whether Two Compounds Are of Molecules with Three or More the Same, Enantiomers, or Diastereomers without Stereocenters? the Need to Spatially Manipulate the Molecule 6.7 What Are the Properties of Stereoisomers? 6.8 How Is Chirality Detected in the CHEMICAL CONNECTIONS Laboratory? 6A Chiral Drugs IN THIS CHAPTER, we will explore the relationships between three-dimensional ob- jects and their mirror images. When you look in a mirror, you see a reflection, or mirror Mirror image The reflection image, of yourself. Now, suppose your mirror image becomes a three-dimensional object. of an object in a mirror. 167 168 CHAPTER 6 Chirality: The Handedness of Molecules We could then ask, “What is the relationship between you and your mirror image?” By relationship, we mean “Can your reflection be superposed on the original ‘you’ in such a way that every detail of the reflection corresponds exactly to the original?” The answer is that you and your mirror image are not superposable. -
Controlling the Shape and Chirality of an Eight- Crossing Molecular Knot
Controlling the Shape and Chirality of an Eight- crossing Molecular Knot John P. Carpenter,‡ Charlie T. McTernan,‡ Jake L. Greenfield, Roy Lavendomme, Tanya K. Ronson and Jonathan R. Nitschke* 1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK ‡ these authors contributed equally *e-mail: [email protected] Abstract The knotting of biomolecules impacts their function, and enables them to carry out new tasks. Likewise, complex topologies underpin the operation of many synthetic molecular machines. The ability to generate and control more complex knotted architectures is essential to endow these machines with more advanced functions. Here we report the synthesis of a molecular knot with eight crossing points, consisting of a single organic loop woven about six templating metal centres, via one-pot self-assembly from a simple pair of dialdehyde and diamine subcomponents and a single metal salt. The structure and topology of the knot were established by NMR spectroscopy, mass spectrometry and X-ray crystallography. Upon demetallation, the purely organic strand relaxes into a symmetric conformation, whilst retaining the topology of the original knot. This knot is topologically chiral, and may be synthesised diastereoselectively through the use of an enantiopure diamine building block. 1 Knots are one of the oldest technologies, having been used for thousands of years to transform the properties of the materials in which they are tied.1 At the molecular level, knots are found in biology in proteins and DNA,2,3