Symmetry of Fulleroids Stanislav Jendrol’, František Kardoš
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Origin of Icosahedral Symmetry in Viruses
Origin of icosahedral symmetry in viruses Roya Zandi†‡, David Reguera†, Robijn F. Bruinsma§, William M. Gelbart†, and Joseph Rudnick§ Departments of †Chemistry and Biochemistry and §Physics and Astronomy, University of California, Los Angeles, CA 90095-1569 Communicated by Howard Reiss, University of California, Los Angeles, CA, August 11, 2004 (received for review February 2, 2004) With few exceptions, the shells (capsids) of sphere-like viruses (11). This problem is in turn related to one posed much earlier have the symmetry of an icosahedron and are composed of coat by Thomson (12), involving the optimal distribution of N proteins (subunits) assembled in special motifs, the T-number mutually repelling points on the surface of a sphere, and to the structures. Although the synthesis of artificial protein cages is a subsequently posed ‘‘covering’’ problem, where one deter- rapidly developing area of materials science, the design criteria for mines the arrangement of N overlapping disks of minimum self-assembled shells that can reproduce the remarkable properties diameter that allow complete coverage of the sphere surface of viral capsids are only beginning to be understood. We present (13). In a similar spirit, a self-assembly phase diagram has been here a minimal model for equilibrium capsid structure, introducing formulated for adhering hard disks (14). These models, which an explicit interaction between protein multimers (capsomers). all deal with identical capsomers, regularly produced capsid Using Monte Carlo simulation we show that the model reproduces symmetries lower than icosahedral. On the other hand, theo- the main structures of viruses in vivo (T-number icosahedra) and retical studies of viral assembly that assume icosahedral sym- important nonicosahedral structures (with octahedral and cubic metry are able to reproduce the CK motifs (15), and, most symmetry) observed in vitro. -
The Cubic Groups
The Cubic Groups Baccalaureate Thesis in Electrical Engineering Author: Supervisor: Sana Zunic Dr. Wolfgang Herfort 0627758 Vienna University of Technology May 13, 2010 Contents 1 Concepts from Algebra 4 1.1 Groups . 4 1.2 Subgroups . 4 1.3 Actions . 5 2 Concepts from Crystallography 6 2.1 Space Groups and their Classification . 6 2.2 Motions in R3 ............................. 8 2.3 Cubic Lattices . 9 2.4 Space Groups with a Cubic Lattice . 10 3 The Octahedral Symmetry Groups 11 3.1 The Elements of O and Oh ..................... 11 3.2 A Presentation of Oh ......................... 14 3.3 The Subgroups of Oh ......................... 14 2 Abstract After introducing basics from (mathematical) crystallography we turn to the description of the octahedral symmetry groups { the symmetry group(s) of a cube. Preface The intention of this account is to provide a description of the octahedral sym- metry groups { symmetry group(s) of the cube. We first give the basic idea (without proofs) of mathematical crystallography, namely that the 219 space groups correspond to the 7 crystal systems. After this we come to describing cubic lattices { such ones that are built from \cubic cells". Finally, among the cubic lattices, we discuss briefly the ones on which O and Oh act. After this we provide lists of the elements and the subgroups of Oh. A presentation of Oh in terms of generators and relations { using the Dynkin diagram B3 is also given. It is our hope that this account is accessible to both { the mathematician and the engineer. The picture on the title page reflects Ha¨uy'sidea of crystal structure [4]. -
Systematics of Atomic Orbital Hybridization of Coordination Polyhedra: Role of F Orbitals
molecules Article Systematics of Atomic Orbital Hybridization of Coordination Polyhedra: Role of f Orbitals R. Bruce King Department of Chemistry, University of Georgia, Athens, GA 30602, USA; [email protected] Academic Editor: Vito Lippolis Received: 4 June 2020; Accepted: 29 June 2020; Published: 8 July 2020 Abstract: The combination of atomic orbitals to form hybrid orbitals of special symmetries can be related to the individual orbital polynomials. Using this approach, 8-orbital cubic hybridization can be shown to be sp3d3f requiring an f orbital, and 12-orbital hexagonal prismatic hybridization can be shown to be sp3d5f2g requiring a g orbital. The twists to convert a cube to a square antiprism and a hexagonal prism to a hexagonal antiprism eliminate the need for the highest nodality orbitals in the resulting hybrids. A trigonal twist of an Oh octahedron into a D3h trigonal prism can involve a gradual change of the pair of d orbitals in the corresponding sp3d2 hybrids. A similar trigonal twist of an Oh cuboctahedron into a D3h anticuboctahedron can likewise involve a gradual change in the three f orbitals in the corresponding sp3d5f3 hybrids. Keywords: coordination polyhedra; hybridization; atomic orbitals; f-block elements 1. Introduction In a series of papers in the 1990s, the author focused on the most favorable coordination polyhedra for sp3dn hybrids, such as those found in transition metal complexes. Such studies included an investigation of distortions from ideal symmetries in relatively symmetrical systems with molecular orbital degeneracies [1] In the ensuing quarter century, interest in actinide chemistry has generated an increasing interest in the involvement of f orbitals in coordination chemistry [2–7]. -
Chapter 1 – Symmetry of Molecules – P. 1
Chapter 1 – Symmetry of Molecules – p. 1 - 1. Symmetry of Molecules 1.1 Symmetry Elements · Symmetry operation: Operation that transforms a molecule to an equivalent position and orientation, i.e. after the operation every point of the molecule is coincident with an equivalent point. · Symmetry element: Geometrical entity (line, plane or point) which respect to which one or more symmetry operations can be carried out. In molecules there are only four types of symmetry elements or operations: · Mirror planes: reflection with respect to plane; notation: s · Center of inversion: inversion of all atom positions with respect to inversion center, notation i · Proper axis: Rotation by 2p/n with respect to the axis, notation Cn · Improper axis: Rotation by 2p/n with respect to the axis, followed by reflection with respect to plane, perpendicular to axis, notation Sn Formally, this classification can be further simplified by expressing the inversion i as an improper rotation S2 and the reflection s as an improper rotation S1. Thus, the only symmetry elements in molecules are Cn and Sn. Important: Successive execution of two symmetry operation corresponds to another symmetry operation of the molecule. In order to make this statement a general rule, we require one more symmetry operation, the identity E. (1.1: Symmetry elements in CH4, successive execution of symmetry operations) 1.2. Systematic classification by symmetry groups According to their inherent symmetry elements, molecules can be classified systematically in so called symmetry groups. We use the so-called Schönfliess notation to name the groups, Chapter 1 – Symmetry of Molecules – p. 2 - which is the usual notation for molecules. -
Can Every Face of a Polyhedron Have Many Sides ?
Can Every Face of a Polyhedron Have Many Sides ? Branko Grünbaum Dedicated to Joe Malkevitch, an old friend and colleague, who was always partial to polyhedra Abstract. The simple question of the title has many different answers, depending on the kinds of faces we are willing to consider, on the types of polyhedra we admit, and on the symmetries we require. Known results and open problems about this topic are presented. The main classes of objects considered here are the following, listed in increasing generality: Faces: convex n-gons, starshaped n-gons, simple n-gons –– for n ≥ 3. Polyhedra (in Euclidean 3-dimensional space): convex polyhedra, starshaped polyhedra, acoptic polyhedra, polyhedra with selfintersections. Symmetry properties of polyhedra P: Isohedron –– all faces of P in one orbit under the group of symmetries of P; monohedron –– all faces of P are mutually congru- ent; ekahedron –– all faces have of P the same number of sides (eka –– Sanskrit for "one"). If the number of sides is k, we shall use (k)-isohedron, (k)-monohedron, and (k)- ekahedron, as appropriate. We shall first describe the results that either can be found in the literature, or ob- tained by slight modifications of these. Then we shall show how two systematic ap- proaches can be used to obtain results that are better –– although in some cases less visu- ally attractive than the old ones. There are many possible combinations of these classes of faces, polyhedra and symmetries, but considerable reductions in their number are possible; we start with one of these, which is well known even if it is hard to give specific references for precisely the assertion of Theorem 1. -
On Polyhedra with Transitivity Properties
Discrete Comput Geom 1:195-199 (1986) iSCrete & Computathm~ ~) 1986 Springer-V©rlagometrvNew York Inc. IF On Polyhedra with Transitivity Properties J. M. Wills Mathematics Institute, University of Siegen, Hoelderlinstrasse 3, D-5900 Siegen, FRG Abstract. In a remarkable paper [4] Griinbaum and Shephard stated that there is no polyhedron of genus g > 0, such that its symmetry group acts transitively on its faces. If this condition is slightly weakened, one obtains" some interesting polyhedra with face-transitivity (resp. vertex-transitivity). In recent years several attempts have been/made to find polyhedral analogues for the Platonic solids in the Euclidean 3-space E 3 (cf. [1, 4, 5, 7-14]). By a polyhedron P we mean the union of a finite number of plane polygons in E 3 which form a 2-manifold without boundary and without self-intersections, where, as usual, a plane polygon is a plane set bounded by finitely many line segments. If the plane polygons are disjoint except for their edges, they are called the faces of P. We require adjacent faces to be non-coplanar. The vertices and edges of P are the vertices and edges of the faces of P. The genus of the underlying 2-manifold is the genus of P. A flag of P is a triplet consisting of one vertex, one edge incident with this vertex, and one face containing this edge. If, for given p- 3, q >- 3 all faces of P are p-gons and all vertices q-valent, we say that P is equivelar, i.e., has equal flags (cf. -
In Boron Chemistry
Bull. Mater. Sci., Vol. 22, No. 5, August 1999, pp. 863-867. © Indian Academy of Sciences. The ubiquitous icosahedral B12 in boron chemistry E D JEMMIS* and M M BALAKRISHNARAJAN School of Chemistry, University of Hyderabad, Hyderabad500 046. India Abstract. Though boranes exhibit a wide variety of polyhedral structures, all the three polymorpbs of elemental boron essentially contain icosahedral Bn units as the predominant building block in their unit cell. Theoretical and experimental studies on boranes show that the icosuhedral arrangement leads to most stable boranes and borane anions. This paper attempts to explain the phenomenal stability associated with the icosahedral Bn structure. Using fragment molecular orbital theory, the remarkable stability of BI2Ht2~ among closo boranes are explained. The preferential selection icosahedral B12 unit by elemental boron is explained by improvising a contrived B84 sub-unit of the ~-rhombohedron, the most stable polymorph. This also leads to a novel covalent way of stuffing fnilerenes with icosahedral symmetry. Keywords. Boron; polyhedral closo borane dianions; icosahedral B12; ~-rhombohedral polymorph; orbital compatibility. 1. Introduction Elemental boron exists in three different polymorphic forms (Wells 1979). The thermodynamically most stable The chemistry of boron formed a vast discipline by itself [t-rhombohedral form has 105 boron atoms in its unit cell. and helped to alter the concept of structure and bonding The next stable ~-rhombohedral form has 12 boron atoms. radically (Lipscomb 1963). Starting from the famous The meta stable ~-tetragonal form has fifty boron atoms three-centre two-electron bond, many of the structural in its unit cell. The icosahedral BI2 unit is the primary features exhibited by boron compounds (most signifi- building block in all of these polymorphic forms. -
Viral Capsids and Self Assembly Viral Capsids
MAE 545: Lecture 22 (12/10) Viral capsids and self assembly Viral capsids helical symmetry icosahedral symmetry complex symmetry Hepatitis B virus conical shaped capsid proteins are wrapped (spherical caps usually around the viral RNA still icosahedral) (e.g. Tobacco Mosaic Virus) Poxvirus Note: many viruses also HIV have envelope (lipid bilayer) around the capsid 2 Icosahedral capsids Brome mosaic Bacteriophage Cowpea Chlorotic L-A virus Dengue virus virus φ X 174 Mottle virus Tobacco Human Hepatitis Sindbis virus Bacteriophage Necrosis virus B Virus Simian virus HK97 Colors correspond to different proteins. 3 Generating Vectors for the Lattice Structures of Tubular and Conical Viral Capsids 129 number, to form with icosahedral symmetry. The quasi-equivalence is demonstrated in the experiment results reported in [30]. There are also many viruses that have tubular or lozenge-like capsids. Mature HIV-1 cores have cone- shaped capsids [1, 11]. Unlike the icosahedral viral capsids, the structures of tubular and conical capsids are not yet fully understood. There have been models for the lattice structures of tubular and conical capsids, see [17, 21] and references therein. However, there is a aw in the Nguyen model [21], which missed the requirement on the cone height and could result in incomplete cones if the model is inappropriately applied. In this paper, we propose new models for tubular and conical capsids in a unied fashion based on an extension of the Capser-Klug quasi-equivalence theory. The new models are easier than the existing models. When applied to the HIV-1 (5,7)-cone (5 pentagons in the narrow end and 7 pentagons in the broad end), the capsid properties derived from our models show good agreement with published experimental data. -
Quartic Surfaces with Icosahedral Symmetry
Adv. Geom. 2018; 18 (1):119–132 Igor V. Dolgachev* Quartic surfaces with icosahedral symmetry DOI 10.1515/advgeom-2017-0040. Received 23 September, 2016; revised 9 April, 2017 3 Abstract: We study smooth quartic surfaces in ℙ which admit a group of projective automorphisms isomor- phic to the icosahedron group. Keywords: Quartic surface, icosahedron group. 2010 Mathematics Subject Classification: 14J10 || Communicated by: I. Coskun 1 Introduction Let A5 be the icosahedron group isomorphic to the alternating group in 5 letters. Starting from Platonic solids, it appears as an omnipresent symmetry group in geometry. In this article, complementing papers [4] and [5], 3 we discuss families of smooth quartic surfaces in ℙ that admit the group A5 as its group of projective sym- metries. It follows from loc. cit. that any smooth quartic surface S with a faithful action of A5 belongs to one of the two pencils of invariant quartic surfaces. One of them arises from a linear irreducible 4-dimensional representation of A5 and was studied in great detail by K. Hashimoto in [10]. It contains a double quadric and four surfaces with 5, 10, 10, or 15 ordinary double points. The other pencil arises from a faithful linear representation of the binary icosahedron group 2.A5. As was shown in [4] and [5], it contains two singular surfaces singular along its own rational normal cubic and two surfaces with 10 ordinary double points. In this paper we show first that one of the surfaces with 10 ordinary double points from Hashimoto’s pencil can be realized as a Cayley quartic symmetroid defined by a A5-invariant web W of quadrics (this result was independently obtained by S. -
Chapter 3: Transformations Groups, Orbits, and Spaces of Orbits
Preprint typeset in JHEP style - HYPER VERSION Chapter 3: Transformations Groups, Orbits, And Spaces Of Orbits Gregory W. Moore Abstract: This chapter focuses on of group actions on spaces, group orbits, and spaces of orbits. Then we discuss mathematical symmetric objects of various kinds. May 3, 2019 -TOC- Contents 1. Introduction 2 2. Definitions and the stabilizer-orbit theorem 2 2.0.1 The stabilizer-orbit theorem 6 2.1 First examples 7 2.1.1 The Case Of 1 + 1 Dimensions 11 3. Action of a topological group on a topological space 14 3.1 Left and right group actions of G on itself 19 4. Spaces of orbits 20 4.1 Simple examples 21 4.2 Fundamental domains 22 4.3 Algebras and double cosets 28 4.4 Orbifolds 28 4.5 Examples of quotients which are not manifolds 29 4.6 When is the quotient of a manifold by an equivalence relation another man- ifold? 33 5. Isometry groups 34 6. Symmetries of regular objects 36 6.1 Symmetries of polygons in the plane 39 3 6.2 Symmetry groups of some regular solids in R 42 6.3 The symmetry group of a baseball 43 7. The symmetries of the platonic solids 44 7.1 The cube (\hexahedron") and octahedron 45 7.2 Tetrahedron 47 7.3 The icosahedron 48 7.4 No more regular polyhedra 50 7.5 Remarks on the platonic solids 50 7.5.1 Mathematics 51 7.5.2 History of Physics 51 7.5.3 Molecular physics 51 7.5.4 Condensed Matter Physics 52 7.5.5 Mathematical Physics 52 7.5.6 Biology 52 7.5.7 Human culture: Architecture, art, music and sports 53 7.6 Regular polytopes in higher dimensions 53 { 1 { 8. -
Exploring Icosahedral Virus Structures with Viper
REVIEWS EXPLORING ICOSAHEDRAL VIRUS STRUCTURES WITH VIPER Padmaja Natarajan, Gabriel C. Lander, Craig M. Shepherd, Vijay S. Reddy, Charles L. Brooks III and John E. Johnson Abstract | Virus structures are megadalton nucleoprotein complexes with an exceptional variety of protein–protein and protein–nucleic-acid interactions. Three-dimensional crystal structures of over 70 virus capsids, from more than 20 families and 30 different genera of viruses, have been solved to near-atomic resolution. The enormous amount of information contained in these structures is difficult to access, even for scientists trained in structural biology. Virus Particle Explorer (VIPER) is a web-based catalogue of structural information that describes the icosahedral virus particles. In addition to high-resolution crystal structures, VIPER has expanded to include virus structures obtained by cryo-electron microscopy (EM) techniques. The VIPER database is a powerful resource for virologists, microbiologists, virus crystallographers and EM researchers. This review describes how to use VIPER, using several examples to show the power of this resource for research and educational purposes. ASYMMETRIC UNIT A wealth of virus-structure information that is useful virus structures or a family of virus structures by visit- The asymmetric unit of an to virologists can be derived from the coordinates of ing the ‘Visual VIPER’ tool from the ‘Utilities/Tools’ icosahedral virus structure is high-resolution icosahedral virus structures depos- section of the VIPER main menu. A researcher can defined as the smallest part of ited in the Protein Data Bank (PDB)1. However, it use the same tool to compare these viruses at various the structure from which the complete structure of the virus can be a challenging task — even for experienced levels of protein-subunit organization in their capsid can be built using a specific set structural biologists — to obtain information such as shells. -
New Perspectives on Polyhedral Molecules and Their Crystal Structures Santiago Alvarez, Jorge Echeverria
New Perspectives on Polyhedral Molecules and their Crystal Structures Santiago Alvarez, Jorge Echeverria To cite this version: Santiago Alvarez, Jorge Echeverria. New Perspectives on Polyhedral Molecules and their Crystal Structures. Journal of Physical Organic Chemistry, Wiley, 2010, 23 (11), pp.1080. 10.1002/poc.1735. hal-00589441 HAL Id: hal-00589441 https://hal.archives-ouvertes.fr/hal-00589441 Submitted on 29 Apr 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal of Physical Organic Chemistry New Perspectives on Polyhedral Molecules and their Crystal Structures For Peer Review Journal: Journal of Physical Organic Chemistry Manuscript ID: POC-09-0305.R1 Wiley - Manuscript type: Research Article Date Submitted by the 06-Apr-2010 Author: Complete List of Authors: Alvarez, Santiago; Universitat de Barcelona, Departament de Quimica Inorganica Echeverria, Jorge; Universitat de Barcelona, Departament de Quimica Inorganica continuous shape measures, stereochemistry, shape maps, Keywords: polyhedranes http://mc.manuscriptcentral.com/poc Page 1 of 20 Journal of Physical Organic Chemistry 1 2 3 4 5 6 7 8 9 10 New Perspectives on Polyhedral Molecules and their Crystal Structures 11 12 Santiago Alvarez, Jorge Echeverría 13 14 15 Departament de Química Inorgànica and Institut de Química Teòrica i Computacional, 16 Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain).