Fundamentals of Crystallography
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Symmetry of Fulleroids Stanislav Jendrol’, František Kardoš
Symmetry of Fulleroids Stanislav Jendrol’, František Kardoš To cite this version: Stanislav Jendrol’, František Kardoš. Symmetry of Fulleroids. Klaus D. Sattler. Handbook of Nanophysics: Clusters and Fullerenes, CRC Press, pp.28-1 - 28-13, 2010, 9781420075557. hal- 00966781 HAL Id: hal-00966781 https://hal.archives-ouvertes.fr/hal-00966781 Submitted on 27 Mar 2014 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. Symmetry of Fulleroids Stanislav Jendrol’ and Frantiˇsek Kardoˇs Institute of Mathematics, Faculty of Science, P. J. Saf´arikˇ University, Koˇsice Jesenn´a5, 041 54 Koˇsice, Slovakia +421 908 175 621; +421 904 321 185 [email protected]; [email protected] Contents 1 Symmetry of Fulleroids 2 1.1 Convexpolyhedraandplanargraphs . .... 3 1.2 Polyhedral symmetries and graph automorphisms . ........ 4 1.3 Pointsymmetrygroups. 5 1.4 Localrestrictions ............................... .. 10 1.5 Symmetryoffullerenes . .. 11 1.6 Icosahedralfulleroids . .... 12 1.7 Subgroups of Ih ................................. 15 1.8 Fulleroids with multi-pentagonal faces . ......... 16 1.9 Fulleroids with octahedral, prismatic, or pyramidal symmetry ........ 19 1.10 (5, 7)-fulleroids .................................. 20 1 Chapter 1 Symmetry of Fulleroids One of the important features of the structure of molecules is the presence of symmetry elements. -
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. -
Types of Lattices
Types of Lattices Types of Lattices Lattices are either: 1. Primitive (or Simple): one lattice point per unit cell. 2. Non-primitive, (or Multiple) e.g. double, triple, etc.: more than one lattice point per unit cell. Double r2 cell r1 r2 Triple r1 cell r2 r1 Primitive cell N + e 4 Ne = number of lattice points on cell edges (shared by 4 cells) •When repeated by successive translations e =edge reproduce periodic pattern. •Multiple cells are usually selected to make obvious the higher symmetry (usually rotational symmetry) that is possessed by the 1 lattice, which may not be immediately evident from primitive cell. Lattice Points- Review 2 Arrangement of Lattice Points 3 Arrangement of Lattice Points (continued) •These are known as the basis vectors, which we will come back to. •These are not translation vectors (R) since they have non- integer values. The complexity of the system depends upon the symmetry requirements (is it lost or maintained?) by applying the symmetry operations (rotation, reflection, inversion and translation). 4 The Five 2-D Bravais Lattices •From the previous definitions of the four 2-D and seven 3-D crystal systems, we know that there are four and seven primitive unit cells (with 1 lattice point/unit cell), respectively. •We can then ask: can we add additional lattice points to the primitive lattices (or nets), in such a way that we still have a lattice (net) belonging to the same crystal system (with symmetry requirements)? •First illustrate this for 2-D nets, where we know that the surroundings of each lattice point must be identical. -
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]. -
Chapter 4, Bravais Lattice Primitive Vectors
Chapter 4, Bravais Lattice A Bravais lattice is the collection of all (and only those) points in space reachable from the origin with position vectors: n , n , n integer (+, -, or 0) r r r r 1 2 3 R = n1a1 + n2 a2 + n3a3 a1, a2, and a3 not all in same plane The three primitive vectors, a1, a2, and a3, uniquely define a Bravais lattice. However, for one Bravais lattice, there are many choices for the primitive vectors. A Bravais lattice is infinite. It is identical (in every aspect) when viewed from any of its lattice points. This is not a Bravais lattice. Honeycomb: P and Q are equivalent. R is not. A Bravais lattice can be defined as either the collection of lattice points, or the primitive translation vectors which construct the lattice. POINT Q OBJECT: Remember that a Bravais lattice has only points. Points, being dimensionless and isotropic, have full spatial symmetry (invariant under any point symmetry operation). Primitive Vectors There are many choices for the primitive vectors of a Bravais lattice. One sure way to find a set of primitive vectors (as described in Problem 4 .8) is the following: (1) a1 is the vector to a nearest neighbor lattice point. (2) a2 is the vector to a lattice points closest to, but not on, the a1 axis. (3) a3 is the vector to a lattice point nearest, but not on, the a18a2 plane. How does one prove that this is a set of primitive vectors? Hint: there should be no lattice points inside, or on the faces (lll)fhlhd(lllid)fd(parallolegrams) of, the polyhedron (parallelepiped) formed by these three vectors. -
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]. -
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. -
Crystal Structure
Physics 927 E.Y.Tsymbal Section 1: Crystal Structure A solid is said to be a crystal if atoms are arranged in such a way that their positions are exactly periodic. This concept is illustrated in Fig.1 using a two-dimensional (2D) structure. y T C Fig.1 A B a x 1 A perfect crystal maintains this periodicity in both the x and y directions from -∞ to +∞. As follows from this periodicity, the atoms A, B, C, etc. are equivalent. In other words, for an observer located at any of these atomic sites, the crystal appears exactly the same. The same idea can be expressed by saying that a crystal possesses a translational symmetry. The translational symmetry means that if the crystal is translated by any vector joining two atoms, say T in Fig.1, the crystal appears exactly the same as it did before the translation. In other words the crystal remains invariant under any such translation. The structure of all crystals can be described in terms of a lattice, with a group of atoms attached to every lattice point. For example, in the case of structure shown in Fig.1, if we replace each atom by a geometrical point located at the equilibrium position of that atom, we obtain a crystal lattice. The crystal lattice has the same geometrical properties as the crystal, but it is devoid of any physical contents. There are two classes of lattices: the Bravais and the non-Bravais. In a Bravais lattice all lattice points are equivalent and hence by necessity all atoms in the crystal are of the same kind. -
Crystals the Atoms in a Crystal Are Arranged in a Periodic Pattern. A
Crystals The atoms in a crystal are arranged in a periodic pattern. A crystal is made up of unit cells that are repeated at a pattern of points, which is called the Bravais lattice (fig. (1)). The Bravais lattice is basically a three dimensional abstract lattice of points. Figure 1: Unit cell - Bravais lattice - Crystal Unit cell The unit cell is the description of the arrangement of the atoms that get repeated, and is not unique - there are a various possibilities to choose it. The primitive unit cell is the smallest possible pattern to reproduce the crystal and is also not unique. As shown in fig. (2) for 2 dimensions there is a number of options of choosing the primitive unit cell. Nevertheless all have the same area. The same is true in three dimensions (various ways to choose primitive unit cell; same volume). An example for a possible three dimensional primitive unit cell and the formula for calculating the volume can be seen in fig. (2). Figure 2: Illustration of primitive unit cells 1 The conventional unit cell is agreed upon. It is chosen in a way to display the crystal or the crystal symmetries as good as possible. Normally it is easier to imagine things when looking at the conventional unit cell. A few conventional unit cells are displayed in fig. (3). Figure 3: Illustration of conventional unit cells • sc (simple cubic): Conventional and primitive unit cell are identical • fcc (face centered cubic): The conventional unit cell consists of 4 atoms in com- parison to the primitive unit cell which consists of only 1 atom. -
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). -
Structural and Electronic Properties of Chalcopyrite Semiconductors
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by ethesis@nitr STRUCTURAL AND ELECTRONIC PROPERTIES OF CHALCOPYRITE SEMICONDUCTORS By Bijayalaxmi Panda Under the Guidance of Prof. Biplab Ganguli Department Of Physics National Institute Of Technology, Rourkela CERTIFICATE This is to certify that the project thesis entitled ” Structural and elec- tronic properties of chalcopyrite semiconductor” being submitted by Bijay- alaxmi Panda in partial fulfilment to the requirement of the one year project course (PH 592) of MSc Degree in physics of National Institute of Technology, Rourkela has been carried out under my supervision. The result incorporated in the thesis has been produced by using TB-LMTO codes. Prof. Biplab Ganguli Dept. of Physics National Institute of Technology Rourkela - 769008 1 ACKNOWLEDGEMENT I would like to acknowledge my guide Prof. Biplab Ganguli for his help and guidance in the completion of my one-year project and also for his enormous motivation and encouragement. I am also very much thankful to Phd scholars of cmputational physics lab whose encouragement and support helped me to complete my project. 2 ABSTRACT We have studied the structural and electronic properties of pure, deffect and doped chalcopyrite semiconductors using Density functional theory (DFT) based first principle technique within Tight binding Linear Muffin Tin orbital (TB-LMTO) method. Our calculated structural parameters such as lattice constant, anion displacement parameter(u) in case of pure chalcopyrite and anion displacement parameter(ux, uy,uz) in case of deffect and doped chal- copyrite, tetragonal distortion(η=c/2a) and bond length are in good agree- ment with other work.