Crystal Builder, Surface Builder, Interface Builder, Polymer Builder, Amorphous Builder. Release 4.0 April 1999 (last full revision March 1997)

Transcription

1 Cerius 2 Builders Crystal Builder, Surface Builder, Interface Builder, Polymer Builder, Amorphous Builder Release 4.0 April 1999 (last full revision March 1997) Scranton Road San Diego, CA / Fax: 619/

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3 Copyright * This document is copyright 1999, Molecular Simulations Inc., a subsidiary of Pharmacopeia, Inc. All rights reserved. Except as permitted under the United States Copyright Act of 1976, no part of this publication may be reproduced or distributed in any form or by any means or stored in a database retrieval system without the prior written permission of Molecular Simulations Inc. The software described in this document is furnished under a license and may be used or copied only in accordance with the terms of such license. Restricted Rights Legend Use, duplication, or disclosure by the Government is subject to restrictions as in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFAR or subparagraphs (c)(1) and (2) of the Commercial Computer Software Restricted Rights clause at FAR , as applicable, and any successor rules and regulations. Trademark Acknowledgments Catalyst, Cerius 2, Discover, Insight II, and QUANTA are registered trademarks of Molecular Simulations Inc. Biograf, Biosym, Cerius, CHARMm, Open Force Field, NMRgraf, Polygraf, QMW, Quantum Mechanics Workbench, WebLab, and the Biosym, MSI, and Molecular Simulations marks are trademarks of Molecular Simulations Inc. IRIS, IRIX, and Silicon Graphics are trademarks of Silicon Graphics, Inc. AIX, Risc System/ 6000, and IBM are registered trademarks of International Business Machines, Inc. UNIX is a registered trademark, licensed exclusively by X/Open Company, Ltd. PostScript is a trademark of Adobe Systems, Inc. The X-Window system is a trademark of the Massachusetts Institute of Technology. NSF is a trademark of Sun Microsystems, Inc. FLEXlm is a trademark of Highland Software, Inc. Permission to Reprint, Acknowledgments, and References Molecular Simulations usually grants permission to republish or reprint material copyrighted by Molecular Simulations, provided that requests are first received in writing and that the required copyright credit line is used. For information published in documentation, the format is Reprinted with permission from Document-name, Month Year, Molecular Simulations Inc., San Diego. For example: Reprinted with permission from Cerius 2 Builders, April 1999, Molecular Simulations Inc., San Diego. Requests should be submitted to MSI Scientific Support, either through electronic mail to support@msi.com or in writing to: * U.S. version of Copyright Page

4 MSI Scientific Support and Customer Service 9685 Scranton Road San Diego, CA To print photographs or files of computational results (figures and/or data) obtained using Molecular Simulations software, acknowledge the source in the format: Computational results obtained using software programs from Molecular Simulations Inc. dynamics calculations were done with the Discover program, using the CFF91 forcefield, ab initio calculations were done with the DMol program, and graphical displays were printed out from the Cerius 2 molecular modeling system. To reference a Molecular Simulations publication in another publication, no author should be specified and Molecular Simulations Inc. should be considered the publisher. For example: Cerius 2 Builders, April San Diego: Molecular Simulations Inc., 1999.

5 Contents 1. Introduction 1 Who should use this documentation How to find information Using other Cerius2 documentation Additional information sources Typographical conventions Crystal Builder 5 Building and unbuilding crystals Building a molecular crystal using general symmetry positions 8 Building a crystal from a 2D periodic model Building an ionic crystal using space groups Changing lattice vectors Creating superstructures from crystals Generating a primitive superlattice Generating a noncrystalline superstructure Generating a superstructure from a facetted crystal18 Unbuilding a crystal Displaying crystals Displaying several cells Drawing Miller planes Displaying crystal facets Calculating cell formula, density, and volume Finding symmetry in a crystal Surface Builder 27 Building and unbuilding surfaces Cleaving a surface from a crystal Building a surface from a nonperiodic model Building a surface by adding atoms Changing surface lattice vectors Creating a surface superstructure Unbuilding a surface Displaying surfaces Cerius 2 Builders/April 1999 v

6 4. Interface Builder 37 About the interface builder Creating an interface Defining the sides of the interface Concepts and general procedure Specifying the sides of the interface Building the interface Editing the interface after it is build Creating a periodic model from an interface Creating a crystal from an interface Creating a surface from an interface Polymer Builder 47 Monomer units Specifying monomer units Monomer files Creating or editing monomers Editing monomers Using monomers created with other programs Homopolymers Building homopolymers Tacticity Monomer head/tail orientation Torsion angles Random copolymers Building random copolymers Random copolymer preferences Reactivities Block copolymers Editing polymers Monomer and polymer display Amorphous Builder 73 How the amorphous builder works Building amorphous structures Building amorphous structures using the default settings 77 Building amorphous structures using custom settings.78 Cloning to create starting models Specifying what torsions to rotate during building Defining rotatable torsions and torsion rules Finding unique rotatable torsions Specifying torsion rotation methods vi Cerius 2 Builders/April 1999

7 Entering data in the state table Editing the state table, specifying rotation methods.. 87 Saving state table data A. References 93 B. Files 95 State table (.ris) file RIS file format Example file Figures Figure 1. Initial crystal orientation with respect to the computer screen Figure 2. Tactic forms of a polymer Cerius 2 Builders/April 1999 vii

8 viii Cerius 2 Builders/April 1999

9 Figure 1. Initial crystal orientation with respect to the computer screen Figure 2. Tactic forms of a polymer Platform Book_name/Month 1997 ix

10 x Platform Book_name/Month 1997

11 1 Introduction Cerius 2 Builders is a complete guide to the specialized builder modules that can be added to the Cerius 2 modeling environment to supplement the basic model sketching capabilities provided in the Visualizer. You need not read this entire documentation set before you start using Cerius 2. Once you are familiar with the information presented in Cerius 2 Modeling Environment, you can read only the sections of this documentation set that describe the builder modules that you want to use. Who should use this documentation This documentation is intended for day-to-day users of Cerius 2 and is of interest to those users who want to use specialized builder modules. Prerequisites You should already be familiar with: The windowing software on your workstation. Use of the mouse on your workstation. Basic UNIX commands. Basic use of the Cerius 2 interface. Quantum mechanical techniques. Your workstation needs to have: Access to a licensed copy of Cerius 2. A home directory in which you can create subdirectories. Cerius 2 Builders/April

12 1. Introduction How to find information If you want to know about Building, visualizing, and editing crystal structures. Constructing 2D periodic systems. Constructing models of crystal interfaces. Building all types of linear polymers. Building amorphous molecular structures of any type. Scientific references. The format of the ris files written by the Analog Builder and Conformers modules. Read Crystal Builder. Surface Builder. Interface Builder. Polymer Builder. Amorphous Builder. References. Files. Using other Cerius 2 documentation You can find additional information about Cerius 2 in several other documentation sets: Cerius 2 Modeling Environment Basic use of the Cerius 2 interface and the C 2 Visualizer module. MSI Forcefield Engines: CDiscover Use of CDiscover in Cerius 2, Insight, and standalone modes. Cerius 2 Simulation Tools The Open Force Field, Force Field Editor, Charges, Minimizer, Dynamics Simulation, Analysis, and Field Calculation modules. Cerius 2 Quantum Mechanics: Quantum Chemistry and Cerius 2 Quantum Mechanics: Physics Quantum-mechanics programs in the Cerius 2 interface. Cerius 2 Command Script Guide How to capture and replay a script of Cerius 2 commands and enhance your command scripts with the features of the Tool Command Language (Tcl). Cerius 2 Installation and Administration Guide Step-by-step instructions for installing and administering Cerius 2 in your operating environment. 2 Cerius 2 Builders/April 1999

13 Additional information sources Additional information sources On-screen help MSI s website On-screen help is available within the Cerius 2 environment. It is accessed by clicking the right mouse button while the cursor is over the item in the interface about which you want information. A brief identification of some items appears when you simply allow the cursor to linger over them. Additional help and some demos are accessed from the Help menu. The URL for the documentattion and customer support areas of MSI s site on the World Wide Web are: Typographical conventions Unless otherwise noted in the text, Cerius 2 Builders uses the typographical conventions described below: Terms introduced for the first time are presented in italic type. For example: Instructions are given to the software via control panels. Keywords in the interface are presented in bold type. In addition, slashes (/) are used to separate a menu item from a submenu item. For example: Select the View/Colors menu item means to click the View menu item, drag the cursor down the pulldown menu that appears, and release the mouse button over the Colors item. Words you type or enter are presented in bold type. For example: Enter in the entry box. UNIX command dialog and examples of lines in files are represented in a typewriter font. For example, the following illustrates a line in a.grf file: Cerius 2 Builders/April

14 1. Introduction CERIUS Grapher File Words in italics represent variables. For example: > cerius2 -b outputfile scriptfile In this example, the name of the file to which text output should be directed replaces the value outputfile, and scriptfile is the name of a file containing a command script. 4 Cerius 2 Builders/April 1999

15 2 Crystal Builder The C 2 Crystal Builder module provides a robust and versatile crystal builder and editor. It also includes plane and facet tools to aid in visualization of crystal structures. Crystal structures are of fundamental importance in materials science. Many other Cerius 2 modules perform calculations and simulations on crystalline structures, including: Crystal Packer Diffraction-Crystal Diffraction-Faulted DLS HRTEM LEED/RHEED Morphology Rietveld Sorption This chapter contains information on: Building and unbuilding crystals Displaying crystals Calculating cell formula, density, and volume Finding symmetry in a crystal Cerius 2 Builders/April

16 2. Crystal Builder For information about Loading and saving crystal structure files. Crystal file formats. Building crystal surfaces. Building crystal interfaces. Energy minimization of crystals. Calculations and simulations involving crystals. See The discussion of loading and saving structure files in Cerius 2 Modeling Environment. Files appendix, Cerius 2 Modeling Environment. Surface Builder. Interface Builder. Crystal Packer module, Cerius 2 Computational Instruments Property Prediction; Minimizer module, Cerius 2 Simulation Tools. Cerius 2 Computational Instruments Property Prediction and Cerius 2 Analytical Instruments. Building and unbuilding crystals Following some introductory material (below), this section contains information on: Building a molecular crystal using general symmetry positions Building a crystal from a 2D periodic model Building an ionic crystal using space groups Changing lattice vectors Creating superstructures from crystals Unbuilding a crystal The C 2 Crystal Builder module enables you to build many types of crystals, from small ionic models to large polymer models. Fragment types can be mixed so that solvent fragments are incorporated into polymer crystals or small-molecule fragments into zeolite structures. (See Cerius 2 Modeling Environment for definitions of fragments, models, molecules, etc.) Usually the crystallographic asymmetric unit consists of only a portion of the unit cell. In such cases, it is more convenient to work with a crystal chemical unit, which consists of a complete molecule, rather than only a part. In C 2 Crystal Builder, the term asym- 6 Cerius 2 Builders/April 1999

17 Building and unbuilding crystals General procedure Accessing the tools metric unit refers to any unit, whether a complete fragment or part of a polymer chain or a group of ions, that can be replicated throughout the unit cell of the crystal. The following are the three necessary steps in building a crystal. Although they need not be, these steps are often performed in the following order: Specify the asymmetric unit. This can be done by loading or sketching a model or by placing individual atoms by entering their coordinates. Specify the crystal lattice type for the unit cell, that is, the crystallographic parameters a, b, c (cell lengths) and α, β, γ (cell angles). Select a space group (either by mnemonic or number) or build it from the various symmetry operators. Controls belonging to the C 2 Crystal Builder module are contained on the CRYSTAL BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the CRYSTAL BUILDER card, click its name so that this card moves in front of the others (if it is not already there: Cerius 2 Builders/April

18 2. Crystal Builder How it works The important commands for building a crystal are grouped in the Crystal Building control panel, which is accessed by selecting the Crystal Building menu item on the CRYSTAL BUILDER card. Tools on this control panel are used to build the crystal and to open other control panels needed to input various crystal parameters. The building process is started by clicking the BUILD CRYSTAL pushbutton in the Crystal Building control panel. The crystal is always built in the current model space, and exactly what happens depends on the contents of the current model space: If a nonperiodic or 2D-periodic model is current, it is used as the asymmetric unit for building the crystal. If the model space is empty, a unit cell box is displayed and atoms can be placed in it afterwards. If a crystal is already present in the current model space, it is rebuilt using the current crystal-building settings. You can return to the asymmetric unit at any time by clicking the UNBUILD CRYSTAL pushbutton in the Crystal Building control panel. In addition to building regular crystals, you can create superlattices and superstructures with the C 2 Crystal Builder module. Generating a superlattice resets the crystal symmetry to P 1 and converts all atoms displayed in the model window (including those that are symmetry copies) into real atoms. In generating a superstructure, the unit cell is removed and all atoms in the model become part of the nonperiodic structure. Building a molecular crystal using general symmetry positions Constructing the starting model Accessing the tools To construct the asymmetric unit, load and/or build a model (in a new model space) using the Sketcher control panel or other Visualizer tools (see the discussion of building models in Cerius 2 Modeling Environment). Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. Open the Crystal Build Preferences control panel by clicking the Preferences pushbutton on the Crystal Building control panel. 8 Cerius 2 Builders/April 1999

19 Building and unbuilding crystals Starting the process Important Specifying unit-cell shape Building the crystal Specifying crystal symmetry Open the Cell Parameters control panel by clicking the Cell Parameters pushbutton on the Crystal Building control panel. Alternatively, select the Unit Cell/Cell Parameters menu item on the CRYSTAL BUILDER card. Open the General Positions control panel by clicking the Edit pushbutton to the right of the POSITIONS control on the Crystal Building control panel. Alternatively, select the Symmetry/General Positions menu item from the CRYSTAL BUILDER card. For most crystal structures, the default display style is best. If this has been changed, you need to choose DEFAULT from the Visualization style popup in the Crystal Build Preferences control panel. If you want bonds across unit cell boundaries and between symmetry copies of atoms to be calculated automatically, assure that the Automatically calculate bonds check box in the Crystal Build Preferences control panel is checked (see the discussion of bond calculation criteria in Cerius 2 Modeling Environment). If the Automatically calculate bonds check box is checked, bonding is automatically recalculated for any crystal loaded from a file. This may result in chemically unreasonable bonds being formed between atoms that are close together. As a result, you may want to turn this option off or adjust the bonding calculation parameters appropriately before loading a crystal later in your Cerius 2 session. To specify the cell size and shape, enter its dimensions and angles in the appropriate entry boxes in the Cell Parameters control panel. If some of these parameters are restrained by symmetry considerations or if some angle values are mutually incompatible, you cannot change their values, or related values are changed to match, whichever is appropriate. To construct the basic unit cell around the model, click the BUILD CRYSTAL pushbutton in the Crystal Building control panel. To specify the crystal symmetry, set the Choose Symmetry Description control in the Crystal Building control panel to POSI- TIONS. The crystal symmetries used for building are listed in the General Positions control panel. Primitive is the default lattice, so: Cerius 2 Builders/April

20 2. Crystal Builder Technical notes If you want a lattice other than primitive, choose the centering type from the Centering popup in the General Positions control panel. If you want to constrain the cell parameters to a particular lattice type, set the Lattice Type popup in the General Positions control panel. By setting the lattice type and the centering, you can specify any of the conventional Bravais lattices. You can enter the general symmetry positions in the Add Symmetry Operator entry box in the General Positions control panel. The format is: rot 1, trans 1, rot 2, trans 2, rot 3, trans 3 Where rot 1, rot 2, and rot 3 are expressions from the set {x, y, z, -x, -y, -z, x-y, y-z, z-x, -x+y, -y+z, -z+x}, which are used to generate the rotational part of the symmetry operation, and where trans 1, trans 2, trans 3 are positive and rational fractions, from the set {+1/ 6, +1/4, +1/3, +1/2, +2/3, +3/4, +5/6} or the decimal equivalents. Examples of symmetry operators are: -x -y -z -x y -z y +1/2 -x +1/2 z +1/2 y -x+y z +1/6 z y x Editing the symmetry Symmetry positions are tested for consistency with the current unit cell parameters, and bad positions are rejected. For example, you cannot enter the symmetry position corresponding to a sixfold rotation axis if the current unit cell is cubic. Conversely, if the cell parameters are altered after the symmetry position is entered, you are warned that some of the symmetries in use are not consistent with the symmetry of the lattice. Whenever any change is made to the cell parameter values, the crystal is updated and redisplayed, although it is not rebuilt (that is, connectivity is unchanged). If you make a mistake, remove a symmetry entry by entering the number of the symmetry entry (from the General Position Operators list box in the General Positions control panel) in the Remove Symmetry Operator entry box. To remove all symmetry entries, 10 Cerius 2 Builders/April 1999

21 Building and unbuilding crystals Additional information use the Clear List of General Positions action button and confirm the action. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Building a crystal from a 2D periodic model Constructing the starting model Accessing the tools Specifying the crystal Building the crystal Load a 2D periodic model (i.e., a surface model) into the current (empty) model space. This can be done by loading such a model from file or by using the C 2 Surface Builder (see Surface Builder) to create one. Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. Open the Crystal Build Preferences control panel by clicking the Preferences pushbutton on the Crystal Building control panel. Open the Find Space Group control panel by selecting the Symmetry/Find Symmetry menu item from the CRYSTAL BUILDER card. For most crystal structures, the default display style is best. If this has been changed, you need to choose DEFAULT from the Visualization style popup in the Crystal Build Preferences control panel. Enter the Vacuum Thickness that you want (in the Crystal Build Preferences control panel). This is the thickness of the empty layer that is created when you make the surface into a crystal. The crystal cell vector perpendicular to the surface is taken to be the thickness of the surface atoms plus the vacuum thickness. Choose the Orientation for the vacuum slab in the Crystal Build Preferences control panel. The vacuum layer is oriented normal to the specified Cartesian axis. The thickness of the surface, together with the vacuum thickness, determines the cell dimension normal to the vacuum slab. Click the BUILD CRYSTAL pushbutton in the Crystal Building control panel. The 2D surface structure is converted into a 3D crystal. The crystal cell parameters are obtained from the surface mesh parameters. Cerius 2 Builders/April

22 2. Crystal Builder Finding the symmetry Additional information The crystal is created without any symmetry defined. If you want to find the symmetry of the crystal you need to use the Find Space Group control panel. If you want the crystal model to be redisplayed according to any symmetry that is found, check the Update Model check box in the Find Space Group control panel. Atoms that are found to be symmetry copies of one another (within the Tolerance) are moved so that they are exact symmetry copies. To start a program that searches for any symmetry that may exist in the current crystal, click the Find Space Group Symmetry action button in Find Space Group control panel. (Periodicity is included if the crystal can be represented with a smaller unit cell.) The symmetry that is found is reported to the text window. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Building an ionic crystal using space groups Accessing the tools Begin with an empty model space. Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. Open the Crystal Build Preferences control panel by clicking the Preferences pushbutton on the Crystal Building control panel. Open the Space Groups control panel by clicking the Edit pushbutton to the right of SPACE GROUP on the Crystal Building control panel. Alternatively, select the Symmetry/Space Groups menu item from the CRYSTAL BUILDER card. Open the Cell Parameters control panel by clicking the Cell Parameters pushbutton on the Crystal Building control panel. Alternatively, select the Unit Cell/Cell Parameters menu item on the CRYSTAL BUILDER card. Open the Add Atom control panel by clicking the Add Atoms pushbutton on the Crystal Building control panel. Alternatively, select the Build/Add Atom menu item from the menu bar in the Visualizer s main control panel. 12 Cerius 2 Builders/April 1999

23 Building and unbuilding crystals Starting the process Building the crystal Specifying crystal symmetry Technical notes For most crystal structures built by this method, the default display or original style is best, so choose DEFAULT or ORIGI- NAL from the Visualization style popup in the Crystal Build Preferences control panel. In the ORIGINAL style, atoms appear exactly as specified by their coordinates. In the DEFAULT style, atoms with coordinates outside the unit cell are drawn translated to within the cell or to the most appropriate location in relation to the connectivity. Fragments whose centers of geometry are on cell faces, edges, and corners are repeated on the opposite face, edges, or corners. To construct the basic unit cell within which to build the model, click the BUILD CRYSTAL pushbutton in the Crystal Building control panel. To specify the crystal symmetry, set the Choose Symmetry Description control in the Crystal Building control panel to SPACE GROUP. Enter the space group number or name in the Space Group entry box (of the Space Groups control panel), by typing it or by choosing it from the associated pulldown. Alternatively, enter the name or number of a space group in the same class as the one you want, then use the Step through groups arrows to find the desired space group. The space groups that are stepped through are restricted to the crystal class to protect against accidentally changing the crystal cell parameters. If the space group has more than one Option, choose the Option that you want to apply. Review the Space Group Information and Symmetry Positions list boxes in the Space Groups control panel for details on the chosen space group. The space groups used by Cerius 2 are those that appear in the International Tables of Crystallography, Volume A (1989). Only the brief symbol is required the Space Group entry box. Cerius 2 also recognizes all nonstandard space group settings. The space group symbol consists of a maximum of four fields of letters and numbers, separated by spaces, and is entered in the Space Group entry box. Input is not case sensitive. Bars above numbers are represented by minus signs in front, and subscripts Cerius 2 Builders/April

24 2. Crystal Builder are entered immediately following the number to which they belong. Here are some examples of space group specifications: Space group number 1: P 1 Space group number 2: P -1 Space group number 17: P Space group number 88: I 41/a Space group number 193: P 63/m c m Space group number 226: F m -3 c Specifying unit-cell shape Choosing the coordinate system Constructing the asymmetric unit Choosing certain space groups forces changes to some cell parameters. For example, selecting a cubic space group sets the cell angles to 90 and sets a = b = c. Some space groups have several options in the International Tables of Crystallography. For the current space group, these are given in the Option pulldown. For example, all monoclinic space groups have a choice of b or c as the unique cell axis. Some also have three alternatives for the cell, giving a total of nine different settings for one space group. Each setting has a different full space group symbol, but they share the same brief symbol. Some orthorhombic, tetragonal, and cubic space groups have more than one choice for the origin of the unit cell, and these are also listed. Some trigonal space groups offer a choice of rhombohedral axes (a = b = c, α = β = γ) or hexagonal axes (a = b c, α = β = 90, γ = 120 ). Use the pulldown to select the appropriate option. To specify the cell size and shape, enter its dimensions and angles in the appropriate entry boxes in the Cell Parameters control panel. If some of these parameters are restrained by symmetry considerations or if some angle values are mutually incompatible, you cannot change their values, or related values are changed to match, whichever is appropriate. To specify what coordinate system you want to use in constructing the model of the asymmetric unit, use the coordinate system popup (located next to the coordinates entry box in the Add Atom control panel). Set the popup to XYZ for the Cartesian system or ABC for the fractional system. For each individual real atom (i.e., those that are not symmetry copies), you use controls in the Add Atom control panel to enter an element type and the x, y, z or a, b, c coordinates. 14 Cerius 2 Builders/April 1999

25 Building and unbuilding crystals Editing the asymmetric unit Additional information You may also want to specify other options: Hybridization, a nonzero Charge, Occupancy, Name, and isotropic and/or anisotropic temperature factors. Click the ADD ATOM pushbutton after each atom is specified. The new atom and any symmetry copies appear in the model window. If you make a mistake and want to remove an atom, use the UNDO pushbutton. You can also select the atom in the model window and choose the Edit/Delete menu item from the menu bar on the main Visualizer control panel. The symmetry copies of the atom are also deleted. Please see the on-screen help for additional information about the controls in all the panels mentioned here. For additional information about the Add Atom control panel, see the discussion of build operations in Cerius 2 Modeling Environment. Changing lattice vectors Accessing the tools Changing the lattice vectors The facility for altering lattice vectors allows you to redefine the lattice vectors of a crystal without changing the crystal structure. You might simply want to reorient the lattice so that the a, b, and c axes point in new directions. An example might be preparing a crystal for the C 2 HRTEM module, where the beam direction is specified relative to the crystal lattice. You may need to alter lattice vectors when you want to reduce a conventional unit cell to a smaller primitive unit cell. Changing the lattice popup in the Lattice Redefinition control panel to PRIMI- TIVE before clicking the Change action button redefines lattice vectors for the primitive unit cell. Open the Lattice Redefinition control panel by selecting the Unit Cell/Redefine Lattice menu item from the CRYSTAL BUILDER card. To preview the new vectors before actually applying them to the crystal, check the Show new lattice vectors check box. To specify new lattice vectors, assure that the lattice popup is set to USER-SPECIFIED and enter the three desired values in the New entry boxes, specifying them in terms of the three current lattice Cerius 2 Builders/April

26 2. Crystal Builder Changing to a primitive lattice Applying the changes to the current crystal Technical notes Caution Additional information vectors. The new vectors should be true lattice vectors and should form a right-handed set. They form the three new cell sides. The new vectors appear as light blue lines on the model if the Show new lattice vectors check box is checked. Alternatively, if you want to change from a conventional lattice to a primitive lattice, change the lattice popup to PRIMITIVE. The New entry boxes are set as appropriate to change the current model to a primitive lattice. As long as the popup is set to PRIMI- TIVE, you cannot edit the new lattice vectors. Click the Change to action button to change the lattice from the old to the new vectors. The redefined crystal overwrites the current model, so you should first save the current model or copy it to another model space if you want to preserve it. If the lattice popup is set to USER-SPECIFIED, the old lattice is lost, as are symmetry descriptions. If the lattice popup is set to PRIMITIVE, Cerius 2 keeps the symmetry descriptions in the model, transforming them as appropriate, and also remembers the old lattice parameters (they are stored with the model) so that you can change them later to a conventional lattice description. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Creating superstructures from crystals Converting a crystal into a superstructure removes the applied symmetry and changes the symmetry-copies of atoms into real atoms. Two types of superstructure can be created from a crystal model: A periodic superlattice The superlattice is a crystal of P 1 symmetry. Building a primitive superlattice is a way of reducing symmetry without altering the crystal structure. Moving atoms and other edits are often easier with a P 1 model, because there 16 Cerius 2 Builders/April 1999

27 Building and unbuilding crystals are no symmetry constraints to interfere, as in the higher symmetries. The superlattice may be quite large, made up of several unit cells. Building a large superlattice and then editing it is a good way of introducing disorder into a crystal structure. For information about disorder, see the relevant chapter in Cerius 2 Modeling Environment. A nonperiodic superstructure A nonperiodic superstructure has the same structure as a crystal, but Cerius 2 treats it like a nonperiodic structure. Thus, you can perform manipulations and calculations on the nonperiodic structure (such as a charge equilibration calculation) that cannot be done on a crystalline model. This section contains information on: Generating a primitive superlattice Generating a noncrystalline superstructure Generating a superstructure from a facetted crystal Caution The current surface is lost when the superlattice or superstructure is built. If you want to save the current surface, copy it into a new model space and/or save it to a file before creating the superstructure. Generating a primitive superlattice Accessing the tools Making a superlattice You need to create a superlattice from a crystal model having higher symmetry before performing tasks such as substitutional disorder and sorption simulations that require models with primitive symmetry. Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. Open the Crystal Visualization control panel by selecting the Visualization menu item from the CRYSTAL BUILDER card. To display the current model in the size that you want the superlattice to be, enter a, b, and c values in the Display Range entry boxes in the Crystal Visualization control panel. Cerius 2 Builders/April

28 2. Crystal Builder Additional information Click the Crystalline Superlattice action button in the Crystal Building control panel. The entire current model is converted into a superlattice with P 1 symmetry and the previous symmetry-copy atoms become real atoms. The superstructure is a new larger unit cell that is the size of the previously displayed collection of cells. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Generating a noncrystalline superstructure Accessing the tools Making a superstructure Additional information Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. Open the Crystal Visualization control panel by selecting the Visualization menu item from the CRYSTAL BUILDER card. To display the current model in the size that you want the superstructure to be, enter a, b, and c values in the Display Range entry boxes in the Crystal Visualization control panel. Click the Non-periodic Superstructure action button in the Crystal Visualization control panel. The entire current model is converted into a nonperiodic superstructure. This structure contains the same atoms as all the displayed cells of the original crystal, including any repeated face atoms. However, the model is nonperiodic, meaning it is not a unit cell. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Generating a superstructure from a facetted crystal Accessing the tools Facetting the crystal Making the superstructure Open the Crystal Facetting control panel by selecting the Facetting menu item from the CRYSTAL BUILDER card. Select the group of atoms to be deleted using the crystal facetting process described under Displaying crystal facets. Uncheck the Display selected atoms check box in the Crystal Facetting control panel so that you can estimate how the superstructure will look. Click the Generate Superstructure from facetted crystal action button at the bottom of the Crystal Facetting control panel. This 18 Cerius 2 Builders/April 1999

29 Displaying crystals Additional information converts the visible part of the structure (deleting the selected atoms) into a nonperiodic superstructure. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Unbuilding a crystal Accessing the tools Unbuilding a crystal Additional information Select the Crystal Building menu item on the CRYSTAL BUILDER card to open the Crystal Building control panel. To return the model to its nonperiodic asymmetric unit, deleting all symmetry copies of atoms and the unit cell, click the UNBUILD CRYSTAL pushbutton. This leaves the atoms of the original model with the original bonding. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Displaying crystals After each crystal building operation, the crystal is displayed in the model window. The initial orientation of the crystal is such that the c axis of the cell is perpendicular to the screen and the projection of the b axis on the screen is vertical (Figure 1). The display options on the Crystal Visualization control panel enable you to change the display. (You can also use the mouse controls to move the model) This section contains information on: Displaying several cells Drawing Miller planes Displaying crystal facets Displaying several cells The number of unit cells of the crystal that are displayed is a display property only that is, all calculations on a crystal model are Cerius 2 Builders/April

30 2. Crystal Builder b c a Figure 1. Initial crystal orientation with respect to the computer screen By default, the c coordinate is perpendicular to the screen, and the b and c coordinates and the axes that are vertical and perpendicular to the screen are all in the same plane. Accessing the tools Changing the number of unit cells displayed Additional information done using periodic boundary conditions and assuming an infinitely repeating lattice. Open the Crystal Visualization control panel by selecting the Visualization menu item on the CRYSTAL BUILDER card or by clicking the Visualization pushbutton on the Crystal Building control panel (see Building and unbuilding crystals). Change the number of displayed cells in the current crystal model by entering values in the three Crystal Cell Display Range entry boxes and clicking the associated ENTER pushbutton. The number of cells drawn is the product of the number of cells along each cell axis (a b c). Please see the on-screen help for additional information about the controls in all the panels mentioned here. Drawing Miller planes Miller planes enable you to display planes in crystal structures, which aids in the study of crystal habit planes. 20 Cerius 2 Builders/April 1999

31 Displaying crystals Accessing the tools Displaying Miller planes for the current crystal model Positioning the Miller planes Open the Crystal Visualization control panel by selecting the Visualization menu item on the CRYSTAL BUILDER card or by clicking the Visualization pushbutton on the Crystal Building control panel (see Building and unbuilding crystals). Open the Miller Plane Options control panel by clicking the More pushbutton on the Crystal Visualization control panel. Check the Show Miller Plane check box in the Crystal Visualization control panel. To display single or multiple Miller planes, choose SINGLE or FAMILY from the Miller Plane popup. To change the color of the Miller plane(s), select the desired color from the Color popup. To adjust the opacity of the plane, change the value in the Transparency entry box in the Miller Plane Options control panel. To reorient the Miller plane(s), enter the desired h, k, and l Miller indices in the three Miller Plane Display entry boxes in the Crystal Visualization control panel and click the associated ENTER pushbutton. Set the position of the Miller plane in one of three ways: Specify a point in fractional coordinates to lie on the plane in the position entry box in the Miller Plane Options control panel. Enter a perpendicular distance in angstroms from the cell origin to the plane in the Origin Distance entry box in the Crystal Visualization control panel. The Origin Distance entry box specifies the perpendicular distance from the plane to the origin in angstroms. The distance is measured in the direction of the conventional plane normal from the origin and may thus be negative. Use the associated up and down arrows to step the plane through the crystal. Use the up and down Origin Distance arrows to step the plane through the crystal. If desired, orient the Miller plane parallel or perpendicular to the computer screen by selecting from the Orient to Screen popup in the Miller Plane Options control panel and clicking the associated action button. Cerius 2 Builders/April

32 2. Crystal Builder Additional information Please see the on-screen help for additional information about the controls in all the panels mentioned here. Displaying crystal facets Accessing the tools Adding facets to the current crystal model Editing facets An additional aid to visualization is the ability to section the crystal by facetting it along Miller planes. Facetting is essentially a tool for mass selection of atoms according to which side of specified planes they lie on. The ability to hide selected atoms and to generate superstructures (see Generating a superstructure from a facetted crystal) from the facetted crystal (removing the selected atoms) allows the study of crystal habits and facetted crystals. These facetting controls are best used when the display range on the Crystal Visualization control panel is greater than 1, 1, 1 (see Displaying several cells). Open the Crystal Facetting control panel by selecting the Facetting menu item on the CRYSTAL BUILDER card. Open the Edit Facet Options control panel by clicking the More pushbutton that appears on the Crystal Facetting control panel when the EDIT FACET popup item is chosen. Check the Facetting on check box in the Crystal Facetting control panel. Assure that the popup below the Display selected atoms check box is set to ADD NEW FACET. Enter the Miller Indices of the facet into the three entry boxes and click the associated ENTER pushbutton. Specify other facet parameters by using the position, Color, and Transparency controls in the Crystal Facetting control panel. Click the Add facet action button. The facet appears in the model window and its description appears in the Current Facets list box in the Crystal Facetting control panel. Repeat the above steps to create more facets. To edit existing facets, change the ADD NEW FACET popup to EDIT FACET. Use the Edit Facet Number entry box to specify which facet to edited (the number matches that in the Current Facets list box). 22 Cerius 2 Builders/April 1999

33 Calculating cell formula, density, and volume Selecting atoms Additional information Then adjust the facet position and/or orientation, change its color, or remove the facets altogether using the various controls that appear on the Crystal Facetting control panel. The Edit Facet Options control panel contains additional controls for editing existing facets. To select atoms based on their positions with respect to the facets, set the Selection Logic popup to OUTSIDE ANY or INSIDE ALL. You may want to uncheck the Display selected atoms check box at this stage to view the effects better. Unchecking the box gives you a preview of how the superstructure (Generating a superstructure from a facetted crystal) will look. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Calculating cell formula, density, and volume Accessing the tools Obtaining the information Additional information You can compare the cell volume and density values of the current crystal model with experimental results to estimate the accuracy of the model structure. Open the Cell Contents control panel by selecting the Unit Cell/ Cell Contents menu item from the CRYSTAL BUILDER card. The list box in the Cell Contents control panel automatically displays information about the unit cell of the current model, including the number of atoms, volume, density, and cell formula. (For 2D periodic and nonperiodic models, appropriate values are displayed.) The contents of this list box in are automatically kept up-to-date with the current model. If you want to display the current information in the text window, click the Print to Text Window action button. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Cerius 2 Builders/April

34 2. Crystal Builder Finding symmetry in a crystal Accessing the tools Setting up Finding the symmetry Additional information You may want to find the space-group symmetry of the current crystal model. For example, you might have performed tasks that required you to change the model into a superlattice and now want to reimpose symmetry. Open the Find Space Group control panel by selecting the Symmetry/Find Symmetry menu item from the CRYSTAL BUILDER card. Choose the tolerance you want to use for finding symmetry. For most models, the default value of 0.1 Å should suffice. You may enter other values by entering any value in the Tolerance entry box or by choosing a defined value from the associated popup. If you want to see what symmetry exists in the model without forcing the model s structure to that symmetry, uncheck the Update Model check box. If you want the found space group to always be the standard setting for the found space group (i.e., the first Option shown in the Space Groups control panel, see Building an ionic crystal using space groups), check the Force to Standard Setting check box. Sometimes this means that the updated model is reoriented from the original. If the Force to Standard Setting box is unchecked, the symmetry finder (after finding the space group) attempts to find a setting that matches the current origin and axes of the model, with minimal change to the model s orientation when the model is updated. Click the Find Space Group Symmetry action button. If the Update Model check box is checked, the model is transformed as appropriate for the newly found cell vectors and symmetry. Atoms that are deemed to be symmetry copies of each other (according to the Tolerance), but whose positions do not exactly match, are moved so as to give an exact symmetry match. Please see the on-screen help for additional information about the controls in all the panels mentioned here. 24 Cerius 2 Builders/April 1999

35 Finding symmetry in a crystal Cerius 2 Builders/April

36 2. Crystal Builder 26 Cerius 2 Builders/April 1999

37 3 Surface Builder The C 2 Surface Builder module is used for constructing 2D-periodic structures by cleaving a plane from a crystal or by placing atoms and fragments within a suitable 2D-surface cell. Surface models are required for calculations with some modules, for example, the C 2 LEED/RHEED module. For calculations using other modules, you can convert surface structures into large nonperiodic superstructures to represent the surface. The C 2 Surface Builder module also helps to visualize surfaces within crystal models that were built with the C 2 Crystal Builder module. This chapter contains information on: Building and unbuilding surfaces Displaying surfaces For information about Loading and saving surface structure files. Surface file formats. Building crystals. Building interfaces from surfaces. Interface Builder. Diffraction from surfaces. Cerius 2 Analytical Instruments. See The discussion of loading and saving structure files in Cerius 2 Modeling Environment. The discussion of Cerius 2 structure files in Cerius 2 Modeling Environment. Crystal Builder. Cerius 2 Builders/April

38 3. Surface Builder Building and unbuilding surfaces Following some introductory material (below), this section contains information on: Cleaving a surface from a crystal Building a surface from a nonperiodic model Building a surface by adding atoms Changing surface lattice vectors Creating a surface superstructure Unbuilding a surface General procedure File formats Accessing the tools The C 2 Surface Builder builds surfaces in which a basic surface unit is repeated using a 2D periodic cell. Many similarities exist between the Crystal Builder module, which builds 3D structures, and the Surface Builder module, which builds 2D structures. You can also use the surface builder to convert surfaces into superstructures and superlattices. Any surface can be unbuilt, converting the surface to one cell of a nonperiodic model. All unit cell information is lost. You can build surfaces in two basic ways: Specify a surface as a slab within a crystal and a thickness for the slab to be cleaved out (cleave-from-crystal method, see Cleaving a surface from a crystal). Specify a 2D unit cell and add nonperiodic models (Building a surface from a nonperiodic model) or atoms (Building a surface by adding atoms) to it (build-from-atoms method). The MSI and CSSR file formats are the only formats that save 2D models, that is, they include the 2D unit cell information. However, once the surface has been converted into a nonperiodic superstructure, any of the file formats used for nonperiodic models can be used to save the structure. Controls belonging to the C 2 Surface Builder module are con- 28 Cerius 2 Builders/April 1999

39 Building and unbuilding surfaces tained on the SURFACE BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the SURFACE BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this: Cleaving a surface from a crystal Constructing the starting model Accessing the tools Beginning the process In building a surface from a 3D crystal, a slab is defined within the crystal and then the slab is cleaved out as a surface. Build (see Building and unbuilding crystals) or load a crystal model to serve as the starting structure. This model must be loaded into the current Cerius 2 session, but need not be the current model. Select the Cleave Crystal Surface menu item on the SURFACE BUILDER card to open the Cleave Crystal Surface control panel. Open the Surface Box control panel by clicking the More pushbutton on the Cleave Crystal Surface control panel. Choose the desired crystal model from the model pulldown near the top of the Cleave Crystal Surface control panel. This assures that the surface is cut from the correct crystal. Cerius 2 Builders/April

40 3. Surface Builder Specifying the surface slab Choose the appropriate Cleave Rule. If you want the surface to be cleaved on an atom-by-atom basis, ignoring bonds, use the ATOMIC rule. If you want Cerius 2 to try to maintain whole molecules, choose the DEFAULT or MOLECULAR rule. For more information about cleave rules, see the on-screen help. From the face to have dangling bonds popup, select how you want dangling bonds to be handled. All the bonding that was present in the crystal model is transferred to the surface model. Additionally, you can use this popup to control whether to display the bonds to atoms that are not included in the surface. These connected atoms appear in the surface model as dummy X atoms. You may view them, but they do not affect calculations. (However, you can select them all by element and change them, for instance, to hydrogens.) Enter the Miller indices for the slab in the Direction entry box. When the Miller indices have been specified, the surface builder selects two vectors, U and V, in the plane of the slab to be the basis vectors for the surface. These are two of the set of shortest lattice vectors lying in the plane. Use the Direction, U, and V entry boxes on the Surface Box control panel to set the shape and position of the cleaving slab with respect to the crystal. Set the thickness of the surface slab by entering a value in one of the Depth entry boxes (in terms of angstroms for the left entry box or number of cells for the right entry box) in the Cleave Crystal Surface control panel. The thickness of the slab in number of cells refers to the crystallographic d-spacing. For example, when you slice the (1 1 0) plane, the depth of one unit cell is 1 d(1 1 0). To display the cleaving slab on the crystal model before splitting it from the crystal (as a yellow dashed line, click the Display Surface Box check box. The contents of the cleaving slab become the basis for the surface model. Adjust the position of the slab by entering an Origin for the cleaving slab (with respect to the crystal coordinates) or by using the six Move box arrows on the Surface Box control panel. You can also move the slab with the Move box perpendicular arrows in the Cleave Crystal Surface control panel. The position of the cleaving box is instantly updated in the model window, so long as the Display Surface Box check box in the Cleave Crystal Surface control panel is checked. 30 Cerius 2 Builders/April 1999

41 Building and unbuilding surfaces Cleaving the surface Caution Additional information Now open a new, empty model space (see Cerius 2 Modeling Environment to review how to do this) to contain the surface model. Click the CLEAVE pushbutton on the Cleave Crystal Surface control panel. The cleaved surface appears in the current model space. If you cleave a crystal while in a nonempty model space, the current model is overwritten, except if it is the crystal from which the surface is being cleaved (for which a warning appears and the procedure is halted). Please see the on-screen help for additional information about the controls in all the panels mentioned here. Building a surface from a nonperiodic model Constructing the starting model Accessing the tools Beginning the process Building a surface from a nonperiodic model involves positioning the model within a surface cell and then generating the surface. The model must be built or read in before the cell is defined. The surface is built in the yz plane, with the v surface vector coincident with the z axis. You should position the model roughly where you want it to be when the surface is built. (See the discussion of moving and manipulating models in Cerius 2 Modeling Environment.) Load or build a nonperiodic model. See Cerius 2 Modeling Environment for information on building, saving, and loading models. Select the Building From Atoms menu item on the SURFACE BUILDER card to open the Building From Atoms control panel. Open the Surface Build Preferences control panel by clicking the Preferences pushbutton on the Building From Atoms control panel. Open the Surface Cell Parameters control panel by clicking the Cell Parameters pushbutton in the Building From Atoms control panel. In the Surface Build Preferences control panel, set the Visualization style to ORIGINAL. If you want bonds across unit cell boundaries and between symmetry copies of atoms to be calculated automatically, assure that Cerius 2 Builders/April

42 3. Surface Builder the Automatically calculate bonds check box in the Surface Build Preferences control panel is checked (see the discussion of bond calculation criteria in Cerius 2 Modeling Environment). Important Specifying the unit surface cell Building the surface If the Automatically calculate bonds check box is checked, bonding is automatically recalculated for any surface loaded from a file. This may result in chemically unreasonable bonds being formed between atoms that are close together. As a result, you may want to turn this option off or adjust the bonding calculation parameters appropriately before loading a surface later in your Cerius 2 session. Enter the dimensions of the surface cell in the u, v, and θ entry boxes of the Surface Cell Parameters control panel. (The choice of coordinate system has no effect until after the surface is built.) However, choosing an unsuitable 2D cell may lead to many atoms overlapping and, consequently, many bonds across cell boundaries. Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model window. As needed, readjust the position of the model with respect to the surface cell using keyboard mouse combinations and/or items in the Move pulldown (on the main control panel s menu bar) and the Sketcher control panel (see Cerius 2 Modeling Environment for details). At this stage, you may want to redisplay the surface according to one of the other visualization styles. Choose a new Visualization style with the popup in the Surface Build Preferences control panel: The DEFAULT option is suitable for most surfaces. All bonded fragments (molecules) are translated so that their centers of geometry lie within the unit cell. Networks are displayed so that, in the repeat direction of the network, atoms fit into the cell. Bonded fragments or atoms that lie on a cell faces or edge are repeated on the opposite face or edge. The ONE-CELL option means to translate each atom into the surface cell. No repeats are shown, resulting in exactly one cell s worth of atoms being shown. 32 Cerius 2 Builders/April 1999

43 Building and unbuilding surfaces The ORIGINAL option makes atoms appear exactly where they were originally defined. No extra translations are added, so atoms may appear outside the unit cell. Additional information Tip Operations such as moving atoms can leave the display inconsistent with the visualization style. Checking the Enable automated recalculation box enables automatic recalculation of the display. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Building a surface by adding atoms Beginning the process Accessing the tools Specifying the unit surface cell Building the surface Adding atoms Building a surface from individually placed atoms involves positioning them within a surface cell and then generating the surface. The cell is generated before the atoms are placed in it. Begin with an empty model space. Select the Building From Atoms menu item on the SURFACE BUILDER card to open the Building From Atoms control panel. Open the Surface Cell Parameters control panel by clicking the Cell Parameters pushbutton in the Building From Atoms control panel. Open the Add Atom control panel by clicking the Add Atoms pushbutton on the Building From Atoms control panel. Alternatively, select the Build/Add Atom menu item in the main Visualizer control panel. Enter the dimensions of the surface cell in the u, v, and θ entry boxes of the Surface Cell Parameters control panel. (The choice of coordinate system has no effect until after the surface is built.) Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model window. Choose the surface fractional (UVd) or Cartesian (XYZ) coordinate system from the popup in the Add Atom control panel. Cerius 2 Builders/April

44 3. Surface Builder Additional information For each atom, you need to enter an element type and x, y, z coordinates (Cartesian) or U, V, d coordinates (surface fractional). The x, y, z, and d coordinates are in angstroms, and U and V in fractional coordinates. You may also want to specify other options for the atom: Hybridization, a nonzero Charge, Occupancy, Name, and isotropic and/or anisotropic temperature factors. Click the ADD ATOM pushbutton after each atom has been specified. The new atom appears in the model window. If you make a mistake and want to remove an atom, you can delete it using the UNDO pushbutton. You can also delete selected atoms with items in the Edit menu on the main Visualizer control panel. Please see the on-screen help for additional information about the controls in all the panels mentioned here. For additional information about the Add Atom control panel, see the discussion of build operations in Cerius 2 Modeling Environment. Changing surface lattice vectors How it works Accessing the tools Changing the lattice vectors Once a surface is built, you may want to edit the lengths and angles of the surface cell vectors, U and V. This is done through the Surface Cell Parameters control panel. All changes made on this control panel are instantly reflected in the model window. The effect of lattice alteration on atom position depends on the coordinate type you want to fix: If the Cartesian coordinates of the atoms remain fixed, the model conformation remains the same, although gaps or bad contacts may result. If the fractional coordinates of the atoms remain fixed, then, for example, an atom in the middle of the surface remains in the middle, but the model conformation is distorted by rescaling. Open the Surface Cell Parameters control panel by selecting the Cell Parameters menu item from the SURFACE BUILDER card or by clicking the Cell Parameters pushbutton on the Building From Atoms control panel. Make the surface model that you want to edit be current. Use the Surface Cell Parameters control panel to choose which coordinate system to fix: CARTESIAN or FRACTIONAL. 34 Cerius 2 Builders/April 1999

45 Building and unbuilding surfaces Additional information Use the u, v, and θ entry boxes and/or the sliders to enter new dimensions for the U and V surface vectors and for the angle θ between the vectors. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Creating a surface superstructure Accessing the tools Size of the new structure Creating a superlattice Creating a nonperiodic superstructure Once a block of surface cells is displayed in the current model space, you may want to convert this display into a surface superlattice model or into a nonperiodic superstructure model. For example: To introduce disorder into a surface structure, generate a superlattice from a block of surface cells, then selectively edit the superlattice. To perform calculations on a surface using Cerius 2 modules that do not explicitly accept 2D-periodic surface models, generate a large nonperiodic superstructure from the surface cells. Open the Surface Visualization control panel by clicking the Visualization menu item on the SURFACE BUILDER card. Alternatively, click the Visualization menu item on the Building From Atoms control panel. Open the Building From Atoms control panel (by selecting the Building From Atoms menu item on the SURFACE BUILDER card) or the Cleave Crystal Surface control panel (by selecting the Cleave Crystal Surface menu item on the SURFACE BUILDER card). Use the Surface Cell Display Range controls in the Surface Visualization control panel to display the number of surface cells that you want included in the superstructure or superlattice. To create one large periodic surface structure (a superlattice) from the displayed atoms, click the Periodic Superlattice action button in the Cleave Crystal Surface or Building From Atoms control panel. Alternatively, to create a nonperiodic superstructure from the displayed atoms, click the Non-periodic Superstructure action button in either panel. Cerius 2 Builders/April

46 3. Surface Builder Caution Additional information The current surface is lost when the superlattice or superstructure is built. If you want to save the current surface, copy it into a new model space and/or save it to a file before creating the superstructure. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Unbuilding a surface Accessing the tools Unbuilding a surface Additional information Open the Building From Atoms control panel by selecting the Building From Atoms menu item on the SURFACE BUILDER card. To return the model to its nonperiodic asymmetric unit, deleting all symmetry copies of atoms and the surface cell, click the UNBUILD SURFACE pushbutton to return the surface model to a nonperiodic model. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Displaying surfaces Accessing the tools Display range Additional information It is often easier to visualize the current surface by displaying a large block of surface cells instead of just one. Open the Surface Visualization control panel by selecting the Visualization menu item from the SURFACE BUILDER card. Alternatively, click the Visualization pushbutton on the Building From Atoms control panel. Enter the number of surface cells to be displayed along the U and V directions. Click the ENTER pushbutton, and a block of surface units of the prescribed dimensions is displayed in the model window. Please see the on-screen help for additional information about the controls in all the panels mentioned here. 36 Cerius 2 Builders/April 1999

47 4 Interface Builder The C 2 Interface Builder module is used for constructing models of a crystal interface between two different crystals or a twin or defect within a crystal. The C 2 Interface Builder module aids in simulating experimental data such as high-resolution transmission electron microscopy images of interfaces (C 2 HRTEM module) and in visualizing epitaxy and structural relationships between crystalline particles in contact. This chapter contains information on: About the interface builder Creating an interface Creating a periodic model from an interface For information about Loading and saving interface structure files. Building crystals. Building surfaces. Microscopy. See The discussion of loading and saving structure files in Cerius 2 Modeling Environment. Crystal Builder. Surface Builder. Cerius 2 Analytical Instruments. About the interface builder How it works The sequence of steps for using the C 2 Interface Builder module is shown below. These steps are described in more detail later in the chapter. 1. Define the right side of the interface Specify the crystal model, Miller plane, match vector, match point, and dimensions of the right side of the interface. Cerius 2 Builders/April

48 4. Interface Builder Accessing the tools 2. Define the left side of the interface Specify the crystal model, Miller plane, match vector, match point, and dimensions of the left side of the interface. 3. Build the interface Specify the interfacial separation and the various atom bonding and superposition criteria. When the interface is built, the two planes are oriented so that the projections of their match points are coincident and their match vectors are parallel. 4. Edit the interface (optional) After the interface has been built, you have another opportunity to automatically remove superimposed atoms. You may also do manual editing. 5. Create a periodic structure (optional) For some applications, you may want to create a crystal or a surface model from the nonperiodic interface model. You can do this with the Crystal Builder or Surface Builder module. Controls belonging to the C 2 Interface Builder module are contained on the INTERFACE BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the INTER- FACE BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this: 38 Cerius 2 Builders/April 1999

49 Creating an interface Creating an interface To construct an interface, you need to define the two sides of the interface, specify some build-control parameters, and then build the interface. Afterwards you may need to remove superimposed atoms from the interface. This section includes information on: Defining the sides of the interface Building the interface Editing the interface after it is build Defining the sides of the interface Concepts and general procedure The starting model(s) Before the interface can be built, the left and right sides of the interface must be specified using the Interface Left Side and Interface Right Side control panels. The names left and right are, of course, only for the purpose of differentiating the interface sides. They refer to the sides of the model window on which each appears when the interface is built. Resetting the screen view also returns the interface to its original left/right orientation. For each side, you need to specify a crystal model from which to take the interface. The model is chosen from the Interface Model pulldown (the left and right control panels contain the same set of controls), which show only crystal models that are suitable for use with the interface builder. The model needs to be chosen first. Usually the crystal used for the left side is different from the crystal for the right side. However, to model a fault or twinning in a crystal, you use the same crystal for both sides of the interface. The interface plane The interface Plane itself is specified by the Miller indices h, k, and l. The convention is that the vector coming out of the built interface (that is, towards the other side) is normal to the interface plane. For the right side of the interface, the vector normal to the Miller plane points in the negative x direction. For the left side of the interface, this vector points in the positive x direction. Cerius 2 Builders/April

50 4. Interface Builder Match point Match vector Mesh shape You also need to specify a Depth for the interface side. This is the thickness of the slab that is taken from the crystal to form the interface model and may be thought of as the amount of pure crystal on the back side of the interface. The Match Point specifies a point in crystal fractional coordinates that should match the match point of the other crystal. The match point is also the origin of the interface slab to be cut from the crystal. If the interface separation is zero, the match points coincide. If not, their projections normal to the interface planes coincide. For each crystal, a match vector must be defined as the First Side of Interface Mesh. Because the two interface planes must be oriented with their match vectors parallel, the match vector and match point together define the relative orientations of the two planes. The match vector is given in the u, v, w fractional coordinate system of the crystal, and the interface builder checks that the vector is indeed in the interface plane. When the interface is built, this vector lies along the z axis. You may want to preserve some periodicity in the direction of the match vector. This is particularly true if you want to put the interface into a 2D or 3D periodic box. If you enter a value in the multiplication (by) entry box to the right of the entry box for specifying the u, v, w coordinates of the first side of the interface, the unit vector length multiplied by this value is the length of the side. Because lattice vectors are necessarily along periodicities in the crystal structure, using an integer multiplication factor ensures a good repeat along the match direction. Two methods are available for specifying the shape of the two interface planes: ORTHOGONAL (the edges of the interface plane meet at right angles, which gives a square or rectangle) and VEC- TOR (the interface may be a parallelogram). The two sides of the interface need not be the same shape or specified by the same method. For the orthogonal method, you must define two edges for each interface: one being the match vector and the other perpendicular to the match vector in the plane of the interface (along the y axis), using the First Side of Interface Mesh and Second Side of Interface Mesh entry boxes. The vector method enables you to specify an interface that is a parallelogram. The first vector is the match vector (First Side of 40 Cerius 2 Builders/April 1999

51 Creating an interface Specifying the sides of the interface Interface Mesh entry box). The second vector (Second Side of Interface Mesh entry box) must also be in the interface plane, and its length can be given explicitly in angstroms or as a multiple of the unit vector. Constructing the starting model Accessing the tools Beginning the process For details on the following steps, please see the previous section (Concepts and general procedure). Perform the following sequence of tasks once for each side of the interface, using the Interface Right Side and Interface Left Side control panels, respectively. Load or build one or two crystals from which the interface is to be constructed. Decide on the Miller planes, one for each side, that you will use to form the interface. You may find it helpful to view the planes using the facilities of the Crystal Visualization or the Crystal Facetting control panels of the Crystal Builder module. For detailed information, please see Crystal Builder. Open the Interface Right Side control panel by selecting the Right Side menu item from the INTERFACE BUILDER card. Alternatively, if you have the Interface Building control panel (see Accessing the tools) open, click its Right Side pushbutton. Open the Interface Left Side control panel by selecting the Left Side menu item from the INTERFACE BUILDER card. Alternatively, if you have the Interface Building control panel (Accessing the tools) open, click its Left Side pushbutton. From the Interface Model pulldown, select the crystal to be used to generate a side of the interface. To specify how the interface slab is sliced from the crystal, choose ATOMIC or MOLECULAR from the Cleave popup, as desired or appropriate for your crystal. MOLECULAR means that the interface is built by cutting complete molecules from the crystal. ATOMIC means that it is built by cutting atoms from the crystal regardless of how they form molecules. The MOLECULAR option can cause atoms to end up outside the volume strictly defined as the interface slab, in particular within the space between the two sides of the interface after it is built. Cerius 2 Builders/April

52 4. Interface Builder Specifying the interface slab Additional information Tip Enter the Miller indices of the interface Plane. Specify the Depth or thickness (in angstroms) of the slab that will form the interface. Enter the match vector for the interface side in the First Side of Interface Mesh entry box. If you attempt to input a vector that is not in the Miller plane, a warning is displayed in the text window. Specify the length of the slab along the match vector in angstroms or in terms of the number of lattice vectors, using one of the entry boxes to the right of the First Side of Interface Mesh entry box. To specify the general shape of the interface mesh, choose ORTHOGONAL or VECTOR from the Mesh popup: If you have chosen an ORTHOGONAL mesh shape, enter a value for the length of the side perpendicular to the first vector, in the Second Side of Interface Mesh entry box. If you have chosen a VECTOR mesh shape, enter a vector and a length to define the second side of the interface, using the Second Side of Interface Mesh entry box and either of the two entry boxes to its right. Enter the Match Point, in terms of fractional crystal coordinates. To use the location of a particular atom as the match point, <Shift>-click the atom with the right mouse button. The atom s coordinates appear in an information box. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Building the interface How it works Once the interface has been correctly defined on both sides, you are ready to build the interface. This is done with the Interface Building control panel. The interface is built from the two sides specified in the Interface Left Side and Interface Right Side control panels. The build operation takes place in the current workspace, which must be empty. The original crystals are not affected by the interface building. 42 Cerius 2 Builders/April 1999

53 Creating an interface Accessing the tools Specifying build parameters The interface is built so that the normals of the left and right Miller planes face each other. The relative positions of the faces are governed by the match vector (First Side of Interface Mesh) and the Match Point specified in the Interface Left Side and Interface Right Side control panels and by the Interfacial Separation, which is specified in the Interface Building control panel. The match vector is aligned with the z axis. Various bonding and atom options can be specified before building. For example, you can specify whether you want to calculate bonding upon building or whether and how superimposed atoms are removed. After defining the interface sides as described above (Specifying the sides of the interface), open the Interface Building control panel by selecting the Interface Building menu item on the INTERFACE BUILDER card. Set the size of the gap between the interface planes (the Interfacial Separation) in angstroms. The effects of various values are: 0 Å No interfacial separation between the left and right sides, likely resulting in superimposed atoms in the interface. > Å This much separation may lead to bonding across the interface if the Calculate bonds on building box is checked. > 2 Å This much separation between the two sides is suitable for visualization purposes. Check the Calculate bonds on building box if you want bonding for the new interface model to be calculated when the interface is built. If this box is unchecked, the bonding in the original crystals is transferred to the equivalent parts of the interface, but no bonding occurs across the gap between the two sides of the interface. Set the dangling bonds popup according to how you would like dangling bonds to be displayed. They may be omitted altogether (NEITHER), drawn on the LEFT or RIGHT side only, or drawn on BOTH sides of the interface. Dangling bonds are a representation of bonds that existed in the crystal across the cleave face of the interface. The atom that is not in the cleaved set is replaced by a dummy atom. Use of this option gives an indication of the bonding patterns that may be required across the interface. Cerius 2 Builders/April

54 4. Interface Builder Building the interface Additional information When the Remove superimposed atoms box is checked, atom pairs at the interface that are superimposed (within the Superimposition tolerance) are replaced by one atom from the interface side specified by the Keep atoms popup. Any bonds to the removed atom are transferred to the retained atom. After the build parameters have been specified, make an existing empty model space current or open a new empty model space. Click the BUILD INTERFACE pushbutton. The new interface is built in the current (empty) model space. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Editing the interface after it is build After the interface is built, the Edit Interface control panel gives you a second chance at removing superimposed atoms, without requiring you to rebuild the interface. This option removes all duplicate atoms and transfers the bonding to the retained atoms. Note For organic crystals, the interface may slice through molecules leaving broken pieces on either side. This also necessitates some manual editing after the interface is built. Please refer to the discussion of editing models in Cerius 2 Modeling Environment. Accessing the tools Open the Edit Interface control panel by selecting the Edit Interface menu item from the INTERFACE BUILDER card. Cleaning up the interface With the interface in the current model window, click the REMOVE DUPLICATES pushbutton. The Superimposition tolerance entry box on the Interface Building control panel also controls the tolerance for duplication here. Additional information Please see the on-screen help for additional information about the controls in all the panels mentioned here. Creating a periodic model from an interface This section includes information on: 44 Cerius 2 Builders/April 1999

55 Creating a periodic model from an interface Creating a crystal from an interface Creating a surface from an interface When an interface is built, it is oriented in a way that makes creating a periodic model from the interface model straightforward. In addition, the crystal and surface cell parameters are set so that building a crystal or surface from an interface model puts the interface in a reasonable plane and assigns default cell or mesh parameters that match the dimensions of the right side of the interface. This enables you to extend interfaces, particularly those where the two sides match. For example, this is necessary for performing HRTEM simulations on an interface, because HRTEM calculations can be applied only to crystal models. Creating a crystal from an interface Accessing the tools Building the crystal Additional information Create an interface in which the left and right face dimensions of the interface are the same. Open the Crystal Building control panel by selecting the Crystal Building menu item from the CRYSTAL BUILDER card. Set various parameters as desired (see Crystal Builder). Click the BUILD CRYSTAL pushbutton. The interface appears correctly placed in a 3D unit cell. Please see the on-screen help for additional information about the controls in all the panels mentioned here. Creating a surface from an interface Accessing the tools Create an interface in which the left and right face dimensions of the interface are the same. Open the Building From Atoms control panel by selecting the Building From Atoms menu item from the SURFACE BUILDER card. Click the Cell Parameters pushbutton to open the Surface Cell Parameters control panel. Cerius 2 Builders/April

56 4. Interface Builder Beginning the process Building the surface Additional information Notice that the u, v, and θ cell parameters in the Surface Cell Parameters control panel are defaulted to the dimensions of the right side of the interface. Set various parameters as desired (see Surface Builder). On the Building From Atoms control panel, click the BUILD SUR- FACE pushbutton. The interface appears correctly placed in a 2D surface cell. Please see the on-screen help for additional information about the controls in all the panels mentioned here. 46 Cerius 2 Builders/April 1999

57 5 Polymer Builder The C 2 Polymer Builder module enables you to build all types of linear polymers: homopolymers, random copolymers, and block copolymers. You can load the monomer units from which polymers are constructed from files supplied with Cerius 2 or create your own monomers. You can also edit the monomers before using them. Almost any of the Cerius 2 simulation and computation modules can be applied to polymer models. Two modules that are particularly applicable to polymer models are C 2 Blends and C 2 Polymer Properties. This chapter contains information on: Monomer units Homopolymers Random copolymers Block copolymers Editing polymers Monomer and polymer display For information about Loading and saving monomer and polymer structure files. See The discussion of loading and saving structure files in Cerius 2 Modeling Environment. Cerius 2 Builders/April

58 5. Polymer Builder For information about Polymer file formats. Building crystals from polymers. Mixtures of polymers. See The discussion of Cerius 2 structure files in Cerius 2 Modeling Environment. Crystal Builder. The discussion of the Blends module in Cerius 2 Computational Instruments Property Prediction. Polymer statistics. The discussion of the Polymer Properties module in Cerius 2 Computational Instruments Property Prediction. Diffraction from polymers. Cerius 2 Analytical Instruments. Accessing the tools Controls belonging to the C 2 Polymer Builder module are contained on the POLYMER BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the POLY- MER BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this: 48 Cerius 2 Builders/April 1999

59 Monomer units Monomer units Following some introductory material (below), this section contains information on: Specifying monomer units Monomer files Creating or editing monomers Editing monomers Using monomers created with other programs Monomers Torsions Chirality Inversion Monomers (or repeat units) are the building blocks of polymers. A Cerius 2 monomer is defined as a model containing one head and one tail group. Thus, only linear polymers can be built when a series of monomers is linked to form a polymer. A monomer head group consists of a special object attached to the designated head atom of the monomer. Similarly, a tail group is a special object attached to the tail atom of the monomer. One kind of monomer may be joined to form a homopolymer, or several types of monomer may be used to form a random or a block copolymer. By default, the torsion angle between monomer units is determined by the conformations of the head and tail groups of the two monomers. However, this can be changed. Monomer chirality is important in determining the configuration of the polymer. Monomers loaded from the Cerius 2 monomer files already have chiral centers defined. You can also define (or redefine) chiral centers as desired. You can also invert the monomer at its chiral center. For example, you might want to create a mirror-image pair of monomers for building an atactic or syndiotactic random or block copolymer. Cerius 2 Builders/April

60 5. Polymer Builder Specifying monomer units Additional information Many of the polymer builder control panels contain one or more generic monomer choosers. These consist of a pulldown that accesses all monomers that are available to the program and an entry box that shows the name of the currently specified monomer unit. The available monomers include all the monomer structure files supplied with Cerius 2 (see Monomer files) and all the models currently loaded that are monomers (that is, models with one head and one tail group defined, see Creating or editing monomers). The monomer chooser pulldown shows the names of individual monomers only in the current directory (class). To see the names of monomers in other directories, click the directory name. You can also enter the name of any valid monomer by typing it in the monomer chooser s entry box. Please see the on-screen help for information about the monomer chooser(s) in any control panel in which they appear. Monomer files Creating or editing monomers Starting the process Cerius 2 provides several directories of structure files for some common monomer types. These directories are subdirectories in the Cerius2-Models directory, which is automatically linked to from the directory in which you start up Cerius 2. They are automatically listed in the monomer chooser pulldowns (see Specifying monomer units). In addition (next section), you can create your own monomers by editing other models supplied with Cerius 2 or can create your own monomer models from scratch. Monomers can be created by assigning head and tail groups in models loaded from file or created using the 3D Sketcher. You may also define backbone atoms in any monomer unit if you want. Begin with the model that you want to convert to a monomer unit. Place it in the current model space. 50 Cerius 2 Builders/April 1999

61 Monomer units Accessing the tools Defining head and tail groups and torsion atoms Remember Removing head and tail definitions You can build the model using the 3D Sketcher and/or other Cerius 2 building tools, or you can load a suitable model from a file. You can load one of the standard monomer files for editing by using the monomer chooser in the Monomer Editor control panel and then clicking the LOAD pushbutton. Open the Monomer Editor control panel by selecting the Edit/ Monomers menu item from the POLYMER BUILDER card. Click the Preferences pushbutton in the Monomer Editor control panel to open the Monomer Preferences control panel. The following instructions mention double-clicking the atom. When you double-click an atom with the Define Head or Define Tail tool, Cerius 2 automatically determines the atoms that will be used to define the torsion between monomers in the built polymer. If you want to define the torsion atoms yourself, you should click the head or tail atom once and then click the other two atoms that define the torsion. Click the Define Head tool. Double-click the atom that you want to be made into the monomer head. By default the monomer head is colored magenta. Click the Define Tail tool. Double-click the atom that you want to be made into the monomer tail. By default the monomer tail is colored light blue. At present, the Polymer Builder can use monomers with only one head and one tail. By default, when you define a head or tail atom, the definition for any previously defined head or tail (respectively) is removed. You can change this behavior by unchecking the Remove old Head/ Tail check box in the Monomer Preferences control panel. If you want to remove head or tail definitions, click the Remove Head or Tail linkage tool and click the incorrectly defined atom to remove the definition. You can also change a head into a tail (and vice versa) without changing the defined torsion atoms by using the Change linkage tool. Cerius 2 Builders/April

62 5. Polymer Builder Defining backbone atoms You may want to define backbone atoms in your monomer units. This is helpful if you might want to easily display or select backbone atoms in your built polymer, which can often give you a better understanding of its overall structure. To define an atom as a backbone atom, use the Define Backbone tool. Help Additional information Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the monomer editor. Please see the on-screen help for additional help on the controls in these panels. Information on building and editing models and on selecting and displaying atoms according to various properties is contained in Cerius 2 Modeling Environment. Editing monomers Starting the process Accessing the tools Defining chiral centers You can edit all monomer models with any of the model-editing tools found in the Visualizer main control panel. In addition, the polymer builder includes tools for defining chiral (tacticity) centers in monomer units. Begin with the model that you want to edit. Place it in the current model space. You can build the model using the 3D Sketcher and/or other Cerius 2 building tools, or you can load a suitable model from a file. You can load one of the standard monomer files for editing by using the monomer chooser in the Monomer Editor control panel and then clicking the LOAD pushbutton. Open the Monomer Editor control panel by selecting the Edit/ Monomers menu item from the POLYMER BUILDER card. Click the Preferences pushbutton in the Monomer Editor control panel to open the Monomer Preferences control panel. Chiral centers are used by the polymer builder to determine inversions, for example when building syndiotactic or atactic polymers (see Tacticity). If the monomer has any chiral centers, define them by setting the RECTUS/SINISTER popup as desired and then clicking the Define center tool and then clicking the center atom. 52 Cerius 2 Builders/April 1999

63 Monomer units Removing chiral definitions Loading and saving File formats Help Additional information By default, rectus (R) chiral centers are yellow and sinister (S) chiral centers are dark pink. You can invert the chiral center: click the Invert center tool and then click the chiral atom. By default, when you define a tacticity (chiral) center, the definition for any previously defined center is removed. You can change this behavior by unchecking the Remove old tacticity center check box in the Monomer Preferences control panel. If you want to remove the definition of a chiral center, click the Remove centers tool and click the incorrectly defined atom to remove the definition. Monomers that you create and/or edit can be saved and loaded just like any other model created in Cerius 2. Since only the monomer files supplied with Cerius 2 are automatically detected by the monomer choosers (see Specifying monomer units), you need to specifically load any custom monomer units that you want to use in future Cerius 2 sessions. For this, select the File/Load Model item from the menu bar in the main Visualizer control panel to access the Load Model control panel. The MSI file format is particularly recommended because it includes chirality information (which is saved within the atom names). Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the monomer editor. Please see the on-screen help for information about all the controls in these control panels. Information on editing, saving, and loading models is contained in Cerius 2 Modeling Environment. Using monomers created with other programs There is no industry-standard description of how monomers and their linkages are represented, so different programs use different representations. However, Cerius 2 enables you to convert files of other formats to the current Cerius 2 format, while properly interpreting the head/tail group information. Cerius 2 Builders/April

64 5. Polymer Builder Accessing the tools Polygraf and Biograf files Old Cerius 2 files Insight II files Additional information Open the Monomer Editor control panel by selecting the Edit/ Monomers menu item from the POLYMER BUILDER card. Click the Convert Formats pushbutton on the Monomer Editor control panel to access the Convert Formats control panel. In the Polygraf and Biograf programs, a monomer head is represented by an atom named HX and a monomer tail by an atom named TX. Click the Convert from Xgraf action button to convert any atoms with these names to hydrogen atoms and add Cerius 2 monomer head or tail groups. Default torsion angles are generated. Prior to version 3.0, Cerius 2 used a different representation for monomer heads and tails. For a monomer head, a pair of dummy atoms (J2 and X) indicated the head position and the torsion to be used for building. Click the Convert from Cerius2 v2.0 action button to replace the J2 atom with hydrogen and to remove the X atom. Similarly, the monomer tail was represented by a pair of atoms (J1 and X). Clicking the Convert from Cerius2 v2.0 action button additionally replaces these by a hydrogen atom and a monomer tail linkage object, respectively. Default torsion angles are generated appropriately. Monomer or polymer structures loaded from Insight II.car/.mdf files do not explicitly contain linkage atoms. Instead they contain knowledge of the backbone going from one hydrogen atom to another. Clicking the Convert from InsightII action button adds head and tail linkages to the atoms at each end of the backbone. By convention, the head is chosen to lie closer to any sidegroup than does the tail. If the assignment of head and tail is not as desired, they can be swapped by using the Change linkage tool on the Monomer Editor control panel (see Editing monomers). Please see the on-screen help for information about all the controls in these control panels. Homopolymers Following some introductory material (below), this section contains information on: Building homopolymers 54 Cerius 2 Builders/April 1999

65 Homopolymers Tacticity Monomer head/tail orientation Torsion angles General procedure A homopolymer is made of a single type of monomer unit. You must specify several options to build a homopolymer: Monomer to be used for building. Number of monomer units. Tacticity. Head/tail orientation of units. Torsion angle between units. Initiator and terminator units. The initiator and terminator options enable you to add a single copy of a different monomer unit to each end of the built polymer chain. A monomer head or tail is chemically defined just as is any other element (it is usually hydrogen), so no capping of the polymer chain is required. Building homopolymers Specifying the monomer unit Accessing the tools Number and type of monomer units Standard monomer units and end units are loaded with monomer choosers on the Homopolymer Builder control panel. However, you are not restricted to the choice of monomers supplied with Cerius 2. If you want a nonstandard monomer, create (see Monomer units) or load (see Loading and saving) it now. Open the Homopolymer Builder control panel by selecting the Homopolymer menu item on the POLYMER BUILDER card. Click the Preferences pushbutton in the Homopolymer Builder control panel to open the Homopolymer Preferences control panel. Specify the type of monomer to be used in the polymerization from the Monomer popup. Enter the number of monomer units for the new polymer in the Number of monomers entry box. Cerius 2 Builders/April

66 5. Polymer Builder Tacticity Head/tail orientation Torsions Other controls Choose any (extra) initiator and/or terminator monomers with the Initiator and/or Terminator popups. These are in addition to the number of monomers specified in the Number of monomers entry box. (For example, if Number of monomers is set to 5 and you also specify an initiator and a terminator, the final polymer will be 7 units long.) If the monomer being polymerized has a single chiral center, change the tacticity if desired. For information on tacticity, see Tacticity. By default, an isotactic polymer (see Figure 2) is built. Change the head/tail orientation of the monomers if desired. By default, they are oriented so that the tail of each monomer is attached to the head of the previous monomer in the sequence. Change the torsion angles if desired. Using the defaults builds a polymer with torsion angles taken from the monomer model. For information on setting torsions, see Torsion angles. Use controls in the Homopolymer Preferences control panel if you want to reset any preferences for how the build proceeds. Tip If you will want to build a polymer crystal, you should retain the head and tail linkages (that is, leave the Make ordinary molecule box unchecked. The polymer then is automatically aligned in the crystal cell, and the repeat of the cell along the c axis is treated correctly. The random-number generator is used in the homopolymer builder for setting tacticity, orientation, or torsions randomly if such options are chosen. Setting the Random seed to a particular value allows regeneration of specific structures. Building the homopolymer Click the BUILD pushbutton in the Homopolymer Builder control panel. The linear homopolymer is built in the current model space, overwriting any existing model (unless specified otherwise in the Homopolymer Preferences control panel). Additional information Please see the on-screen help for information about all the controls in these control panels. See Specifying monomer units for information on using monomer choosers. 56 Cerius 2 Builders/April 1999

67 Homopolymers Tacticity Concepts Homopolymers containing chiral centers can be polymerized in several stereoconfigurations. Cerius 2 offers a choice of three tacticity options (Figure 2): Isotactic. Syndiotactic. Atactic (you need to specify the meso diad ratio). Figure 2. Tactic forms of a polymer The isotactic (top), syndiotactic (middle), and atactic (bottom) forms of polystyrene are shown. The equivalent meso diad ratios are 1.0, 0.0, and 0.5, respectively. Cerius 2 Builders/April

68 5. Polymer Builder Preparing the monomer Accessing the tools Setting monomer tacticity Additional information In the isotactic form, all the R groups lie on the same side of the backbone chain. In the syndiotactic form, the R groups alternate from one side to the other. There is no regular tacticity. In the atactic form, both isotactic and syndiotactic sequences exist. The meso diad ratio is the relative proportion of isotactic monomer pairs in a given polymer. Thus, a polymer with a meso diad ratio of 0.0 is a syndiotactic polymer, a polymer with a ratio of 0.5 is a random atactic polymer, and a polymer with a ratio of 0.90 is a predominantly isotactic polymer containing some syndiotactic diads. For syndiotactic and atactic homopolymers, the monomer to be polymerized must have a chiral center. If the chiral center has not already been defined, follow the instructions under Defining chiral centers. Open the Homopolymer Builder control panel by selecting the Homopolymer menu item on the POLYMER BUILDER card. Click the Tacticity pushbutton on the Homopolymer Builder control panel to open the Polymer Tacticity control panel. Choose one of the three tacticity options: ISOTACTIC, SYNDIO- TACTIC, or ATACTIC or specify the appropriate Meso-Diad Ratio (see, for example, Figure 2). Please see the on-screen help for information about all the controls in these control panels. Monomer head/tail orientation How it works The typical orientation of monomer units in a polymer is head-totail, that is, the tail of the monomer being added is connected to the head of the previously added monomer. However, this behavior can be changed by setting two probability values the probability of an exposed head group on the growing polymer chain connecting with the head of a monomer being added to the chain and the probability of an exposed tail group connecting with the tail of a monomer being added. The default values of 0.0 for both probabilities gives head-to-tail connections. A value of 1.0 for both probabilities gives strictly alternating head head and tail tail connections. Any other combi- 58 Cerius 2 Builders/April 1999

69 Homopolymers Accessing the tools Setting the orientation probabilities Additional information nation of the two probabilities gives a mixed, randomly selected, arrangement of connections. Open the Homopolymer Builder control panel by selecting the Homopolymer menu item on the POLYMER BUILDER card. Click the Orientation pushbutton on the Homopolymer Builder control panel to open the Monomer Orientation control panel. Choose HEAD-TO-TAIL, ALTERNATING, or MIXED to set the head-to-head and tail-to-tail probabilities to one of three standard pairs of values. The actual values used are shown in the probability entry boxes. For more flexibility in defining the orientation, use the Head-to- Head prob and Tail-to-Tail prob entry boxes to set the probability that a monomer head is followed by another head and that a monomer tail is followed by another tail. Please see the on-screen help for information about all the controls in these control panels. Torsion angles How it works As the polymer chain is built, the torsion angle between each successive pair of monomer units can be determined in one of three ways. This torsion angle can be: Chosen at random for each link. Taken from the monomer models (the default). The torsion between units is equal to 360 minus the sum of the linkage torsions of the two participating monomer linkage groups. A fixed angle that you specify. Note The torsion angles within the monomer are not affected by the Polymer Torsions control panel. Torsion angles within monomer units can be changed by selecting the Move/Bond Geometry or Build/3D-Sketcher item from the menu bar in the main Visualizer control panel. Accessing the tools Open the Homopolymer Builder, Random Copolymer Builder, or Block Copolymer control panel by selecting the Homopolymer, Random Copolymer, or Block Copolymer menu item (respectively) on the POLYMER BUILDER card. Cerius 2 Builders/April

70 5. Polymer Builder Setting torsion angles for linkages Note Additional information Click the Torsions pushbutton on any of these control panels to open the Polymer Torsions control panel. Choose one of the three torsion options: RANDOM, DEFAULT, or ANGLE. If you choose ANGLE, you also need to specify the torsion angle in the Degrees entry box. This torsion angle setting applies to all monomers and is irrespective of polymer type (homopolymer or copolymer). Please see the on-screen help for information about all the controls in these control panels. Information on editing torsion angles within models is contained in Cerius 2 Modeling Environment. Random copolymers Following some introductory material (below), this section contains information on: Building random copolymers Random copolymer preferences Reactivities General procedure A copolymer is made up of two or more monomer building blocks. In a random copolymer, the sequence of monomers in the polymer chain is irregular. Statistically, the proportion of each monomer type and the probability of one monomer following another are determined by the relative concentrations of the monomers and their relative reactivities. The random copolymer builder in Cerius 2 enables you to specify the following: Monomers to be used for building. Monomer concentrations. Number of monomer units. 60 Cerius 2 Builders/April 1999

71 Random copolymers Monomer reactivities. Torsion angle between units. Initiator and terminator units. The initiator and terminator options enable you to add a single copy of a different monomer unit to each end of the built polymer chain. A monomer head or tail is chemically defined just as is any other element (it is usually hydrogen), so no capping of the polymer chain is required. Building random copolymers Specifying the monomer unit Accessing the tools Number and types of monomer units Standard monomer units and end units are loaded with monomer choosers on the Random Copolymer Builder control panel. However, you are not restricted to the choice of monomers supplied with Cerius 2. If you want a nonstandard monomer, create (see Monomer units) or load (see Loading and saving) it now. Open the Random Copolymer Builder control panel by selecting the Random Copolymer menu item on the POLYMER BUILDER card. Specify the types of monomer to be used in the polymerization from the Monomer popups. If you change your mind and want to remove a monomer from the list, simply delete its name from the entry box of the relevant Monomer chooser. Alternatively, you can set its concentration to (below). Enter the number of monomer units for the new copolymer in the Number of monomers entry box. This is the sum of repeat units of all monomer types in the copolymer (except for the initiator and terminator units). Choose any (extra) initiator and/or terminator monomers with the Initiator and/or Terminator popups. These are in addition to the number of monomers specified in the Number of monomers entry box. (For example, if Number of monomers is set to 5 and you also specify an initiator and a terminator, the final polymer will be 7 units long.) Cerius 2 Builders/April

72 5. Polymer Builder Monomer concentrations Monomer reactivities Tacticity and head/tail orientation Torsions Other controls Building the copolymer Additional information Enter the concentrations of each monomer type in the respective Conc entry box. These are relative concentrations and therefore need not sum to unity. However, concentrations can be normalized (so they do sum to unity) by clicking the Normalize Conc action button. To specify relative reactivities of the monomers, click the Reactivities pushbutton to open the Monomer Reactivities control panel. For information on setting monomer reactivities, please see Reactivities. Set the inversion (Invert entry boxes) and Flip probabilities for each monomer type. These control s (respectively) set the probability for inverting the chiral center and for flipping the monomer unit head-for-tail when the monomer unit is added to the growing polymer chain. Set the torsion angles if you want something other than the default behavior. Using the defaults builds a copolymer with torsion angles taken from each of the monomer models. For information on setting torsions, see Torsion angles. Use controls in the Random Copolymer Preferences control panel (see Random copolymer preferences) if you want to reset any preferences for how the build proceeds. Click the BUILD pushbutton in the Random Copolymer Builder control panel. The described random copolymer is built in the model space that is specified in the Random Copolymer Preferences control panel. Please see the on-screen help for information about all the controls in these control panels. See Specifying monomer units for information on using monomer choosers. Random copolymer preferences Several preference options are available for controlling the building of random copolymers. You can: Choose the location for the built polymer (the current or a new model space). 62 Cerius 2 Builders/April 1999

73 Random copolymers Accessing the tools Setting some preferences Decide whether to use reactivities in combination with concentrations to determine the probabilities used in growing the polymer chain. Enforce the concentrations specified in the Random Copolymer Builder control panel. Otherwise, the actual concentrations for repeated builds follow a Gaussian distribution about the specified concentration. Remove any subunit and linkage information from the built polymer. Print or not print building information to the text window. Specify how many components to include in the polymer name. The polymer name is usually generated from the names of the contributing monomers. You can restrict the number of component names to use, to decrease the length of the polymer s name. Reset the seed for the random-number generator. This is useful for recreating particular structures. Open the Random Copolymer Builder control panel by selecting the Random Copolymer menu item on the POLYMER BUILDER card. Click the Preferences pushbutton in the Random Copolymer Builder control panel to open the Random Copolymer Preferences control panel. Check the Use reactivities box if you want to use both monomer reactivities (Reactivities) and concentrations to determine the frequency of monomers in the built chain. Check the Force concentrations box to enforce the specified monomer concentrations. Otherwise the actual concentrations in repeated builds form a Gaussian distribution around the desired value. Check the Make ordinary molecule box if you want the subunit and linkage information to be removed from the final model. This information is useful for selection and display of components of the built polymer, as well as for using this polymer to build more complex polymers. Cerius 2 Builders/April

74 5. Polymer Builder Additional information Specify the maximum number of monomer components that contribute to the polymer name in the Maximum components in name entry box. If the polymer is built with more than this many components, the name is set to Random Copolymer instead of being generated from the component names. Please see the on-screen help for information about all the controls in these control panels. Reactivities Concepts The two factors that determine the probability of a monomer of a given type joining the growing end of a copolymer chain are the concentration of the monomer [Mj] and the reactivity k ij of monomer j with the growing chain s end i, so that k ij [Mj] probability of monomer j joining a copolymer chain ending in group i. For the copolymerization of a terpolymer (three monomer types), nine rate constants are involved: k 11 * * M 1 + M 1 M 1 M 1 k 21 * * M 2 + M 2 M 1 M 1 k 31 * * M 3 + M 3 M 1 M 1 k 12 * * M 1 + M 1 M 2 M 2 k 22 * * M 2 + M 2 M 2 M 2 k 32 * * M 3 + M 3 M 2 M 2 k 13 * * M 1 + M 1 M 3 M 3 k 23 * * M 2 + M 2 M 3 M 3 k 33 * * M 3 + M 3 M 3 M 3 To copolymerize these monomers, the relative reactivity rates are entered into the Cerius 2 relative reactivity matrix as shown in Table 1. The rate constants for the self-propagating reactions are on the diagonal (k 11, k 22, k 33 ), and the cross-propagation rate terms are on the off-diagonals (k ij, i j). Experimental results on monomer reactivities (Young 1975) are often presented as reactivity ratios, r 1 and r 2, for polymer pairs: k 11 r 1 = k 12 Eq Cerius 2 Builders/April 1999

75 Random copolymers Table 1. Relative monomer reactivity rates Monomer Relative reactivities no. name M 1 k 11 k 12 k 13 2 M 2 k 21 k 22 k 23 3 M 3 k 31 k 32 k 33 k 22 r 2 = k 21 Eq. 2 Accessing the tools Setting monomer reactivity A reactivity ratio greater than one indicates a preference for like monomers to link. Reactivities can be entered into the Cerius 2 matrix and viewed as either relative reactivities or reactivity ratios. Monomer concentration values are set with the Random Copolymer Builder control panel (see Monomer concentrations). Monomer reactivities are set with the Monomer Reactivities control panel (this section). Open the Random Copolymer Builder control panel by selecting the Random Copolymer menu item on the POLYMER BUILDER card. Click the Reactivities pushbutton in the Random Copolymer Builder control panel to open the Monomer Reactivities control panel. Click the Preferences pushbutton on the Random Copolymer Builder control panel to open the Random Copolymer Preferences control panel. Decide whether you want to use RELATIVE reactivities or reactivity RATIOS and select the appropriate Reactivities button in the Monomer Reactivities control panel. For an explanation of relative reactivities and reactivity ratios, see above. In the scrollable array of entry boxes in the Monomer Reactivities control panel, enter the relative reactivities or reactivity ratios for each of the monomer pairs that may appear in the copolymer. (If you enter, say, ratios and want to change them to relative reactivities, simply select the RELATIVE button and the values in the table are appropriately recalculated.) Cerius 2 Builders/April

76 5. Polymer Builder Additional information Check the Use reactivities box in the Random Copolymer Preferences control panel. The reactivities are applied when the copolymer is constructed. Please see the on-screen help for information about all the controls in these control panels. Block copolymers General procedure Specifying the monomer unit Accessing the tools Number and types of monomer units Block copolymers are polymers with regularly repeating sequences. The Cerius 2 block copolymer builder enables you to build linear chains of repeating block sequences. The following must be specified to define a block copolymer: Monomers to be used for building. Repeating block sequence. Number of repeating blocks. Torsion angle between units. Initiator and terminator units. Standard monomer units and end units are loaded with monomer choosers on the Block Copolymer Builder control panel. However, you are not restricted to the choice of monomers supplied with Cerius 2. If you want a nonstandard monomer, create (see Monomer units) or load (see Loading and saving) it now. Open the Block Copolymer Builder control panel by selecting the Block Copolymer menu item on the POLYMER BUILDER card. Click the Preferences pushbutton to access the Block Copolymer Preferences control panel. Click the Torsions pushbutton to access the Polymer Torsions control panel. Specify the types of monomer to be used in the polymerization from the Monomer popups. If you change your mind and want to remove a monomer from the list, simply delete its name from the entry box of the relevant Monomer chooser. 66 Cerius 2 Builders/April 1999

77 Block copolymers Defining the super unit size, tacticity, and head/ tail orientation Torsions Other controls Choose any initiator and/or terminator monomers with the Initiator and/or Terminator popups. Enter the number of superunit blocks for the new copolymer in the Number of super units entry box. The superunit is made up of several monomer units. For each monomer forming part of the superunit, enter the block Size and specify the Tacticity and the monomer Orientation. The tacticity is specified by choosing ISO or SYN for an isotactic sequence or syndiotactic sequence (respectively) or by entering a number between 0.0 and 1.0, representing the meso diad ratio of an atactic sequence. For more information on tacticity, see Tacticity The monomer orientation is specified by choosing HEAD-TAIL or ALTERNATE from the pulldown for constant head-to-tail or alternating head-to-head and tail-to-tail connections (respectively) or by entering two numbers, each between 0.0 and 1.0, specifying the probabilities of head-to-head and tail-to-tail connections, respectively. For more information on orientation, see Monomer head/tail orientation. Set the torsion angles if you want something other than the default behavior. Using the defaults builds a copolymer with torsion angles taken from each of the monomer models. For information on setting torsions, see Torsion angles. Use controls in the Block Copolymer Preferences control panel if you want to reset any preferences for how the build proceeds. For example, check the Make ordinary molecule box if you want the subunit and linkage information to be removed from the final model. This information is useful for selection and display of components of the built polymer, as well as for using this polymer to build more complex polymers. Specify the maximum number of monomer components that contribute to the polymer name in the Maximum components in name entry box. If the polymer is built with more than this many components, the name is set to Block Copolymer instead of being generated from the component names. The random-number generator is used in the block copolymer builder for setting tacticity, orientation, or torsions randomly if Cerius 2 Builders/April

78 5. Polymer Builder Building the block copolymer Additional information such options are chosen. Setting the Random seed to a particular value allows regeneration of specific structures. Click the BUILD pushbutton in the Block Copolymer Builder control panel. The linear block copolymer is built in the current model space, overwriting any existing model (unless specified otherwise in the Homopolymer Preferences control panel). Please see the on-screen help for information about all the controls in these control panels. See Specifying monomer units for information on using monomer choosers. Editing polymers Starting the process A certain amount of editing can be performed on polymers that have been built using the polymer builder. The backbone can be defined or redefined, tacticity centers can be inserted or removed, and the model can be inverted about the tacticity center. In addition, a list can be obtained of the groupings within the model. Place the polymer model that you want to edit in the current model space. Accessing the tools Open the Polymer Editor control panel by selecting the Edit/Polymers menu item on the POLYMER BUILDER card. Defining backbone atoms You may want to define backbone atoms in your polymer. This is helpful if you might want to display or select the backbone atoms of your polymer, which can often give you a better understanding of its overall structure. To define atoms as backbone atoms, use the Define Backbone tool. Defining chiral centers You can define chiral centers by setting the RECTUS/SINISTER popup as desired, clicking the Define center tool, and then clicking the center atom. By default, rectus (R) chiral centers are yellow and sinister (S) chiral centers are dark pink. You can invert the chiral center: click the Invert center tool and then click the chiral atom. 68 Cerius 2 Builders/April 1999

79 Editing polymers Removing chiral definitions Listing atomic groupings Help Additional information If you want to remove the definition of a chiral center, click the Remove centers tool and click the incorrectly defined atom to remove the definition. Clicking the List atomic groupings action button prints a list of the types and classes of all atomic groupings in the current model to the text window. The repeat unit layer is the lowest (most descendent) level of groupings, followed by the monomer layer, which identifies the monomers used to build the polymer. The superunit layer is the most ascendent level of atom groupings found in the model. The block layer is defined as the level, if such exists, underneath the super block layer. Typically, in a block copolymer the superunits become superunit groupings, consisting of several blocks, each in turn consisting of several monomers. If the monomers were originally built as some sort of polymer themselves, then they may contain even smaller groupings identified as subunits and repeat units. Otherwise, the monomers and repeat units are usually identical. In a simple isotactic homopolymer built of basic library monomers, all levels are identical. However, in a syndiotactic homopolymer, each syndiotactic pair unit can be distinguished as a superunit. The type of the grouping is typically the name of a monomer from the monomer library, and the class of the grouping relates to the directory from which the monomer was chosen. More generally, the names of the types are intended to identify groupings of the same detailed structure, and the class is intended to identify groupings of the same general chemical nature. For example, PE (polyethylene) and PP (polypropylene) are considered different types but share the same class : Olefin. Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the monomer editor. Please see the on-screen help for additional help on the controls in these panels. Information on editing models and on selecting and displaying atoms according to various properties is contained in Cerius 2 Modeling Environment. Cerius 2 Builders/April

80 5. Polymer Builder Monomer and polymer display Accessing the tools Several options are available that affect the visualization of monomers and polymers. These include: The ability to color the linkage atoms, to label them, and to display the torsion geometry. The ability the color the backbone and to show only the backbone atoms. The ability to color and label tacticity centers. The ability to color and label according to different atom groupings. Open the Display Editor control panel by selecting the Edit/Display menu item on the POLYMER BUILDER card. Click the Coloration Preferences pushbutton in the Display Editor control panel to open the Display Preferences control panel. Changing linkage displays Use the Color Heads and Tails action button in the Display Editor control panel to color heads and tails of a monomer or polymer in the current model space. Specify what colors to use by choosing from the Head and Tail popups in the Display Preferences control panel. Use the Label Heads and Tails action button in the Display Editor control panel to label any heads or tails in the current model. Use the Label Torsion Geometry action button to display the linkage geometry for the current model. The torsion-defining atoms and the current torsion value are shown. Use the Remove Linkage Labels action button to remove the linkage label graphics from the display of the current model. The linkage atoms may remain colored. Changing backbone display If the Show Only Backbone Atoms action button in the Display Editor control panel is clicked, non-backbone atoms in the current model become invisible. If any atoms are selected, then only those selected in the current model that are not backbone atoms become invisible. 70 Cerius 2 Builders/April 1999

81 Monomer and polymer display Changing display of chiral centers If the Show All Atoms action button is clicked, all atoms in the current model become visible. If the Color Backbone action button is clicked, any backbone atoms in the current model are given the distinct backbone color. Specify what colors to use by choosing from the Backbone popup in the Display Preferences control panel. If any atoms are selected, then only those atoms have their color changed. If the Remove Backbone Color action button in the Display Editor control panel is clicked, the color of any backbone atoms in the model (or selected backbone atoms if any atoms are selected) changes back to that used before the backbone color was applied. Use the Color Tacticity Centers action button in the Display Editor control panel to color any tacticity centers in the model with the tacticity center color. Specify what colors to use by choosing from the Tacticity popups in the Display Preferences control panel. Use the Remove Tacticity Color action button in the Display Editor control panel to change the color of the atoms back to what they were before the tacticity center color was used. Use the Label Tacticity Centers action button to label atoms in the model according to their tacticity center nature, R for rectus or S for sinister. If only some atoms are selected, then that subset alone is labeled according to tacticity. Display of atom groupings Use the Groupings popup to set the level of atom groupings at which you want to edit the display. Please see Listing atomic groupings for information on the various levels of grouping, types, and classes. Use the Color Atoms action button to color atom groupings according to the attribute selected in the associated popup. The NUMBER popup item is particularly useful for distinguishing boundaries between groupings of the same symbol or class. Use the Label Grouping action button to label atom groupings according to the selected attribute. If a subset of the atoms in the model is selected, then labels are applied only to the atom grouping subunits containing those selected atoms. Use the associated popup to choose whether to label groupings by TYPE or by CLASS. Cerius 2 Builders/April

82 5. Polymer Builder Additional information Use the Remove Grouping Labels action button to remove atom grouping labels. Please see the on-screen help for information about all the controls in these control panels. 72 Cerius 2 Builders/April 1999

83 6 Amorphous Builder The C 2 Amorphous Builder module builds amorphous molecular structures, which can be represented in the molten state, in solution, or in the semicrystalline state. The amorphous structure can be built nonperiodically as an isolated single or multiple chain or as a 3D-periodic system to represent the bulk state. The structures are generated by varying the rotatable torsions using a random method or a rotational isomeric state (RIS) method. Features are available that make it easy to generate several structures, automatically relax them to relieve strain, and save their coordinates for analysis. Most of the Cerius 2 simulation, computation, and analysis modules can be used with amorphous structures. This chapter contains information on: How the amorphous builder works Building amorphous structures Cloning to create starting models Specifying what torsions to rotate during building Specifying torsion rotation methods For information about Mixtures of polymers. Diffraction from amorphous structures. The format of the ris files written by the amorphous builder. See The discussion of the Blends module in Cerius 2 Computational Instruments Property Prediction. The discussion of the Diffraction-Amorphous module in Cerius 2 Analytical Instruments. Files. Cerius 2 Builders/April

84 6. Amorphous Builder Accessing the tools Controls belonging to the C 2 Amorphous Builder module are contained on the AMORPHOUS BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the AMORPHOUS BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this: How the amorphous builder works The starting structure Varying the torsions The amorphous builder works on the current model. This can be a single- or multiple-chain structure that has been read in or built using the Polymer Builder, the 3D-Sketcher, or one of the other builders. You can make multiple copies of structures and place them in the model window (Cloning to create starting models). Solvents, plasticizers, or additives can also be included in the current model space. The amorphous structure is grown by varying the angles of rotatable torsions. You can specify that certain types of torsions be considered not rotatable (Fixing torsions), for example, torsions involving single-bond sp 2 sp 2 interactions, double bonds, or methyl groups. 74 Cerius 2 Builders/April 1999