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Cerius2 BuildersCrystal Builder, Surface Builder, Interface Builder, Polymer

Builder, Amorphous Builder

Release 4.0 April 1999(last full revision March 1997)

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This document is copyright © 1999, Molecular Simulations Inc., a subsidiary of Pharma-copeia, 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 Molec-ular 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.

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Trademark AcknowledgmentsCatalyst, Cerius2, 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 Sim-ulations 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 trade-mark 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.

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Reprinted with permission from Cerius2 Builders, April 1999, Molecular Simula-tions Inc., San Diego.

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Computational results obtained using software programs from Molecular Simu-lations Inc.—dynamics calculations were done with the Discover® program, using the CFF91 forcefield, ab initio calculations were done with the DMol pro-gram, and graphical displays were printed out from the Cerius2 molecular mod-eling system.

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Cerius2 Builders, April 1999. San Diego: Molecular Simulations Inc., 1999.

Cerius2 Builders/April 1999 v

Contents

1. Introduction 1

Who should use this documentation . . . . . . . . . . . . . . . . . . 1How to find information . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Using other Cerius2 documentation . . . . . . . . . . . . . . . . . . 2Additional information sources . . . . . . . . . . . . . . . . . . . . . . 3Typographical conventions . . . . . . . . . . . . . . . . . . . . . . . . . 3

2. Crystal Builder 5

Building and unbuilding crystals. . . . . . . . . . . . . . . . . . . . . 6Building a molecular crystal using general symmetry positions

8Building a crystal from a 2D periodic model. . . . . . . . 11Building an ionic crystal using space groups . . . . . . . 12Changing lattice vectors . . . . . . . . . . . . . . . . . . . . . . . 15Creating superstructures from crystals . . . . . . . . . . . . 16

Generating a primitive superlattice . . . . . . . . . . . 17Generating a noncrystalline superstructure . . . . . 18Generating a superstructure from a facetted crystal18

Unbuilding a crystal . . . . . . . . . . . . . . . . . . . . . . . . . . 19Displaying crystals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Displaying several cells . . . . . . . . . . . . . . . . . . . . . . . . 19Drawing Miller planes. . . . . . . . . . . . . . . . . . . . . . . . . 20Displaying crystal facets . . . . . . . . . . . . . . . . . . . . . . . 22

Calculating cell formula, density, and volume. . . . . . . . . . 23Finding symmetry in a crystal . . . . . . . . . . . . . . . . . . . . . . 24

3. Surface Builder 27

Building and unbuilding surfaces . . . . . . . . . . . . . . . . . . . 28Cleaving a surface from a crystal . . . . . . . . . . . . . . . . 29Building a surface from a nonperiodic model . . . . . . . 31Building a surface by adding atoms . . . . . . . . . . . . . . 33Changing surface lattice vectors . . . . . . . . . . . . . . . . . 34Creating a surface superstructure . . . . . . . . . . . . . . . . 35Unbuilding a surface . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Displaying surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

vi Cerius2 Builders/April 1999

4. Interface Builder 37

About the interface builder . . . . . . . . . . . . . . . . . . . . . . . . . 37Creating an interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Defining the sides of the interface . . . . . . . . . . . . . . . . 39Concepts and general procedure . . . . . . . . . . . . . . 39Specifying the sides of the interface . . . . . . . . . . . . 41

Building the interface . . . . . . . . . . . . . . . . . . . . . . . . . . 42Editing the interface after it is build . . . . . . . . . . . . . . . 44

Creating a periodic model from an interface. . . . . . . . . . . . 44Creating a crystal from an interface . . . . . . . . . . . . . . . 45Creating a surface from an interface . . . . . . . . . . . . . . . 45

5. Polymer Builder 47

Monomer units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Specifying monomer units . . . . . . . . . . . . . . . . . . . . . . 49Monomer files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Creating or editing monomers . . . . . . . . . . . . . . . . . . . 50Editing monomers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Using monomers created with other programs . . . . . . 53

Homopolymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54Building homopolymers . . . . . . . . . . . . . . . . . . . . . . . . 55Tacticity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Monomer head/tail orientation . . . . . . . . . . . . . . . . . . 58Torsion angles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Random copolymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Building random copolymers . . . . . . . . . . . . . . . . . . . . 60Random copolymer preferences . . . . . . . . . . . . . . . . . . 62Reactivities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Block copolymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Editing polymers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68Monomer and polymer display. . . . . . . . . . . . . . . . . . . . . . 69

6. Amorphous Builder 73

How the amorphous builder works . . . . . . . . . . . . . . . . . . 74Building amorphous structures. . . . . . . . . . . . . . . . . . . . . . 76

Building amorphous structures using the default settings77

Building amorphous structures using custom settings. 78Cloning to create starting models . . . . . . . . . . . . . . . . . . . . 82Specifying what torsions to rotate during building . . . . . . 82

Defining rotatable torsions and torsion rules . . . . . . . . 83Finding unique rotatable torsions. . . . . . . . . . . . . . . . . 84

Specifying torsion rotation methods . . . . . . . . . . . . . . . . . . 85

Cerius2 Builders/April 1999 vii

Entering data in the state table . . . . . . . . . . . . . . . . . . 87Editing the state table, specifying rotation methods . . 87Saving state table data . . . . . . . . . . . . . . . . . . . . . . . . . 91

A. References 93

B. Files 95

State table (.ris) file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95RIS file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96Example file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Figures

Figure 1. Initial crystal orientation with respect to the computer screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Figure 2. Tactic forms of a polymer . . . . . . . . . . . . . . . . . . . . . 57

viii Cerius2 Builders/April 1999

Platform Book_name/Month 1997 ix

Figure 1. Initial crystal orientation with respect to the computer screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Figure 2. Tactic forms of a polymer . . . . . . . . . . . . . . . . . . . . . 57

x Platform Book_name/Month 1997

Cerius2 Builders/April 1999 1

1 Introduction

Cerius2 Builders is a complete guide to the specialized builder mod-ules that can be added to the Cerius2™ 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 Cerius2. Once you are familiar with the information pre-sented in Cerius2 Modeling Environment, you can read only the sec-tions 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 Cerius2 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 Cerius2 interface.

� Quantum mechanical techniques.

Your workstation needs to have:

� Access to a licensed copy of Cerius2.

� A home directory in which you can create subdirectories.

2 Cerius2 Builders/April 1999

1. Introduction

How to find information

Using other Cerius2 documentation

You can find additional information about Cerius2 in several other documentation sets:

� Cerius2 Modeling Environment—Basic use of the Cerius2 inter-face and the C2•Visualizer module.

� MSI Forcefield Engines: CDiscover—Use of CDiscover in Cerius2, Insight, and standalone modes.

� Cerius2 Simulation Tools—The Open Force Field, Force Field Editor, Charges, Minimizer, Dynamics Simulation, Analysis, and Field Calculation modules.

� Cerius2 Quantum Mechanics: Quantum Chemistry and Cerius2 Quantum Mechanics: Physics—Quantum-mechanics programs in the Cerius2 interface.

� Cerius2 Command Script Guide—How to capture and replay a script of Cerius2 commands and enhance your command scripts with the features of the Tool Command Language (Tcl).

� Cerius2 Installation and Administration Guide—Step-by-step instructions for installing and administering Cerius2 in your operating environment.

If you want to know about… Read…

Building, visualizing, and editing crystal structures. Crystal Builder.Constructing 2D periodic systems. Surface Builder.Constructing models of crystal interfaces. Interface Builder.Building all types of linear polymers. Polymer Builder.Building amorphous molecular structures of any type. Amorphous Builder.Scientific references. References.The format of the ris files written by the Analog Builder

and Conformers modules.Files.

Additional information sources


Additional information sources

On-screen help On-screen help is available within the Cerius2 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.

MSI’s website The URL for the documentattion and customer support areas of MSI’s site on the World Wide Web are:

http://www.msi.com/doc/

http://www.msi.com/support/

Typographical conventions

Unless otherwise noted in the text, Cerius2 Builders uses the typo-graphical 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 addi-tion, slashes (/) are used to separate a menu item from a sub-menu 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 exam-ple:

Enter 0.001 in the entry box.

� UNIX command dialog and examples of lines in files are repre-sented in a typewriter font. For example, the following illus-trates a line in a .grf file:


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.


2 Crystal Builder

The C2•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 sci-ence. Many other Cerius2 modules perform calculations and sim-ulations on crystalline structures, including:

Crystal PackerDiffraction-CrystalDiffraction-FaultedDLSHRTEMLEED/RHEEDMorphologyRietveldSorption

This chapter contains information on:

Building and unbuilding crystals

Displaying crystals

Calculating cell formula, density, and volume

Finding symmetry in a crystal


2. Crystal Builder


Following some introductory material (below), this section con-tains 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 C2•Crystal Builder module enables you to build many types of crystals, from small ionic models to large polymer models. Frag-ment types can be mixed so that solvent fragments are incorpo-rated into polymer crystals or small-molecule fragments into zeolite structures. (See Cerius2 Modeling Environment for defini-tions 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 mole-cule, rather than only a part. In C2•Crystal Builder, the term asym-

For information about See

Loading and saving crystal structure files.

The discussion of loading and saving structure files in Cerius2 Modeling Environment.

Crystal file formats. Files appendix, Cerius2 Modeling Environment.Building crystal surfaces. Surface Builder.Building crystal interfaces. Interface Builder.Energy minimization of crystals. Crystal Packer module, Cerius2 Computational Instruments Prop-

erty Prediction; Minimizer module, Cerius2 Simulation Tools.Calculations and simulations

involving crystals.Cerius2 Computational Instruments Property Prediction and

Cerius2 Analytical Instruments.



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.

General procedure 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 crys-tallographic 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.

Accessing the tools Controls belonging to the C2•Crystal Builder module are con-tained 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:


2. Crystal Builder

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.

How it works 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 superlat-tices and superstructures with the C2•Crystal Builder module. Generating a superlattice resets the crystal symmetry to P1 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

To construct the asymmetric unit, load and/or build a model (in a new model space) using the Sketcher control panel or other Visu-alizer tools (see the discussion of building models in Cerius2 Mod-eling Environment).

Accessing the tools 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 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/Gen-eral Positions menu item from the CRYSTAL BUILDER card.

Starting the process For most crystal structures, the default display style is best. If this has been changed, you need to choose DEFAULT from the Visual-ization style popup in the Crystal Build Preferences control panel.

If you want bonds across unit cell boundaries and between sym-metry 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 Cerius2 Modeling Environment).

Important

Specifying unit-cell shape 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.

Building the crystal To construct the basic unit cell around the model, click the BUILD CRYSTAL pushbutton in the Crystal Building control panel.

Specifying crystal symme-try

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:

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 Cerius2 session.


2. Crystal Builder

� 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 Symme-try Operator entry box in the General Positions control panel.

Technical notes The format is:

rot1, trans1, rot2, trans2, rot3, trans3

Where rot1, rot2, and rot3 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 trans1, trans2, trans3 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 +0.5-y +1/2 -x +1/2 z +1/2 y -x+y z +1/6 z y x

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).

Editing the symmetry If you make a mistake, remove a symmetry entry by entering the number of the symmetry entry (from the General Position Oper-ators list box in the General Positions control panel) in the Remove Symmetry Operator entry box. To remove all symmetry entries,



use the Clear List of General Positions action button and confirm the action.

Additional information 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


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 C2•Surface Builder (see Surface Builder) to create one.



Open the Find Space Group control panel by selecting the Symme-try/Find Symmetry menu item from the CRYSTAL BUILDER card.

Specifying the crystal For most crystal structures, the default display style is best. If this has been changed, you need to choose DEFAULT from the Visual-ization 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 crys-tal cell vector perpendicular to the surface is taken to be the thick-ness 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.

Building the crystal Click the BUILD CRYSTAL pushbutton in the Crystal Building control panel. The 2D surface structure is converted into a 3D crys-tal. The crystal cell parameters are obtained from the surface mesh parameters.


2. Crystal Builder

Finding the symmetry 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 sym-metry 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.


Building an ionic crystal using space groups

Begin with an empty model space.



Open the Space Groups control panel by clicking the Edit… push-button to the right of SPACE GROUP on the Crystal Building con-trol 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.



Starting the process For most crystal structures built by this method, the default dis-play 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 out-side the unit cell are drawn translated to within the cell or to the most appropriate location in relation to the connectivity. Frag-ments whose centers of geometry are on cell faces, edges, and cor-ners are repeated on the opposite face, edges, or corners.

Building the crystal To construct the basic unit cell within which to build the model, click the BUILD CRYSTAL pushbutton in the Crystal Building control panel.

Specifying crystal symme-try

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 choos-ing 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 cho-sen space group.

Technical notes The space groups used by Cerius2 are those that appear in the International Tables of Crystallography, Volume A (1989). Only the brief symbol is required the Space Group entry box. Cerius2 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


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 1Space group number 2: P -1Space group number 17: P 2 2 21Space group number 88: I 41/aSpace group number 193: P 63/m c mSpace group number 226: F m -3 c

Choosing certain space groups forces changes to some cell param-eters. 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 sym-bol, but they share the same brief symbol. Some orthorhombic, tet-ragonal, 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.

Specifying unit-cell shape 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.

Choosing the coordinate system

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.

Constructing the asym-metric unit

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.



You may also want to specify other options: Hybridization, a non-zero 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.

Editing the asymmetric unit

If you make a mistake and want to remove an atom, use the UNDO pushbutton. You can also select the atom in the model win-dow 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.

Additional information Please see the on-screen help for additional information about the controls in all the panels mentioned here. For additional informa-tion about the Add Atom control panel, see the discussion of build operations in Cerius2 Modeling Environment.

Changing 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 C2•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.

Accessing the tools Open the Lattice Redefinition control panel by selecting the Unit Cell/Redefine Lattice menu item from the CRYSTAL BUILDER card.

Changing the lattice vec-tors

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


2. Crystal Builder

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.

Changing to a primitive lattice

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.

Applying the changes to the current crystal

Click the Change to action button to change the lattice from the old to the new vectors.

Caution

Technical notes 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, Cerius2 keeps the sym-metry descriptions in the model, transforming them as appropri-ate, and also remembers the old lattice parameters (they are stored with the model) so that you can change them later to a conven-tional lattice description.


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 P1 sym-metry. 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 P1 model, because there

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.



are no symmetry constraints to interfere, as in the higher sym-metries.

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 infor-mation about disorder, see the relevant chapter in Cerius2 Mod-eling Environment.

� A nonperiodic superstructure—A nonperiodic superstructure has the same structure as a crystal, but Cerius2 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

Generating a primitive 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 prim-itive symmetry.


Open the Crystal Visualization control panel by selecting the Visu-alization menu item from the CRYSTAL BUILDER card.

Making a superlattice To display the current model in the size that you want the super-lattice to be, enter a, b, and c values in the Display Range entry boxes in the Crystal Visualization control panel.

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.


2. Crystal Builder

Click the Crystalline Superlattice action button in the Crystal Building control panel. The entire current model is converted into a superlattice with P1 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.


Generating a noncrystalline superstructure


Open the Crystal Visualization control panel by selecting the Visu-alization menu item from the CRYSTAL BUILDER card.

Making a superstructure To display the current model in the size that you want the super-structure 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 Crys-tal Visualization control panel. The entire current model is con-verted 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 nonpe-riodic, meaning it is not a unit cell.


Generating a superstructure from a facetted crystal

Accessing the tools Open the Crystal Facetting control panel by selecting the Facetting menu item from the CRYSTAL BUILDER card.

Facetting the crystal 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 Fac-etting control panel so that you can estimate how the superstruc-ture will look.

Making the superstructure Click the Generate Superstructure from facetted crystal action button at the bottom of the Crystal Facetting control panel. This

Displaying crystals


converts the visible part of the structure (deleting the selected atoms) into a nonperiodic superstructure.


Unbuilding a crystal


Unbuilding a crystal 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.


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 projec-tion 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)


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 dis-play property only—that is, all calculations on a crystal model are


2. Crystal Builder

done using periodic boundary conditions and assuming an infi-nitely repeating lattice.

Accessing the tools Open the Crystal Visualization control panel by selecting the Visu-alization menu item on the CRYSTAL BUILDER card or by click-ing the Visualization… pushbutton on the Crystal Building control panel (see Building and unbuilding crystals).

Changing the number of unit cells displayed

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 num-ber of cells drawn is the product of the number of cells along each cell axis (a × b × c).


Drawing Miller planes

Miller planes enable you to display planes in crystal structures, which aids in the study of crystal habit planes.

Figure 1. Initial crystal orientation with respect to the computer screenBy 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.

c

b

a

Displaying crystals


Accessing the tools Open the Crystal Visualization control panel by selecting the Visu-alization menu item on the CRYSTAL BUILDER card or by click-ing 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.

Displaying Miller planes for the current crystal model

Check the Show Miller Plane check box in the Crystal Visualiza-tion 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 Trans-parency entry box in the Miller Plane Options control panel.

Positioning the Miller planes

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 Crys-tal 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 ori-gin to the plane in the Origin Distance entry box in the Crystal Visualization control panel.

The Origin Distance entry box specifies the perpendicular dis-tance 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.


2. Crystal Builder


Displaying crystal facets

An additional aid to visualization is the ability to section the crys-tal 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 gener-ate 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).

Accessing the tools 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.

Adding facets to the cur-rent crystal model

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.

Editing 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 Fac-ets list box).



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.

Selecting atoms 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 superstruc-ture from a facetted crystal) will look.



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.

Accessing the tools Open the Cell Contents control panel by selecting the Unit Cell/Cell Contents menu item from the CRYSTAL BUILDER card.

Obtaining the information The list box in the Cell Contents control panel automatically dis-plays information about the unit cell of the current model, includ-ing the number of atoms, volume, density, and cell formula. (For 2D periodic and nonperiodic models, appropriate values are dis-played.)

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.



2. Crystal Builder


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.

Accessing the tools Open the Find Space Group control panel by selecting the Symme-try/Find Symmetry menu item from the CRYSTAL BUILDER card.

Setting up 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 forc-ing 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 set-ting 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.

Finding the symmetry Click the Find Space Group Symmetry action button.

If the Update Model check box is checked, the model is trans-formed as appropriate for the newly found cell vectors and sym-metry. 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.



2. Crystal Builder


3 Surface Builder

The C2•Surface Builder module is used for constructing 2D-peri-odic 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 C2•LEED/RHEED module. For calculations using other modules, you can convert surface structures into large nonperiodic superstructures to represent the surface.

The C2•Surface Builder module also helps to visualize surfaces within crystal models that were built with the C2•Crystal Builder module.


Building and unbuilding surfaces

Displaying surfaces


Loading and saving surface structure files.


Surface file formats. The discussion of Cerius2 structure files in Cerius2 Modeling Envi-ronment.

Building crystals. Crystal Builder.Building interfaces from surfaces. Interface Builder.Diffraction from surfaces. Cerius2 Analytical Instruments.


3. Surface Builder



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

The C2•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 super-structures and superlattices.

Any surface can be unbuilt, converting the surface to one cell of a nonperiodic model. All unit cell information is lost.

General procedure 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).

File formats The MSI and CSSR file formats are the only formats that save 2D models, that is, they include the 2D unit cell information. How-ever, once the surface has been converted into a nonperiodic superstructure, any of the file formats used for nonperiodic mod-els can be used to save the structure.

Accessing the tools Controls belonging to the C2•Surface Builder module are con-



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

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 Cerius2 session, but need not be the current model.

Accessing the tools 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… push-button on the Cleave Crystal Surface control panel.

Beginning the process 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.


3. Surface Builder

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 Cerius2 to try to maintain whole mole-cules, 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 con-nected 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.)

Specifying the surface slab

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 cleav-ing 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 Dis-play Surface Box check box in the Cleave Crystal Surface control panel is checked.



Cleaving the surface Now open a new, empty model space (see Cerius2 Modeling Envi-ronment to review how to do this) to contain the surface model. Click the CLEAVE pushbutton on the Cleave Crystal Surface con-trol panel. The cleaved surface appears in the current model space.

Caution


Building a surface from a nonperiodic model

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 coin-cident with the z axis. You should position the model roughly where you want it to be when the surface is built. (See the discus-sion of moving and manipulating models in Cerius2 Modeling Envi-ronment.)


Load or build a nonperiodic model. See Cerius2 Modeling Environ-ment for information on building, saving, and loading models.

Accessing the tools 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 con-trol panel.

Beginning the process In the Surface Build Preferences control panel, set the Visualiza-tion style to ORIGINAL.

If you want bonds across unit cell boundaries and between sym-metry copies of atoms to be calculated automatically, assure that

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).


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 Cerius2 Modeling Environment).

Important

Specifying the unit sur-face cell

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 bound-aries.

Building the surface Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model win-dow.

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 Cerius2 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.

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 Cerius2 session.



� 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.

Tip


Building a surface by adding atoms

Building a surface from individually placed atoms involves posi-tioning them within a surface cell and then generating the surface. The cell is generated before the atoms are placed in it.

Beginning the process Begin with an empty model space.

Accessing the tools 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 con-trol panel.

Open the Add Atom control panel by clicking the Add Atoms… pushbutton on the Building From Atoms control panel. Alterna-tively, select the Build/Add Atom… menu item in the main Visu-alizer control panel.

Specifying the unit sur-face cell

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.)

Building the surface Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model win-dow.

Adding atoms Choose the surface fractional (UVd) or Cartesian (XYZ) coordinate system from the popup in the Add Atom control panel.

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.


3. Surface Builder

For each atom, you need to enter an element type and x, y, z coor-dinates (Cartesian) or U, V, d coordinates (surface fractional). The x, y, z, and d coordinates are in angstroms, and U and V in frac-tional 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.

Additional information Please see the on-screen help for additional information about the controls in all the panels mentioned here. For additional informa-tion about the Add Atom control panel, see the discussion of build operations in Cerius2 Modeling Environment.

Changing surface 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.

How it works 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.

Accessing the tools 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.

Changing the lattice vec-tors

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.



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.


Creating a surface superstructure

Once a block of surface cells is displayed in the current model space, you may want to convert this display into a surface super-lattice model or into a nonperiodic superstructure model. For example:

� To introduce disorder into a surface structure, generate a super-lattice from a block of surface cells, then selectively edit the superlattice.

� To perform calculations on a surface using Cerius2 modules that do not explicitly accept 2D-periodic surface models, gener-ate a large nonperiodic superstructure from the surface cells.

Accessing the tools Open the Surface Visualization control panel by clicking the Visu-alization menu item on the SURFACE BUILDER card. Alterna-tively, 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).

Size of the new structure Use the Surface Cell Display Range controls in the Surface Visu-alization control panel to display the number of surface cells that you want included in the superstructure or superlattice.

Creating a 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.

Creating a nonperiodic superstructure

Alternatively, to create a nonperiodic superstructure from the dis-played atoms, click the Non-periodic Superstructure action but-ton in either panel.


3. Surface Builder

Caution


Unbuilding a surface

Accessing the tools Open the Building From Atoms control panel by selecting the Building From Atoms menu item on the SURFACE BUILDER card.

Unbuilding a surface 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.


Displaying surfaces

It is often easier to visualize the current surface by displaying a large block of surface cells instead of just one.

Accessing the tools Open the Surface Visualization control panel by selecting the Visu-alization menu item from the SURFACE BUILDER card. Alterna-tively, click the Visualization… pushbutton on the Building From Atoms control panel.

Display range 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.


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.


4 Interface Builder

The C2•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 C2•Interface Builder module aids in simulating experimental data such as high-resolution transmis-sion electron microscopy images of interfaces (C2•HRTEM mod-ule) and in visualizing epitaxy and structural relationships between crystalline particles in contact.


About the interface builder

Creating an interface

Creating a periodic model from an interface

About the interface builder

How it works The sequence of steps for using the C2•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 dimen-sions of the right side of the interface.


Loading and saving interface structure files.


Building crystals. Crystal Builder.Building surfaces. Surface Builder.Microscopy. Cerius2 Analytical Instruments.


4. Interface Builder

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 projec-tions of their match points are coincident and their match vec-tors are parallel.

4. Edit the interface (optional)—After the interface has been built, you have another opportunity to automatically remove super-imposed 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.

Accessing the tools Controls belonging to the C2•Interface Builder module are con-tained 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:




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

Before the interface can be built, the left and right sides of the inter-face 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.

The starting model(s) 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 crys-tal 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.



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 inter-face model and may be thought of as the amount of pure crystal on the back side of the interface.

Match point 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 crys-tal. If the interface separation is zero, the match points coincide. If not, their projections normal to the interface planes coincide.

Match vector 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 sys-tem 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 inter-face into a 2D or 3D periodic box. If you enter a value in the mul-tiplication (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 vec-tor 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.

Mesh shape 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 perpendic-ular 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



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 mul-tiple of the unit vector.

Specifying the sides of the interface

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 infor-mation, please see Crystal Builder.

Accessing the tools Open the Interface Right Side control panel by selecting the Right Side menu item from the INTERFACE BUILDER card. Alterna-tively, if you have the Interface Building control panel (see Access-ing 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. Alterna-tively, if you have the Interface Building control panel (Accessing the tools) open, click its Left Side… pushbutton.

Beginning the process 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 inter-face 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.



Specifying the interface slab

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 Sec-ond 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.

Tip


Building the interface

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.

How it works The interface is built from the two sides specified in the Interface Left Side and Interface Right Side control panels. The build opera-tion takes place in the current workspace, which must be empty. The original crystals are not affected by the interface building.

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.



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 gov-erned 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 build-ing. For example, you can specify whether you want to calculate bonding upon building or whether and how superimposed atoms are removed.

Accessing the tools 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.

Specifying build parame-ters

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.

� > 0–1.5 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 bond-ing 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 bond-ing patterns that may be required across the interface.



When the Remove superimposed atoms box is checked, atom pairs at the interface that are superimposed (within the Superim-position 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.

Building the interface Click the BUILD INTERFACE pushbutton. The new interface is built in the current (empty) model space.


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

Accessing the tools Open the Edit Interface control panel by selecting the Edit Inter-face 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 tol-erance entry box on the Interface Building control panel also con-trols the tolerance for duplication here.



This section includes information on:

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 Cerius2 Modeling Environment.



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 creat-ing 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 inter-face. This enables you to extend interfaces, particularly those where the two sides match. For example, this is necessary for per-forming HRTEM simulations on an interface, because HRTEM cal-culations can be applied only to crystal models.

Creating a crystal from an interface

Create an interface in which the left and right face dimensions of the interface are the same.

Accessing the tools Open the Crystal Building control panel by selecting the Crystal Building menu item from the CRYSTAL BUILDER card.

Building the crystal Set various parameters as desired (see Crystal Builder).

Click the BUILD CRYSTAL pushbutton. The interface appears correctly placed in a 3D unit cell.


Creating a surface from an interface

Create an interface in which the left and right face dimensions of the interface are the same.

Accessing the tools 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.



Beginning the process 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.

Building the surface 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.



5 Polymer Builder

The C2•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 con-structed from files supplied with Cerius2 or create your own monomers. You can also edit the monomers before using them.

Almost any of the Cerius2 simulation and computation modules can be applied to polymer models. Two modules that are particu-larly applicable to polymer models are C2•Blends and C2•Poly-mer Properties.


Monomer units

Homopolymers

Random copolymers

Block copolymers

Editing polymers

Monomer and polymer display


Loading and saving monomer and poly-mer structure files.



5. Polymer Builder

Accessing the tools Controls belonging to the C2•Polymer Builder module are con-tained 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:

Polymer file formats. The discussion of Cerius2 structure files in Cerius2 Modeling Environment.

Building crystals from polymers. Crystal Builder.Mixtures of polymers. The discussion of the Blends module in Cerius2 Computa-

tional Instruments Property Prediction.Polymer statistics. The discussion of the Polymer Properties module in Cerius2

Computational Instruments Property Prediction.Diffraction from polymers. Cerius2 Analytical Instruments.


Monomer units


Monomer units


Specifying monomer units

Monomer files

Creating or editing monomers

Editing monomers

Using monomers created with other programs

Monomers Monomers (or repeat units) are the building blocks of polymers. A Cerius2 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.

Torsions By default, the torsion angle between monomer units is deter-mined by the conformations of the head and tail groups of the two monomers. However, this can be changed.

Chirality Monomer chirality is important in determining the configuration of the polymer. Monomers loaded from the Cerius2 monomer files already have chiral centers defined. You can also define (or rede-fine) chiral centers as desired.

Inversion 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.


5. Polymer Builder

Specifying monomer units

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 Cerius2 (see Monomer files) and all the models cur-rently 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.

Additional information Please see the on-screen help for information about the monomer chooser(s) in any control panel in which they appear.

Monomer files

Cerius2 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 Cerius2. They are auto-matically 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 Cerius2 or can create your own monomer models from scratch.

Creating or editing monomersMonomers 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.

Starting the process Begin with the model that you want to convert to a monomer unit. Place it in the current model space.

Monomer units


You can build the model using the 3D Sketcher and/or other Cerius2 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.

Accessing the tools 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 con-trol panel to open the Monomer Preferences control panel.

Defining head and tail groups and torsion atoms

The following instructions mention double-clicking the atom. When you double-click an atom with the Define Head or Define Tail tool, Cerius2 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 col-ored light blue.

Remember

Removing head and tail definitions

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.

At present, the Polymer Builder can use monomers with only one head and one tail.


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 back-bone atoms in your built polymer, which can often give you a bet-ter understanding of its overall structure.

To define an atom as a backbone atom, use the Define Backbone tool.

Help Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the monomer editor.

Additional information 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 Cerius2 Modeling Environment.

Editing monomers

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.

Starting the process 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 Cerius2 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.


Click the Preferences… pushbutton in the Monomer Editor con-trol panel to open the Monomer Preferences control panel.

Defining chiral centers Chiral centers are used by the polymer builder to determine inver-sions, 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.

Monomer units


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.

Removing chiral defini-tions

By default, when you define a tacticity (chiral) center, the defini-tion 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.

Loading and saving Monomers that you create and/or edit can be saved and loaded just like any other model created in Cerius2.

Since only the monomer files supplied with Cerius2 are automati-cally 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 Cerius2 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.

File formats The MSI file format is particularly recommended because it includes chirality information (which is saved within the atom names).


Additional information Please see the on-screen help for information about all the controls in these control panels. Information on editing, saving, and load-ing models is contained in Cerius2 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, Cerius2 enables you to convert files of other formats to the current Cerius2 format, while properly inter-preting the head/tail group information.


5. Polymer Builder


Click the Convert Formats… pushbutton on the Monomer Editor control panel to access the Convert Formats control panel.

Polygraf and Biograf files In the Polygraf and Biograf programs, a monomer head is repre-sented 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 Cerius2 monomer head or tail groups. Default torsion angles are gener-ated.

Old Cerius2 files Prior to version 3.0, Cerius2 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 but-ton 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.

Insight II files 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).

Additional information Please see the on-screen help for information about all the controls in these control panels.

Homopolymers


Building homopolymers

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 poly-mer chain is required.

Building homopolymers

Specifying the monomer unit

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 sup-plied with Cerius2. If you want a nonstandard monomer, create (see Monomer units) or load (see Loading and saving) it now.

Accessing the tools 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.

Number and type of monomer units

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.


5. Polymer Builder

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.)

Tacticity If the monomer being polymerized has a single chiral center, change the tacticity if desired. For information on tacticity, see Tac-ticity. By default, an isotactic polymer (see Figure 2) is built.

Head/tail orientation 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.

Torsions 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.

Other controls Use controls in the Homopolymer Preferences control panel if you want to reset any preferences for how the build proceeds.

Tip

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 informa-tion on using monomer choosers.

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.

Homopolymers


Tacticity

Concepts Homopolymers containing chiral centers can be polymerized in several stereoconfigurations. Cerius2 offers a choice of three tactic-ity options (Figure 2):

� Isotactic.

� Syndiotactic.

� Atactic (you need to specify the meso–diad ratio).

Figure 2. Tactic forms of a polymerThe isotactic (top), syndiotactic (middle), and atactic (bottom) forms of polysty-rene are shown. The equivalent meso–diad ratios are 1.0, 0.0, and 0.5, respec-tively.


5. Polymer Builder

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 atac-tic 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 pre-dominantly isotactic polymer containing some syndiotactic diads.

Preparing the monomer 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.


Click the Tacticity… pushbutton on the Homopolymer Builder control panel to open the Polymer Tacticity control panel.

Setting monomer tacticity Choose one of the three tacticity options: ISOTACTIC, SYNDIO-TACTIC, or ATACTIC or specify the appropriate Meso-Diad Ratio (see, for example, Figure 2).


Monomer head/tail orientation

How it works The typical orientation of monomer units in a polymer is head-to-tail, 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 connect-ing 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-

Homopolymers


nation of the two probabilities gives a mixed, randomly selected, arrangement of connections.


Click the Orientation… pushbutton on the Homopolymer Builder control panel to open the Monomer Orientation control panel.

Setting the orientation probabilities

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 probabil-ity 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.


Torsion angles

How it works As the polymer chain is built, the torsion angle between each suc-cessive 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 tor-sions of the two participating monomer linkage groups.

� A fixed angle that you specify.

Note

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 (respec-tively) on the POLYMER BUILDER card.

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.


5. Polymer Builder

Click the Torsions… pushbutton on any of these control panels to open the Polymer Torsions control panel.

Setting torsion angles for linkages

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.

Note

Additional information 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 Cerius2 Modeling Environment.

Random copolymers


Building random copolymers

Random copolymer preferences

Reactivities

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.

General procedure The random copolymer builder in Cerius2 enables you to specify the following:

� Monomers to be used for building.

� Monomer concentrations.

� Number of monomer units.

This torsion angle setting applies to all monomers and is irrespective of polymer type (homopolymer or copolymer).

Random copolymers


� Monomer reactivities.



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 poly-mer chain is required.

Building random copolymers


Standard monomer units and end units are loaded with monomer choosers on the Random Copolymer Builder control panel.


Accessing the tools Open the Random Copolymer Builder control panel by selecting the Random Copolymer menu item on the POLYMER BUILDER card.

Number and types of monomer units

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 0.000 (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.)


5. Polymer Builder

Monomer concentrations 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.

Monomer reactivities To specify relative reactivities of the monomers, click the Reactiv-ities… pushbutton to open the Monomer Reactivities control panel. For information on setting monomer reactivities, please see Reactivities.

Tacticity and head/tail ori-entation

Set the inversion (Invert entry boxes) and Flip probabilities for each monomer type. These control s (respectively) set the probabil-ity 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.

Torsions 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.

Other controls Use controls in the Random Copolymer Preferences control panel (see Random copolymer preferences) if you want to reset any prefer-ences for how the build proceeds.

Building the copolymer 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 Prefer-ences control panel.


Random copolymer preferences

Several preference options are available for controlling the build-ing of random copolymers. You can:

� Choose the location for the built polymer (the current or a new model space).

Random copolymers


� Decide whether to use reactivities in combination with concen-trations 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 speci-fied 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 poly-mer ’s name.

� Reset the seed for the random-number generator. This is useful for recreating particular structures.

Accessing the tools 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.

Setting some preferences Check the Use reactivities box if you want to use both monomer reactivities (Reactivities) and concentrations to determine the fre-quency of monomers in the built chain.

Check the Force concentrations box to enforce the specified mono-mer 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.


5. Polymer Builder

Specify the maximum number of monomer components that con-tribute 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.


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 kij of mono-mer j with the growing chain’s end i, so that kij [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:

To copolymerize these monomers, the relative reactivity rates are entered into the Cerius2 relative reactivity matrix as shown in Table 1. The rate constants for the self-propagating reactions are on the diagonal (k11, k22, k33), and the cross-propagation rate terms are on the off-diagonals (kij, i ≠ j).

Experimental results on monomer reactivities (Young 1975) are often presented as reactivity ratios, r1 and r2, for polymer pairs:

Eq. 1

k11——M1

*M1+ ——M1M1

*→

k12——M1

*M2+ ——M1M2

*→

k13——M1

*M3+ ——M1M3

*→

k21——M2

*M1+ ——M2M1

*→

k22——M2

*M2+ ——M2M2

*→

k23——M2

*M3+ ——M2M3

*→

k31——M3

*M1+ ——M3M1

*→

k32——M3

*M2+ ——M3M2

*→

k33——M3

*M3+ ——M3M3

*→

r1

k11

k12-------=

Random copolymers


Eq. 2

A reactivity ratio greater than one indicates a preference for like monomers to link. Reactivities can be entered into the Cerius2 matrix and viewed as either relative reactivities or reactivity ratios.

Accessing the tools Monomer concentration values are set with the Random Copoly-mer 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.

Setting monomer reactiv-ity

Decide whether you want to use RELATIVE reactivities or reactiv-ity 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 reactivi-ties, simply select the RELATIVE button and the values in the table are appropriately recalculated.)

Table 1. Relative monomer reactivity rates

Monomer Relative reactivities

no. name 1 2 3

1 M1 k11 k12 k13

2 M2 k21 k22 k23

3 M3 k31 k32 k33

r2

k22

k21-------=


5. Polymer Builder

Check the Use reactivities box in the Random Copolymer Prefer-ences control panel. The reactivities are applied when the copoly-mer is constructed.


Block copolymers

Block copolymers are polymers with regularly repeating sequences. The Cerius2 block copolymer builder enables you to build linear chains of repeating block sequences.

General procedure The following must be specified to define a block copolymer:

� Monomers to be used for building.

� Repeating block sequence.

� Number of repeating blocks.




Standard monomer units and end units are loaded with monomer choosers on the Block Copolymer Builder control panel.


Accessing the tools 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 Copoly-mer Preferences control panel.

Click the Torsions… pushbutton to access the Polymer Torsions control panel.

Number and types of monomer units

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.

Block copolymers


Choose any initiator and/or terminator monomers with the Initi-ator 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.

Defining the super unit—size, tacticity, and head/tail orientation

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 alter-nating 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, respec-tively. For more information on orientation, see Monomer head/tail orientation.

Torsions 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.

Other controls 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 com-ponents of the built polymer, as well as for using this polymer to build more complex polymers.

Specify the maximum number of monomer components that con-tribute 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


5. Polymer Builder

such options are chosen. Setting the Random seed to a particular value allows regeneration of specific structures.

Building the block copoly-mer

Click the BUILD pushbutton in the Block Copolymer Builder con-trol 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).


Editing polymers

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 addi-tion, a list can be obtained of the groupings within the model.

Starting the process 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/Poly-mers 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 click-ing 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.

Editing polymers


Removing chiral defini-tions

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.

Listing atomic groupings 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 mono-mers, 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 gen-erally, the names of the “types” are intended to identify groupings of the same detailed structure, and the “class” is intended to iden-tify groupings of the same general chemical nature. For example, PE (polyethylene) and PP (polypropylene) are considered differ-ent “types” but share the same “class”: “Olefin”.


Additional information 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 Cerius2 Modeling Environment.


5. Polymer Builder


Several options are available that affect the visualization of mono-mers and polymers. These include:

� The ability to color the linkage atoms, to label them, and to dis-play the torsion geometry.

� The ability the color the backbone and to show only the back-bone atoms.

� The ability to color and label tacticity centers.

� The ability to color and label according to different atom group-ings.

Accessing the tools Open the Display Editor control panel by selecting the Edit/Dis-play 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 link-age 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 link-age label graphics from the display of the current model. The link-age atoms may remain colored.

Changing backbone dis-play

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.



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.

Changing display of chiral centers

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 Edi-tor 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 group-ings 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 group-ing subunits containing those selected atoms. Use the associated popup to choose whether to label groupings by TYPE or by CLASS.


5. Polymer Builder

Use the Remove Grouping Labels action button to remove atom grouping labels.



6 Amorphous Builder

The C2•Amorphous Builder module builds amorphous molecular structures, which can be represented in the molten state, in solu-tion, 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, automat-ically relax them to relieve strain, and save their coordinates for analysis.

Most of the Cerius2 simulation, computation, and analysis mod-ules can be used with amorphous structures.


How the amorphous builder works

Building amorphous structures

Cloning to create starting models

Specifying what torsions to rotate during building

Specifying torsion rotation methods


Mixtures of polymers. The discussion of the Blends module in Cerius2 Computa-tional Instruments Property Prediction.

Diffraction from amorphous structures. The discussion of the Diffraction-Amorphous module in Cerius2 Analytical Instruments.

The format of the ris files written by the amorphous builder.

Files.


6. Amorphous Builder

Accessing the tools Controls belonging to the C2•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:


The starting structure 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). Sol-vents, plasticizers, or additives can also be included in the current model space.

Varying the torsions The amorphous structure is grown by varying the angles of rotat-able torsions. You can specify that certain types of torsions be con-sidered not rotatable (Fixing torsions), for example, torsions involving single-bond sp2–sp2 interactions, double bonds, or methyl groups.



Random and RIS build methods

Several algorithms can be used to generate the amorphous struc-ture: a Monte Carlo method that assigns random values to all tor-sions and two rotational isomeric state (RIS) methods:

� The random method results in a random distribution of torsion angles.

� The RIS ratio method refines this by enabling you to explicitly specify a distribution of isomeric states (i.e., torsion angles, along with angle tolerances and a relative frequencies) for the torsion type.

� The RIS energy method calculates the appropriate distribution of isomeric states (torsion angles) using the Boltzmann parti-tion function, given the specified RIS temperature and relative energies of the various isomeric states.

A method is specified for each unique rotatable torsion, thus allowing a combination of methods to be used (Specifying torsion rotation methods).

Building 3D periodic sys-tems

If the structure is to be built as a 3D-periodic system, the amor-phous builder constructs a cube of the appropriate volume to con-tain the structure at a requested density. Whenever the chain leaves the cell while it is being built, its periodic image is generated on the opposite face of the cell and growth continues into the cell. By the end of the building process, the complete chain may effec-tively traverse many unit cells.

Bump checking A bump-checking algorithm is used to control how close together nonbonded atoms are allowed to come when the amorphous structure is being built. The minimum nonbond distance allowed is equal to the sum of the two atoms’ van der Waals radii multi-plied by the van der Waals scale. The number entered is used for a hard-sphere van der Waals approximation.

van der Waals scale values can range from 0 to 0.89. If 0 is used, all bumps are disregarded and phantom chain growth is permitted. The maximum value is 0.89, which is the distance at which the Lennard–Jones 12–6 potential becomes strongly repulsive:

U (0.89 r0) = 0

Here U is the potential energy and r0 is the minimum-energy dis-tance. van der Waals scale values close to 0.300 (the default) are recommended. As the van der Waals scale gets larger, the van der



Waals energy of the system becomes more favorable. However, because the atoms are not allowed to come as close together, this makes it more difficult to construct an atomistic model. For many systems, values greater than 0.600 may prevent Cerius2 from building a structure.

The smaller the value used for the van der Waals scale, the faster structures are generated, but subsequent energy minimization cal-culations take longer.

By default, hydrogen atoms are included when performing the van der Waals bump checking. You can specify otherwise, how-ever (Bump checking).

Retry attempts You can specify how many attempts should be made to find an acceptable angle for each rotatable torsion (Torsion placement attempts). If an acceptable value is not found after this many attempts, Cerius2 backs up to the previous torsion, sets a new value for its angle, and then tries the problem bond again. Cerius2 may have to back up several bonds before acceptable values are found. You can also specify how many times Cerius2 should back up all the way to the beginning and start building again before it aborts building a conformation and goes on to the next one (Torsion placement attempts).

Relaxing the structures The amorphous structures can be automatically relaxed by energy minimization after each one is built.



Building amorphous structures using the default settings

Building amorphous structures using custom settings

Technical notes Initiating the build process by clicking the RUN BUILD pushbut-ton in the Amorphous Builder control panel initiates the build pro-cess using the current model and the current settings in the amorphous builder control panels. If a torsion search has not already been performed, it is automatically done before running the build. (A torsion sort is also done if required.)



Structure-building continues until the specified number of sam-ples have been generated. A statistically unique conformation is generated each time. If it is not possible to build a structure with the current parameter values, a message to that effect is displayed in the text window.

The model window is updated with the coordinates of the new structures after they are generated. If the structures are to be relaxed, plots showing the energies and rms force can be dis-played.

The build process can be stopped at any time by clicking the INTERRUPT button in the Processing… dialog box.

Building amorphous structures using the default settings

The default settings The amorphous builder defaults are set up so that you can easily build a single nonperiodic amorphous structure using the random method. The rotatable torsions are determined by excluding sin-gle-bond sp2–sp2 interactions, double bonds, and methyl rotors; torsions that differ only in chirality or atom name are not consid-ered unique. The VdW Scale is set to 0.30 for a quick build, and hydrogen atoms are included in the bump checking. The structure generated appears in the model window but is not relaxed or saved.

Starting the process Place the starting structure in the current model space.

The starting structure can be loaded from a file or built using the polymer builder or one of the other builders. Multiple copies can easily be made by using the Amorphous Builder Clone control panel (Cloning to create starting models).

Accessing the tools Open the Amorphous Builder control panel by selecting the Build menu item on the AMORPHOUS BUILDER card.

Building the structure To start the build, click the RUN BUILD pushbutton.

Additional information Please see the on-screen help for information about all the controls in this control panel. Using the polymer builder is discussed under Polymer Builder. Information on building and editing models is contained in Cerius2 Modeling Environment, published separately by MSI.



Building amorphous structures using custom settings

Typical build process Generally, you start building an amorphous structure by finding all the unique rotatable torsions for your structure and assigning a build method to each (the random method is generally the default). For torsions where data are available, you would proba-bly want to use the RIS ratio or RIS energy method. For these methods, you must specify the angles, tolerances, and ratios or energies for each isomeric state. For the latter, you also need to specify the temperature.

You should specify values for the periodic density if you are build-ing a 3D-periodic structure.

You also need to specify a van der Waals scale (for bump checking, see Bump checking) that is appropriate for your system and that takes performance issues into account.

Some trial builds may be required to determine optimal settings, and you may find that you need to modify the retry parameters to achieve a successful build.

You will probably want to generate several structures, relax them, and save them in a trajectory file for later analysis.

Starting the process Place the starting structure in the current model space.

The starting structure can be loaded from a file or built using the polymer builder or one of the other builders. Multiple copies of a structure can easily be made using the Amorphous Builder Clone control panel (Cloning to create starting models).

Accessing the tools Open the Amorphous Builder control panel by selecting the Build menu item on the AMORPHOUS BUILDER card.

Click the Output… pushbutton to open the Amorphous Builder Output control panel.

Click the Preferences… pushbutton to open the Amorphous Builder Preferences control panel.

Rotatable torsions Define the rules used to determine which torsions are rotatable (see Defining rotatable torsions and torsion rules).

If you are not using the random method for all torsions, find the unique rotatable torsions and assign a build method and RIS vari-



ables to each (see Finding unique rotatable torsions and Specifying tor-sion rotation methods).

Bump checking Enter a value for the VdW Scale (0 to 0.89) in the Amorphous Builder control panel. This value is used to determine how closely atoms can approach one another before they are considered to be too close (Bump checking).

Hydrogens are included in bump checking by default, resulting in a lower-energy structure. However, you may want to exclude hydrogens when building large structures, to speed up the build process.

To exclude hydrogen atoms from van der Waals bump checking, check the Ignore H’s in VdW Bump Checking check box in the Amorphous Builder Preferences control panel.

Type of structure Select Nonperiodic in the Amorphous Builder control panel to build a nonperiodic amorphous structure or 3D Periodic to con-struct a 3D-periodic system to represent the bulk state.

If you are building 3D-periodic structures, enter the desired unit cell density for the bulk state in g cm-3 in the Periodic Density entry box.

Number of structures Enter the Number of Samples (in the Amorphous Builder control panel) to be generated. If you want more than one sample, you should save (in a trajectory file) the coordinates of each structure generated (Saving structures).

Torsion placement attempts

Sometimes steric hindrance prevents a given torsion from being placed, so Cerius2 can go back in the build process to change pre-vious torsions. Retry options are set to prevent Cerius2 from get-ting stuck in an endless loop, so that it will abort a nonproductive build and move on to the next conformation.

Enter the Maximum Attempts Per Torsion allowed (in the Amor-phous Builder Preferences control panel) before going back to the previous rotatable bond. This entry box specifies the number of attempts that can be made to find an acceptable value for each unique torsion. If an acceptable value is not found after this many attempts, Cerius2 goes back to the previous rotatable bond, sets a new value for its torsion, and tries the problem bond again. (Max-imum Attempts Per Torsion are allowed each time.)



Build restarts Cerius2 may have to go back several bonds, or even go all the way back to the beginning, before an acceptable value is found.

To abort building a conformation when more than some Maxi-mum Restarts (from the beginning) are required:

� Check the Abort After Maximum Restarts check box in the Amorphous Builder Preferences control panel.

� In the Maximum Restarts entry box in the Amorphous Builder Preferences control panel, enter the number of restarts allowed before aborting. This specifies the number of times that Cerius2 can back up all the way to the beginning when trying to build a structure.

If Cerius2 needs to abort the build for the current conformation, a message to that effect is displayed in the text window. Cerius2 then goes on to build the next conformation. (The total number of con-formations generated will thus be fewer than the number of sam-ples requested, above.)

Tip

Interrupt controls Interrupts are allowed by default, so that you can stop the build at any time. However, this can be turned off, or the frequency of checking for interrupts can be decreased. This speeds up the build process somewhat.

To disable build interruptions, uncheck the Allow User Interrupts check box.

To allow the build process to be interrupted if necessary:

� Check the Allow User Interrupts check box.

� Enter a value for the Interrupt Check Interval. The default is each time 2.0% of the process has been completed.

Relaxing the structures If you want to minimize the structures, check the Relax Structure check box in the Amorphous Builder Preferences control panel. The amorphous structure generated from each build appears in the model window and then is minimized.

You can increase the likelihood of generating a conformation by decreasing the value for the periodic density or van der Waals scale and/or by increasing the tolerance scale, maximum attempts per torsion, or maximum restarts and then starting a new build.



Important

If you are writing the built structures to a trajectory file (below), the coordinates of the final structure are saved.

Updating the model dis-play

To repeatedly update the model display as the build proceeds, check the Update Model check box in the Amorphous Builder Output control panel and enter a value for the Update Frequency (entering n means to update each time n% of the rotatable torsions are placed).

To update the display only at the end of the build, uncheck the box.

Saving structures To save the generated amorphous structures in a trajectory file:

� Check the Create POLYGRAF Trajectory File check box in the Amorphous Builder Output control panel.

� Enter any desired comments in the Comments entry boxes.

� Enter a filename prefix in the Filename entry box (the .trj exten-sion is added automatically).

If a file of the same name already exists, a dialog box opens. Click Overwrite File to overwrite the file or click Ignore Action and specify a different filename.

If you do not want to save the structures, uncheck the Create POLYGRAF Trajectory File check box.

Building the structure To start the build, click the RUN BUILD pushbutton in the Amor-phous Builder control panel.

Additional information Please see the on-screen help for information about all the controls in these control panels. Using the polymer builder is discussed under Polymer Builder. Information on building and editing mod-els is contained in Cerius2 Modeling Environment, published sepa-rately by MSI.

If you want nondefault minimization conditions, you need to go to the Minimizer module (see Cerius2 Simulation Tools) to set up the minimization job before starting the build.



Cloning to create starting models

The Amorphous Builder works on the current model. If you want to create multiple-chain models, you can use the Edit/Copy and Edit/Paste items on the menu bar in the main Visualizer control panel (see Cerius2 Modeling Environment, published separately by MSI) to create such a model from single-chain structures. How-ever, this method copies only one structure at a time.

The Amorphous Builder Clone control panel enables you to quickly make one or more copies of several different structures and place them in the same model space. The cloned structures are placed in a new model space.

Starting the process Read in or build the structures from which you want to create clones. If you are using more than one structure and want different numbers of copies of each, put them in separate model spaces.

Accessing the tools Open the Amorphous Builder Clone control panel by selecting the Clone menu item from the AMORPHOUS BUILDER card.

Specifying the copies To specify the models you want to copy, click the Show Model Information action button at the bottom of the Amorphous Builder Clone control panel. The names of suitable models cur-rently in Cerius2’s memory are listed in the Model Name list box.

Enter the number of copies you would like in the Copies entry box next to each model listed.

Making the copies To make the copies, click the CLONE pushbutton.

Additional information Please see the on-screen help for information about all the controls in this control panel. Please see Cerius2 Modeling Environment for information about other ways of copying models from one space to another.



Defining rotatable torsions and torsion rules



Finding unique rotatable torsions

Defining rotatable torsions and torsion rules

Technical notes The amorphous structure is grown by selecting the angles for the rotatable torsions. Which torsions are defined as rotatable is cru-cial in determining how the structure is built. You can exclude cer-tain types of torsions from those that are allowed to vary, for example, torsions involving single-bond sp2–sp2 interactions, multiple bonds, or methyl rotors.

Torsions that differ only in chirality or atom name are not consid-ered unique. The atom name option is provided so that you can make a particular torsion unique by assigning a different name to one of its atoms. This enables you to specify a different build method or RIS variables for that torsion.

Unique torsions need to be found and specified before starting the build (Building amorphous structures).

Accessing the tools Open the Amorphous Builder Torsions control panel by selecting the Torsions menu item from the AMORPHOUS BUILDER card.

Click the Rules… pushbutton to open the Amorphous Torsion Rules control panel.

Setting torsion rules To exclude torsions involving single-bond sp2–sp2 interactions from the list of rotatable torsions, check the Ignore SP2-SP2 Single Bonds check box. It might be useful to include such torsions for biphenyl-like molecules (for the single bond joining the rings), but probably not where more planar structures are involved (for example, the N–C bond in amide-like compounds).

To exclude torsions involving double, triple, or resonant bonds from the list of rotatable torsions, check the Ignore Multiple Bonds check box.

To exclude torsions involving —CH3 groups from the list of rotat-able torsions, check the Ignore Methyl Rotors check box.

To specify that torsions that are the same except for chirality are not considered to be different torsion types, uncheck the Ignore Chirality check box.



To specify that torsions that are the same except for atom name(s) are not considered to be different torsion types, uncheck the Ignore Atom Names check box.

Sorting bond arrays after torsion search

To always have the bond arrays sorted after a torsion search, check the Always Sort Bond Arrays check box. (When this box is unchecked, sorts are automatically done if needed.)

Because the sort process takes time (nearly doubling the find time), this box should be checked only when anomalous behavior is observed during a build (for example, when parts of the molecule flash in the display—as can be seen if the Update Model check box on the Amorphous Builder Output control panel is checked). This indicates that Cerius2 is not accounting for all possibilities in deter-mining when a sort is needed, so a forced sort is required.

Additional information Please see the on-screen help for information about all the controls in this control panel.

Finding unique rotatable torsions

Technical notes You can find all the unique rotatable torsions for a structure with the Amorphous Builder Torsions control panel. When the search ends, all torsions that satisfy the current torsion rules are listed in the unique torsions table in that control panel. The atom names comprising each torsion type are listed, and torsion names are assigned sequentially (t1, t2, etc.).

If overlapping bond vectors are found during the search, the tor-sions are sorted. That is, they are reordered so that no overlap occurs. (Overlap prevents the build from proceeding properly.) However, you can force a sort following every torsion search (but this can nearly double the find time).

The torsion types listed in the unique torsions table also appear in the Amorphous Builder State Table control panel, which allows you to change the build method and RIS variable assignments (Specifying torsion rotation methods).

Accessing the tools Open the Amorphous Builder Torsions control panel by selecting the Torsions menu item on the AMORPHOUS BUILDER card.



Click the Edit… pushbutton in the Amorphous Builder Torsions control panel to open the Amorphous Builder State Table control panel.

Finding the torsions To find all the unique torsions types that meet the rules set in the Amorphous Torsion Rules control panel (Defining rotatable torsions and torsion rules), click the FIND pushbutton in the Amorphous Builder Torsions control panel.

All unique rotatable torsion types are found and listed in the unique torsions table (which lists the names of the atom types con-stituting each torsion) in the Amorphous Builder Torsions control panel.

Renaming torsions If you want to rename torsion types, select a name from the Table Entry popup in the unique torsions table for the torsion to be renamed. You might, for example, want to use this feature if you want two different torsion types to be treated identically during building, if you created new torsion entries in the Amorphous Builder State Table control panel (Entering data in the state table), or if you created or edited some entries in that control panel.

If merely want to give a torsion type an easy-to-remember name, simply enter the new name in the appropriate Table Entries entry box in the Amorphous Builder State Table control panel (Editing the state table, specifying rotation methods).

Viewing the torsions You can display torsion types on the model:

� To display all torsions of a given type, set the Display Mode popup to ALL. To show just the first occurrence of the torsion type, set it to FIRST.

� Click the Show action button associated with the desired tor-sion type. The four atoms and three bonds constituting the tor-sion(s) are highlighted.

Additional information Please see the on-screen help for information about all the controls in this control panel.


The build method, RIS variables, and couplings assigned to each unique rotatable torsion are specified in the Amorphous Builder



State Table control panel (this section). Data can easily be entered, edited, and saved.


Entering data in the state table

Editing the state table, specifying rotation methods

Saving state table data

Random and RIS build methods

As mentioned previously (Random and RIS build methods), the amorphous builder provides three building methods: a Monte Carlo method that assigns random values to torsions and two RIS methods.

A method is specified for each unique rotatable torsion type, which allows a combination of methods to be used in the model. For example, you might have data on the distribution of isomeric states for some, but not all, torsion types. You could assign the RIS ratio method to these torsions and use the random method for the others.

Fixing torsions You can also specify that particular torsions be fixed (that is, not rotated). This is done by choosing IGNORED for the building method.

Tolerances With the two RIS methods, you can specify a tolerance for the tor-sion angle for each of the isomeric states. The angle tolerance value affects performance: loose tolerances speed the process of generat-ing a trial structure but may increase the number of computational cycles required to optimize the structure later. Conversely, tight tolerances slow the building process but result in a better (that is, lower-energy) structure that requires fewer optimization steps.

All the specified tolerances are multiplied by a tolerance scale fac-tor (default = 1.0). This enables you to increase or decrease all tol-erances at once without having to enter new values for each.

Coupling Considerable evidence supports the interdependence of bond rotations for neighboring bonds in chain molecules (Flory et al. 1989). When using one of the RIS build methods, you can couple the angle selected for a torsion to the isomeric state chosen for the bond immediately preceding it.



Entering data in the state table

Data can be entered in the torsion state table by:

� Clicking the FIND pushbutton on the Amorphous Builder Tor-sions control panel (Finding unique rotatable torsions).

or:

� Loading a .ris file (this section).

When you import data from a .ris file it also appears in the unique torsions table (Amorphous Builder Torsions control panel). If the RIS variable and coupling values are not all appropriate for the torsions in your current model, you can edit them (Editing the state table, specifying rotation methods).

Accessing the tools Open the Load State Table control panel by selecting the State Table/Load menu item from the AMORPHOUS BUILDER card.

Loading data from a .ris file

Use the file browser to find and load the appropriate .ris file.

The data in the file appear in the Amorphous Builder State Table control panel and can be edited if desired (Editing the state table, specifying rotation methods).

Additional information Please see the on-screen help for information about all the controls in this control panel. Operation of file selector controls is covered in Cerius2 Modeling Environment.

Editing the state table, specifying rotation methods

Options make it easy to edit the state table. You can edit the torsion rotation methods and the parameters governing the RIS methods. Entries can also be created, copied, or deleted. The entry names can be changed if desired.

Technical notes Only the torsions whose entry names correspond to those listed in the unique torsions table (in the Amorphous Builder Torsions con-trol panel, see Finding unique rotatable torsions) are used during building. These are listed as “used” in the state table (a u appears next to the Edit check box for the used torsions in the Amorphous Builder State Table control panel).



Accessing the tools Open the Amorphous Builder control panel by selecting the Build menu item from the AMORPHOUS BUILDER card. Then click the Preferences… pushbutton in the Amorphous Builder control panel to open the Amorphous Builder Preferences control panel.

Open the Amorphous Builder State Table control panel by:

� Selecting the State Table/Edit menu item from the AMOR-PHOUS BUILDER card.

or:

� Selecting the Torsions menu item from the AMORPHOUS BUILDER card to open the Amorphous Builder Torsions con-trol panel, then clicking the Edit… pushbutton.

Entering data Load torsion information into the state table by finding torsions in the model (Finding unique rotatable torsions) or by loading them from a .ris file (Entering data in the state table).

Creating a new entry In addition to entries that are automatically loaded into the state table (above), you can create new entries. To do so, click the Create Entry pushbutton in the Amorphous Builder State Table control panel. The new entry appears at the end of the list and is labeled new in its Table Entries entry box.

Selecting a torsion entry for editing

To edit an entry in any way, first check the Edit check box (in the Amorphous Builder State Table control panel) for the torsion to be edited, deleted, or copied. (You can edit only one torsion type at a time.)

Changing an entry name If you want to change the name of a torsion type, make the torsion editable (above) and enter a new name in the appropriate Table Entries entry box in the Amorphous Builder State Table control panel. If there is a corresponding entry in the unique torsions table (in the Amorphous Builder Torsions control panel), it is renamed too.

Defaults for torsion rota-tion method

By default, all rotatable torsions are assigned the random build method. This enables you to run a random build without defining any torsion variables.

To make all rotatable torsions have no rotation method assigned by default, uncheck the Default All Torsions to RANDOM check box in the Amorphous Builder Preferences control panel. Then you need to define each one yourself (in the Amorphous Builder State Table control panel).



Changing the torsion rota-tion method

If you want to change the build method for a torsion type, make the torsion editable (above) and choose a method from the Type popup (RANDOM, RIS RATIO, or RIS ENERGY, see Random and RIS build methods) for that torsion type in the Amorphous Builder State Table control panel.

If you choose one of the RIS methods, you need to examine and may want to change the RIS variables and/or the coupling (below).

Fixed torsions You can fix the torsion at its current value (that is, not rotate it) by setting the Type popup in the Amorphous Builder State Table con-trol panel to IGNORED.

Changing RIS variables To change the number of states that a torsion type can take as it rotates, enter a new value for Number of States in the Amorphous Builder State Table control panel. Each “state” is a torsion angle value, along with the angle tolerance and a ratio or energy value.

Define each state by entering new values for Angle, Tolerance, and Ratio or Energy, as needed, for each isomeric state.

The Tolerance value is multiplied by the Tolerance Scale (set in the Amorphous Builder control panel) and both added to and sub-tracted from the angle to determine the acceptable torsion range for the isomeric state. Changing the tolerance scale enables you to increase or decrease the acceptable range of angles for all the states simultaneously. For example, given values of 60°, 10°, and 1.5 for Angle, Tolerance, and Tolerance Scale, respectively, the torsion could range from 45° to 75°.

The Ratio specifies the ratio for the corresponding isomeric state and, together with the ratios given for the other states, determines the distribution when building with the RIS ratio method. For example, for a 1:4:1 distribution of a torsion among three angle val-ues, you would enter 1 for state 1, 4 for state 2, and 1 for state 3.

The Energy specifies the energy for the corresponding isomeric state (in kcal mol-1) and applies only for building with the RIS energy method. The relative energies of the various isomeric states are used together with the RIS temperature and the Boltzmann partition function to calculate the distribution of a torsion among angle values.

If you are using the RIS energy method, enter the RIS Tempera-ture in Kelvin in the Amorphous Builder control panel. This tem-



perature is used together with the relative energies specified for each state and the Boltzmann partition function to determine the distribution of rotational isomeric states.

Changing the coupling If you want to couple the state of a torsion to the state of the torsion about the bond immediately preceding it, check the Couple check box in the Amorphous Builder State Table control panel. Then:

� If needed, enter a new value for Number of Preceding States.

and/or:

� Enter new RIS ratio or energy values, as needed, for each of the Preceding States listed in the coupled RIS state table at the bot-tom of the Amorphous Builder State Table control panel.

The top row of entry boxes under the Preceding States heading specifies the angles for the preceding torsion’s isomeric state. The values under Angle and Tolrnc are the same as those spec-ified for Angle and Tolerance in the RIS table (above). Instead of specifying only one RIS ratio or energy value for each iso-meric state, the rest of the table specifies the RIS ratio or energy values for each isomeric state, given the preceding torsion’s iso-meric state.

Copying a torsion To duplicate a torsion-type entry, make the torsion editable (above) and click the Copy Entry pushbutton in the Amorphous Builder State Table control panel. A new entry labeled copy appears at the end of the state table list. It can be edited like any other entry (above).

Deleting a torsion To delete a torsion-type entry, make the torsion editable (above) and click the Delete Entry pushbutton in the Amorphous Builder State Table control panel. (Only unused torsions can be deleted.)

Deleting all unused tor-sions

To remove all unused torsion-type entries from the state table list, click the Delete All Unused pushbutton in the Amorphous Builder State Table control panel. All torsions without a u next to their Edit check box are deleted from the table.




Saving state table data

The state table can be saved as a .ris file that can be read in later using the Load State Table control panel (Entering data in the state table). This enables you to create .ris files customized for your mod-els.

Accessing the tools Open the Save State Table control panel by selecting the State Table/Save menu item from the AMORPHOUS BUILDER card.

Saving the data Use the file browser tools to specify the filename (the .ris extension is added automatically).

You may enter up to five lines of comments into the file by entering them in the Comments entry boxes.

Additional information Please see the on-screen help for information about all the controls in this control panel. Operation of file selector controls is covered in Cerius2 Modeling Environment.


A References

Flory, P. J.; Jackson, C. J.; Wood, J. Statistical Mechanics of Chain Mol-ecules, Oxford University Press: New York; 49–94 (1989).

Young, L., “Copolymerization reactivity ratios”, in Polymer Hand-book, 2nd Edit., Brandrup, J.; Immergut, H. E., Eds.; John Wiley & Sons: New York; 105–386 (1975).


A. References


B Files

The file format described in this appendix is for .ris files written by the Cerius2•Conformers (see Cerius2 Conformational Search and Analysis, published separately by MSI) and Amorphous Builder modules.

State table (.ris) file

File sections The state table file format consists of the following sections (in this order):

� Header information—A VERSION record followed by optional COMMENT records.

� Torsion entry information—The following set of records is included for each torsion entry:

Label and build method—LABEL and TYPE records (in that order).

RIS information (uncoupled)—NSTATES, COUPLED, and STATE records (in that order). These records are included only if one of the RIS build methods is used and the torsion is not coupled.

RIS information (coupled)—NSTATES, COUPLED, NPR-ESTATES, PRESTATE, and STATE records (in that order). These records are included only if one of the RIS build methods is used and the torsion is coupled.

� End-of-file record (END).

Record identifiers Each record begins with a left-justified keyword consisting of ten characters (the letters specified in this appendix, plus trailing spaces).


B. Files

RIS file format

Header information

Torsion entry: Label and build method

Torsion entry: Uncoupled RIS information

These records are included only if a RIS build method is used (TYPE RIS ENERGY or TYPE RIS RATIO) and the torsion is not coupled (COUPLED NO).

Keyword Format Value Description

VERSION (2A10) string Version number (currently RIS.0.1).COMMENTa (A10,A70) string Remarks on the state table file (optional).

aUp to 5 comment lines can be entered when saving the state table with the Amorphous Builder; one COMMENT record is produced for each line entered. However, more lines can be added by editing the file with a text editor later.


LABEL (2A10) string Torsion name.TYPE (2A10) RANDOM, RIS

ENERGY, RIS RATIO, or IGNORED

Torsion rotation method during build.


NSTATES (A10,I3) integer Number of states (maximum 15).COUPLED (2A10) NO (YES if torsion is coupled) NO if not coupled.STATEa (A10,3F8.3) 3 reals Angle, tolerance, and value. Values are ener-

gies in kcal mol-1 for TYPE RIS ENERGY or population ratios for TYPE RIS RATIO.

aA STATE record should be included for each isomeric state. The number of states is specified by NSTATES.

State table (.ris) file


Torsion entry: Coupled RIS information

These records are included only if using an RIS build method (TYPE RIS ENERGY or TYPE RIS RATIO) and the torsion is coupled (COUPLED YES).

End-of-file record

Example file

VERSION RIS.0.1 COMMENT There was a ship, quoth he.

LABEL t1 TYPE RIS ENERGYNSTATES 3COUPLED NO STATE 60.000 20.000 1.000STATE 180.000 20.000 0.000STATE 300.000 20.000 1.000

LABEL t2 TYPE RIS ENERGYNSTATES 3COUPLED YES NPRESTATES 3


NSTATES (A10,I3) integer Number of states (maximum 15).COUPLED (2A10) YES YES if torsion is coupled (NO if not cou-

pled).NPRESTATES (A10,I3) integer Number of preceding states p (maxi-

mum 6).PRESTATE (A10,16X,6F8.3) p reals Angles for the preceding torsion.STATEa (A10,8F8.3) (p + 2)

realsAngle, tolerance, and NPRESTATES val-

ues. Values are energies in kcal mol-1 for TYPE RIS ENERGY or population ratios for TYPE RIS RATIO.

aA STATE record should be included for each isomeric state. The number of states is specified by NSTATES.

Keyword Format Description

END (A10) End-of-file marker.


B. Files

PRESTATE 60.000 180.000 300.000STATE 60.000 20.000 1.000 1.000 99.000STATE 180.000 20.000 0.000 0.000 0.000STATE 300.000 20.000 99.000 1.000 1.000

LABEL t3 TYPE RIS RATIO NSTATES 3COUPLED NO STATE 60.000 20.000 1.000STATE 180.000 20.000 5.000STATE 300.000 20.000 1.000

LABEL t4 TYPE RIS RATIO NSTATES 3COUPLED YES NPRESTATES 3PRESTATE 60.000 180.000 300.000STATE 60.000 20.000 1.000 1.000 0.000STATE 180.000 20.000 5.000 5.000 5.000STATE 300.000 20.000 0.000 1.000 1.000

LABEL t5 TYPE RANDOM

LABEL t6 TYPE IGNORED …END

Product_group Book_name/Month 1997 99

2D-periodic structures 273D-periodic structures 5, 79

AAdd Atom control panel 12, 15, 33, 34amides 83AMORPHOUS BUILDER card 74Amorphous Builder Clone control panel 82Amorphous Builder control panel 77, 78, 88Amorphous Builder module 73Amorphous Builder Output control panel 78Amorphous Builder Preferences control panel

78, 88Amorphous Builder State Table control panel

85, 88Amorphous Builder Torsions control panel 83,

84amorphous structures 73

3D-periodic 75, 79aborting a build 80anomalous behavior during builds 84building 74building in general 78building with default settings 77bump checking 75, 78, 79bump checking, hydrogens 79cloning starting structures 82display 81finding unique rotatable torsions 84, 85minimization conditions 81minimizing 80Monte Carlo method 75nonperiodic 79periodic density 78relaxing 76, 80repeated building attempts 76, 79RIS methods 75rotatable torsions 83rotation methods 86saving 81simple build 77

starting a build 81stopping a build 80torsions 78, 83torsions used during building 87troubleshooting 80unique torsions table 85van der Waals scale 75

Amorphous Torsion Rules control panel 83asymmetric unit 7

constructing 8atoms

adding 14, 34backbone 52, 68converting symmetry copies into real 16coordinates 42deleting symmetry copies 19, 36display 70exact symmetry positions 24groupings in polymers 69names 83, 84options 15, 34removing 15, 18, 34selecting in crystals 22, 23superimposed 44

Bbiphenyl 83Block Copolymer Builder control panel 66Block Copolymer control panel 59Block Copolymer Preferences control panel 66block copolymers 47, 66, 69

building 66, 68composition 66number of superunit blocks 67preferences 67superunit groupings 69superunit size 67

bold type, meaning 3bond arrays, sorting 84bonds

automatic calculation 9, 31

Index

100 Product_group Book_name/Month 1997

C

crystals 9dangling 43interfaces 43multiple 83surfaces 30, 31

Bravais lattices 10BUILDERS 1 card deck 7, 29, 38, 48, 74Building From Atoms control panel 31, 33, 35,

36, 45

CCell Contents control panel 23Cell Parameters control panel 9, 12Cleave Crystal Surface control panel 29, 35Convert Formats control panel 54coordinate system 14

fixing 34coordinates

Cartesian 14, 33crsytal interfaces 39fractional 14orientation to computer screen 20surface fractional 33

copolymers 47, 60, 66Crystal Build Preferences control panel 8, 11,

12CRYSTAL BUILDER card 7Crystal Builder module 5Crystal Building control panel 8, 11, 12, 17, 18,

19, 45Crystal Facetting control panel 18, 22Crystal Visualization control panel 17, 20, 21crystals

accuracy of model 23asymmetric unit 8bonds 9building 7cell size and shape 9cell volume 23connectivity 10constructing from atoms 12creating from interfaces 38, 45default orientation 20defects 37density 23disorder 17display 19

display range 19display style 9, 11, 13facetting 18, 22faults 39from surface 11generating nonperiodic superstructures 16generating superlattices 16, 17habit planes 20initial orientation 19interfaces 37lattice 10Miller planes 20nonperiodic model 17number of displayed cells 20polymer 6polymers 56redisplaying 12reverting to nonperiodic asymmetric unit

19sectioning 22selecting atoms 22simulations 5structural relationships between particles

37symmetry 9, 10, 12, 13twinning 37, 39unbuilding 19unit cell, constructing 13updating 12, 24vacuum slab 11vacuum thickness 11

DDisplay Editor control panel 70Display Preferences control panel 70

EEdit Facet Options control panel 22Edit Interface control panel 44epitaxy 37

Ffacets

adding 22color and transparency 22

G


creating 22crystal 22displaying 22editing 22positioning 22removing 23

files2D unit cell information 28Biograf 54conversion 53CSSR 28example .ris 97formats 95Insight II 54monomers 53, 54MSI 28old Cerius2 54Polygraf 54.ris 87, 91, 95rotatable torsions 95state table 95surface information 28trajectory 79, 81

Find Space Group control panel 11, 24Flory, P. J. 86, 93

GGeneral Positions control panel 9

Hhelp, on-screen 3high-resolution transmission electron micros-

copy 37Homopolymer Builder control panel 55, 58, 59Homopolymer Preferences control panel 55homopolymers 47

atomic groupings 69building 55, 56composition 55preferences 56

IINTERFACE BUILDER card 38Interface Builder module 37, 38Interface Building control panel 43

Interface Left Side control panel 41Interface Right Side control panel 41interfaces

alignment of sides 40building 44creating crystals from 45creating surfaces from 45crystal 37duplicated atoms 44editing 44gap 43match point 40, 42match vector 40, 42Miller indices 42Miller planes 41orientation of sides 40periodicity 40setting up 41shape 40, 42slab thickness 42superimposed atoms 44vector conventions 39

italic type, meaning 3, 4

JJackson, C. J. 93

Llattice

Bravais 10infinite assumed 20primitive 16reorienting 15specifying 9symmetry 10type 10

Lattice Redefinition control panel 15lattice vectors

changing 15display 16new 15previewing changes 15redefining 15user-specified 15

Load State Table control panel 87


M

Mmethyl rotors 83Miller indices 21Miller Plane Options control panel 21Miller planes 20

color 21display 21facetting along 22opacity 21positioning 21reorienting 21transparency 21

models2D periodic 11, 27amorphous 73copying 82crystal 5crystal interfaces 37ionic 6monomers 52multiple-chain 82polymers 6, 47surface 11, 27

Molecular Simulations, Inc.customer support 3website 3

molten state 73monomer choosers 50Monomer Editor control panel 51, 52, 54Monomer Orientation control panel 59Monomer Preferences control panel 51, 52Monomer Reactivities control panel 65monomers 49

available to polymer builder 50backbone atoms 52chiral centers 49, 52, 53, 57chirality 49choosing types 55, 61, 66color use 70concentrations 62concentrations, exact 63creating 50definition 49display 70editing 52files 49, 50head group 49, 51, 70head/tail orientation 56, 58, 62, 67

inversion at chiral center 49, 53, 62labelling 70loading 51, 52, 53number of units 55, 61reactivities 62, 63reactivity ratios 64, 65relative concentrations 60, 62relative reactivities 60, 62, 65saving 53tail group 49, 51, 70torsions between 51, 56, 59, 62, 67torsions within 59

PPOLYMER BUILDER card 48Polymer Builder module 47, 48Polymer Editor control panel 68Polymer Tacticity control panel 58Polymer Torsions control panel 60, 66polymers

atactic 58atomic groupings 69, 71backbone atoms 68backbone display 70, 71building 47, 61, 66chemical nature 69chiral centers 68, 71color use 70, 71configuration 49, 57copolymers 60, 66crystals 56display 70editing 68filenames 64, 67grouping classes 69grouping types 69head group 70initiator 55, 61, 67inversion at chiral center 68isotactic 58labelling 70, 71levels of atomic groupings 69meso–diad ratio 58monomer units 49, 61names 64, 67of polymers 63random-number generator 56, 63, 67stereoconfigurations 57

R


structure 69superunit blocks 67syndiotactic 58tacticity 56, 57, 62, 67tacticity, illustration 57tail group 70terminator 55, 61, 67torsion between monomer units 49, 56, 59,

62, 67visualization 70

RRandom Copolymer Builder control panel 59,

61, 63, 65Random Copolymer Preferences control panel

63, 65random copolymers 47, 60

building 61, 62composition 61, 64preferences 62rate constants 64

RIS energy method 75, 89, 90temperature 89

RIS methods 73, 78number of states 89specifying 87, 89tolerance 86, 89tolerance scale factor 86, 89

RIS ratio method 75, 89, 90RIS variables 85rotational isomeric state methods 73

SSave State Table control panel 91semicrystalline state 73single-bond sp2–sp2 interactions 83solution 73solvent 6space group

cell origin 14class 13example specifications 14hexagonal axes 14information 13monoclinic 14name 13

nonstandard 13number 13options 13, 14, 24reference 13rhombohedral axes 14specifying 13standard 24symbol 13

Space Groups control panel 12superlattices

generating from crystals 16, 17generating from surfaces 35primitive 17size 17, 35unit cell 18

superstructuresgenerating from crystals 16generating from facetted crystals 18generating from surfaces 35noncrystalline 18nonperiodic 17, 18, 19, 35previewing 23size 18, 35

Surface Box control panel 29Surface Build Preferences control panel 31SURFACE BUILDER card 29Surface Builder module 27surface cell

deleting 36dimensions and angles 32, 33

Surface Cell Parameters control panel 31, 33, 34, 45

surface cell vectorschanging 34new 35redefining 34

Surface Visualization control panel 35, 36surfaces

basis vectors 30bonds 30, 31cell, constructing 32cleaving slab 29constructing from atoms 33creating from crystals 29, 31creating from interfaces 38, 45creating from nonperiodic models 31disorder 35display 30, 36display range 36


T

display style 32generating nonperiodic superstructures 35generating superlattices 35Miller indices 30number of displayed surface cells 36positioning slab 30redisplaying 32, 33reverting to nonperiodic asymmetric unit

36slab shape and position 30surface cell, constructing 33thickness 30unbuilding 36updating 30

symmetrycell parameters 10constraints 9, 14constraints, removing 17crystal 9, 12, 13editing 10exact match of atom positions 24finding 12, 24positions 10primitive 17reducing 15, 16reimposing 24tolerance 24

Ttorsions

acceptable 79build methods 78chirality 83coupling 85, 86, 90display 70, 85excluded 83file 95fixed 86, 89information 88labelling 70range of angles 89renaming 85, 88rigid 86rotatable 83rotation methods 78, 85, 87, 88, 89rules 83, 85searches 84sorting 84

state table 87states 89types 85unique rotatable 78, 83unique torsions table 87

typewriter font, meaning 3typographical conventions 3

Uunit cell 6

changing to primitive 15constructing 13deleting 19density 23, 79dimensions and angles 9, 14formula 23information 23number displayed 19number of atoms 23volume 23

WWood, J. 93

YYoung, L. 64, 93

Zzeolite structures 6

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