Difference between revisions of "Quick Start Guide for CrystalExplorer17"

Latest revision as of 03:32, 24 June 2019

What is CrystalExplorer?

CrystalExplorer, showing a list of crystals (top right) with m-nitroaniline selected and shown in the graphics window.

CrystalExplorer is a standard tool for investigating intermolecular interactions and packing in crystalline materials using Hirshfeld surface analysis.

CrystalExplorer also includes powerful tools to generate surfaces based on ab initio quantum mechanical property densities.

By mapping these properties and other distance- and curvature-related metrics on Hirshfeld surfaces, CrystalExplorer provides unique insights into the in-crystal environment.

CrystalExplorer can also readily display and quantify voids in crystal structures.

Most recently, CrystalExplorer17 implements the accurate and efficient calculation of intermolecular interaction energies and energy frameworks.

Opening a CIF

CrystalExplorer reads crystal structures from Crystallographic Information Files (CIF).

To open a CIF, either

• Click the Open File button on the Main Toolbar, or
• Choose File → Open from the Main Menu.

Each time a CIF is opened, CrystalExplorer adds all the crystal structures contained within it to the current project.

A list of all the crystal structures is shown in the selection box in the top-right of the main window.

Clicking in the selection box on a chosen crystal will cause it to be displayed in the graphics window.

Changing the View

CrystalExplorer allows you to rotate, zoom in/out and translate so that you can achieve a particular orientation of the structure.

CrystalExplorer has three modes: rotation, zooming and translation which are selected using the main toolbar.

By default CrystalExplorer starts in the rotation mode. To rotate the structure, left-click in the graphics windows in the background, and drag the mouse around.

Since left-clicking is also used to selected atoms/molecules is important to only left-click on the background if you want to change the view.

When in the rotation mode it is also possible to rotate about the z-axis (out the screen) by holding down the shift key and left-click-dragging the mouse.

The View Toolbar

The view toolbar, shown below, appears the the bottom of the graphics window.

Using the view toolbar, you can precisely rotate or scale the structure.

Or, you can choose a view down one of the crystallographic axes a, b or c.

The Recenter button resets the center of rotation to be at the center of the atoms displayed.

Recentering is useful after a large, asymmetrical cluster has been created.

Selecting and Deselecting Atoms and Molecules

Atoms and molecules need to be selected before surfaces or clusters can be made.

An atom is selected when it is highlighted by a golden mesh.

Select atoms and molecules by left-clicking on them:

• To select a single atom, left-click on it.
• To select a whole molecule or fragment, double left-click on an atom or bond.
• To select everything, right-click to bring up the context menu and choose the menu item Select All Atoms.

To help with choosing atoms you can show the atom labels.

By repeating the left-click operation an item can be deselected.

Left-clicking in the background of the graphics display is the fastest way to deselect everything.

Generating Clusters

CrystalExplorer provides a number of methods for building up clusters of atoms or molecules.

Complete Fragments

Many options in CrystalExplorer can produce 'incomplete' molecular fragments.

Indeed, a cif file may contain only an incomplete asymmetric molecular fragment.

By clicking on the fragment completion button in the main toolbar all bonded atoms in a fragment or molecule are generated, and only whole molecules are displayed.

Generate Unit Cells

This button generates multiple copies of the unit cell including any surfaces which you have made within.

A dialog box allows the user to choose the number of copies and direction in which to make the unit cell copies.

This is especially useful when combined with crystal void surfaces to show empty pores and channels in the structure.

Show/Hide Contact Atoms

The red and black atoms are close-contact ghost atoms

By clicking on theShow/Hide contact atoms button CrystalExplorer shows ghost atoms.

These ghosts representing atoms close to the real atoms shown in the graphics window.

By left-clicking on the ghosts, they become real atoms, and a new set of close-contact atoms is displayed.

By repeated clicking on the ghost atoms, the connectivity of the crystal structure can be explored.

In this way, the cluster of atoms representing the crystal structure can be expanded.

The ghost atoms are turned off by clicking the Show/Hide contact atoms button again.

Generate Atoms Within Radius

This feature allows the user to generate a cluster of atoms within a specified distance of any atom currently selected.

When the button is clicked, a popup window appears; simply enter the desired distance.

Surfaces and Surface Properties

CrystalExplorer can generate the following surfaces:

• Hirshfeld
• Promolecule
• Crystal Voids
• Electron Density
• Deformation Density
• Electrostatic Potentials
• Molecular Orbitals
• Spin density

One of the most powerful features of CrystalExplorer is the ability to map properties onto surfaces with color. Some of these properties e.g. the electron density property must be chosen when generating the surface but there are a number of built-in properties that are always available to these surfaces. At present only Hirshfeld, Promolecule and Electron Density surfaces can have properties mapped onto them.

For further information see: Surfaces in CrystalExplorer and Surface Properties.

Generating Surfaces

General procedure for generating surfaces is:

• Using the mouse, select the atoms you want included in the surface. In general you'll want to select a complete molecule, although CrystalExplorer will often allow surfaces to be generated for any selection including single atoms.
• Click the toolbar button to bring up the Surface Generation dialog.
• In the Surface Generation dialog you must choose the surface type, any surface properties and the resolution (quality). Surfaces can be further customised with surface options e.g. the surface's isovalue. Click the OK button to generate the surface.

Some of the surfaces and surface properties are quantum mechanical in nature and require a wavefunction. CrystalExplorer automatically enlarges the Surface Generation dialog when a wavefunction calculation is required.

Wavefunction calculations can be performed with the built-in Tonto program or with Gaussian program. In order for CrystalExplorer to be able to use Gaussian follow these the steps on the "Setting up Gaussian" page. Note: Gaussian is not distributed with CrystalExplorer and must be purchased separately.

Surface Information

All generated surfaces appear in that crystal's surface list. A green tick next to a surface name tells CrystalExplorer to show that surface in the graphics window. By clicking on the green tick, it will be changed to a red cross and the surface will be hidden from view. This is useful if you have many surfaces and only want to keep the display from getting cluttered.

The Surface Controller (located at the bottom right hand side of the CrystalExplorer Window) gives you details about the surfaces and allows you to change features of the surface ― for example, which property is currently mapped on its surface. The Surface Controller has three tabs,

• Options Tab: allows you to set all aspects of the surface, including the property mapped on the surface, the color range for the property, and whether the surface is displayed semi-transparent
• Info Tab: displays information such as the surface area and volume, globularity and asphericity
• Property Info Tab: provides the min, max and mean values of each property mapped on the surface

All Hirshfeld surfaces have the following properties mapped by default:

• None (a monochrome surface; colour can be changed in the Preferences → Graphics dialog)
• d_i
• d_e
• d_norm
• Shape index
• Curvedness
• Fragment patch (surface patches adjacent to neighbouring surfaces are coloured separately)

Cloning Surfaces

Sometimes it is desirable to generate a cluster of molecules with identical Hirshfeld surfaces (and a property mapped on these surfaces). The Clone Surface button performs this function without the need for repeated (and time-consuming) generation of all the surfaces. Once a single Hirshfeld surface has been created it can be copied onto all symmetry-related molecules in the graphics window by clicking on the toolbar button. Once these surfaces have been generated they exist as separate entities and can be individually decorated with different surface properties.

Displaying Fingerprint Plots

To display a fingerprint plot^[1], first select a Hirshfeld surface (in the surface list) and then click on the Display Fingerprint Plot button . This button is located in the Surface Controller in the bottom right of the CrystalExplorer window.

The fingerprint window includes options for,

• Translating or expanding the fingerprint plot to cater for structures with longer distance contacts.
• Saving the fingerprint plot (Tip: For best reproduction save the fingerprint as an .eps file).
• Creating filtered fingerprint plots.

Filtered Fingerprint Plots

Filtered fingerprint plots^[2] are produced by applying a filter to highlight only close contacts between pairs of atoms of particular chemical elements. Only contributions from those contacts are shown in the fingerprint plot, with the rest greyed out.

By clicking on the fingerprint plot, highlight "cones" can also be displayed on the Hirshfeld surface showing which points on the surface correspond to a certain di/de pairs

• 

  Fingerprint plot of benzene-dicarbaldehyde with no close contact filtering

• 

  Hirshfeld surface of benzene-dicarbaldehyde with no close contact filtering

• 

  Filtered fingerprint plot with close contacts shown for O atoms inside the surface and H atoms outside

• 

  Close contact decomposition mapped onto the Hirshfeld surface

• 

  Highlight "cones" on Hirshfeld surface produced by clicking on the fingerprint plot. The cone color can be changed in the Graphics tab of the CrystalExplorer Preferences dialog.

For more information, see Fingerprint Plots.

Measuring distances and angles

Measuring distances, angles, dihedral angles and out-of-plane bends.

CrystalExplorer also includes basic tools for conventional structure analysis.

You can measure distance and angle between objects by clicking on the appropriate toolbar buttons before selecting your objects to measure.

Measuring distances

• Select two atoms (using left-click); the atoms are highlighted in green and the distance is shown.
• Select an atom then (left) click a point on a surface; the distance between the atom and the selected surface point is shown.
• Tip: Double (left) click on an atom or a surface; then single or double (left) click on another atom or surface; the minimum distance between the two objects is shown. Nice.

Measuring angles

• Select three atoms in sequence. An arc will be drawn between the first and third atoms, with the second atom at the centre. The angle will be displayed on the screen.
• For the dihedral angles, in-plane and out-of-plane bends you need to select four atoms. These angles include a translucent green plane to help the user visualise the angle. This translucent green plane is best viewed on a non-white, non-black background.

The button removes that last measurement made and the button exits measurement mode and reverts to normal selection mode.

Show Crystal Information

This button on the far right of the top toolbar provides a wealth of information about the analysis of the crystal structure under consideration. It has four tabs:

• Crystal - Summarizes brief details from the CIF.

• Atoms - Gives two lists of coordinates for atoms in the graphics window, the first in Cartesian coordinates (Å) and the second in crystal fractional coordinates.

• Surface - Provides a convenient summary of detailed information about each molecular surface: minimum, maximum and mean values of surface properties; details of breakdown (%) of the Hirshfeld surface associated with atom···atom filtering of fingerprint plots; fragment patch information; surface property statistics (especially useful when mapping the electrostatic potential on surfaces).

• Energies - Details of energy components and total energies resulting from computation of model energies for molecule/ion pairs.

Context Menu

Context Menu.

Right-clicking in the graphics window brings up the Context Menu and allows fast access to many common operations.

The options presented depend on whether you right-clicked on the background, an atom or a surface i.e. they depend on the context in which you right-clicked.

Footnotes

1. ↑ M.A. Spackman, J.J. McKinnon, CrystEngComm, 2002, 4 ,378-392:
   Fingerprinting Intermolecular Interactions in Molecular Crystals
2. ↑ J.J. McKinnon, D. Jayatilaka, M.A. Spackman, Chem Commun., 2007 ,3814 - 3816:
   Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces