Building Molecules

AMSinput Building structures SMILES Ligands Metal complexes Cluster Nanotubes

In the previous tutorial you have learned how to construct a molecule by building it out of atoms. For bigger molecules this process can be quite time-consuming. Therefore, AMSinput provides various tools to help you with building molecules.

This tutorial will cover easy ways to add molecules or solvents:

• The quickest is to search () for a molecule inside AMSinput, using available structures from the built-in database

• When searching for molecules on the Internet, in open-source datasets or with chemical suppliers, you can directly load provided xyz files or SMILES strings

We show how to use the structure tool in AMSinput to build larger molecules:

• Building a small peptide chain

• Building metallo-organic complexes

• Creating your own structures library

Finally, you can use the crystal tools to:

• Cut a nanoparticle from a crystal

• Create carbon nanotubes

Start AMSinput

We start by creating a new folder where we will save our molecules:

Start AMSjobs

Select File → New Directory from the main menu

Enter a folder name

Double-click on the folder name to move to the new directory

Start AMSinput via SCM → New Input

Search for ethanol

For common molecules, the easiest way to get the coordinates is to search for them in AMSinput.

Press ctrl/cmd-F to activate the search box (or click the search icon in the panel bar)

Enter ‘ethanol’ as search text (without quotes)

Click on the ‘C2H6O: Ethanol (ADF)’ match

Rotate to get a good view

Your ethanol is ready. The (ADF) in the search results means that the molecule has already been optimized by ADF. (Unless states otherwise, these optimizations were done with the BP86 XC potential, TZP basis set and small core.)

Import XYZ for ethanol

AMSinput allows importing coordinates from various different file types, including the .ams files obtained when running jobs with AMS.

For files obtained from online sources, the xyz format is the most common.

AMSinput can also be used to generate these xyz files:

Use the File → Export Coordinates (System) → .xyz menu command

Enter ‘ethanol.xyz’ as the filename. (The save location should be the empty folder created earlier)

Click Save

Your xyz file should now be visible in the AMSjobs browser:

Use the File → Close job menu command in AMSinput

Click ‘No’ when asked if you want to save your changes

Click in the AMSjobs window to activate it

Enable Filter → Other (if it is not yet enabled)

Use the Job → Refresh List menu command (or press F5)

Click the triangle in front of example to show the example.xyz file

Double click on the .xyz file (listed in Local files)

AMSinput will start and automatically import the .xyz file. To import a molecule when AMSinput is already open (for instance, if you want to add solvent molecules), you can use the File → Import Coordinates… command:

Use the File → New menu command in AMSinput

Click ‘No’ when asked if you want to save your changes

Select the File → Import Coordinates menu command

Select the ethanol.xyz file

Tip

It is also possible to copy/paste data directly into AMSinput. This works for many formats, including xyz, SMILES or InChI strings.

The coordinates for ethanol are:

C       0.01247000       0.02254000       1.08262000
C      -0.00894000      -0.01624000      -0.43421000
H      -0.49334000       0.93505000       1.44716000
H       1.05522000       0.04512000       1.44808000
H      -0.64695000      -1.12346000       2.54219000
H       0.50112000      -0.91640000      -0.80440000
H       0.49999000       0.86726000      -0.84481000
H      -1.04310000      -0.02739000      -0.80544000
O      -0.66442000      -1.15471000       1.56909000

Use the File → New menu command in AMSinput

Click ‘No’ when asked if you want to save your changes

Copy the xyz coordinates of ethanol above (select the coordinates above and press ctrl/cmd-C)

Click on the AMSinput window to activate it

Paste the xyz coordinates (ctrl/cmd-V or Edit → Paste)

Import SMILES string

AMSinput can also interpret SMILES strings. In case of ethanol:

Use the File → New menu command in AMSinput

Click ‘No’ when asked if you want to save your changes

Copy the SMILES string: CCO

Click on the AMSinput window to activate it

Paste the SMILES string (ctrl/cmd-V or Edit → Paste)

Click the empty space in the drawing area to clear the selection

Because SMILES strings do not contain information on the 3D structure, the coordinates that we obtain are different from the optimized structure from ADF.

It is typically recommended to first pre-optimize () the structure with UFF when loading from SMILES. This results in more reasonable structures and helps speed up subsequent simulations done using e.g. ADF or BAND.

Build ethanol using the structure tool

As a demonstration on how to use the structure tool , we start by building a methane molecule:

Use the File → New menu command in AMSinput

Click ‘No’ when asked if you want to save your changes

Select the C-tool

Click anywhere in the drawing area to make a carbon atom

Select Atoms → Add Hydrogen , or use the shortcut (ctrl/cmd-E)

The next step is to add a methyl group, using the structure tool :

Select the → Alkyl Chains → Methyl structure

Notice that the button of the structures menu is now glowing, indicating that the structure tool is active.

Double-click on one of the hydrogen atoms

Zoom out if needed (with right mouse button or mouse wheel)

You will see that the hydrogen is replaced by a methyl group.

Note that:

• The methyl is orientated along the newly formed C-C bond and the new hydrogens point away from the existing ones.

• The carbon on the newly-placed methyl group was designated as the ‘replacing’ atom. This carbon atom has been placed at the location of the substituted hydrogen atom. All structures in the structure tool have a predefined ‘replacing’ atom.

• The background glow from the ‘Structures’ tool has moved to the ‘Pointer’ tool button; the ‘Pointer’ tool is active again.

To create ethanol, we need to add a hydroxyl group:

Select the → Ligands → OH structure

Double-click on one of the hydrogen atoms

Again, the hydrogen is replaced by the structure. In this case, the oxygen replaces the selected atom. The O-H bond is aligned along the C-O bond and points away from the rest of the molecule. This shows you the very general way in which the structures will align according to the bonds in the original molecule and those in the structure. In this case, the hydroxyl group is not automatically oriented as it normally would be in an ethanol molecule.

Pre-optimize by selecting

Add solvent molecules using the structure tool

The structure tool includes several commonly-used solvent molecules, allowing you to easily add solvents to your system. Ethanol is also included in this list:

Select the → Solvents → Ethanol structure

Left-click in an empty space near the hydroxyl group

We can select the new molecule to orient it to a different position:

The oxygen atom on the new ethanol molecule should still be selected after using the structure tool

Use the Select → Select Molecule menu command (or ctrl/cmd-M)

Use the mouse to rotate (left mouse button) and translate (right mouse button) the ethanol molecule

Building a peptide chain using the structure tool

Larger biomolecules or macromolecules can be assembled using the basic building blocks in the structure tool. We will look at a small peptide chain as an example.

Select File → New

Click ‘No’ when asked to save your changes

Select the → Amino Acids → AA Backbone structure

Place it in the drawing area

The AA backbone structure contains 2 subunits of a basic peptide chain. We can extend the peptide backbone by adding additional subunits.

Tip

Press the space bar to reuse the previous structure tool

Click in empty space to deselect the nitrogen

Select the → Amino Acids → AA Backbone structure (or just press the space bar)

Double click on the (non double-bonded) terminal oxygen

You may want to use View → Reset View

In a similar fashion, you can replace the hydrogens on the backbone by amino acid side groups of your choice. These can be found in the → Amino Acid → AA Side Groups sub-menu.

Metal complexes and ligands

In the sub-menu ‘Metal Complexes’ you can find a set of predefined complexes corresponding to commonly encountered geometries. A set of ligands has also been provided, including typical monodentates, bidentates and polydentates. These can be used to quickly construct metallo-organic structures.

Predefined Metal Complex Geometries

Select the File → New command

Click ‘No’ (do not save changes)

Select the → Metal Complexes → ML6 Octahedral structure and place it in the drawing area

Notice that six dummy (“Xx”) atoms have been placed around the metal center in an octahedral fashion.

Select one of the dummy atoms by clicking on it

Select the Select → Select Atoms Of Same Type menu command

When replacing multiple atoms with the same side-group, instead of using the structure tool, we can access the ligands selection through the Atoms menu:

Select the Atoms → Replace By Structure → Ligands → CN command

Click in empty space to clear the selection

Reset the View if needed

Notice that all the dummy atoms in the selection have been replaced by CN ligands.

Bidentate Ligands

In order to use the bidentate ligands, we must start with a bare metal center.

Select the File → New command

Click ‘No’ (do not save changes)

Click the X button in the toolbar to open the periodic table menu

Select an iron atom and place it in the drawing area

Select the → Ligands → Bidentates → Ethylenediamine structure

Double-click on the metal atom

For the bidentate ligands, the Structure Tool attaches the ligand to the selected atom, instead of replacing it. Other multidentate ligands are defined in a similar fashion.

Press space bar to re-select the previous ligand

Double-click on the metal atom

Notice that the second ligand appears opposite the existing one.

Modifying the Plane Angle

To change the relative orientation of two bidentate ligands, we can change the plane angle. The planes are defined by two sets of three atoms, the central one being present in both sets. In this case this will, of course, be the metal atom.

Select, in order, the two nitrogens on the first ligand, the metal atom, and the nitrogens on the second ligand

Change the plane angle to 90 degrees using the slider

In this way, you can easily change the environment around the metal from square planar to tetrahedral. This feature works as long as you choose the atoms in the right order, and if the defined planes can freely rotate relative to each other.

Your own structures library

You can make your own structure library for use with the Structure Tool. This allows you to easily access frequently-used building blocks that are relevant to your research.

By default, user-defined structures will be stored in the .scm_gui/Structures directory.

Defining your structures

To be able to actually use the structures as described earlier, it is necessary to define one of the atoms as having xyz-coordinates (0,0,0). This atom will be designated as the ‘replacing’ atom. By using the ‘Save As Structure’ command, this step will be done for you.

Select the File → New command

Click ‘No’ (do not save changes)

Build methane

Replace three of the hydrogens by chloride atoms

Delete the remaining hydrogen and pre-optimize the structure

Select the central carbon atom

Use the → Save As Structure … command

Enter the name of the structure (Trichloromethyl)

The selected atom (currently the C atom) will be used as the ‘replacing’ atom

The new structure will appear in the Structures menu and can be used immediately.

Using dummy atoms

Dummy (“Xx”) atoms are treated differently when used in structures. A dummy atom will not replace an existing atom when it is defined as the ‘replacing atom’. Instead, the double-clicked atom will remain and will accept the bonds that the dummy atom had in the structure. (As with the bidentates shown earlier.)

Build a methane molecule

Replace the carbon atom by a nitrogen atom

Select one of the hydrogens and replace it by a dummy atom (the ‘Xx’ atom type, in the periodic system menu)

Select the dummy atom

Save the structure using the → Save As Structure … command

Select the new structure from the Structures menu

Double-click on one of the hydrogens

Because a dummy atom was used, the NH3 group has been attached to the hydrogen atom instead of replacing it. This way, dummy atoms can be used to conveniently add complex building blocks such as multidentate ligands or monomer units.

If you want to clean up your structures, you can use the → Manage Structures… command. If you use it, AMSjobs will open and show the contents of your Structures directory. As the structures are just (simplified) .ams files, you can open them using AMSinput for viewing or editing. Using AMSjobs, you can rename or delete the files. The Structure Tool will update automatically.

A sphere of Cu atoms, cut out of the crystal

When constructing single crystals or nanoparticles, it is often easiest to start from a crystalline bulk material. We will showcase this procedure here for a copper particle.

We start by making a Cu crystal. We will use a super cell to obtain a large number of Cu atoms.

To build the crystal, we need to use the Periodic tools. These will work only for engines supporting periodicity (e.g BAND).

Start AMSinput (or use File → New in the currently open AMSinput window)

Search () for ‘copper’

Click on ‘Cu’ in the Crystals section of the search results

Edit → Crystal → Generate Super Cell…

Enter ‘5’ to change the top left element to 5 (the other diagonal elements should automatically adjust)

Click OK in the pop-up-window

Now we have a block of Cu, with explicit Cu atoms. Next we will center this block, and select a sphere of atoms around the origin.

Make sure the origin is in the center of the block: Edit → Set Origin → X, Y and Z

Select → Select Atom Close To Origin

Select → Select Within Radius

Click OK

Select → Invert Selection

Press the Backspace key to delete the selected atoms

Switch to the ADF engine BAND → ADF

You may need to rotate the structure a little before the drawing area updates

You should now have a (very small) sphere consisting of Cu atoms in the molecular ADF program:

To make bigger spheres, simply choose a bigger super cell and use a larger radius when selecting atoms.

Tip

For building mono-metallic Wulff particles, one can also use the dedicated nanoparticle builder.

Working with nanotubes

A carbon nanotube segment is included in the AMSinput database (). Nanotubes with alternate structures or elemental compositions can be obtained through online databases, or by using the free TubeGen tool.

Because nanotubes are periodic structures, they are typically provided as CIF files:

data_nanotube

_audit_creation_method       '(3,3) Nanotube -- TubeGen 3.3, J T Frey, University of Delaware'

_cell_length_a         7.4762
_cell_length_b         7.4762
_cell_length_c         2.4643
_cell_angle_alpha     90.00
_cell_angle_beta      90.00
_cell_angle_gamma    120.00

_symmetry_space_group_name_H-M   'P 1'
_symmetry_Int_Tables_number       1

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C         0.7762    0.5000    0.0000
C         0.8138    0.7061    0.0000
C         0.7762    0.7762    0.5000
C         0.6077    0.8138    0.5000
C         0.5000    0.7762    0.0000
C         0.2939    0.6077    0.0000
C         0.2238    0.5000    0.5000
C         0.1862    0.2939    0.5000
C         0.2238    0.2238    0.0000
C         0.3923    0.1862    0.0000
C         0.5000    0.2238    0.5000
C         0.7061    0.3923    0.5000

Now we want to get this structure into AMSinput:

Copy the CIF information shown above

Start AMSinput

Edit → Paste

View → Axes

Edit → Set Origin → X, Y and Z

View → Periodic → Periodic View Type → Repeat Unit Cell

Rotate to get a good view

We see a piece of nanotube, which is repeated in all directions. In the periodic view, 9 nanotubes are visible side-by-side.

In order to obtain a model of a single nanotube, we can set the periodicity to be one-dimensional in AMSinput. 1D systems in AMS always assume that the structure is oriented along the X-axis. However, the structure that we imported here has the nanotubes oriented along the Z-axis instead. To change our nanotube structure into a single tube, we therefore need to rotate it first.

Use the Edit → Rotate 90 → Rotate Y menu command to make the nanotube lie along the X-axis

Change the Periodicity to be one-dimensional (chain)

The ‘Rotate 90’ command not only rotated the coordinates of the atoms, but also the lattice vectors.

We now have a small piece of nanotube. (Since the periodic view already includes adjacent cells, the repeat unit is actually quite small.) If you want to build a larger model, this is easily achieved using the super cell method:

Edit → Crystal → Generate Super Cell

Enter 10 in the top-left cell

Click OK to repeat the unit cell 10 times

Switch to some non-periodic code (like ADF) if you wish to treat this piece of nanotube without infinite symmetry.

If you have a large system you can sometimes get a better view by introducing Fog.

View → Fog

Click the Done button (or play with the sliders first if you want to change the fog parameters)