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 ([image: Search][image]) 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 [image: Search][image] in the panel bar)
   Enter 'ethanol' as search text (without quotes)
   Click on the 'C2H6O: Ethanol (ADF)' match
   Rotate to get a good view

   [image]

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**)

   [image]


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

   [image]

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 ([image:
PreOptimTool][image]) 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** [image:
StructTool][image], 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)

   [image]

The next step is to add a methyl group, using the **structure tool**
[image: StructTool][image]:

   Select the [image: StructTool][image] **→ 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)

   [image]

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 [image: StructTool][image] **→ Ligands → OH** structure
   Double-click on one of the hydrogen atoms

   [image]

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 [image: PreOptimTool][image]

   [image]


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 [image: StructTool][image] **→ 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

   [image]


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 [image: StructTool][image] **→ Amino Acids → AA Backbone** structure
   Place it in the drawing area

   [image]

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 [image: StructTool][image] **→ 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**

   [image]

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
[image: StructTool][image] **→ 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 [image: StructTool][image] **→ 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

   [image]

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

   [image]

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 [image: StructTool][image] **→ Ligands → Bidentates → Ethylenediamine** structure
   Double-click on the metal atom

   [image]

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

   [image]

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

   [image]

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 [image: PreOptimTool][image] the structure
   Select the central carbon atom
   Use the [image: StructTool][image] **→ 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

   [image]

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 [image: StructTool][image] **→ Save As Structure ...** command

   [image]

   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 [image:
StructTool][image] **→ 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 ([image: Search][image]) 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

   [image]

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

   [image]

   **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:

   [image]

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
([image: Search][image]). 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

   [image]

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**)

   [image]

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

   [image]

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)

   [image]
