The first basic operation you need to learn in order to start building your own molecules with the Molecular Builder is to insert the atomic elements of the molecule that you wish to build. There are two ways of accomplishing this task in VNL

In this tutorial, we will use both approaches to construct the two simple molecules shown below, namely methane (CH₄) and silane (SiH₄).

To launch the Molecular Builder tool, double-click the Molecular Builder icon on the VNL Toolbar.

The main window of the Molecular Builder tool now appears

First, make sure that the option Autoadjust has been enabled.

Now, insert a carbon atom by pressing the C key. This inserts an sp³ hybridized carbon atom into the 3D-View. In addition, since Autoadjust is active, the Molecular Builder by default inserts four monovalent hydrogen atoms to satisfy the valency of the carbon atom. Since the carbon atom is sp³ hybridized, the hydrogen atoms are positioned as the four corners of a tetrahedron with the sp³ hybridized carbon atom as the tetrahedron center.

As a result, the finished methane molecule has been constructed. The Molecular Builder main window should now displays the CH₄ molecule, as shown in Figure 5.

To use the methane molecule in a different VNL tool, first save it to the disk as a NanoLanguage script by pressing the Save/Save As button. Drag-and-drop from Molecular Builder into another open VNL tool is also supported in the following cases: the Atomic Manipulator, the Nanoscope, the NanoLanguage Scripter, and the Script Editor; see drag-and-drop.

The carbon atom in the methane molecule was inserted by pressing the C key on the keyboard. This keyboard operation cannot be used for inserting elements whose atomic symbols consist of two letter combinations. Pressing S followed by I to insert the element Si would not work, since one sulfur and one iodine atom would be inserted into the 3D-View instead.

Instead, to insert silicon, you must use the Periodic Table tool.

First, make sure that the 3D-View is empty by pressing either the New button or using the keyboard short cut Ctrl-A + Delete.

Then launch the Periodic Table tool by pressing the button Periodic Table. The Periodic Table window then appears.

Click on the element symbol Si in the Periodic Table tool and change to the 3D-View of the main window. To insert the selected Si atom, either

Since the option Autoadjust is enabled, the four hydrogen atoms of the silane molecule are inserted automatically in a tetrahedral arrangement centered around the sp³ hybridized silicon atom. The finished silane molecule is shown in Figure 7.

The next task we will solve is building the two molecules carbon tetrachloride and 2,2-dimethyl propane. The structure of both molecules is shown below.

First, keep tapping the undo button until you get back to the state with the finished methane molecule. Then left-click and select all four hydrogen atoms. The 3D-View should now look as follows

Then launch the Periodic Table tool by pressing the Periodic Table button and select the element Cl (chlorine). Switch back to the 3D-View, then press the Insert key or right-click and choose Replace [Chlorine (Cl)]. All the selected hydrogen atoms are replaced by chlorine yielding the desired carbon tetrachloride molecule.

Again, tap the undo button until you reach the state with the finished methane molecule. Then select all four hydrogen atoms, and press the C key. As a result, all hydrogen atoms are replaced by methyl groups yielding the molecule 2,2-dimethyl propane. The molecule displayed in the 3D-View is shown below.

As you saw in the previous section, building a molecule such as methane is an almost trivial task in the Molecular Builder provided that the option Autoadjust is enabled. In this case, the properties and geometry of the entire molecule is handled automatically by the Molecular Builder.

In many other situations, however, you will need to add some level of hand tuning when constructing your molecules. In this case, you may use the Geometry Manager tool for putting the molecule into place. Doing this will allow you to specify the

between the atomic elements of a molecule. If Autoadjust is enabled, changing atomic properties (elements, hybridization, charge, or bond order) will trigger automatic adjustments. To avoid this, disable the Autoadjust option.

To learn to master the Geometry Manager tool, we will use it for constructing a methane molecule, but this time with Autoadjust disabled.

First start an empty Molecular Builder window by double-clicking the icon

If the 3D-View is not empty, either

Now, insert a carbon atom in the center of the 3D-View by pressing the C key. After this, insert three hydrogen atoms positioned as a triangle centered around the carbon atom. Position one of the hydrogen atoms above the central carbon atom. You insert the hydrogen by first placing the mouse cursor at the desired position followed by pressing the H key.

If the initial carbon atom takes up too much space, press Ctrl and drag the mouse in the 3D-View while pressing the left mouse button until an acceptable view has been reached. Your initial setting should now look similar to this

In the 3D-View, select the top-most hydrogen atom, then the carbon atom, and finally one of the two remaining hydrogen atoms. Select the atoms by left-clicking each atom in the order H–C–H. Then launch the Geometry Manager tool by pressing the Geometry Manager button.

Now, edit and change the two Distance fields to the value 1.09 corresponding to the correct value of the C–H bond length. Since geometric operations performed in the Geometry Manager tool always operate on the last selected atom, the above change will reposition the carbon atom as well as the last selected hydrogen atom.

Change the bond angle for the H–C–H bond to 109.5 in the Angle field and use the Bond Order drop-down menu to set the bond-order of the two C–H bonds to single.

Switch back to the 3D-View and deselect the last selected hydrogen atom and select the other non-selected hydrogen atom. In a similar fashion, for the last selected atom, use the Geometry Manager tool for setting the respective bond order, bond length, and bond angle to single, 1.09, and 109.5. The 3D-View and Geometry Manager tool now look as follows

First, switch to the 3D-View and press Clear Selection (Ctrl-A). Then left-click one of the bottom hydrogen atoms, the carbon atom, the top hydrogen atom, and finally the other bottom hydrogen atom.

Switch to the Geometry Manager tool and change the Dihedral angle to either 120 or -120.

Change to the 3D-View and press Clear Selection (Ctrl-A). Rotate and zoom the view to observe that the four atoms are positioned with the three hydrogen atoms as corners of a tetrahedron face with the carbon atom as the tetrahedron center.

In the 3D-View, use the mouse to rotate and zoom the system until the carbon atom is centered with the three hydrogen atoms positioned behind the carbon atom

Position the mouse cursor slightly off the central carbon atom and insert the fourth hydrogen atom by pressing the H key.

Select the carbon atom and the newly inserted hydrogen atom in the order C–H and use the Geometry Manager tool to change the bond length to 1.09.

First select an arbitrary H–C–H bond among the back-facing hydrogen atoms. Then select the last inserted hydrogen atom. Launch the Geometry Manager tool and notice the value of the displayed dihedral angle . Change the dihedral to either 120 or -120 depending on which value is closest to the currently displayed dihedral angle.

To finalize the construction of the methane molecule, choose any H–C–H bond with the first hydrogen atom chosen among the back-facing atoms and the last hydrogen atom chosen as the newly inserted hydrogen atom. Switch to the Geometry Manager tool. First set the H–C–H bond angle to 109.5. Then change the bond order of the last C–H bond to single.

Press Ctrl-R (or choose Camera → Reset in the 3D-View context menu) to reset the 3D-View. The finished methane will look similar to the one seen in this figure

In nature, the stable conformation of the molecule ethane (C₂H₆) is the so-called staggered form , where the two methyl groups are rotated 60° relative to each other around the axis connecting the two carbon atoms. In this staggered conformation, all 8 atoms are positioned as far from each other as possible giving rise to the energetically lowest possible conformation of ethane.

As the rotation angle between the two methyl groups is increased, the energy of the molecule also increases reaching its maximum value at 60° where the C–H bonds of the methyl groups are pairwise parallel. This conformation of ethane is called the eclipsed conformation . The eclipsed conformation is meta-stable since any infinitesimal perturbation will make the molecule relax back to the staggered state. The geometry of both the staggered and the eclipsed state is shown in Figure 8 .

When you build ethane and have the option Autoadjust enabled, the Molecular Builder will always construct the staggered version of ethane. In this tutorial, we will show you how to construct an eclipsed ethane molecule with the Molecular Builder.

Our first step will be to construct a staggered ethane molecule. Afterwards, we then convert this into the desired eclipsed conformation.

First, launch an empty the Molecular Builder window by double-clicking the icon

and check that the 3D-View is empty (Ctrl-A + Delete). In addition, make sure that the option Autoadjust has been enabled.

Now, position the mouse cursor in the center of the screen and build a methane molecule by pressing the C key.

Position the mouse cursor over one of the four hydrogen atoms and press the C key. As shown below, the entire structure will be converted into a staggered ethane molecule.

To change the staggered conformation into the eclipsed, select a sequence of four atoms in the order H–C–C–H with the two hydrogen atoms rotated 60° relative to each other.

The eclipsed conformation can now be obtained by changing the dihedral angle between the two planes spanned by the H–C–C and C–C–H bonds. Clearly, the two planes should coincide implying that the dihedral angle should be 0°.

To accomplish this, launch the Geometry Manager tool by pressing the Geometry Manager button. Change the value of the Dihedral Angle field to 0. This operation generates the eclipsed ethane conformation

In this tutorial, we will construct an ethanol molecule (C₂H₅OH) using the Join feature of the Molecular Builder as well as the Molecule Cupboard tool. The final goal of the tutorial, the ethanol molecule, is shown below

Start by building a staggered ethane molecule as discussed here.

Launch the Molecule Cupboard tool by pressing the Molecule Cupboard. Either type the string h2 in the search field or use the drop-down list and select the item Functional group. Then select the water molecule (H2O) from the list of displayed molecules.

Switch to the 3D-View and position the mouse cursor away from the ethane molecule. Press the Insert key. The water molecule will be inserted into the 3D-View.

Left-click to select a hydrogen atom on both the water and the ethane molecule. Right-click in the 3D-View and choose Join from the context menu. The water and ethane molecule will be joined at the selected positions.

Once you have selected the water molecule, first notice that one of the hydrogen atoms of the molecule have been selected as displayed in the preview window of the Molecule Cupboard tool. Then switch to the 3D-View, and position the mouse cursor over one of the hydrogen atoms of the ethane molecule. Then press Insert upon which the water and ethane molecule get joined.

Alternatively, first select the water molecule in the Molecule Cupboard. Then switch to the 3D-View and select a hydrogen atom on the ethane molecule. Finally, right-click and choose Insert & Join

Furthermore, during the Join operation, auto adjustments are always active. For the current setting, this implies that Molecular Builder automatically removes one of the hydrogen atoms in order to obtain a valency preserving bond between the sp³ hybridized carbon and the oxygen atom. As a result, the molecule ethanol has been built.

Here, we will show you how to construct the aldehyde molecule acetaldehyde. To this end, we will first construct an ethanol molecule and use the bond order parameter from the Geometry Manager to add the required changes to the bond between the C–O bond. An acetaldehyde molecule is shown below.

Start the Molecular Builder with an empty 3D-View and make sure that the Autoadjust option is enabled. Then position the mouse cursor in the 3D-View and press the C key. This will construct a methane molecule.

Then position the mouse cursor over one of the four hydrogen atoms and press the C key. The hydrogen atom is then converted into a carbon atom changing the methane molecule to ethane.

Finally, position the mouse cursor over one of the six hydrogen atoms and press the O key. As displayed below, the ethane molecule is converted into ethanol.

In order to finalize the construction of the acetaldehyde molecule , we need to change the bond order of the C–O from a single to a double bond.

First, left-click to select both the oxygen and carbon atom that make up the C–O bond.

Then press the Geometry Manager button and use the drop-down menu to change the bond order of the C–O bond from single to double. As a result, the desired acetaldehyde molecule has been generated. Note also, that the hybridization of both the carbon and the oxygen atom has been changed from sp³ to sp² as expected in a double bond.

We have already seen how the Join feature can be used for attaching molecular structures to each other. When molecules are joined in the Molecular Builder, a single bond between the two are established. In some situations, however, more than a single bond must be established in order to obtain the desired structure. In this case, you should use the Fuse functionality to build your molecule. Here, we will illustrate the use of Fuse operations by constructing the molecule naphthalene from two benzene rings:

Start the Molecular Builder with an empty 3D-View and launch the Molecule Cupboard. Scroll through the Molecules list and select benzene (C₆H₆).

Switch back to the 3D-View and press the Insert key twice. To avoid overlaps between the inserted rings, make sure to reposition the mouse cursor in-between the insertions. Your Molecular Builder window should look as shown below.

Now, left-click to select the following two sequences of atoms H–C–C–H and C–C–C–C. Notice, that the order of selections is important. Your selections should look as below

Finally, in the 3D-View, right-click on any of the selected atoms and select Fuse from the context menu. As a result of the operation, the two benzene rings get fused at the selected atoms thereby generating the desired naphthalene molecule. A 3D representation is shown below.

The final molecule that we will construct here is p-benzene-dithiol – that is, a benzene ring where two oppositely positioned hydrogen atoms have been substituted by thiol groups . A 3D representation of p-benzene-dithiol is shown below.

Start the Molecular Builder with an empty 3D-View and press Molecule Cupboard to launch the Molecule Cupboard tool.

Scroll though the list of Molecules and select benzene. Switch to the 3D-View and press Insert to add the selected benzene molecule.

Switch back to the Molecule Cupboard dialog and select Hydrogen sulfide. In the 3D-View, press the Insert key twice to insert an H₂S molecule above and below the benzene ring. The 3D-View should look as follows:

Now, select a hydrogen atom belonging to one of the two H₂S molecules. In addition, select the hydrogen atom located closest to the previously selected hydrogen atom.

Right-click in the 3D-View, and choose Join from the context menu. As a result, the first thiol group has been added to the benzene ring.

To obtain a p-benzene-dithiol molecule, similar to the one shown in Figure 10, repeat the above procedure to add the remaining thiol group.

Once the benzene ring has been added to the 3D-View, position the mouse cursor over two mutually para oriented hydrogen atoms and do one of the following operations for each hydrogen atom: