Molecular Builder

Table of Contents

The Molecular Builder tool is a powerful tool designed for automating the task of building and editing molecules. Put shortly, you can use the tool either to

In many situations, for example when setting up the central region molecule of a two-probe system, you will often find that defining the molecule by hand-typing the coordinates of all atoms can be a time-consuming and error prone business.

In this chapter, we will give a detailed account of the tools and functionality available in the Molecular Builder tool, and provide several examples of how typical molecular structures can be build using the tool.

When you have finished building your molecule you can either

However, before we start to discuss all the technical aspects of the tool, let us look at a few examples, and see how the basic features of the Molecular Builder can be used to build some simple molecules.

Starting the Molecular Builder

In order to start using the Molecular Builder tool, double-click the icon

on the VNL Toolbar. An empty Molecular Builder window should then be available on your desktop (a Molecular Builder in use is shown in Figure 3). The black window is the 3D-View which is used for displaying 3D renderings of the molecules you build.

If the 3D-View is not empty, left-click to activate the window, and do either of the following to clear the view

  • Press Ctrl-A followed by pressing the Delete key.

  • Right-click and choose Select all from the context menu, then press the Delete key.

  • Left-click the New button. Note that this also clears the content of the “undo stack” unlike when you use the Delete key.

The Molecular Builder tool: Main window (left), Periodic Table (center) and Molecular Cupboard window (right).

Figure 3: The Molecular Builder tool: Main window (left), Periodic Table (center) and Molecular Cupboard window (right).


Building simple molecules

In this section, we will use the Molecular Builder tool to insert atoms and construct some relatively simple molecules, namely

  • Methane (CH4)

  • Water (H2O)

  • Ammonia (NH3)

Images of the three molecules are shown below.

In this section, we will not get into the finer technical details of how to use the Molecular Builder, but instead focus on some simple work-flows that can be used to construct even relatively complicated molecular structures.

[Important] Important

Before you try out the examples discussed below, make sure that the option Autoadjust is enabled in the main Molecular Builder window.

Methane

The first molecule we will build is a methane molecule (CH4). If you have not started the Molecular Builder already, please follow the instruction given previously.

Now lets start building the methane molecule. Simply press the C key on your keyboard. This inserts a carbon atom into the 3D-View. However, a single carbon has a valency of four and is as such an unsaturated compound. Since the option Autoadjust is enabled, the Molecular Builder automatically inserts four hydrogen atom bonded to the central carbon atom that we just inserted.

The result, obtained simply by pressing C on your keyboard is the finished methane molecule. Your newly build methane molecule should look like this:

Methane molecule (CH4) constructed with the Molecular Builder tool.

Figure 4: Methane molecule (CH4) constructed with the Molecular Builder tool.


Finally, to use your newly built methane molecule in other VNL tools, press the button Save, which will save the methane molecule configuration to a NanoLanguage script.

Water

Changing our newly built CH4 molecule into other molecules is a straightforward task. In the 3D-View, hover the mouse cursor over the carbon atom and press the key O on the keyboard. The carbon atom will change into an oxygen atom. Since the valency of oxygen is 2, two of the four hydrogen atoms are automatically removed. As a result, the methane molecule has been converted into a water molecule (H2O) as shown in Figure 5.

Water molecule constructed with the Molecular Builder. The molecule was obtained simply by placing the mouse cursor over the carbon atom in the CH4 molecule shown in and pressing the O key.

Figure 5: Water molecule constructed with the Molecular Builder. The molecule was obtained simply by placing the mouse cursor over the carbon atom in the CH4 molecule shown in Figure 4 and pressing the O key.


Ammonia

Using the combination of placing the mouse cursor and selecting atomic symbols with the keyboard, provides a convenient technique for making simple changes to a molecule. As a final example, we will use the same technique for converting the water molecule into the gaseous ammonia molecule (NH3). Again, hover the cursor over the oxygen atom in the water molecule, and press the N key. The oxygen atom changes into a nitrogen atom. In this case, the valency of nitrogen is 3, so the Molecular Builder automatically adds an extra hydrogen atom yielding the desired ammonia molecule. A 3D rendering of the molecule is shown in Figure 6.

Ammonia molecule (NH3) constructed with the Molecular Builder.

Figure 6: Ammonia molecule (NH3) constructed with the Molecular Builder.


[Note] Note

Elements whose atomic symbol is composed of two letters cannot be inserted using the keyboard. To insert such elements into your structure, you need to use the The Periodic Table tool.

Using the techniques illustrated for constructing CH4, H2O, and NH3, you can build a range of molecules. As a second exercise, you could try to construct slightly more complicated molecules, for example, ethanol (C2H5OH), formic acid (HCOOH), and butane (C4H10) using the technique you have learned so far.

However, in order to construct more advanced molecules, you need to get acquainted with the finer details of the tools available in the Molecular Builder tool. We cover these in the subsequent sections.

[Tip] Tip

In case you want to use your molecule configuration in another tool, but are not interested in saving it to your file system, you can just as well drag-and-drop the configuration directly from the Molecular Builder to the tool icon, see the drag-and-drop section.

Adjusting molecules

The Molecular Builder comes with a sophisticated set of tools for adjusting the geometric properties of the molecules you build. You can either choose to enable the option Autoadjust in the main window or apply your own User adjustments to the molecule geometry.

The two alternatives are described in the following two sections.

Autoadjustments

If you enable the option Autoadjust in the main Molecular Builder window, the local geometry and valencies of the structure you build are taken care of by the Molecular Builder. This includes bond distances, bond angles, and dihedral angles, which are adjusted according to a molecular template pattern recognition scheme.

If a suitable template is not found, adjustments only include bond angles determined by the hybridization of the selected atom, whereas bonded atoms are removed to match the valency of the selected atom. In addition, bond distances are determined either from a table of typical values or by the covalent radii of the involved atoms.

[Important] Important

Be aware, that auto-adjustments only affect the “central atom”, that is, the atom upon which you operate. Auto-adjustments is not a global operation, and you must make sure yourself that the final structure is correct.

User adjustments

When you choose to disable the option Autoadjust, the Molecular Builder will only do exactly what it is told to do. When atoms are inserted, geometric features such as the atom valency and bond angles are not adjusted as you build up your structures.

You can, however, instruct the Molecular Builder to adjust the geometry of a certain selection of atoms by using the operations Set Ideal Angles and Adjust Geometry available from the context menu in the 3D-View. The two options differ in the level of the applied adjustments

  • Set Ideal Angles: Only bond angles are adjusted according to the hybridization of the selected atom (109.5° for sp3, 120° for sp2, and 180° for sp). For example, the bond angle for a H–C–H bond in methane will be set equal to 109.5° corresponding to the bond angle in methane.

  • Adjust Geometry: In this case, a full scale adjustment as described under the section called “Autoadjustments” is applied.

To illustrate the difference between the two methods, disable the Autoadjust option, and build the following “sketchy” methane molecule by inserting a square of four hydrogen atoms around a central carbon atom. Each hydrogen atom should be single bonded to the central carbon atom.

Left-click to select the central carbon atom and choose Adjust Geometry from the context menu of the 3D-View. As a result, all angles are adjusted to 109.5° since the inserted carbon atom by default is sp3 hybridized. If you use the Geometry Manager tool to inspect the bond distances in the molecule, you'll notice that the bond length of the C–H also has been changed to the experimental value of 1.092 Å.

Now, keep pressing the undo button until you reach the state of the system just before the Adjust Geometry operation was executed. Then choose Set Ideal Angles from the context menu. If you inspect the resulting molecule with the Geometry Manager tool, you will notice that only the angles of the H–C–H bonds have changed, whereas the bond lengths are kept at the values determined by the positions where you originally inserted the five atoms.

The Periodic Table tool

To start the Periodic Table, press the button Periodic Table in the main Molecular Builder window.

Depending on the state of the scene in the 3D-View, the following alternatives apply

  • If no atoms are selected in the 3D-View, additional atoms and molecules are inserted into the 3D-View at the position pointed to by the mouse cursor.

  • If the cursor is located over a previously inserted atom, this atom will be replaced by your insertion.

  • If one or more atoms already are selected in the 3D-View, pressing Insert will replace all these atoms by the atom selected in the Periodic Table window.

Inserting elements whose atomic symbol is expressed by a single letter is most easily accomplished by pressing the corresponding keyboard symbol. For example, to insert an oxygen or nitrogen atom, press the respective keys O or N on your keyboard.

For inserting elements such as silicon or sodium whose atomic symbol is composed of two-letter combinations, this approach will not work. In this case, you can use the Periodic Table tool for inserting such atoms. As shown in Figure 7, the layout of the Periodic Table GUI uses the conventions of a traditional periodic table.

Using the Periodic Table for inserting atoms is simple:

Just left-click on the element you wish to insert. Then go to the 3D-View in the main window, and press the Insert key on your keyboard. Alternatively, right-click anywhere in the 3D-View and insert the atom from the context menu. If several identical elements should be inserted, continue to move the cursor to the right place and press the Insert key until the desired number has been reached.

[Note] Note

Remember to reposition the mouse cursor between each insertion; otherwise, all atoms will be positioned right on top of each other.

The Periodic Table tool. Select the desired element by Left-clicking in the periodic table, and insert it by pressing either the Insert key on your keyboard in the 3D-View, or by choosing the Insert entry from the context menu of the 3D-View.

Figure 7: The Periodic Table tool. Select the desired element by Left-clicking in the periodic table, and insert it by pressing either the Insert key on your keyboard in the 3D-View, or by choosing the Insert entry from the context menu of the 3D-View.


The Molecule Cupboard

The Molecular Builder comes with a selection of predefined molecule templates that you can use as building blocks for setting up complicated molecular structures. These templates can be accessed by using the Molecule Cupboard. Here, you can choose a molecule and insert it into the 3D-View. So instead of building a toluene molecule from scratch, choose the benzene ring template from the Molecule Cupboard, build a separate methane molecule and use the Join feature to add the required methyl group.

You invoke the Molecule Cupboard by pressing the Molecule Cupboard button in the main window. The tool is shown in Figure 8.

The Molecule Cupboard tool. Scroll and Left-click in the Molecules box to select the desired molecule template. The template can now be inserted in the 3D View by pressing the Insert key on your keyboard or by choosing the entry Insert from the context menu of the 3D-View. insert

Figure 8: The Molecule Cupboard tool. Scroll and Left-click in the Molecules box to select the desired molecule template. The template can now be inserted in the 3D View by pressing the Insert key on your keyboard or by choosing the entry Insert from the context menu of the 3D-View.


The Molecule Cupboard contains four different box elements:

  • Filter: Use the filter for searching for specific templates. A selection of predefined filters accessed via the drop-down list is also available.

  • Molecules: Displays the list of molecule templates available showing the empirical formula, the molecule name, and the group category of the molecule. If the molecule has an alternative name, this will also be displayed. If the filter has been used, this box only displays the templates matched by the search.

  • Molecule information: Here you will find some specific information about the currently selected molecule template.

  • Preview: A 3D rendering of the currently selected molecule template. Notice that a hydrogen atom always is preselected in the displayed preview. This indicates the atomic position that will be used when molecules from the Molecule Cupboard are joined with preexisting molecules in the 3D-View.

To use the Molecule Cupboard do the following: Launch the tool by pressing the Molecule Cupboard. Scroll through the list in the Molecules box and left-click to select the desired molecule template.

After you have made your selection, switch to the Molecular Builder 3D-View and point the mouse cursor at the location where you want the molecule to be inserted. Then, press the Insert key or choose Insert from the context menu of the 3D-View. The selected template has been inserted into the 3D-View and is ready for further manipulations. If the mouse cursor is located over an existing atom, a Join operation is attempted.

Alternatively, if an atom or molecule already has been selected in the 3D-View, pressing the Insert key will result in a join operation: In this case, the molecular template selected in Molecule Cupboard will be joined with the molecule in the 3D-View. The join operation takes place at the selected atom of the template molecule and the selected atom of the molecule in the 3D-View. Observe that the selected atom of the template molecule is shown in the 3D preview window in the Molecule Cupboard tool.

Filtering templates

It is often handy to narrow down the number of templates that are displayed in the Molecules box. Access the drop-down list located on the right from the Filter edit field and select among a set of predefined search filters. For more refined and specific searches, you can use the edit field Filter in order to display only a selection of the templates that meets certain criteria. For example:

  • To choose among all alkane and alkyne templates, type the string “alk” in the Filter edit field. If you extend your string to “alka”, only alkanes gets displayed.

  • To locate all hexane templates with a ring structure, type the string “hexa ring” in the Filter edit field. The filter then chooses all templates matching both the string “hexa” and “ring”.

Joining and fusing molecules

A typical work-flow when using the Molecular Builder for constructing complicated structures is first to assemble the building blocks of the structures and then join these. There are two techniques for accomplishing this task, namely joining and fusing molecules. We will discuss these separately in the subsequent two sections.

Join

Joining molecules can be accomplished in the Molecular Builder either by

  • joining two molecules directly in the 3D-View

  • joining a molecule selected in the Molecule Cupboard with a molecule in the 3D-View.

We will discuss both approaches in the following.

To join molecules directly in the 3D-View, left-click in the 3D-View to select a terminal atom in each of the two structures that you wish to join. Then right-click to open the context menu of the 3D-View, and select the entry Join. As a result, the two molecules have been joined.

To join a molecule from the Molecule Cupboard with one from the 3D-View, first select the desired molecule template in the Molecule Cupboard tool. The chosen molecule is displayed in the 3D Preview window. Here, you left-click to choose the terminal atom of the molecule displayed in the Preview window.

Now, switch to the molecule in the 3D-View of the main window and position the mouse cursor over the terminal atom where the join operation should take place. Finally, to join the two molecules, press the Insert key on your keyboard or right-click to launch the context menu.

Let us illustrate each of the above approaches with some examples: We start off by building the molecule biphenyl (C12H10) which consist of two benzene ring connected through a C–C bond. The biphenyl molecule is shown below

Start up the Molecular Builder with an empty 3D-View, press the Molecule Cupboard button, and select the benzene ring template from the Molecules box. Insert two benzene rings into the 3D-View by pressing the Insert on the keyboard twice. Reposition the mouse cursor in-between the two inserts to avoid having the rings overlapping each other.

Then left-click to select two terminal hydrogen atoms, one on each benzene ring. Then press Ctrl-J or right-click in the 3D-View window and choose Join from the context menu. The two benzene will be joined generating the desired biphenyl molecule.

An alternative approach for joining molecules is to join a molecule in the 3D-View directly with a molecule selected in the Molecule Cupboard. Here is how to do it:

First press Molecule Cupboard and select the entry for benzene. Then add a single benzene molecule to the 3D-View by pressing the Insert button. Notice that a terminal hydrogen atom already has been selected on the benzene molecule displayed in the Preview window of Molecule Cupboard tool. Switch back to the 3D-View window and place the mouse cursor over any of the hydrogen atoms of the displayed benzene ring. Finally, press the Insert button. The benzene ring from the Molecule Cupboard has been joined with benzene ring from the 3D-View. Alternatively, you can also first select one the H atoms on the benzene ring in the 3D-View, then right-click and select Insert and Join from the context menu.

[Note] Note

Even if the option Autoadjust is disabled, it always becomes active during join operations to ensure that the correct bond structure appears after the join.

Fuse

When constructing molecules and adding functional groups to a molecule that requires more than one bond to be broken, a join operation will not suffice. In this case, you should instead use the Fuse operation. The Fuse operation is available from the context menu of the 3D-View window or can be activated by the keyboard shortcut Ctrl-J.

The primary usage of the Fuse operation is as a “ring-joining” tool for merging two or more ring-structured molecules. For example using benzene as the building block for constructing molecules such as naphthalene, anthracene, anthraquinone, and phenanthrene (see Figure 9 below).

Examples of ring-structured molecules: naphthalene (a), anthracene (b), anthraquinone (c), and phenanthrene (d).

Figure 9: Examples of ring-structured molecules: naphthalene (a), anthracene (b), anthraquinone (c), and phenanthrene (d).


As an example, we will use a fuse operation for building the molecule naphthalene shown above in Figure 9:

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 setup 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, right-click 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 rendering similar to that shown in Figure 9 will show up in your 3D-View.

Chirality and cis/trans isomers

The 3D structure of many molecules is not preserved if the molecule is reflected through a mirror plane. A molecule, that cannot be superimposed onto its mirror image, is called chiral. The two mirror image molecules are called enantiomers. For example, the molecule CHFClI (methane with three different halogen substituents), exists in two distinct forms (both of which are shown in Figure 10).

Generating the mirror image of a chiral molecule in the Molecular Builder is a simple task: in the 3D-View, right-click to open the context menu and choose Mirror. As a result, the mirror image or stereo isomer of the original molecule gets generated. The two mutual stereo images are shown in Figure 10.

The two distinct forms of the molecule CHFClI. Both molecules are each others mirror image and cannot be superimposed on each other.

Figure 10: The two distinct forms of the molecule CHFClI. Both molecules are each others mirror image and cannot be superimposed on each other.


Cis-trans isomers

In some situations, you do not want to mirror the entire molecule you have build, but just some of the substituents on certain parts of the molecule. In this case, you use the operation Swap Substituents, which is available from the context menu in the 3D-View:

To Swap groups on a specific atom

  1. Left-click in the 3D-View on the atom whose substituents you want to swap

  2. Right-click to bring up the context menu and choose the entry Swap Substituents.

For example, suppose that we have built the molecule trans-1,2-dichloroethene shown below.

The molecule trans-1,2-dichloroethene.

Figure 11: The molecule trans-1,2-dichloroethene.


To convert trans-1,2-dichloroethene into its cis conformation, cis-1,2-dichloroethene, first left-click to select either of the two carbon atoms. Then right-click in the 3D-View and select the entry Swap Substituents. The resulting cis isomer is shown below.

The molecule trans-1,2-dichloroethene can be converted into its cis form cis-1,2-dichloroethene by selecting either of the two carbon atoms followed by selecting the operation Swap Substituents from the context menu of the 3D-View.

Figure 12: The molecule trans-1,2-dichloroethene can be converted into its cis form cis-1,2-dichloroethene by selecting either of the two carbon atoms followed by selecting the operation Swap Substituents from the context menu of the 3D-View.


Try yourself to built the cis and trans isomers of the molecule 2-butene shown below

The cis form of the molecule 2-butene.

Figure 13: The cis form of the molecule 2-butene.


The Geometry Manager tool

The Geometry Manager tool is the fundamental tool for specifying the constituents and the geometry of the molecules you build. The tool is launched by pressing the button Geometry Manager in the main window of the Molecular Builder. You use the Geometry Manager tool to set

  • the atomic element of an atom

  • the electrical charge of an atom

  • the hybridization of an atom

  • the bond order between two atoms

  • the distance between two atoms

  • the angle between three atoms

  • the dihedral angle between four atoms

[Important] Important

When saving the configuration as a NanoLanguage script, information about electrical charge, hybridization, and bond order will be lost. Since this information is not used in any of the subsequent tools, it is usually not a problem. If you want to keep this information, you should instead save the configuration as a VNL file using Save As.

Defining the element type

When you insert atoms using the Molecular Builder, you can use the Geometry Manager tool for both setting and changing the element type of a given atom. To do this, start the tool by pressing the button Geometry Manager in the main Molecular Builder window. Now, left-click to select an atom in the 3D-View. The selected atom is now present in the Geometry Manager table view. In the Element column, select the desired element for the selected atom from the drop-down list. Your choice should now be reflected in the 3D-View.

For example, to build a methanol molecule (CH3OH), start by building a methane molecule. Now, in the main window, press the button Geometry Manager, select any of the four hydrogen atoms bonded to the central carbon atom, and make sure the option Autoadjust is enabled. Change to the Geometry Manager window, and change the element type of the hydrogen atom to oxygen. That's it, the methane molecule has now been converted into methanol.

The entire periodic table is available from the drop-down list in the Element column. Elements may also be inserted by using the The Periodic Table tool.

Building ions – setting atomic charges

Many substances, such as NH4+ and Cl- exist in nature as stable charged structures called ions. By setting the charge quantity given in the Charge column of the Geometry Manager window, you can use the Molecular Builder for setting up and constructing ions. You do that by selecting the relevant atom in the 3D-View, and assigning its charge using the spin-box available from the Charge column of the Geometry Manager window.

For example, to construct the ammonium ion NH4+, start off by building the ammonia molecule NH3. Then left-click on the central nitrogen atom in the 3D-View to select the atom. Afterwards, select the Geometry Manager tool and use the Charge spin-box to change the charge on the nitrogen atom from 0 to 1. Provided that the option Autoadjust is enabled in the main window, the Molecular Builder will then add an extra hydrogen atom bonded to the central nitrogen atom, thereby generating the ammonium ion NH4+. The structure is shown below in Figure 14.

Ammonium ion constructed from an ammonia molecule by using the Geometry Manager tool to change the charge of the central nitrogen atom from 0 to +1.
Ammonium ion constructed from an ammonia molecule by using the Geometry Manager tool to change the charge of the central nitrogen atom from 0 to +1.

Figure 14: Ammonium ion constructed from an ammonia molecule by using the Geometry Manager tool to change the charge of the central nitrogen atom from 0 to +1.


[Note] Note

Configurations containing charged molecules (ions) build with the Molecular Builder are currently not fully supported; instead they are treated in NanoLanguage scripts as being neutral.

Hybridization

To explain the geometry and bond properties of molecular structures, the so-called hybridization model is of substantial importance. In this model, the bond forming orbitals of individual atoms are described by using appropriate linear combinations of the s and p orbitals describing the valence shell of each atom.

The specified hybridization of an atom is primarily used in the Molecular Builder to determine the characteristic bond geometry of the specific atom. So when you specify the hybridization of an atom, you also determine the geometric layout of the bonds it can form. The hybridization is specified in the Geometry Manager tool in the Hybridization column. Use the drop-down list to select the desired hybridization. The following hybridization models are available

  • mono: The hybridization of a hydrogen atom

  • sp3: The hybridization of an atom that form single bonds, for example the carbon atoms in CH4 and C2H6. The bonds from an sp3 hybridized atom will approximately have tetrahedral geometry with bond angles close to 109.5°

  • sp2: The hybridization of an atom forming double bonds, for example the carbon atoms found in C2H4 The bonds from an sp2 hybridized carbon atom approximately gives rise to planar geometries with bond angles close to 120.0°.

  • sp: The hybridization of an atom forming triple bonds, for example the carbon atoms found in C2H2 and the nitrogen atoms in the N2 molecule. The bonds from an sp hybridized carbon atom approximately gives rise to linear geometries with bond angles close to 180.0°.

  • undefined: If the hybridization of an atom is set to undefined, the user-specified geometry associated with this atom is preserved when geometry adjustments of the molecule are performed.

The typical geometry of tetrahedral, planar, and linear arrangements found in sp3, sp2, and sp hybridized molecules are shown in Figure 15 below.

Molecular geometries corresponding to the respective hybridizations sp3, sp2, and sp.

Figure 15: Molecular geometries corresponding to the respective hybridizations sp3, sp2, and sp.


Let us use the Geometry Manager tool and the hybridization parameter to build the molecule hydrogen cyanide (HCN) shown below

First start by building an ethane molecule and make sure the option Autoadjust is enabled. Then place the mouse cursor over the C–C bond and press the 3 key. The single bond will change into a triple bond yielding the molecule ethyne (C2H2).

Place the mouse cursor over one of the two carbon atoms and press N on the keyboard. The carbon atom is replaced with an sp3 hybridized nitrogen atom with two additional bonded hydrogen atoms.

Finally, left-click to select the newly entered nitrogen atom and launch the Geometry Manager tool. In the Hybridization field, choose sp from the drop-down list. In order to preserve the valency of the nitrogen atom, this operation also removes the two hydrogen atoms bonded to the nitrogen atom; as a result, the desired hydrogen cyanide molecule has been built. A rendering of the resulting molecule from the 3D-View is displayed in Figure 16.

A hydrogen cyanide molecule (HCN) with an sp hybridized nitrogen atom.
A hydrogen cyanide molecule (HCN) with an sp hybridized nitrogen atom.

Figure 16: A hydrogen cyanide molecule (HCN) with an sp hybridized nitrogen atom.


[Tip] Tip

Instead of building ethyne from scratch, the operation discussed above could have been simplified by importing the ethyne molecule directly from the Molecule Cupboard.

Setting the bond order

The central carbon atom in the methane molecule is a so-called sp3 hybridized atom implying that all C-H pairs are single-bonded with each bond sharing exactly one electron pair. In a broad category of chemical species, however, atoms may also be sp2 and sp hybridized giving rise to double– and triple bond connections between bonded atoms. The order of the chemical bonds for molecular structures that you are working with in Molecular Builder can defined with the Geometry Manager tool.

Setting the bond order between an atom pair requires that both atoms have been selected in the 3D-View. After the atom pair has been selected, you may then use the drop-down list from the Bond Order column in the Geometry Manager tool to set the bond order of the selected pair. Here, you may choose among the following values

  • None: The atom pair is not connected with a bond. You can use this setting to break a bond between an atom pair.

  • Single: A single bond sharing one electron pair between the bonded atoms, for example bonds in H2O, NH3, and C2H6.

  • Double: A double bond sharing two electron pairs between the bonded atoms, for example as in the linear carbon dioxide molecule (CO2) and the planar molecule ethene (C2H4).

  • Triple: A triple bond between the atom pair with three electron pairs being shared between the bonded atoms. An example is the linear molecule acetylene (C2H2).

  • 1.5: A bond, corresponding to the bond structure found in cyclic ring structures such as the benzene molecule (C6H6). In benzene, nine electron pairs are shared between six equivalent carbon atoms, leading to a bond order equal to 1.5. For the same reason, a bond-order need not be an integer number.

  • pseudo: Inserting a pseudo bond between two atoms serves the purpose of a geometric guide for easing manipulations of the molecule. The bond is completely ignored when automatic adjustments of the molecule are performed.

In order to illustrate the usage of the bond order parameter, we will use the Geometry Manager tool to set up the planar molecule ethene (C2H4) where the two carbon atoms are connected with a double bond (this molecule is sometimes also referred to as ethylene). The ethene molecule is shown below.

Start off by building methane and make sure that Autoadjust is enabled. Then left-click one of the four hydrogen atoms, followed by pressing the key C. The hydrogen atom is then converted into a carbon atom. As a result, since the option Autoadjust is active, the methane molecule is converted into an ethane molecule (C2H6). The 3D-View should now look similar to this

Now, make sure that the newly added carbon atom still is selected in the 3D View. After this, select the other carbon atom by left-clicking the atom in the 3D-View. The bond characteristics of the two selected carbon atoms can now be changed with the Geometry Manager tool. Launch the tool by pressing the Geometry Manager button in the main window. The last of the selected carbon atoms will have an active drop-down list in the Bond Order column. Select the bond order “double” from the list. The planar ethene molecule including the double bond between the two carbon atoms can now be viewed in the 3D-View. A typical rendering is shown in Figure 17.

An ethene molecule constructed by changing the bond order between the two carbon atoms of ethane from single to double.

Figure 17: An ethene molecule constructed by changing the bond order between the two carbon atoms of ethane from single to double.


[Note] Note

Even though bond orders are mostly used for visualization purposes, they are important elements for automatic geometry adjustments in the Molecular Builder, where it serves the role as pattern recognition elements involved in bond distance, bond angle, and dihedral angle adjustments.

Adjusting bond distances

When you set up chemical bonds through Join and Fuse operations between the atoms in your constructed molecules, the Molecular Builder chooses the bond distances from either pattern recognition templates or from a data base of tabulated typical values. If the Molecular Builder cannot locate a suitable bond length for a given atom pair, it will use the sum of the covalent radii of the two atoms. If this bond length is not what you want, you may use the Geometry Manager tool to define your preferred values. You do it like this:

Select two atoms by left-clicking them in the 3D-View and start up the Geometry Manager tool. Type in the desired bond length in the edit field in the column labeled Distance. To display your updated distance in the 3D-View either press Return or simply click anywhere in the background of the 3D-View.

[Important] Important
  • When you change the distance between two atoms, it is always the last selected atom, as well as all groups connected to it, that change position. In contrast, the first selected atom, as well as all groups connected to it, remain unchanged.

  • If the Distance field in the Geometry Manager tool is unresponsive, this implies that this particular distance cannot be changed. The distance may for example be locked in a ring structure, such as benzene where changing the C–C distance is not allowed.

Bond angles

Consider a molecule subsystem with two atoms bonded to a central atom as shown in Figure 18. As the figure illustrates, the three bonded atoms define a unique bond angle θ describing the bending of the chemical sub-chain. For example, for a water molecule, the experimental value of the H–O–H bond angle is θ = 104.5°. The Molecular Builder uses several molecule templates for choosing optimized bond values. In situations where you wish to alter or fine tune a bond angle, you proceed as follows:

Setting bond angles in the Molecular Builder requires that you first select the three atoms that define the bond angle. Do this in the 3D-View by left-clicking the three atoms. Once this has been done, start the Geometry Manager tool and type in the relevant angular value (given in units of degrees) and finish by pressing Return.

[Important] Important
  • When you change the angle between three atoms, it is always the last selected atom, as well as all groups connected to it, that change position. In contrast, the first selected atom, as well as all groups connected to it, remain unchanged.

  • The bonding angle depends on the order in which you select the three atoms that define the angle. Always make your selections such that the central atom becomes the second in your succession of selections. For example, for water, the atoms should be selected in the order

    • Correct: H–O–H

    • Wrong: H–H–O or O–H–H

  • If the Angle field in the Geometry Manager tool is unresponsive, this implies that this particular angle cannot be changed. The angle may for example be locked in a ring structure, such as benzene where changing a C–C–C angle is not allowed.

Definition of the bond angle θ using the C–O–H bond in methanol as an example.

Figure 18: Definition of the bond angle θ using the C–O–H bond in methanol as an example.


Dihedral angles

Consider the sub-chain of atoms labeled as H1–C2–C3–H4 in the ethane molecule shown in Figure 19. Each of the three-atom sets H1–C2–C3 and C2–C3–H4 define two respective planes labeled as α and β in Figure 19. The intersection angle ϕ between the two planes is the so-called dihedral angle. Just as for bond distances and angles, the Molecular Builder uses a set of optimized molecule templates for choosing appropriate dihedral values for the molecules you build. In situations where the dihedral angles require adjustment, you can alter it with the Geometry Manager tool as follows:

First left-click in the 3D-View on the four atoms that define the dihedral angle that you wish to change. Then start the Geometry Manager tool by pressing the button Geometry Manager. Finally, edit the value of the dihedral angle in the field in the column Dihedral Angle to the desired value and press Return. Your changes will be reflected in the 3D-View.

[Important] Important
  • When you change the dihedral angle between four atoms, it is always the last selected atom, as well as all groups connected to it, that change position. In contrast, the first selected atom, as well as all groups connected to it, remain unchanged.

  • If the Dihedral Angle field in the Geometry Manager tool is unresponsive, this implies that this particular angle cannot be changed. The angle may for example be locked in a ring structure, such as benzene where changing a C–C–C–C angle is not allowed.

  • Always select the atoms that define the dihedral angle in their natural order. The dihedral angle depends on the order of selection, and its geometric meaning becomes very difficult to interpret if you do not choose the natural selection order. For example, for the sub-chain shown in Figure 19 select the atoms in the order H1–C2–C3–H4 or H4–C3–C2–H1.

Definition of the dihedral angle ϕ using the molecule ethane as an example: The angle ϕ is defined as the intersection angle between the two planes α and β spanned by the respective atom chains H1–C2–C3 and C2–C3–H4.

Figure 19: Definition of the dihedral angle ϕ using the molecule ethane as an example: The angle ϕ is defined as the intersection angle between the two planes α and β spanned by the respective atom chains H1–C2–C3 and C2–C3–H4.


Keyboard shortcuts.

Table 2: Keyboard shortcuts available in the 3D-View window. The equivalent context menu entries of the 3D-View are also displayed.

Action Shortcut Context menu
Reset 3D-View Ctrl-R CameraReset
Export 3D-View scene to graphics file Ctrl-E CameraExport View...
Print 3D-View scene Ctrl-P CameraPrint View...
Undo last action Ctrl-Z  
Redo Ctrl-Y  
Join molecules Ctrl-J Join
Fuse molecules Ctrl-J Fuse
Select all Ctrl-A Select All
Delete all selected items. If no items are selected, delete item pointed to by mouse cursor. Delete Delete
Join/Insert/Replace molecule from Molecule Cupboard or Periodic Table Insert Insert “molecule or Insert “atom
Insert/Replace atom with single letter atomic symbol symbol C, H, B, N, O, F, P, S, K, V, Y, I, W, and U  
Change bond order ½, 0, 1, 2, and 3  

[Important] Important

When no atoms are selected, the actions of the shortcut keys depend on the positional context of the mouse cursor:

  • background:

    • Insert: Insert selected molecule/atom from Molecule Cupboard or Periodic Table.

    • C, H, B, N, O, F, P, S, K, V, Y, I, W, and U: Insert atom associated with single letter atomic symbol.

  • atom:

    • Insert: Join the atom with selected terminal atom of the molecule from Molecule Cupboard or replace atom with selected element from Periodic Table.

    • Delete: Delete atom.

    • C, H, B, N, O, F, P, S, K, V, Y, I, W, and U: Replace atom with atom associated with single letter atomic symbol.

  • bond:

    • Delete: Delete the bond.

    • ½, 0, 1, 2, and 3: Replace bond-order with new bond order.

Instead, if one or more atoms are selected, the short cut keys work on the selection:

  • Insert: Insert and Join for each atom selected.

  • Delete: Delete each atom in selection.

  • C, H, B, N, O, F, P, S, K, V, Y, I, W, and U: Replace each atom in selection with the atom associated with pressed single letter atomic symbol.