Teaching the computational chemistry for students with Chemcraft

The latest version of Chemcraft can perform some semi-empirical computations (more exactly, it has an integration with a freeware program xtb). These computations are not as powerful as those performed by professional software like Gaussian or Orca, but they are very simple and can help students understand the basics of computational chemistry.

Additionally, we believe that Chemcraft can offer some new approaches in teaching organic chemistry: now the students don't have to memorize many empirical facts and pieces information. Instead, they can use Chemcraft to quickly compute anything they need (it will be often easier to compute data than to search for it online). When the students are taught concepts like sp2 hybridization, they will be able to quickly perform some computations to visualize these concepts on the screen.

Below, we present some tutorials for performing simple computations in Chemcraft, which illustrate the points mentioned above:

1. Let's consider that you want to know the characteristic frequency of the -NH2 group in an IR spectrum. Do the following:

1) Run Chemcraft;

2) Choose "Edit/Add fragment/-R/-C6H5", then click the blank screen at the main window. You will see the fragment C6H5X added to your current molecule:

3) Return to the fragments window above and choose "-R/-NH2"; then left-click the dummy atom at the main window. The NH2 group will be added instead of this dummy atom, resulting in the aniline molecule. You can then close the fragments window at the top;

4) Choose "Compute/Optimize geometry/Perform computation using Chemcraft optimizer (slow)", then wait for 1 minute and press Stop (this step is necessary to avoid finding saddle points instead of the minimum in the next step);

5) Choose "Compute/Geometry optimization + frequencies job". The vibrational spectrum of this molecule will be computed:

6) Select N, H, H atoms by left-clicking, then press the "Tools" button in the bottom left corner and choose "Find frequencies in which the selected atoms are mostly involved". You will see that these atoms of the NH2 group are mostly involved in the frequencies 35 and 36;

7) Expand the "Frequencies" node at the left, then click "35 Frequency ..." node. You will see the animation of this vibrational mode. Another way to visualize it is to click "Show displacement vectors" at the left:

8) You can also view the entire vibrational spectrum of this molecule by clicking the "Frequencies" node and then "Show spectrum" below. Note, however, that this xtb computation assumes the gas phase, and because of this, the IR intensities of these two vibrational modes are significantly underestimated:

2. Let's consider that you want to know the heats of formation or heats of combustion of some simple compounds: methane, ethane, propane, acetylene, benzene. Do the following:

1) Launch Chemcraft, then select "Edit/Add fragment/Molecules/Simple compounds/CH4", and then click on the main screen. A methane molecule will appear on the screen;

2) Click "Compute/Geometry optimization + frequencies job";

3) Delete all the atoms at the screen by first selecting "Edit/Select all", then "Edit/Delete selected";

4) Select "Edit/Add fragment/Molecules/Simple compounds/C2H6", add this fragment to the screen, and compute again via "Compute/Geometry optimization + frequencies job";

5) Delete the atoms again and perform the same routine with "Edit/Add fragment/Molecules/Simple compounds/C3H8", then "Edit/Add fragment/Molecules/Simple compounds/C2H2", and then "Edit/Add fragment/Molecules/Rings/Benzene";

6) Then do the same for the O2 molecule, choosing "Edit/Add atom/O" and clicking twice on the same location in the main window. Perform the computation for O2. Then perform the same steps for two more molecules: "Edit/Add fragment/Molecules/Simple compounds/CO2" and "Edit/Add fragment/Molecules/Simple compounds/H2O". Then you will have 16 nodes in the hierarchical list at the left:

7) Now you have calculated the energies of 8 substances in the gas phase: CH4, C2H6, C3H8, C2H2, C6H6, O2, CO2, H2O. Each of these energies can be viewed and copied by clicking on Frequencies on the left, expanding its subitems, then clicking on "Single point geometry" and then switching to "Abstract":

8) Then, you will need to open the reaction energy calculation window through "Tools/Simple utilities/Calculate the energy of a reaction" (for this purpose, it may be more convenient to open another Chemcraft window, i.e., click the Chemcraft icon again):

In the energy calculation window, you need to click the plus signs and then "Paste", calculating the energies for the following reactions:

CH4+2O2->CO2+2H2O

2C2H6+7O2->4CO2+6H2O

2C3H8+10O2->6CO2+8H2O

2C2H2+5O2->4CO2+2H2O

2C6H6+15O2->12CO2+6H2O

After computing these energies, you will get approximately the following values:

1209.87705

2149.06027

3079.56651

1874.07124

4941.35676

If you paste these values into Excel or Origin together with the experimental data from Wikipedia (https://en.wikipedia.org/wiki/Heat_of_combustion), you will get the following correlation:

The heats of formation are slightly more difficult to compute with quantum chemistry than the energies of combustion, because for the former, we need to compute the total energies of elements in their standard states, which can be more difficult to compute than the energies of substances in gas phase like e.g. CO2. Anyway, it is easy to recalculate the heats of combustion into heats of formation using the empirical data, and if users ask us, we will add a tool to Chemcraft for this conversion.

3. Let's consider that you want to study the internal rotation in a molecule like ethane. Do the following:

1)  Launch Chemcraft, then select "Edit/Add fragment/Molecules/Simple compounds/C2H6", then click on the main screen. An ethane molecule will appear on the screen, and then you can close the fragments window above;

2) Select the H, C, C, H atoms by left-clicking, that determine the dihedral H-C-C-H which describe the internal rotation of methyl groups (two H atoms must belong to different methyl groups):

3) Choose "Compute/Relaxed PES scan by selected parameter/Perform scan in Chemcraft", then press "Ok";

4) When the computation is finished, click "View scan graph/Energy vs scan step" in the bottom left. You will see the following graph:

You can find more information on performing the semi-empirical xtb computations with Chemcraft at this webpage.

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