3.Preparing a molecule for calculation

When you want to start a new ORCA calculation on a new molecule you have to make a few choices:

- Where am I going to get the original coordinates for the molecule?

For most exercises in this course, the molecules will be simple but will still be too difficult to write the coordinates out manually (only for diatomics and triatomics is that straightforward). We will thus use the molecular builder feature of Chemcraft to build up a starting structure most of the time. Sometimes, you might also want to take an optimized structure from ORCA, visualize in Chemcraft and make some changes (e.g. to find a new conformer or substitute chemical groups).

If the molecule is large or so complicated that it is time-consuming to do it in Chemcraft, it is quite common to get starting coordinates from another source. Perhaps coordinates from a similar molecule that someone else calculated or perhaps from an experimental X-ray crystallographic structure.

- What type of job should I do and what level of theory should I use?

In the exercises you will usually be told what to use although sometimes you can choose. In the real world you need to make intelligent choices about what type of job you want to run and what level of theory (what method and what basis set). Making these choices comes from reading the literature and experience. Often your choice will be dependent on your system size and your computational facilities. In most cases the jobtype you want is a geometry optimization (or a single-point energy calculation on a previously optimized geometry) and the method might be a cheap but reasonably accurate HF or DFT method.

Building a molecule using Chemcraft

You can build your molecule atom by atom if you like but most of the time it is easiest to find a fragment from the Chemcraft library and modify it to your needs.

See the following Chemcraft tutorials on how to build molecules:

Constructing molecules

Working with fragments

See also this page: Chemcraft basics

Note that Chemcraft has some features that can be quite handy for building molecules:

e.g.

- you can symmetrize your starting structures for a particular pointgroup. Edit menu -> Set pointgroup.

- clean up bad bond lengths and angles. Edit menu-> Clean.

Once you are happy with your starting structure (the key thing is to make sure that you don't have atoms too close to each other that are not forming a chemical bond) we can export those coordinates. Also note that it does not matter if Chemcraft sometimes shows a single bond when you think there should be a double bond, or no bond when there should be a bond. Chemcraft just guesses the bond order based on distances and often makes mistakes. Just make sure that your bond distances and bond angles are sensible (see e.g. Standard Bond Lengths and Bond Angles), otherwise ORCA will struggle to solve the quantum mechanical equations. Use your chemical intuition!

The only information that we will take from Chemcraft are the Cartesian coordinates of the nuclear positions. This information we get by clicking the "Coord" tab in the Chemcraft window. Then you can copy these coordinates into an ORCA inputfile, see below.

Creating the ORCA inputfile for a geometry optimization and frequency calculation

The figure above shows the structure of an ORCA inputfile (click for a larger version). The inputfile always needs the following:

- A simpleinputline beginning with a ! symbol. This is where you put ORCA keywords. Here HF-3c (method), opt (geometry optimization job) and freq (vibrational frequency job)

- A coordinate block beginning with a * symbol and ending with *. You also specify the charge and the spin multiplicity here, followed by the coordinates (usually Cartesian coordinates in Angstrom). These coordinates can for example come from Chemcraft or perhaps from a previous ORCA job (optimimized coordinates).

There is an entire webpage dedicated to how to construct ORCA inputfiles: The ORCA Input Library

It is recommended to start reading the "General Input" page.