Usage

Timeo functions can be run from the Olex2 console as spy.Timeo.* or from the panels under Tools > Timeo.

Selecting atoms

All analyses use the same selection rules:

• One atom selected: the neighbouring atoms are taken into account to form a centered shape, such as a coordination complex.
• Several atoms selected: they are interpreted as a non-centered shape, such as a borane cluster.

Grown Structures

Selecting symmetry-generated atoms from a grown structure will result in either an error or a wrong calculation. Selecting an atom whose neighbours are outside the unit cell is no problem.

Workflow:

1. Open a structure in Olex2.
2. Select the atoms you want to include.
3. Run a function from the console or the panel. See Cosmochlore, autoSHAPE and octahedral distortion.

Function	Analysis
spy.Timeo.autoCSHM()	Continuous shape measures (Cosmochlore).
spy.Timeo.autoCSOM()	Continuous symmetry operation measures (Cosmochlore).
spy.Timeo.autoODIS()	Octahedral distortion (Cosmochlore).
spy.Timeo.autoSHAPE()	Continuous shape measures through SHAPE 2.1.
spy.Timeo.autoOCTADIST()	Octahedral distortion (Timeo’s own implementation).

π-bonded ligands

Timeo can detect ηⁿ π-bonded ligands. When merge_ligands is enabled, the coordinates of all the donor atoms of each ligand are averaged to its centroid before measuring, following Cirera et al.¹.

Note

Centroid search does not work with ligands outside the asymmetric unit.

Use exclude_h to leave hydrogen and deuterium atoms out of the coordination polyhedron. Both options are described in settings.

Disorder

Disorder is handled automatically. If more than two parts are found in the selected structure, the calculation is run on each part separately.

By default every measurement uses part 0 plus part N. If the selected atom is in part 0 and has connected atoms in parts 1 and 2, the measures run on parts 0 + 1 and 0 + 2.

You can set the parts yourself with part codes (part_codes in settings). Codes are separated by spaces, and each code is measured as one structure. Every digit of a code is a part:

Part codes	Measurements
(empty)	Part 0 with each other part (default).
0	Atoms in part 0 only.
01	Atoms in parts 0 and 1.
01 02	Two measurements: parts 0 + 1 and parts 0 + 2.
12 34	Two measurements: parts 1 + 2 together, and parts 3 + 4 together.

Output

Results are printed to the Olex2 console. Files are written next to the structure:

Analysis	Location
Cosmochlore (autoCSHM, autoCSOM, autoODIS)	<FilePath>/cosmochlore/
autoSHAPE	<FilePath>\autoSHAPE\<FileName>_<part>_<atoms>\<run>
autoOCTADIST	<FilePath>/OH_distortion

1.

Cirera, J., Ruiz, E. & Alvarez, S. Continuous Shape Measures as a Stereochemical Tool in Organometallic Chemistry. Organometallics 24, 1556–1562 (2005).