Sterimol.py

A command line Python program for the calculation of multi-dimensional Sterimol parameters: L, B1 and B5 for half-sandwich complexes and organic molecules. If used on half-sandwich complexes, it also generates Tolman cone angles and metal to ring-centroid (unweighted) distances. The results have been validated against the original Fortran77 code compiled with gfortran on OSX v10.11.3 27/03/2016. Code developed in the Paton group at Colorado State University.

This code is no longer actively supported. We recommend using wSterimol which provides expanded functionality for flexible substituents and a graphical interface through PyMol.

Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters Brethomé, A. V.; Fletcher, S. P.; Paton, R. S. ACS Catalysis 2019, 9, 2313-2323 DOI: 10.1021/acscatal.8b04043

Installation

Sterimol runs as a Python module. There are two ways to make this work below. In both cases, you won't need to copy the scripts to your working directory.

1. The easy way: pip install sterimol
2. Download the package from https://github.com/bobbypaton/Sterimol. Set the environment variable PYTHONPATH to point to the location of the 'Sterimol' folder. For example in OSX, this is done by adding the following (example) line to .bash_profile: export PYTHONPATH=$PYTHONPATH:/Users/username/Documents/Sterimol
3. Now run the script with Gaussian input or output files as python -m sterimol file(s)

N.B. If you do want to run the scripts directly (i.e. not as a module) you may need to delete a single period on line 24 of sterimol.py (i.e. from sterimoltools import * )

Correct Usage

For half-sandwich complexes

sterimol.py file(s)

• This program will read Gaussian input or output files or half-sandwich complexes.

For organic molecules

python -m sterimol (-a1 atom A) (-a2 atom B) (-radii radius-model) file(s)

• -a1 and -a2 specify atoms A and B atoms for the calculation - these fields are mandatory as they specify the axis along which Sterimol parameters are calculated.
• The -radii option specifies the radial model used; it may be set to -radii bondi or -radii cpk for either van der Waals radii from Bondi or CPK. If left blank, the default setting uses the original CPK radii.

Example 1:

Calculating Tolman cone angles, metal to ring-centroid distances, and Sterimol parameters for a half-sandwich complex from a Gaussian output file.

python -m sterimol examples/RhCpMe5Cl2PMe3.log

Sandwich Analysis
STERIMOL: using original CPK Van der Waals parameters

Structure                 Tolman_CA   MC_dist         L        B1        B5
RhCpMe5Cl2PMe3.log           173.97     1.833     4.016     3.902     4.304

The output shows the tolman cone angle (in degrees) and metal to centroid distance, L, B1 and B5 (all in Angstrom). Cone angles and Sterimol parameters are calculated using the original CPK atomic radii.

Example 2:

Calculating Sterimol parameters for an organic functional group (e.g. tert-butyl) from a Gaussian-formatted input file.

python -m sterimol -a1 2 -a2 1 examples/tBu.com

   STERIMOL: using original CPK Van der Waals parameters
   Atoms 1 and 2 define the L-axis and direction [ 1.1  0.   0. ]

   Atom       Xco/A     Yco/A     Zco/A    VdW/pm
   ##############################################
   H          0.000     0.000     0.000     100.0
   C         -1.100     0.000     0.000     150.0
   C         -1.610     1.030     1.030     150.0
   H         -2.710     1.030     1.030     100.0
   H         -1.250     0.760     2.030     100.0
   H         -1.250     2.030     0.760     100.0
   C         -1.610     0.380    -1.400     150.0
   H         -2.710     0.380    -1.400     100.0
   H         -1.250     1.380    -1.670     100.0
   H         -1.250    -0.360    -2.140     100.0
   C         -1.610    -1.400     0.380     150.0
   H         -2.710    -1.400     0.380     100.0
   H         -1.250    -2.140    -0.360     100.0
   H         -1.250    -1.670     1.380     100.0

   Structure                      L        B1        B5
   examples/tBu.gjf            4.11      2.76      3.17

The output in this case returns the element types, Cartesian coordinates and atomic radii according to the CPK radial definitions. The Sterimol parameters for the structure are underneath; L, B1 and B5 are all given in Angstroms.

Example 3:

Calculating parameters for a dimeric half-sandwich complex from a Gaussian output file.

python -m sterimol examples/Rh_AsymmetricDimer.log

Sandwich Analysis
STERIMOL: using original CPK Van der Waals parameters

   Structure                 Tolman_CA   MC_dist         L        B1        B5
   Rh_AsymmetricDimer.log      191.283     1.763     6.184     3.381     5.607
   Rh_AsymmetricDimer.log      190.174     1.766     6.239     3.386     5.608

In this example two sets of parameters are produced - this occurs when the dimeric complex does not have a symmetry plane and thus measurements from each of the two metal centres yields different results. In the case of symmetric dimers, only a single set of parameters is generated (as they would be the same when measured from either metal centre).

Tips and Troubleshooting

• Errors will occur if this program is used on systems containing atoms for which there are no CPK defined radii.
• When running on organic molecules, the directionality of -a1 and -a2 is important - make sure the -a1 to -a2 vector is pointing towards the functional group being measured.
• It is possible to run on any number of files at once, for example using wildcards to specify all of the Gaussian files in a directory (*.out)
• The python file doesn’t need to be in the same folder as the Gaussian files. Just set the location of sterimol.py in the $PATH variable.

Papers using Sterimol.py

1. Correlating Reactivity and Selectivity to Cyclopentadienyl Ligand Properties in Rh(III)-Catalyzed C-H Activation Reactions: an Experimental and Computational Study Piou, T.; Romanov-Michailidis, F.; Romanova-Michaelides, T.; Jackson, K. E.; Semakul, N.; Taggart, T. D.; Newell, B S.; Rithner, C. D.; Paton, R. S.; Rovis, T. J. Am. Chem. Soc. 2017 139, 1296–1310 DOI: 10.1021/jacs.6b11670
2. Improved correlation between animal and human potency of non-steroidal anti-inflammatory drugs using quantitative structure–activity relationships (QSARs). Dearden, J.; Hewitt, M. M.; Bresnen, G. N.; Gregg, C. SAR and QSAR in Environmental Research. 2017, 28 1-9 DOI: 10.1080/1062936X.2017.1351391
3. Enantiodivergent Pd-catalyzed C–C bond formation enabled through ligand parameterization Zhao, S.; Gensch, T.; Murray, B.; Niemeyer, Z. L.; Sigman, M. S.; Biscoe, M. R. Science 2018, eaat2299 DOI: 10.1126/science.aat2299
4. Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters Brethomé, A. V.; Fletcher, S. P.; Paton, R. S. ACS Catalysis 2019, 9, 2313-2323 DOI: 10.1021/acscatal.8b04043

References for the underlying theory

1. Verloop, A. Drug Design Vol. III, Academic P.; Ariens, E. J., Ed.; 1976.