Sterimol

Calculate Sterimol descriptors L, Bmin, and Bmax.

Introduction

The multidimensional Sterimol parameters were developed by Verloop and the original Sterimol program by Verloop and Hoogenstraaten to capture the dimensions and thus the steric interactions of a substituent along different directions. Using Corey-Pauling-Koltun molecular models (CPK-model), major axes Bmin, Bmax, and L can be defined around the binding point of a given substituent. In short, Bmin represents the shortest distance perpendicular to the primary attachment axis, while Bmax represents the longest distance. These two sub-parameters can be considered the minimum and maximum width of a substituent and are influenced by the extent of branching. The last subparameter L is the total distance that follows the primary bond axis and thus refers to the length.

An example of how the Sterimol descriptors of an ethane molecule along the C2-C5 bond are constructed is shown below (depiction is taken from here). For the calculation of Sterimol descriptors kallisto uses van-der-Waals radii that are obtained from atomic static polarizabilities as described in the section van-der-Waals Radii.

The applied Sterimol algorithm has been initially implemented in the Morfeus software package and was integrated by permission of its main developer.

Define the Subcommand

stm

> kallisto stm options arguments

options

# Note that the atom count starts at 0
--origin <int>
(required)
description:
 number of the origin atom

# Note that the atom count starts at 0
--partner <int>
(required)
description:
 number of the partner atom
 
--out <string> 
(optional)
description: 
 write output to file

arguments

input file is given as (positional) argument

Application

To calculate Sterimol parameter for an ethane molecule along the C2-C5 bond, we use the subcommand stm

> cat ethane.xyz
8
ethane
H    0.00 0.00 0.00
C    0.00 0.00 -1.10
H    -1.00 0.27 -1.47
H    0.27 -1.00 -1.47
C    1.03 1.03 -1.61
H    1.03 1.03 -2.71
H    2.03 0.76 -1.25
H    0.76 2.03 -1.25
# Note that the counting of atoms starts at 0
> kallisto stm --origin 1 --partner 4 ethane.xyz
Calculated for atom 1 (origin) and atom 4 (partner)
L, Bmin, Bmax / au:  6.29  4.27  4.54
L, Bmin, Bmax / A:  3.33  2.26  2.40
# Save output to file 'stm'
> kallisto stm --out stm --origin 1 --partner 4 ethane.xyz
> cat stm
Calculated for atom 1 (origin) and atom 4 (partner)
L, Bmin, Bmax / au:  6.29  4.27  4.54
L, Bmin, Bmax / A:  3.33  2.26  2.40