van-der-Waals Radii

Calculate atomic van der Waals radii.

Introduction

Atomic van-der-Waals (vdW) radii are calculated from atomic polarizabilities as recently introduced by Fedorov et al. (see their arXiv). In their work, they obtained a quantum-mechanical relation between atomic polarizabilities and vdW radii.

$$R_{vdw}(\alpha) = \theta_a \alpha^{1/7},$$

where thetaa = 2.54 has been obtained by fitting to reference data for noble gases. Since the present model should be easily applicable to all elements up to Radon, an additional element-wise parameter thetab is introduced and fitted to reproduce theoretically determined vdW radii (see works of Rahm and Mantina).

$$R_{vdw}(\alpha) = \theta_a \theta_b\alpha^{1/7}$$

We apply static atomic polarizabilities for the calculation of vdW radii. The graphic below depicts calculated vdW radii (vdwtype=rahm) for all atoms up to Radon (CN = 0, q = 0).

Define the Subcommand

vdw

> kallisto vdw options arguments

options

--chrg <int>
(optional, default: 0)
description:
 absolute charge (qtotal) of the input structure (Lagrangian constraint)

 --vdwtype <string>
 (optional, default: rahm)
 description:
  reference atomic van der Waals radii
   rahm: 10.1002/chem.201700610
   truhlar: 10.1021/jp8111556

--angstrom (flag)
(optional, default: false)
description:
 calculate van-der-Waals radii in Ångström
 
--out <string> 
(optional)
description: 
 write output to file

arguments

input file is given as (positional) argument

Application

To calculate atomic van-der-Waals radii for a neutral charged Alanine-Glycine molecule, we call the subcommand vdw

> kallisto vdw alanine-glycine.xyz
3.3065606171598922
3.38164759676716
3.4391750162303536
3.311855692814488
3.3790680338248973
3.2967634203187104
3.4727151121721547
3.2976318319108247
3.3094215076503897
2.420916892530216
2.4135730093586507
3.356462625678808
2.5457085831894677
2.4274072320381417
2.5251614207290154
2.527093029228339
2.409141369050233
2.540154025796337
2.536646925483585
2.5536833297719026
# Save output to file 'vdw'
> kallisto vdw --out vdw alanine-glycine.xyz
3.3065606171598922
3.38164759676716
3.4391750162303536
3.311855692814488
3.3790680338248973
3.2967634203187104
3.4727151121721547
3.2976318319108247
3.3094215076503897
2.420916892530216
2.4135730093586507
3.356462625678808
2.5457085831894677
2.4274072320381417
2.5251614207290154
2.527093029228339
2.409141369050233
2.540154025796337
2.536646925483585
2.5536833297719026

Now we obtain a list of atomic van-der-Waals radii. However, we can furthermore calculate van-der-Waals radii for the cationic (or anionic) Alanine-Glycine molecule by incorporating the chrg option as described in the subcommand definition.