X-Ray DDSQC

CONTACTS:


Address:
Nauky ave. 60 Kharkiv,
61178 Ukraine

Tel.: +38-057-341-02-58
Fax: +38-057-340-93-39
E-mail: sveta@xray.isc.kharkov.com

Head of Department: Dr. Svitlana V. Shishkina


Crystal packing

Our approach was described in the publications:

  1. Shishkin OV, Dyakonenko VV, Maleev AV (2012) Supramolecular architecture of crystals of fused hydrocarbons based on topology of intermolecular interactions. Cryst Eng Comm 14:1795-1804
  2. Shishkin OV, Zubatyuk RI, Shishkina SV, Dyakonenko VV, Medviediev VV (2014) Role of supramolecular sunthons in the formation of the supramolecular architecture of molecular crystals revisited from an energetic viewpoint. Phys Chem Chem Phys 16:6773-6786
  3. Shishkin OV, Zubatyuk RI, Maleev AV, Boese R (2014) Investigation of topology of intermolecular interactions in the benzene-acetylene co-crystal by different theoretical methods. Structural Chemistry 25:1547-1552

 

Calculations of pairwise interaction energies and visualization of the obtained data using energy-vector diagrams.

 

You need the programs:

 

Download scripts

Steps of the calculations:

    1. Save your structure in Mercury’s .cif format. 
    2. Copy your structure and all scripts in the one directory.
    3. Activate your scripts with command: chmod +x *.py
    4. Activate the library with command: module load chem/openbabel
    5. Use the script “MolShellSplit” with command: ./ MolShellSplit.py cifname

      Comments: 
      The script will read CIF file, normalize positions of hydrogen atoms (C-H: 1.089, N-H: 1.015, O-H: 0.993) and calculate the first coordination sphere (defined as all molecules which have contacts with the base molecule within VdW radii sum + 1 Ǻ) for each molecule found in the unit cell asymmetry part. The obtained part of the crystal structure will be divided on the dimers where one molecule is the basic and other belongs to its first coordination sphere.Output:cifname.symm —  each line contains symmetry operation and IDs of base and symmetry related molecule for all dimers separated out.cifname-m##.xyz – geometry of the basic molecule.cifname-s##.xyz – geometry of the basic molecule and its first coordination sphere.cifname-d###.xyz — geometries of dimers

    6. Use the script “mkinps-orca-dim” with command: ./mkinps-orca-dim.py –b cifname

      Comments:
      This script will create three input files for each dimer to calculate DFT+BSSE interaction energy.

    7. Run calculations.
    8. Use the script “geten_orca” with command: ./geten_orca.py –b cifname

      Comments:
      This script will generate list of interaction energies in cifname.ene file.

    9. Use the script “urchins” with command: ./urchins.py cifname

      Comments:
      This script will read cifname.cif, cifname.symm and cifname.ene files and output PDB file with energy-vector diagrams (EVD) suitable for viewing with Mercury.If the basic molecule forms the strongest interaction with only one neighboring molecules such a dimer should be consider the complex building unit. You should create the text file cifname.map in the format:2

      (SymOp(‘symmetry operation’),)

      ((0,N),) 

       

      Where 

      Instead of symmetry operation should be inserted the corresponding symmetry operation for the strongest bound dimer;

      N – the number of the second molecule in this dimer.

 

 
All steps should be repeated. The dimer will be used as the building unit instead of the molecule.