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(The files for the programs mentions below can be found here avicci.zip )
To build the gas hydrate lattice, you need to obtain the coordinates of the oxygen atoms in a unit cell and use the program Avicci to insert hydrogen atoms in such a way as to minimize the overall dipole of the unit cell while abiding by the Bernal–Fowler ice rules. The program then fills the cages of hydrate slab as the the input specifies.
Getting Oxygen Atom Coordinates
Go to http://www.crystallography.net/cod/ Click on Search under Accessing COD Data on the left side Search by DOI: 10.1021/ja049247c
Paper associated with above DOI: “Gas Hydrate Single-Crystal Structure Analyses by Michael T. Kirchner, Roland Boese, W. Edward Billups, and Lewis R. Norman
For structure I, use COD ID: 4112809 For structure II, use COD ID: 4112807 Click on “CIF” under next to the COD ID to download the .cif file (see 4112809.cif and 4112807.cif)
You can use the software Avagadro to open the .cif file You can download Avagadro from here: https://avogadro.en.softonic.com/
Open the .cif file with Avagadro You will see a unit cell for the structure Click on Build→Cartesian Editor Sort by Element Delete all the non-oxygen atoms and their coordinates (delete all lines that do not start with the letter O) click apply and exit out of the Cartesian Editor You should see a less crowded unit cell with only the Oxygen atoms Now we will save the coordinates as a .pdb file click on “File→Save as”, select PDB under “Save as type” and save the file (see 4112809_justOxygen.cif and 4112807_justOxygen.cif)
Using Avicci
You will need to have Java installed to use this program. Click on Avicci.jar to launch the program Specify the inputs: - Input path: - Output path: - Structure: - Fraction Methane in Small Cages: - Fraction Methane in Large Cages: - Fraction Cyclohexane in Large Cages: - Fraction Benzene in Large Cages: - Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ): - Slab Size A: - Slab Size B: - Slab Size C: - Number of spaces to 1st coordinate:
(see 4112809_justOxygen_output.cif and 4112807_justOxygen_output.cif)