Inorganic Structure Prediction

2       Cation Locator menu card

This chapter discusses Cation Locator, a menu card in the Cerius2 Structure Solve deck of cards.

Introduction

Sections in this chapter

The algorithm 26

Methodology 27

Running a calculation 27

General methodology 29

Settings for the energy calculation 29

Setting energy calculation options for a simulation 30

Setting up and running the simulation 32

For information about		See
Making a superlattice		"Crystal Builder" chapter in the Cerius2 Builders manual
Forcefields		Forcefield-Based Simulations manual
Open Force Field (OFF)		"Open Force Field" chapter in the Cerius2 Simulation Tools manual
Minimum image convention		Cerius2 Forcefield-Based Simulations manual
Setting charges		"Preparing the System" chapter in the Cerius2 Forcefield Engines manual

Select STRUCTURE SOLVE from the list of modules and click CATION LOCATOR to bring the CATION LOCATOR menu card to the fore.

The algorithm

The Cation Locator algorithm

1.   A forcefield is first selected and potential parameters and charges assigned to the host and cation species. The cvff_aug_ ionic_400_1.01 forcefield is the recommended forcefield to use when adding cations to zeolites.

2.   A grid is constructed commensurate with the framework structure. Typically, a grid spacing of ~0.5Å is used, the exact value being adjusted to conform to the underlying symmetry of the structure, so a symmetry operator will exactly map one grid point onto another. This is the only stage at which the symmetry of the framework is imposed, for reasons of expediency.

3.   The cation-framework non-bond interaction is computed at each grid point using symmetry to reduce the number of unique sites and speed up the calculation. Ewald summation is used to compute the electrostatic interactions, and a short range cutoff used for the van der Waals interactions.

4.   A second grid, of identical dimensions, is constructed. A single cation is placed at the origin, and the interaction of a second cation at each grid point is computed, again using Ewald summation.

5.   A cation is placed in the host lattice at the lowest energy position determined from step 3, above.

6.   The host-guest interaction reference grid is then updated, as the host lattice now contains an additional cation, with which any additional cation will react. The grid can be rapidly re-computed by combining the host-cation grid with the cation-cation grid, centered about the location of the recently added cation. After the addition of cations, the initial symmetry of the grid is disrupted, and has reduced to triclinic.

7.   The lowest energy position is again determined, and populated. Steps 6 and 7 are repeated until the desired number of cations have been added.

8.   If multiple cations have been added, an additional Monte Carlo exchange phase may be incorporated. Here, pairs of cations are selected at random and their positions swapped. If the resulting structure is of lower energy, this conformation will be saved.

9.   The cation locations may then be optimized using molecular mechanics, with the framework initially held rigid.

Methodology

Cation Locator is used to identify possible locations for extra-framework cations within a charged framework structure, to produce an electrically neutral structure. Multiple cation types may be added in a single run, up to a maximum of 5. In such cases, the full complement of each cation will be loaded in turn, in the order in which they were specified.

Running a calculation

1.   Prepare the framework model

Cerius2-Models/zeolites 

2.   Choose a forcefield to be used during the simulation. A number of forcefields are provided in the

Cerius2-Resources/FORCE-FIELD 

directory. The recommended forcefield for cation addition in aluminosilicates is the cvff_aug_ionic_400_0.1 forcefield.

For more information on forcefields, see the Forcefield-Based Simulations book.

3.   Assign atom types and charges for each cation type to be added.

4.   If multiple cation types are to be added, and a Monte Carlo exchange is required, specify the number of Monte Carlo steps.

5.   Run the calculation.

The cation locator first creates an energy table, then grids for the host framework and cation interactions. The specified cations will then be added sequentially until the target number is reached for each specified cation type. If a Monte Carlo exchange has been requested, this procedure will be performed once the addition of all the cations has been completed. This stage can be interrupted at any time.

6.   Upon completion of the calculation, the resulting structure can then be optimized using standard energy minimization techniques. Note that if the cvff_aug_ionic_400 forcefield has been selected, all the bonds in the structure must first be deleted, since this forcefield contains only non-bond terms.

Cation Locator relies on the Open Force Field (OFF) for loading the forcefield and calculating and assigning atom types (and possibly charges). However, unlike the OFF modules such as Minimizer and Dynamics Simulation, and in common with Sorption, Cation Locator does not use the energy terms selection or any of the calculation preferences from OFF, except when performing the Monte Carlo exchange.

You may wish to familiarize yourself with OFF before running the calculations. For more information, see the Cerius2 Simulation Tools manual.

van der Waals energy

van der Waals energy is calculated by summing all pair interactions within a specified sphere, the radius of the sphere being determined by the interaction cutoff distance.

Minimum image
convention

The minimum-image convention is used to approximate van der Waals energy in the periodic framework. In the minimum image convention, an atom is considered to interact only with its closest neighbor atoms in a periodic box around it.

For more about the minimum image convention, see the Forcefield-Based Simulations book and Allen and Tildesley (1987).

When the minimum-image convention is applied to the evaluation of inter-sorbate energy, the sorbate molecules are treated as whole unit, and not split across minimum-image borders. That is, if the center of a molecule lies within the border, the energy interactions of the whole sorbate molecule are considered, not just those of atoms within the border. This differs from the treatment of framework/sorbate interactions, because sorbates are not considered to repeat periodically in the way that the framework does.

Note

Coulomb energy

The inclusion of Coulomb interactions in the calculation is obligatory, and is performed using the Ewald summation method.

Ewald summation method

Sorbate/framework electrostatics are evaluated using the Ewald summation method. This method accelerates the long-range Coulomb calculation by splitting the slowly converging real-space sum into a quickly converging real-space sum and a reciprocal-space sum.

For more information on the Ewald sum, see Forcefield-Based Simulations book.

Setting energy calculation options for a simulation

1.   Open the Atom Typing control panel by selecting Atom Typing from the CATION LOCATOR menu card.

2.   If the default forcefield and atom typing rules (including charge assignment) are adequate for the simulation, check the Perform Automatic Typing checkbox, and skip to step 5 below.

The default forcefield is usually the Universal 1.02 forcefield. To see which forcefield is set as the default, open the Load Preferences control panel in Open Force Field (Go to OFF SETUP and select Energy Expression Automate Setup on the OPEN FORCE FIELD menu card to open the Automate Energy Setup control panel. Then select the Preferences... button to open the Load Preferences control panel).

3.   To use a forcefield other than the default, but have atom types for that forcefield automatically calculated:

a.   Check the Perform Automatic Typing checkbox in the Atom Typing control panel.

b.   Load your choice of forcefield.

4.   To override or alter calculated atom types:

a.   Uncheck the Perform Automatic Typing checkbox.

b.   Load your choice of forcefield as described in step 2.

c.   Assign and alter forcefield atom types either using the Calculate Atom Type button or by selecting atoms and using the Assign Atom Type button. A list of forcefield atom types is provided for convenience.

5.   Check that reasonable charges have been assigned to the framework by labelling the structure using the CHARGES menu card under the OFF SETUP deck of cards. Note that the framework should have an overall negative charge, which will be compensated by the addition of the requisite number of cations. Some forcefields assign charges as part of the atom typing procedure, others do not.

6.   If the charge on the framework is incorrect then set or calculate more appropriate values. The exact magnitude of the charge is dependent on the potential model adopted. To manually set charges use the Edit Atoms... command under the Build menu at the top of the Visualizer window. Alternatively, to calculate charges you may wish to use the CHARGES menu card under OFF SETUP. For more information on this command refer to the Cerius2 Forcefield Engines manual, "Preparing the System".

7.   If you wish you may alter the interaction cutoff from its default value. Because the interaction cutoff must be consistent with the minimum-image convention, its size is limited by the cell dimensions.

8.   You may also wish to alter the accuracy to which the electrostatic energy is calculated by adjusting the Ewald Accuracy parameter. You should be aware that increasing the accuracy of the calculation will also increase the duration of the calculation.

9.   The Cation Locator uses a method of overlapping grids to determine the location of energy minima. The resolution of this grid can be controlled using the Grid Resolution popup on the Parameters control panel. Increasing the fineness of the grid will increase the duration of the calculation.

10.   To calculate the total charge on the framework:

11.   Open the Run Cation Locator control panel by clicking Run on the CATION LOCATOR menu card.

12.   Use the Report Total Charge on Host button.

13.   Enter the cation Element and Ionic Charge.

14.   Specify how many cations you wish to add in Number of Ions to Add.

15.   Give the Atom Type to be used for the cation. A list of atom types is presented for convenience, and can be filtered by element type.

16.   Repeat steps 13 and 15 for each cation of interest.

17.   Ensure that the framework model is the current model, then press the RUN button.