IFM Chemistry Computational Chemistry 2010, 7.

5 hp LAB4
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Computer laboratory exercise 4 (LAB4):

Modeling inorganic systems using Materials Studio


Introduction:
The objective of the fourth computer laboratory exercise is to model inorganic and
inorganic-organic systems using molecular mechanics (MM) calculations and
molecular dynamics (MD) simulations with periodic boundary conditions. Three
different systems systems, a bulk crystal structure, a surface model and water
solutions will be studies using the molecular modeling program Materials Studio.
A lab report is required for LAB4. Hand in the report by submitting it on Its learning
in Computer labs > Computer lab4 > Lab report LAB4, select Submit answer and
upload your file.

Materials Studio
In this computer laboratory exercise, the molecular modeling program Materials
Studio from Accelrys Inc. (http://accelrys.com) will be used. Materials Studio is a
program package for molecular modeling that includes functions for building and
editing models of molecules, crystalline materials, surfaces, and polymers, and
functions for calculation of properties for molecules and periodic structures with
quantum chemical methods such as DFT, QM/MM and semi-empirical methods, as
well as classical methods including MM, MD, and MC methods in combination with
force fields. I addition, the program includes functions for visualization and analysis.
The program is used both in industry and academia for chemical, materials and
pharmaceuticals development research. The version that will be used in this lab is
Materials Studio 4.0 for Windows. The latest version available is Materials Studio 5.0.
In all exercises a force field, called COMPASS, will be used. COMPASS is an ab
initio force field that has been parameterized and validated using condensed-phase
properties, in addition to various ab initio and empirical data for molecules in
isolation. The force field can be used for a broad range of molecules in isolation and
in condensed phases, and under a wide range of conditions of temperature and
pressure. The molecular mechanics module in Materials Studio is called Forcite, the
module from which both MM minimizations and MD simulations are started.

IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB4
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Practical guide

Start the program
To start the program first search for the file gwstart.bat (select the Start menu, and in
Search programs and files, type gwstart.bat. In Search again in: click Computer),
create a shortcut for this file on the desktop (Select gwstart from the list and r-drag it
to the desktop) and then start by double clicking the shortcut.
Then go to Start > All Programs > Accelrys MS Modeling 4.0 to start the program.

Create a new project
The program collects all files in a folder called Projects. The program generates many
files for every calculation. Therefore it is recommended to start a new project when
starting on a new exercise.
Go to File > New Project, enter a name for the project and press OK.

Import a molecular structure
To import an existing structure choose File > Import. Select directory and file to
import and press Import. The program contains a structural library that can be found
in the file MS Modeling 4.0/Structures/.

Manipulating the structure in the molecular window
When the 3D Viewer Selection Mode or 3D Viewer Rotation Mode has been selected,
the molecular model can be
Rotated by: R-drag
Translated by: M-drag
Zoomed by: M-scroll the mouse wheel
Selection of atoms in the model is done by L-clicking an atom or L-dragging an area
that encloses the atoms to be selected.

Changing the periodic structure to a non-periodic superstructure and back again
To be able to add atoms and molecules to a crystal structure, one has to change it to a
non-periodic structure first:
Select Build > Symmetry > Non-Periodic Superstructure
When the new structure is finished create a periodic structure by:
Select Build > Crystals >Build Crystal, enter group 1 P1 and press Build

Adding atoms to the model
To add atoms to the molecular model use the Add atoms icon button. When pressing
the icon button a dialog box appears. Enter what element to add from the list or select
an element in the periodic table that appears when clicking [] Then click add.
Remove the dialog box by pressing [X].
Move the atom in the molecular window to a good position by first selecting the atom
(L-click) and then moving it with Shift+M-drag. Rotate or move the entire system
with R-drag and M-drag.
Add hydrogens to free valences by pressing the Adjust Hydrogen icon button.

Recalculate bonds and display hydrogen bonds
After changing the structure, a recalculation of the bonds can be useful. Do this by
clicking the Calculate bonds icon.
IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB4
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To calculate and display hydrogen bonds in a structure, click the Calculate Hydrogen
Bonds icon.

Measure bond distances and angles
To measure distances and angles, press the Measure/Change icon button, and then
click on atoms or bonds in the molecular model.

Save the model
When a new model has been created save it with File > Save as.

Change display style
R-click in the molecular window and select Display Style. In the Atom tab in the
dialog box choose a display style. Remove the dialog box by pressing [X]. It is also
possible only to change the display style for selected atoms.
For periodic structures, the view of the periodic cell changed in the Lattice tab, by
changing the range of A, B and C.

Changing the charges of atoms
To change the charges of atoms in the model (for example before performing a
calculation with the energy option Charges: Use current) select Modify > Charges.
In the Atomic Charges tab, first use the Method: QEq, and press Calculate to calculate
the charges of all atoms (make sure that no atoms are selected).
Then select an atom and in the Atomic Charges tab, Set all charges to: value, and
press Assign.
It can be useful to show the charges of selected atoms to see that the charges change.
This is done by first selecting the atom, R-clicking in the molecular window, and
selecting Label. Choose Object type: Atom and Properties: Charge and press Apply.

Running an MM geometry optimization
Press the Forcite icon and select Calculation. In the Setup dialog tab, select Task:
Geometry Optimization and Quality: Medium. In the Energy dialog tab, select
Forcefield: COMPASS and Charges: Forcefield assigned. When geometry
optimization parameters have been selected, press Run to start the calculation.

Running an MD simulation
Press the Forcite icon and select Calculation.
In the Setup dialog tab, select Task: Dynamics and Quality: Medium. Press the More
button and enter parameters for the simulation, e.g. Time step, Number of steps, and
Frame output energy (how many steps to save for analysis). Remove the Forcite
Dynamics dialog box by clicking [X].
In the Energy tab, select Forcefield: COMPASS. Enter either Charges: Forcefield
assigned or Use current (depending on the problem at hand). In exercise 3, select
Charges: Use current, and press the More button. In the Forcite Preparation Options
dialog, untick Calculate Automatically, and click Calculate. When an error message is
shown press Yes, untick List all Forcefield types, and select an appropriate FF and
click Assign. Remove the dialog box by pressing [X].
Start the calculation by pressing Run in the Forcite Calculation dialog.

Animate the saved frames from an MD simulation
IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB4
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To animate the frames from an MD simulation, open the trajectory file and animate by
using the Play/Stop/Step buttons (View > Toolbars > Animation).

Making radial distribution function plots
After an MD simulation has finished, the trajectory file (filename.xtd) can be used to
extract information from, e.g. to plot radial distribution functions, g(r).
First select sets, e.g. atom types to analyze.
To make a set with one atom in the model, first select the atom in the molecule
window. Then go to Edit > Edit Sets. Click New and give a name for the selection,
and OK.
To make a set with all atoms of a specific element, go to Edit > Atom Selection. Select
by Property: Element, Is, and select an element. Tick Create a new selection from all
visible atoms and then click Select. Then go to Edit > Edit Sets. Click New and give a
name for the selection, and OK.
Press the Forcite icon and select Analysis. Select Radial distribution function from the
list and then select Sets: to analyze. Start the analysis by pressing Analyze.
R-click on graph to remove unwanted curves from the plot.


IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB4
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Exercises

Create a new directory, Lab4, to save all your files for the fourth computer laboratory
exercise in. Create a new project for every exercise.


Exercise 1: Crystal Stability of zeolites

Zeolites are alumino-silicates that have a microporous crystalline structure with a
framework that contains cavities and tunnels that can accommodate e.g. ions or water
molecules.

In this exercise, a silicate (ACO) will be studied using MM geometry optimization.
Examine the geometry and energy for the silicate alone and compare with the cases
when a water molecule is incorporated in a small or large cavity. To be able to
compare the energies of the three systems, also perform a calculation with only one
water molecule. The crystal structure ACO.xsd is found in the structures library. Use
the COMPASS force field and medium quality for geometry optimization.



Exercise 2: Surface model Coordination of carboxylic acid to a TiO
2
surface

Metal oxide electrodes can be used in solar cells due to their ability to convert
absorbed light into electricity. However, the photon energy required for
photoexcitation in these systems is situated in the UV region of the solar spectrum,
and most of the radiant power is in the visible region. By adsorbing a layer of dye
molecules to the surface, photoexcitation can occur at wavelengths of visible light,
and the excited electron can then be transferred to the conducting metal oxide. The
dye molecules are often attached to the surface via carboxylic functional groups. Solar
cells based on this approach are called dye-sensitized solar cells or Grtzel cells.

In this exercise, investigate how formic acid (HCOOH) binds to the (101) surface of
the TiO
2
crystal structure anatase. Use a surface model, a so-called slab model, to
study the system. A structure is provided in file hcooh+tio2.msi. What modes of
adsorption are possible?
Examine three adsorption modes and determine the order of stability. What
differences in adsorbate-surface bonds can be seen? Optimize the geometries using
the COMPASS force field and medium quality. For dissociative adsorption modes
place the proton on the opposite side of the slab and use current charges.


IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB4
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Exercise 3: Liquid Structure of water and coordination of metal ions

Metal ions solvated in aqueous occur in many contexts. Solvated ions appear in living
organisms, where their presence or absence can fundamentally alter the functions of
life. Both magnesium and silver ions are present in sea water and drinking water.
Magnesium is together with other alkali metals responsible for water hardness. Silver
is considered in the WHO guidelines for quality of drinking water with a maximum
recommended concentration.

Perform an MD simulation on liquid water (aq64.msi). Run another MD simulation
for Mg
2+
in aqueous solution (mgaq.msi). Replace the magnesium ion with Ag
+
and
run yet another MD simulation. Perform the simulations using the COMPASS force
field at medium quality. Run in 0.2 fs time steps for at least 1000 steps, and frame
output for every step. For the aqueous solutions, use current charges by assigning
mg+2 and ag-o silver +1 oxide to the ions, and modify the charges by setting them to
2,0 and 1,0 e, respectively. Analyze the structure by examining the last structure of
the simulation, as well as constructing the radial distribution function, g(r), from the
trajectory file. For liquid water, plot g(O-O), and for the aqueous solutions, plot g(ion-
O). What is the difference in analyzing the structure in these two ways? Identify the
coordination geometry and coordination distance.