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Table of Contents
Dye anchoring to TiO$_2$
In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in Dye-Sensitized Solar Cells as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: http://dx.doi.org/10.1021/jp4117563
1. Task: Familiarize yourself
The coordinate of the two binding modes are provided you as mode1.xyz
and mode2.xyz
. Visualize the two geometries with VMD and familiarize yourself with the system.
2. Task: Bond induced density differences
Compute the density difference induced by the bonding for the first binding mode. For this you will have to run three separate energy calculations:
- combined system bound in the first mode (file
mode1.xyz
) - lone acetic acid molecule (just remove slab's coordinates from
mode1.xyz
) - lone TiO$_2$ slab (just remove the acid's coordinates from
mode1.xyz
)
In order to output the electronic densities as cube files, your input file has to contain the following snipped:
&DFT &PRINT &E_DENSITY_CUBE &END E_DENSITY_CUBE &END &END DFT
bsub -n 16
.
To process the cube files we are going to use the cubecruncher tool. It is part of CP2K, but not installed on brutus.
Therefore, a compiled binary of the tool is provided at /cluster/home03/matl/schuetto/cubecruncher.x
. To simplify the following steps you should create a symbolic link to it in your working directory:
you@brutusX ~$ ln -s /cluster/home03/matl/schuetto/cubecruncher.x .
Now subtract the densities of the lone systems from the bonded system:
you@brutusX ~$ cubecruncher.x -i mode1_combined.cube -subtract mode1_slab.cube -o tmp.cube you@brutusX ~$ cubecruncher.x -i tmp.cube -subtract mode1_acid.cube -o mode1_delta.cube
The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:
you@brutusX ~$ cubecruncher.x -center geo -i mode1_delta.cube -o mode1_delta-centered.cube
You can visualize the resulting file mode1_delta-centered.cube
with VMD. This has been covered in a previous exercise.
3. Task: Bonding energies
Compute the binding energy for both binding modes:
\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]
For this you will need the energy values of four systems:
- lone acetic acid molecule (run geometry optimization first)
- lone TiO$_2$ slab (you can use the already geometry optimized coordinates from
relaxed_slab.xyz
at the end of the exercise) - combined system bound in the first mode (can be reused from previous task)
- combined system bound in the second mode (file
mode2.xyz
)
Questions
- Sketch briefly the two binding modes.
- Report the system energy for the two binding modes, lone slab, and lone acid molecule.
- Which binding mode is more stable?
- Briefly report the bond induced density difference on the system.
Required Files
- mode1.inp
&GLOBAL ! change name for each different run performed PROJECT mode1 RUN_TYPE ENERGY &END GLOBAL &FORCE_EVAL METHOD Quickstep &DFT &PRINT &E_DENSITY_CUBE ! section to print the electronic density of the system (Task 2) &END E_DENSITY_CUBE &END BASIS_SET_FILE_NAME BASIS_SETS ! This keyword refers the input to an external basis file, which has to be in the same directory as this input file POTENTIAL_FILE_NAME POTENTIALS ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file &SCF ! Ensures convergence of SCF and simulations stability. This section should not be changed MAX_SCF 50 &OT PRECONDITIONER FULL_SINGLE_INVERSE &END OT &OUTER_SCF MAX_SCF 10 &END &END SCF &XC &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL ABC 10.2270 11.3460 20.000 &END CELL &COORD ! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this: @INCLUDE 'mode1_coord' ! The mode1_coord file must be present in the same directory as the input. ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning &END COORD &KIND H ! All basis sets and potentials are looked up in the external files specified above. BASIS_SET DZVP-MOLOPT-GTH ! search in the external basis file (specified above) the one named DZVP-MOLOPT-GTH for H. POTENTIAL GTH-PBE-q1 ! search in the external potential file (specified above) the one named GTH-PBE-q1 for H. &END KIND &KIND C BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q4 &END KIND &KIND O BASIS_SET DZVP-MOLOPT-GTH POTENTIAL GTH-PBE-q6 &END KIND &KIND Ti BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL GTH-PBE-q12 &END KIND &END SUBSYS &END FORCE_EVAL
- POTENTIALS
################################################################################ # # Potential data base file for CP2K (Quickstep) # ################################################################################ # ----------------------------------------------------- # # Literature: - S. Goedecker, M. Teter, and J. Hutter, # Phys. Rev. B 54, 1703 (1996) # - C. Hartwigsen, S. Goedecker, and J. Hutter, # Phys. Rev. B 58, 3641 (1998) # - M. Krack, # Theor. Chem. Acc. 114, 145 (2005) # # Potential for the PBE functional # ################################################################################ # H GTH-PBE-q1 1 0.20000000 2 -4.17890044 0.72446331 0 # C GTH-PBE-q4 2 2 0.33847124 2 -8.80367398 1.33921085 2 0.30257575 1 9.62248665 0.29150694 0 # O GTH-PBE-q6 2 4 0.24455430 2 -16.66721480 2.48731132 2 0.22095592 1 18.33745811 0.21133247 0 # Ti GTH-PBE-q12 4 6 2 0.38000000 2 8.71144218 -0.70028677 3 0.33777078 2 2.57526386 3.69297065 -4.76760461 0.24253135 2 -4.63054123 8.87087502 -10.49616087 0.24331694 1 -9.40665268
- BASIS_SETS
######################################################################### # # This is a library of molecularly optimised basis functions as described in the paper: # # Gaussian basis sets for accurate calculations on molecular systems # in gas and condensed phases # # Joost VandeVondele and Juerg Hutter # J. Chem. Phys. 127, 114105 (2007) # # URL: http://link.aip.org/link/?JCP/127/114105 # DOI: 10.1063/1.2770708 # ########################################### H DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q1 1 2 0 1 7 2 1 11.478000339908 0.024916243200 -0.012512421400 0.024510918200 3.700758562763 0.079825490000 -0.056449071100 0.058140794100 1.446884268432 0.128862675300 0.011242684700 0.444709498500 0.716814589696 0.379448894600 -0.418587548300 0.646207973100 0.247918564176 0.324552432600 0.590363216700 0.803385018200 0.066918004004 0.037148121400 0.438703133000 0.892971208700 0.021708243634 -0.001125195500 -0.059693171300 0.120101316500 C DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q4 1 2 0 2 7 2 2 1 6.132624767898 -0.105576563700 0.024850587600 0.035098108400 -0.056712999000 0.037469425800 2.625196064782 -0.174866621100 0.147440856000 0.114197930900 -0.076743951500 0.071047574800 1.045456957247 0.064464981400 -0.421418379200 0.215908137300 -0.528056757000 0.619330561200 0.478316330874 0.830447035300 0.823051336800 0.355929151000 0.394594045700 0.710730857000 0.178617414302 0.371911373800 0.184880712100 0.271541842000 0.721247475800 0.389148235000 0.075144725465 0.006174464000 -0.742086051600 0.056256557700 0.733902531700 0.346374124100 0.030286753006 0.008966477300 0.083382192000 0.004998059700 0.248172175500 -0.005142430900 O DZVP-MOLOPT-GTH DZVP-MOLOPT-GTH-q6 1 2 0 2 7 2 2 1 12.015954705512 -0.060190841200 0.065738617900 0.036543638800 -0.034210557400 0.014807054400 5.108150287385 -0.129597923300 0.110885902200 0.120927648700 -0.120619770900 0.068186159300 2.048398039874 0.118175889400 -0.053732406400 0.251093670300 -0.213719464600 0.290576499200 0.832381575582 0.462964485000 -0.572670666200 0.352639910300 -0.473674858400 1.063344189500 0.352316246455 0.450353782600 0.186760006700 0.294708645200 0.484848376400 0.307656114200 0.142977330880 0.092715833600 0.387201458600 0.173039869300 0.717465919700 0.318346834400 0.046760918300 -0.000255945800 0.003825849600 0.009726110600 0.032498979400 -0.005771736600 Ti DZVP-MOLOPT-SR-GTH DZVP-MOLOPT-SR-GTH-q12 1 2 0 3 6 3 2 2 1 7.884569925997 0.004750577412 -0.002690702837 0.075105591562 -0.108736525246 0.023185061556 0.052842407451 -0.038307431199 -0.002442658125 3.894698463070 0.499503858222 0.103956524568 0.048602853477 0.100912855636 -0.027189036213 0.195986532018 -0.076880250937 0.013119020987 1.513588828959 -0.664995883766 -0.256641947580 0.079732563787 0.527328996047 -0.230044390357 0.330343722079 -0.242486488988 -0.206817889885 0.596768079836 -0.726044574739 -0.451591547817 1.660896378972 0.468197803110 -0.126795185046 0.396808432313 -0.118369379707 -0.546596492823 0.222222125842 -0.029011079755 0.165167622946 -2.748651632733 0.077640626075 0.343517279356 0.347092399871 0.038099375809 -0.279145975103 0.077078461321 0.075171747143 0.993127316430 1.368227638651 -0.007523238420 0.946960702315 0.132320900948 1.046553050597 0.934394052863
- mode1.xyz
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- mode2.xyz
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