Video tutorials

Timestamps

• 00:00 (opens in a new tab) – Introduction and Overview
• 00:23 (opens in a new tab) – Setting up New Project and Molecular Geometry
• 01:55 (opens in a new tab) – Configuring Calculation Parameters (Basis Set, Method)
• 02:43 (opens in a new tab) – Running Geometry Optimization
• 03:23 (opens in a new tab) – Analyzing Optimization Results
• 04:17 (opens in a new tab) – Vibrational Frequency Analysis Setup
• 04:49 (opens in a new tab) – Frequency Results and Structure Validation
• 05:54 (opens in a new tab) – Conclusion

Useful resources

• Input Files used in the tutorial: Project_and_Input_Files_TM_Tut_01_Ibuprofen_Geo_Opt_Vib_Freq.zip (opens in a new tab)
• Ibuprofen Coordinate file after xTB pre-optimization (XYZ format): Ibuprofen_init.xyz (opens in a new tab)

Timestamps

• 00:00 (opens in a new tab) – Introduction and Overview
• 00:23 (opens in a new tab) – Creating a New Project and Importing the Silicon CIF File
• 01:03 (opens in a new tab) – Exploring the Structure, Periodicity, and Supercells
• 02:02 (opens in a new tab) – Assigning Basis Sets and Atomic Attributes
• 02:30 (opens in a new tab) – Setting Molecular Attributes and Generating Initial MOs
• 03:00 (opens in a new tab) – Selecting Functional, Grid, and K-Point Mesh
• 03:46 (opens in a new tab) – Performing Geometry Optimization with Cell Relaxation
• 04:18 (opens in a new tab) – Checking Convergence and Extracting Band Gap
• 04:53 (opens in a new tab) – Setting Up and Running Band Structure Calculations
• 05:47 (opens in a new tab) – Visualizing and Interpreting the Band Structure
• 06:27 (opens in a new tab) – Calculating Cohesive Energy from Bulk and Atomic Energies
• 08:13 (opens in a new tab) – Results, Discussion, and Conclusion

Useful resources

• Silicon Primitive Cell CIF File: Si_primitive_Turbomole_Tutorial.cif (opens in a new tab)
• Project and Input Files used in this tutorial: TM_Tut_02_Silicon_PBC_Band_Cohesive.zip (opens in a new tab)

What you will learn

• Setting up 2D PBC DFT calculations in TmoleX
• Importing structures and defining periodic cells
• Geometry optimization of:
  • hBN monolayer (32-atom, 4×4 supercell)
  • Isolated water molecule
  • Water adsorbed on hBN
• Monitoring jobs via terminal (ls, cat, tail -f)
• Adsorption energy formula:
  Eads = E(hBN + H2O) − [E(hBN) + E(H2O)]
• Why BSSE matters for localized basis sets
• Comparison with literature (PBE functional)

Adsorption energy result

• From TURBOMOLE (BSSE uncorrected):
  −0.00439 Ha ≈ −0.119 eV ≈ −119 meV
• After Counterpoise BSSE correction:
  ≈ −45 meV (excellent agreement with plane-wave DFT values)

WolframAlpha

• Raw adsorption energy:
  https://www.wolframalpha.com/input?i=(…) (opens in a new tab)
• Conversion to eV:
  https://www.wolframalpha.com/input?i=(…)*27.211324570273 (opens in a new tab)

Download files

• All coord files (water, hBN, water+hBN):
  coord_files_used_in_tutorial_for_water_hBN_and_waterhBN.zip (opens in a new tab)
• Complete TmoleX project files:
  TM_tut_3_Project_Files_Generated_during_Tutorial_for_Adsorption_Energy_of_water_on_hBN.zip (opens in a new tab)

Optimized structures (XYZ / CIF)

• Water: optimized_water.xyz (opens in a new tab)
• hBN (2D periodic): optimized_hBN_2D_periodic-1.cif (opens in a new tab)
• Water + hBN (adsorbed): optimized_water_hBN_2D_periodic.cif (opens in a new tab)

Reference paper

• “Interaction of water with hBN” – JCP 142, 181101 (2015)
  pubs.aip.org/aip/jcp/article/142/18/181101/193687 (opens in a new tab)

Recommended video

• How to apply BSSE / Counterpoise Correction in TURBOMOLE:
  How to Calculate BSSE-Corrected Adsorption Energy using TURBOMOLE? [TUTORIAL] (Pt. 2) (opens in a new tab)

Useful shell commands

• ls
  Lists directory contents (useful for checking job.last, control, MO files, etc.).
• cat filename
  Prints file contents (used here to inspect the first optimization step inside job.last).
• tail -f filename
  Follows a growing file (perfect for watching SCF/optimization progress live).

Energies extracted from TURBOMOLE