ORCA---Computational-Chemistry/C2/Generate--Molecular-Orbitals-of-Water/English

Title of the script: Generate Molecular Orbitals of Water

Author: Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan

Keywords: orca, molecular orbitals of water, gedit text editor, auto optimization, molecular orbitals, homo, lumo, ucsf chimera, computational chemistry, video tutorial.

Visual Cue	Narration
Slide Number 1 Title slide	Welcome to the Spoken tutorial on Generate Molecular Orbitals of Water.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Open the XYZ file. Add commands to create the input file. Run the input file in ORCA environment to get the ORCA output. View the molecular orbital data in the output file.
Slide Number 3 System Requirements	To record this tutorial, I am using; Ubuntu Linux OS version 22.04 ORCA version 6.0.1 Gedit Text Editor version 41.0 Windows users may use notepad or any other text editor.
Slide Number 4 Pre-requisites	To follow this tutorial, learners should be familiar with ORCA software.
Slide Number 5 Code Files The following code file is required to practice this tutorial 1.water.xyz 2. commands.txt These files are provided in the Code Files link of this tutorial page	The following code files are required to practice this tutorial. These files are provided in the Code Files link of this tutorial page.
Show the downloaded and extracted file to Home directory	Download and extract water folder from the Code files link to the Home directory.
Right-click on the file From the context menu select Open With Text Editor.	Let us open the water.xyz file using a text editor.
Select and Delete 3 from the first row. Press Ctrl+ S to save the file.	Delete 3 from the first row and save the file.
Right-click on the commands.txt file and Open With Text Editor	Now we will open commands.txt file using a text editor.
Copy the commands(Ctrl+ C) Paste in the water.xyz(Ctrl+V)	Copy and paste the commands from the file in the first row of the water.xyz file.
Type * at the end of the coordinates.	At the end of the coordinates row type an asterisk (*) We will now go through the code.
! B3LYP def2-SVP TightSCF Opt Highlight ! Highlight B3LYP ! B3LYP def2-SVP Highlight def2-SVP Highlight TightSCF Opt	The command line starts with an exclamation mark. Here B3LYP is the dft functional. def2-SVP is the basis set. TightSCF Opt is the command for geometry optimization.
%output Print[P_MOs] 1 end	This block of code is used to print the molecular orbitals of water.
Point to * xyz 0 1 Point to the asterisk at the start and end.	Here xyz specifies the coordinates of the molecule. 0 is the charge and 1 is the spin multiplicity. The coordinates start and end with an asterisk (*).
Point to the numbers and xyz coordinates. Highlight the xyz coordinates. Point to the entire code.	The numbers in rows are the xyz coordinates of the atoms in Angstrom units. This is the ORCA input file for generating molecular orbitals of water.
Click on the 3 lines icon next Save button. In the drop down menu select Save As option. Delete .xyz and .inp as the extension. In the Save dialog box type the file name as water.inp. Choose location as water folder. Click on the Save button.	Let us now save the file as an input file. Click on the 3 lines icon next to the Save button. In the drop down menu select Save As option. In the Save dialog box type the file name as water.inp. Choose the water folder to save the file. Click the Save button.
Open the Home directory Open the water folder by double clicking on it.	Let us go to the Home directory and open the water folder. It contains the water.inp file.
To open the terminal in water folder, Right-click and from the context menu select Open in Terminal.	Let us now open the terminal in water folder. Right-click and from the context menu select Open in Terminal.
type at the prompt file water.inp point to the output water.inp: Unicode text, UTF-8 (with BOM) text	To check the file format of water.inp, at the prompt type file water.inp Press Enter. Terminal shows the below output. If the terminal shows water.inp: ASCII text as output, please skip the following steps.
Copy paste the command at the prompt sed -i '1s/^\xEF\xBB\xBF//' water.inp Press Ctrl + Shift +V to paste in the terminal Press Enter.	We need to convert the Unicode text to ASCII text as ORCA reads only the ASCII text file. Let’s open the commands.txt file again. Copy and paste the command from commands.txt file to the terminal. Press Enter
Type file water.inp Point to the output. water.inp: ASCII text	To check the file format of water.inp at the prompt type file water.inp This time terminal shows the below output. Now let us run the input file in ORCA.
Type orca water.inp > water.out Press Enter	Type orca space water.inp space > space water.out Here a greater than(>) sign is used to channel the output to the same folder. Press Enter.
Point to files in the water folder, in the HOME directory	After the calculation is complete the output file water.out is generated. The output file is available in the water folder in the HOME directory.
Type less water.out The .out file opens on the terminal and then press “/” and write in capital “ORBITAL ENERGIES” and press “Enter”.	At the prompt type less space water.out. The .out file opens on the terminal. Now let us search for the keyword ORBITAL ENERGIES. At the colon prompt on the terminal, Press back slash (/) and then type in capital letters ORBITAL ENERGIES. Press Enter.
The Orbital energies Table will appear. point to the table.	The orbital energies table is displayed on the terminal.
highlight the Second column which tells about the population and the first column which tells about the Orbital Number. point to the second column. point to orbital 4 and its population.	In this table, look at the second column. It tells us about the population of the orbitals. Note that for the water molecule the highest occupied orbital number 4 has least energy. It has the last highest population of 2.0000. Number 4 orbital is HOMO.
point to orbital 5 and its population.	Now observe orbital number 5. It has the first least population and least energy among the unoccupied orbitals. Number 5 orbital is LUMO.
point to HOMO and LUMO	We will visualize HOMO and LUMO orbitals using Chimera in the upcoming tutorial.
Only Narration	Please refer to the additional reading material to learn more about the molecular orbitals of water.
With this we come to the end of this tutorial.
Slide Number 6 Summary In this tutorial, we have learnt to, Open the XYZ file. Add commands to create the input file. Run the input file in ORCA environment to get the ORCA Output. View molecular orbital data in the output file.	Let us summarize.
Slide Number 7 Assignment Create ORCA input files for carbon monoxide and ammonia. Run the input files in ORCA environment using the terminal to generate the output files. View HOMO and LUMO orbital data in the output files.	As an assignment please do the following.
	Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak