Computational Training Class

Skill #C1: Building a molecule

Level Up Skill #C1: Demonstrate proficiency in GaussView software to build molecules including their chemical characteristic:

Bond types: single, double, triple

Bond length: 1.53Å, 1.33 Å, and 1.18 Å.

Conformations: eclipse, staggered, chair, boat.

Molecular geometry: tetrahedral, trigonal planar, square planar, linear.

Bond rotation: angles, dihedral angles.

 

Skill #C2: Submiting your first job to the supercomputer

Level Up Skill #C2: Choose appropriate computational methods for specific systems (organic compounds, organometallic reagents, radicals, anions, etc.)

Level Up Skill #C2: Understand and apply principles of density functional theory (empiricaldispersion=gd3, cpcm, sdm, nosymm guess=(mix, always), dispersion, etc.)

Level Up Skill #C2: Demonstrate proficiency in computational software (GaussView, FileZilla, Terminal, Python) and commands to submit, execute, and analyze computational calculations.

Level Up Skill #C2: Monitor your computational calculations.

 

Skill #3: Building a transition state

Level Up Skill #C3: Read and understand prior literature in the field to create an initial 3D structure that resembles the geometry of your transition state.

Level Up Skill #C3: Perform a partial optimization of the reaction coordinate to find a maximum energy structure.

Level Up Skill #C3: Use your optimized structure with key computational commands (e.g. opt=(ts, noeigen, calcfc) to obtain the real transition state.

Level Up Skill #C3: Verify your transition state by performing vibrational frequency analysis and confirming that there is exactly one imaginary frequency (negative eigenvalue).

Level Up Skill #C3: Visualize the vibration corresponding to the imaginary frequency to ensure it represents the correct bond breaking and bond forming step or refine the initial geometry if necessary and resubmit calculation.

 

Skill #4: Validating the results

Level Up Skill #C4: Ensure calculation was completed properly.

Level Up Skill #C4: Verify that the results are accurate and compared to experimental data or literature values.

Level Up Skill #C4: Estimate the energies of reactants, transition states, and products.

Level Up Skill #C4: Represent your results in a reaction coordinate diagram using the energies obtained from your computational calculation.