Computational Examples

In response to students querying the usefulness and reason for learning about MOs, last year there was a greater emphasis on "real" MOs and thus a connection to research and higher levels of investigation.

As part of this course you are expected to be able to carry out a calclation and to be familar with the output files and MO visualisation. You are expected to be able to interpret real MOs in terms of a LCAOs. Thus, many of the self-study and exam preparation problems this year include a computational aspect, and then interpretation of the real MOs to allow you practice at this.

You are also strongly encouraged to explore computational chemistry and carry out your own calculations to test your answers to building MO diagrams, this also means you can see the real 3d MOs of more complex systems. You are also encouraged to have a go! Try carrying out calculations on molecules that interest you.

If you are at home and have no access to gaussview (which is installed on all of the chemistry department computers). There is a solution! You can visualise the results on your own computer (you will still need to generate the output files on one of the college computers)

• A free molecular viewer program which you can download and install on your computer or laptop is called avagadro.
• I have generated a selection of files for you (related to your self-study problems and exam preparation questions). These are the outputs from an optimisation and MO calculation. You can also use formated checkpoint files that you have created.
• start up avagadro and goto File:Open (select all file types) and select the *.fchk files you have downloaded.
• the default background colour is black and does not show the orbitals well, so goto View:Set background color ... choose a pale colour, I use a pale blue.
• now to display the MOs goto Extensions:Molecular Orbitals ... then highlight the orbital you wish to view
• if the MO does not have a blue bar you will need to select Render button
• Avagadro does not read the orbital energies, but it can render the MOs

  

Formatted checkpoint files:

1. diatomic
   • pop_n2_opt_freq.fchk
   • pop_f2_opt_freq.fchk
   • pop_no_plus_opt_freq.fchk
   • pop_cn_minus_opt_freq.fchk
   • pop_co_opt_freq.fchk
   pop_o2_triplet_opt_freq.fchk
   • pop_lih_opt_freq.fchk
2. triatomic
   • pop_h2o_opt_freq.fchk
   • pop_beh2_opt_freq.fchk
   • pop_hf2_opt_freq.fchk
   • pop_i3_anion_opt_freq.fchk
3. complex
   • pop_bh3_opt_freq.fchk
   • pop_nh3_opt_freq.fchk
   • pop_allene_anion_opt_freq.fchk
   • pop_b2h6_opt_freq.fchk
   • pop_ch2N_opt_freq.fchk
   • pop_ch2O_opt_freq.fchk
   • pop_cs2nh2_opt_freq.fchk
   • pop_ph5_opt_freq.fchk
   • pop_pf5_opt_freq.fchk
   • pop_ph3cl2_opt_freq.fchk
4. transition metal complexes
   • pop_mocoph34_opt_freq.fchk
   • pop_wcl6_opt_freq.fchk
   • pop_pdcl4_opt_freq.fchk
   • pop_pdnh34_opt_freq.fchk
   • pop_cocl2nh3_cis_opt_freq_pop.fchk
   • pop_cocl2nh3_trans_opt_freq_pop.fchk

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