IMSE Computational Chemistry Lab

Introduction

While water is apparently a very simple molecule it is in actually a very complex liquid. In this lab you will compute the energy for a H-bond between two water molecules. You will explore creating large clusters and examine some of the information that can be obtained from a calculation.

important

  • During this lab you will receive feedback from demonstrators and myself when we answer your questions.
  • You will be assessed through a mini-report which will be graded out of 30, the first part is worth 10 marks, the second part 20 marks
  • If you are ill and/or have a personal problem contact me if at all possible BEFORE the lab is due, extensions will require a medical certificate
  • The full hands-on lab should take approximately 5 hrs, and your write-up should not take more than 3-4hrs. If you find it taking longer contact me!

Hand-in

  • A zipped directory containing
    • Lab report (pdf or word document)
    • Log files for optimisations and scans
    • the directory MUST be named: IMSE_Lab_Your_Name
    • note there are no spaces only underscores!

Lab Outline

  • Part1: A Water Molecule (2.5 hrs)
  • Part1: Write-up (0.5 hr), you should write this part of your report before the last lab session, and ask the demonstrator to give you rapid feedback on the content. Have you included (10 marks):
    • molecule name
    • calculation method
    • basis set
    • final energy E(RB3LYP) in atomic units (au)
    • the point group of your molecule
    • the "Item" section from your output
    • geometric data
    • the vibrational frequencies and intensities
    • the vibrational spectrum
    • answers to the IR questions
    • the NBO charges
    • the NBO charge distribution colour map
    • answers to the NBO questions
    • completed water MO diagram with the real MOs added
    • submit your log file, file names must contain no spaces!
  • Part2: Clusters and Reactions (2 hrs) In this section follow a similar procedure as in Part 1. You are meant to be working more independently now and so the instructions are not as detailed. My advice is to complete as much of this section as you can in the second lab session write it up and then use the last lab session to ask any questions and for help solving any proplems that arise.
    • compute the water monomer at the HF/3-21G level)
    • download the water dimer input file I have created for you (re-name the extension!) and run the file (optimise/frequency/NBO/MOs).
    • it is important to always start with a reasonable geometry, notice that I have arranged one of the H-atoms of one water molecule to point towards the lone-pair of the O-atom of the other water molecule
    • notice we are working at the HF/3-21G level because your laptops are not very powerful, normally we would do this at a higher level. I've also removing the int=grid=ultrafine which turns off the accurate integration grid, this is only sensible when using a more accurate basis set.
    • now you are going to determine the dissociation curve for the H-bond formed by the dimer. When scanning a coordinate we always work "away from" the optimised geometry, so you will need to run two separate jobs.
      • start from your optimised dimer
      • click on the two O-atoms
      • use the Tools, Redundant Coordinates option to add the "Bond" O-O coordinate
      • select "Scan Coordinate"
      • allow 11 steps in units of +0.2 Å (job 1)
      • under "Job Type" remove optF and select Scan
      • sometimes gaussview tries to put "genchk" in, if this happens ask the demonstrator for help, remove all "chk" commands
      • save to a new input file
      • now we need to scan in the other direction, scan the O-O distance from its current value (≈ 2.80 Å) for 3 steps in units of -0.2 Å (job 2)
      • the longer one may take a little while, you can complete it out of the lab, but you should start the smaller one in the lab to make sure you have all the input correct.
      • when your job is finished open "Results" "Scan" and a graph will appear. Click on the graph and choose save data to save the energies to a txt file.
  • Part2: Write-up (4 hrs)
    • present key information describing the method, convergence and final energy of the monomer and dimer files. Provide the optimisation and scan files.(3 marks)
    • Compare and contrast the O-H bond distances. What effect has forming the H-bond had on the O-H bond distances? (1 mark)
    • List the vibrations in a table, provide a snap-shot of the vibrational spectra. (2 marks)
    • What is the general nature of the lowest energy vibrations ≤500cm-1? What is the energy in kJ/mol of vibrations of ≈ 500cm-1 (1 mark)
    • Identify the two symmetric stretching modes for each water molecule, note these modes are mostly but not completely decoupled. Compare this to symmetric stretch mode of the isolated water molecule. What has been the effect of the H-bond? (2 marks)
    • Present the NBO charges in a table and using a colour map. Comment on any changes due to the formation of a H-bond.(2 marks)
    • Visualise the occupied MOs. Take a snap shot of the HOMO, which monomer MO is this? Take a snap shot of the HOMO-1, which monomer MOs interact to form this MO? Take a snap shot of the MO that best represents the H-bond, which MO is this? Which monomer MOs contribute to the cluster MO?(3 marks)
    • The energy of a normal O-H single bond ≈464kJ/mol. Compute the energy of the H-bond, E(dimer)-2*E(monomer) in kJ/mol. What is the relative strength of the H-bond compared to the covalent O-H bond? (2 marks)
    • Plot the H-bond dissociation curve, relative to the optmised dimer energy in kJ/mol (ie presenting the gaussview curves is NOT sufficient) What is the dissociation energy? (4 marks)
  • Extra for experts! (not graded)
    • What is the total energy of the monomer for each different method? Why are the energies so different?
    • The two "dissociation" energies computed above will differ slightly, why is this?
    • Save an animated gif of your favourite vibration, I will pick one to post on twitter, and you could perhaps use one of these in your "u-tupe" clip.If you are very "advanced" you could make an animated gif of one of your MOs using VMD (completely optional). Look here for some I have produced previously
    • Below is a sample from a MD trajectory of 16 water molecules, one water molecule has been highlighted in blue. Here is an input file for one cluster from the trajectory, optimise the cluster (do NOT do a frequency analysis as it will take too long).
    • 16_water_droplet
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