Properties of H2O

  • copy the water_freq.com to water_prop.com, copy the checkpoint files as well.
  • now vi the water_prop.com file and change the %chk filename
  • we still need to read the electronic structure and geometry from the checkpoint file
  • however we are not doing a frequency analysis, so remove that keyword and replace it with sp which stands for "single point" it means we are going to optimise the electronic stucture for this geometry (from checkpoint file), this will be very quick since we are reading in the electronic structure (guess=read).
  • we also need new keywords primarily the pop with selected options
    full to get the MOs
    nbo to do an NBO analysis
    CHelpG for the ESP derived charges
    ESPdipole to ensure the ESP charges reproduce the computed dipole moment
    the full keyword is pop=(full,nbo,chelpg,espdipole) 
    
%chk=water_prop.chk
%mem=3600MB
%nproc=2

# b3lyp/6-311g(d,p) sp guess=read geom=checkpoint  
  pop=(full,nbo,chelpg,espdipole)

single molecule water properties

0 1
  • run the job
    qsub -N water_prop -v in=water_prop rng2_4
  • check the job has terminated normally using "tail -f water_prop" 
    
[phunt@login-0]/work/phunt/liquids $ tail water_prop.log
 0.9941756,-0.6063404,0.,0.\PG=C02V [C2(O1),SGV(H2)]\\@


     "IF I COULD JUST GET IT ON PAPER"
 LIFE AND INK, THEY RUN OUT AT THE SAME TIME,
 OR SO SAID MY OLD FRIEND THE SQUID.
     -- JIMMY BUFFETT, 1981
 Job cpu time:  0 days  0 hours  0 minutes  9.7 seconds.
 File lengths (MBytes):  RWF=      5 Int=      0 D2E=      0 Chk=      1 Scr=      1
 Normal termination of Gaussian 09 at Sun Jan 23 16:33:09 2011.
  • pop=full causes all the molecular orbital (MOs) to be printed, these are best viewed using gaussiview and the checkpoint file, follow the instructions from the 3rd year computational chemistry lab for visualising MOs.
  • You will need to open the *.chk file! Note that the images will be slightly different because they are using guassview on their laptops and not on cx1, and they are carrying out the calculations on BH3 not H2O.
  • I find the orbitals easier to visualise as a mesh, from the File tab choose properties, in the window that opens choose surfaces and switch from solid to mesh, click OK and your surfaces should appear as a mesh showing the atoms inside.
  • Look at all the occupied MOs of water ...
  • I give a whole course on MO theory at the second year level, it can be found here, however of most interest to you is lecture 3 where we derive the MO diagram for water.
  • now use vi to open the water_prop.log file and explore the goodies inside. ([control]F allows you to move down a file a half screen at a time)
  • pop=nbo does an NBO analysis, this is quite extensive and complex, follow the instructions from the 3rd year comp chemistry lab for NBOs, you want the NBO charges for your water atoms (ignore the bonding analysis unless you are particularly interested!) 
    
 Summary of Natural Population Analysis:

                                       Natural Population
                Natural  -----------------------------------------------
    Atom  No    Charge         Core      Valence    Rydberg      Total
 -----------------------------------------------------------------------
      O    1   -0.87670      1.99983     6.86657    0.01030     8.87670
      H    2    0.43835      0.00000     0.55498    0.00667     0.56165
      H    3    0.43835      0.00000     0.55498    0.00667     0.56165
 =======================================================================
   * Total *    0.00000      1.99983     7.97654    0.02363    10.00000
  • The NBO analysis takes a delocalised MO picture and turns it back into the "organic chemists" picture of directional bonding. If you want to find out more about the NBO analysis (this is OPTIONAL) go to the NBO web-site The information can be quite technical, but the beginners tutorial provides a good starting point.
  • find the ESP charges 
    
Fitting point charges to electrostatic potential
 The dipole moment will be constrained to the correct value
 Charges from ESP fit, RMS=   0.00258 RRMS=   0.11974:
 Charge=   0.00000 Dipole=     0.0000     0.0000    -2.0699
 Tot=     2.0699
              1
     1  O   -0.726305
     2  H    0.363152
     3  H    0.363152
  • we can also visuallise the ESP, this is a bit complex. We need to create a density iso-surface to map the ESP onto
    1. from the Results tab choose Surfaces and Contours
    2. from Cube Actions button choose New Cube and then Total Density and OK
    3. from Cube Actions button choose New Cube and then ESP and OK
    4. two new cube files should appear (in red box)

    5. highlight the SCF density cube and then from Surface Actions button choose New Surface and OK
    6. leave the SCF density cube highlighted and then from Surface Actions button choose New Mapped Surface and then the ESP (only option highlighted) and then click on OK
    7. highlight the electron density surface (under surfaces available) and then choose under Surface Actions button Hide Surface and OK, this should leave only the ESP surface showing.
    8. I find that these are better viewed as a solid surface that is cliped, to do this choose View then Display Format then Surface set the format button to Solid and the Z-clip slider in about 1/3. (Display format changes the particular picture, changing the Preferences resets all surfaces.) 

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