Celeste Wiki

== 10/10/2011 Computational Labs - Day 1 ==

Introductory Talk Computational Chemistry Labs 2011-12 File:Trial molecule 1.cml

Crucial link where it's all at: http://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page
Importance of computational chemistry

Find minima to calculate what you can’t see .: beneficial to do first

Can use to predict spectra (e.g. IR spectra from molybdenum last year)

If there is water in a sample, computational chemistry can be used to sift through to make usable data

There are 3 modules to this course: In short these can be summarized as:

organic = molecular mechanics (http://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic)
inorganic - qm
transition states

Administration:

Important to check: Late breaking news
Demonstrator: 12-1 and 2-4 in tutorial room (staff: 2-3)

For module 2: hunt (http://www.huntresearchgroup.org.uk/teaching.html)and 3: bearpark

Deadlines on website

Notes on Using Programmes

http://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:mechanics
in ChemBio 3D the shortcode mm means molecular mechanics#
we are expected to have movable molecules like Monosaccharide chemistry: glycosidation in our wiki pages
Note it is important to use SCAN if molecules too big (e.g. in Mod 2 some calc overheat computer therefore use SCAN which can compute in 4-6 hours = overnight vs Mod 1 where most calculations take second to minutes)
Key thought: If it doesn’t work after 32-4 times ASK for HELP

Schrodinger equation

Parts of the Hamiltonian: e-e exchange, coulomb part, kinetic energy --> summarize as H = Vee + Vnn + Vne + Ek
For the Coulombic it's important to note that there are further things involved such as permitivity, charges, distance
Nuclei are treated "classically" therefore no QM or movement
For wavefunction use hydrogenic atomic orbitals (see atkins for these)

for these equations it's important to know that there are three parts: Coefficient, exponent and polynomial

To describe orbitals we usually use gaussian functions; the more functions, the better/more accurate = because easy to work with
Usually one HAO = 3 functions

Notes on Different Program Examples

Force field – proteins
Dft lda hf – can use qm
Dft – density
Correlation – important once start to break bonds
QM fully – have nuclei with wavefunction as well

In this course we don’t use last 2 mentioned here (they're more advanced)

Will be using chem3d and gaussian

Different systems available because for each type of system there are different types of approximations which can be used
If we don't want to use Gaussian, Orcha is an optional and free alternative

Important to think about

Ave bond – 100-300 kj mol-1
Auccuracy and error reporting should be to correct number of decimal places
Hartrees and atomic units ? kJ mol-1

Degrees of Freedom

Example: Ammonia – NH3

   # degrees of freedom
   4 atoms each with x,y,x = 12 different numbers to put 4 atoms somewhere
   3 coord redundant (can turn and move without changing)
   = 6

Increase #atoms = increase #degrees of freedom
Relationship force gradient : equivalent (mass term too)

Notes on Programming

Hf: fairly accurate energy surfaces but not necessarily a good energy difference
Sto-3g: slater type obitals
Opt freq – code
Use derivatives to get to the bottom of a hill
1: singlet
* No qm definition of a bond .: ignore bonds b/c draws bonds based on distance

http://wiki.ch.ic.ac.uk/wiki/images/f/f3/Yr3lab_pes_rev.pdf

== 10/10/2011 Computational Labs - Day 2 ==

Just learned the importance of saving! Had a piece of text typed which is now gone ...

Pictures - as seen below = how to make smaller? on the side of the text? with a caption?
Jmol - lots of different examples available however so far only posted a "link" of sorts to one (see yesterdays entry)
Table - as seen above I have been able to convert a table (using the copy & paste online Excel-Wiki converter) however it needs refinement
Equations - attempted to enter one "freehand" however was unsuccessful and got error messages therefore attempted to download the two suggested programs because they didn't seem to be available on this laptop however no administrator rights therefore unable to download.
File - pdf file of my notes made during the lecture has been added to this page however it is not very successful as there is a picture of the file as opposed to a small icon to link to it as expected ... basically I had expected what happened to the jmol file to happen to the pdf and vice versa - is it something to do with how they're uploaded?

Energy (kJ mol-1)	Data 1	Data 2
24	0.45	1000
345	0.67	1200.03
25.605	0.98	2505
394.605	2.1	4705.03

File:Notes made during introductory talk.pdf

TESTING Jmol function: