THEORETICAL CHEMISTRY EXPERIMENT
Practical for the Quantumchemistry course
Theoretical Chemistry Group
Joop van Lenthe
Vakgroep Theoretische Chemie
3584 CH Utrecht-De Uithof
tel. (030)-532733 / 532744
- Joop van Lenthe
- Koos Verbeek
- Remco Havenith
A premise of Quantum chemistry (mechanics) is the existence of a wave
function that describes a system of particles (e.g. electrons and nuclei)
completely. If you have this function, you may examine all kind of properties
without having to deal with the actual system. For a chemist this means
knowing the wave function of chemically interesting entities (molecules,
ions, radicals) may contribute to the chemical insight into reactions and
properties. One might consider the relative stability of different isomers,
the optimal geometrical and electronic structure, force constants for chemical
bonds, spectral properties like excitation energies, etc. A nice feature
of theoretical calculations is that not-stable or exotic (and therefore
experimentally not (easily) accessible) molecules are in principal not
more cumbersome than run of the mill molecules. Thus one may consider short-lived
intermediates and transition states. Wave functions are obtained by "solving"
the Schrödinger equation. In practice one needs to approximate the
calculation method (Hartree-Fock, Configuration Interaction, Generalized
Valence Bond) as well as the chemical system (e.g. we treat only the relevant
part of an enzyme and keep various bond-lengths fixed).
- Learning to handle quantum chemical methods and to interpret the results.
This also entails selecting the proper calculational method for the chemical
problem at hand, where the cost (in computer time) of the project is not
- Learning about bigger computer systems (in contrast to PC's). E.g.
using programs like editors and plotting programs and using batch mode
to get the calculations done.
- Seeing that Ab Initio Quantum chemistry may contribute to better
- Practice formulating a problem, organising the experiment and to evaluate
the results critically.
The introductory reading material is about quantum chemistry. You are
required to read the material, to get an idea of the possibilities and
limitations of quantum chemistry, and to dream up a chemical problem, where
quantum chemistry might help. Please note, that the experiment is not expected
One needs to end up with a chemical interpretation of the results. The
numbers coming from your calculations should form the basis for your conclusions.
For example a conclusion like "The SCF-energy of 2-fluorpyridine in
an STO-3G basis is 1234.5678 Hartree" is by itself not very meaningful
. A bit more sense makes "2-fluorpyridine is more stable than 3-fluorpyridine",
though this is still not very exciting.
The reading material comprises :
- The contents of the first year course quantum chemistry (i.e. the quantum
chemistry chapters in "P.W. Atkins, Physical Chemistry"
- Quantumchemie II chapter VII (in Dutch) 'Ab
Initio berekeningen in de praktijk'.
- Atkins , Quanta, a handbook of concepts,
The part on the LCAO method, as well as something on basis sets.
- Szabo & Ostlund, Modern Quantum Chemistry
§3.6 POLYATOMIC BASIS SETS and more if you are interested in the methods.
- J.A.Pople , Two-Dimensional Chart of Quantum Chemistry, J.Chem.Phys.
43 (1965) S229
Also we supply a concise manual for the workstation manual
for the workstation
Find the other literature yourself.
You may also have a look at the Theoretical Chemistry Groups publications.
We are interested for this experiment in what kind of chemical information
you can get from the calculations and not in all kinds of formulas.
Within the time available one can do SCF (Hartree-Fock) for systems
up to some 100 electrons in a normal basis set (e.g. SV 3-21G or SV 6-31G).
Calculations on bigger systems are possible with smaller basis sets. Always
think about what you want to achieve, when choosing basis set and method.
If you want to get a quantitative result a big basis set is nearly always
required, but for a rough estimate of the geometry of a organic molecule,
a minimal basis may suffice. For the calculation of UV spectroscopic data
and for calculations on systems which can't be described with a single
determinantal wave functions, CI-like method are required. These calculations
take more time than a SCF calculation, so it is sensible to restrict yourself
to a small system (20-40 electrons). For including electron correlation
cheap methods like MP2/MP3 are also available. See the example
Available programs/methods in Utrecht
- Gradient (MC)SCF en MP2/MP3 geometry optimisation and saddle-point
(reaction-barrier) and reaction path determination
- Various CI methods.
- Calculation of a large number of properties of molecules, like charge
densities and polarisabilities.
- The calculation of UV/Vis and IR, RAMAN data.
- Relativistic effects (under development)
- Valence Bond methods (TURTLE)
- Solvent effects (under scrutiny)
- Some fit and plot and specialised programs
Try to think of a chemical problem, that, you think, is doable within
of experiments done in the past:
- Calculations on boorhydrids (BH3,B2H6,B3H9),
to establish their relative stability, and to look into the existence of
- Calculation of the structure of CH2=CM2, with
M = H,Li,Na. Is substituted ethene always flat ?
- Calculations on ethane and 1,2-difluorethane. What is the energy difference
between the "staggered" and the "eclipsed' conformation,
and how high is the rotation-barrier ?
- Is there from an energetics viewpoint a preference for the axial or
equatorial position of the nitrogen-proton in a piperidine ring ?
- Acid rain is formed (among others) from SO2 and H2O.
What does the transition state look like.
- The pyramidal inversion and the tunnel effect of the sulfurhydrid-cation
- What does the tropylium-ion look like, and what is it stability compared
to the benzyl-analogon.
- Can you explain (and calculate) that CO binds stronger to Haemoglobine
We prefer to see a problem devised by yourself.
To every experiment there is some work in the library to look up
experimental data, reference calculations, molecular geometries ,etc. This
may (and should) mainly be done while the calculations are running.
We hope that the experiment goes something like this .. (read for Monday
: first day) :
On Monday one starts with finding the assistant and reading the introductory
literature. In the afternoon the goal of the experiment is discussed. The
end of the afternoon may be used to play a bit with the workstation/X-terminal.
When the problem to be solved, is set (Tuesday), the method and programs
should be chosen and hopefully the first calculations are started. The
remaining days are spent doing the calculations and (simultaneously) looking
up literature about the system under study. (Useful references may be found
in the books by Richards et al ('Bibliography of ab initio Molecular
A formal report is not required, however for the discussion supply
- Aim of the experiment
- Which methods are used and why.
- Results and Discussion
- The relevant data with explanation
- Conclusions : What can you conclude from the results ?
The evaluation of this and the experiment and the discussions
about this are an essential part of the practicals.
The judging is strictly subjective and inconsequential and concerns amongst others:
Commitment and insight, planning of the experiment,critically examining
the results, inventiveness and originality.