THEORETICAL CHEMISTRY EXPERIMENT

Practical for the Quantumchemistry course

Theoretical Chemistry Group

2004

 

Coordination

Joop van Lenthe
Vakgroep Theoretische Chemie
Centrumgebouw Noord
Padualaan 14
3584 CH Utrecht-De Uithof
tel. (030)-532733 / 532744

Instruction :

Joop van Lenthe
Koos Verbeek
Remco Havenith

Introduction

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).

Objectives

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 to "succeed".

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 :

  1. The contents of the first year course quantum chemistry (i.e. the quantum chemistry chapters in "P.W. Atkins, Physical Chemistry"
  2. Quantumchemie II chapter VII (in Dutch) 'Ab Initio berekeningen in de praktijk'.
  3. Atkins , Quanta, a handbook of concepts,
    The part on the LCAO method, as well as something on basis sets.
  4. Szabo & Ostlund, Modern Quantum Chemistry
    §3.6 POLYATOMIC BASIS SETS and more if you are interested in the methods.
  5. 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 experiments.


Available programs/methods in Utrecht


Try to think of a chemical problem, that, you think, is doable within a week.

Examples of experiments done in the past:

  1. Calculations on boorhydrids (BH3,B2H6,B3H9), to establish their relative stability, and to look into the existence of 3-center bonds.
  2. Calculation of the structure of CH2=CM2, with M = H,Li,Na. Is substituted ethene always flat ?
  3. 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 ?
  4. Is there from an energetics viewpoint a preference for the axial or equatorial position of the nitrogen-proton in a piperidine ring ?
  5. Acid rain is formed (among others) from SO2 and H2O. What does the transition state look like.
  6. The pyramidal inversion and the tunnel effect of the sulfurhydrid-cation
  7. What does the tropylium-ion look like, and what is it stability compared to the benzyl-analogon.
  8. Can you explain (and calculate) that CO binds stronger to Haemoglobine then oxygen?

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 Wave functions")


A formal report is not required, however for the discussion supply

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.