Computational chemistry and molecular modelling

 

Approximate molecular orbital methods, such as Hückel Theory, have been useful in helping chemists develop ideas and understanding of molecules. 

 

However, the development of computers, and sophisticated ‘ab initio’ molecular orbital methods (based on the same basic approaches such as the variational principle), mean that it is now possible to calculate molecular properties on desktop PCs.  Nowadays, computers are important tools in nearly all areas of chemical research.  For example:

 

· Pharmaceutical industry (e.g. drug design)

· Materials science

· Biotechnology

· Catalysis (e.g modelling catalysis in zeolites and transition metal complexes)

· Spectroscopy

· Atmospheric chemistry

· Crystallography

· Reaction dynamics

 

as well as investigating organic reactivity problems. 

 

Modelling and calculations can given insight beyond experiments in many cases. Modelling and experiments are best done in conjunction: modelling helps interpret experiments, and experiments test computer models.

 

Many different computational chemistry and molecular modelling methods are used - you’ll learn about some of these in the future. 

 

To understand a chemical reaction, we need to know the transition state structure for the reaction.  Transition states are difficult to study directly by experiment.  Instead, their structures can be calculated and analysed.

 


Modelling reactivity: calculations can make useful predictions even for reactions in large, complex systems like enzymes

 

Calculated transition state structure for the reaction in the enzyme phenol hydroxylase (an OH group is transferred to the ortho carbon of phenol): 

 

(Phenol hydroxylase is involved in biodegradation of aromatic pollutants). 

 

Linear correlation between the natural logarithm of the experimental rate constants and the calculated energy barriers (Eact) for conversion of phenol derivatives by phenol hydroxylase

 

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