Computational chemistry is the name used to indicate the use of computational techniques in chemistry, ranging from the quantum mechanics of molecules to the dynamics of large complex molecular aggregates. Modelling techniques like quantum mechanics and density functional theory (QM-DFT) can be used to model atom – to – atom interactions in the most comprehensive way at present, however, this only applies to limited numbers of atoms over relatively short timescales. In contrast, molecular dynamics (MD) is capable of simulating systems up to millions of atoms in microsecond timescales. Increases in the efficiency of computations is achieved through the reduced theoretical description of atomic interactions – i.e. by replacement of strict solutions by their empirical approximations. Very often QM-DFT methods are used to complement MD simulations, i.e. provide input data. Pectin compounds were also the object of theoretical discussions. Due to the size of the systems, most calculations were performed using the methods of molecular dynamics, molecular mechanics, or semi-empirical methods. Recently, we have demonstrated a simulation of AFM experiments on galacturonic acid oligomers by means of the density functional method (DFT) with the enforced geometry optimization (EGO) approach.