Molecular Modeling

This chapter begins by looking at how molecular graphics can help to understand the structures of typical molecules and complexes that one encounters in physical organic chemistry and in related fields of bioorganic chemistry, organometallic chemistry, theoretical and computational chemistry, catalysis, photochemistry, electrochemistry, supramolecular chemistry, polymer chemistry, materials science and nanotechnology. It presents a description of quantum mechanical reactivity indices, highlighting their use in understanding reactions between organic molecules. The chapter looks at modelling of noncovalent, physisorbed complexes such as those arising in self-assembly of macromolecular aggregates in solution and on surfaces, which require classical molecular dynamics simulations. Quantum chemical calculations may be now routinely performed on desktop computers and to obtain properties such as molecule-surface binding energies and distributions of atomic charges in molecules in different solvents. The use of high-performance computing clusters allows larger, and more, systems to be rapidly calculated.