Molecular Modeling of Inorganic Compounds

Part 1 Theory: parameterization, approximations and limitations - concepts, potential energy functions, band stretching, angle bending, torsions, cross-terms, van der Waals interactions, electrostatic interactions, hydrogen bonding interactions, out-of-plane terms, force field parametres, spectroscopic force fields, model and reality, electronic effects, the environment, entropic effects; computation - input and output, energy minimization, simplex method, gradient method, conjugate gradient methods, Newton-Raphson method, least-squares method, constraints and restraints; the multiple minima problem - deterministic methods, stochastic methods, molecular dynamics, practical considerations, making use of experimental data. Part 2 Applications: structural aspects - accuracy of structure predictions, molecular visualization, isomer prediction, analysis of structural trends, unravelling crystallographic disorder, comparison with solution properties; stereoselectivities - conformational analysis, enantioselectivities, racemate separation, stereoselective synthesis, structure evaluation, mechanistic information; metal ion selectivity - chelate ring size, macrocycle hole size, preorganization; spectroscopy - vibrational spectroscopy, electronic spectroscopy, EPR spectroscopy, NMR spectroscopy; electron transfer - redox potentials, electron transfer rates; electronic effects - d-orbital directionality, trans influence, Jahn-Teller distortions; bioinorganic chemistry - complexes of amino-acids and peptides, metalloproteins, metalloporphyrins, metal-nucleotide and metal-DNA interactions, other systems; organometallics - metallocenes, transition metal-allyl systems, transition metal-phosphine compounds, metal-metal bonding, carbonyl cluster compounds; compounds with s, p and f block elements - alkali and alkaline earth metals, crown ethers, crpybands, spherands, biologically relevant ligands, main group elements, lanthanides and actinides. Part 3 Practice of molecular mechanics: developing a force field - bond length deformation, valence angle deformation, torsion angle deformation, out-of-plane deformation, non-bonded interactions, electrostatic interactions, hydrogen bonding interactions; carrying out the calculations - setting up a starting model, energy minimization procedures, scanning potential energy surfaces, mapping potential energy surfaces; interpreting and using the result - structural outcomes, energy outcomes.