Biological & organic reactions

The density functional formalism provides a method for calculating the energy of molecular systems as a function of the atomic positions. In principle, it then provides a means for determining the heats and paths of reaction. There have been many such applications to organic molecules, and studies of biological systems are under way. An example is provided by the reaction of water with adenosine 5'-triphosphate (ATP). ATP is the most important energy carrier in cellular metabolism, and each human being produces its own weight of ATP each day. We show a model system for which we have studied two possible reactions (carbon atoms grey, oxygen orange, hydrogen white, nitrogen blue, phosphorus yellow). The magnesium atoms (green) act as catalysts.

( R. O. Jones, J. Akola)

Polymerization: Beyond the limits of DF calculations

Phase transitions involve the collective motion of many particles, and one might think that the restricted scope of density functional calculations (around 100 atoms, time scales up to a few picoseconds) renders them of little value in this context. This is not the case. Density functional calculations provide an extensive (and extendible) data base of structures, energy barriers, and vibration frequencies for molecules and clusters, which can be used to parameterize classical force fields. These can then be used in Monte Carlo and molecular dynamics simulations for thousands of atoms, long time scales, and a range of temperatures. An example is provided by the temperature and pressure induced transitions in phosphorus from a molecular liquid (P4-tetrahedra) to the polymeric state, such as that shown in the figure.

( R. O. Jones, P.Ballone)

Organic molecules on surfaces - molecular electronics

The possibilities of incorporating organic molecules into existing technologies and building molecule-based nanoscale electronic circuits with rectifying, logic, and switching functions have stimulated experimental and theoretical efforts to study and predict their properties. The development of organic/inorganic interfaces depends critically on understanding the bonding and lateral interactions that govern the orientation, conformation, and two-dimensional arrangement of molecules at surfaces. Density functional (DFT) calculations provide new insight into this problem, particularly the interactions between such molecules, and we have used the EstCoMPP program, a projector augmented plane-wave package, to investigate the geometrical and electronic structure of several molecular layers that use the carboxylate group as an anchor to metal surfaces.

( N.Atodiresei)

Mechanical & thermo-mechanical properties of materials

The DF method can determine energies as a function of atomic positions, and it should be able in principle to predict mechanical and thermo-mechanical properties, such as thermal expansion coefficients or elastic constants of crystalline materials.The theory of thermal expansion by Born and Grüneisen requires a knowledge of the phonon frequencies and the way they change with changing unit cell size. This is a great computational challenge and our success in explaining the thermal expansion of ß-eucryptite - the basic material of all cooktops - is quite remarkable.

( R. O. Jones)