Overview of Distance Geometry as a General Model Builder

Overview of Distance Geometry as a General Model Builder 

Distance geometry can rapidly determine the existence and uniqueness of a model for most problems we are usually interested in answering whether any model exists that satisfies our experimental and hypothetical constraints, and if so, how unique the model is. If only a small number of different structures meet our constraints, we can use molecular mechanics and dynamics to eliminate high energy structures and in favorable cases home in on the correct model. 

Usually, several low energy solutions will remain, but it is often possible to design experiments that can differentiate between them. On the other hand, if there are many degenerate solutions to the model, we can conclude that the model is underdetermined. Finally, distance geometry s random sampling of models often produces surprises, which occasionally lead to new ideas. 

Distance geometry - is a general method for converting a set of distance ranges or bounds into a set of Cartesian coordinates consistent with these bounds. A molecular structure is described by the set of all pairwise interatomic distances in a distance matrix. Cartesian and internal coordinates have been used historically primarily for mathematical and computational convenience for many modeling applications a distance matrix representation is simpler because chemical struaure information is often described by distances. 

---