Generalized electronic diabatic approach to structural similarity in two-dimensional potential energy surfaces of various topologies

Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two-dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open-shell transition state) coupled in an external field. The "effective" 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential-energy-surface topologies (consistent with three-state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product. (c) 2007 Wiley Periodicals, Inc.