Molecular reaction dynamics in the adiabatic representation is complicated by the existence of conical intersections and the associated geometric phase effect. The first-derivative coupling vector between the corresponding electronically adiabatic states can, in general, be decomposed into longitudinal ͑removable͒ and transverse ͑nonremovable͒ parts. At intersection geometries, the longitudinal part is singular, whereas the transverse part is not. In a two-electronic-state Born-Huang expansion, an adiabatic-to-diabatic transformation completely eliminates the contribution of the longitudinal part to the nuclear motion Schro ¨dinger equation, leaving however the transverse part contribution. We report here the results of an accurate calculation of this transverse part for the 1 2 AЈ and 2 2 AЈ electronic states of H 3 obtained by solving a three-dimensional Poisson equation over the entire domain U of internal nuclear configuration space Q of importance to reactive scattering. In addition to requiring a knowledge of the first-derivative coupling vector everywhere in U, the solution depends on an arbitrary choice of boundary conditions. These have been picked so as to minimize the average value over U of the magnitude of the transverse part, resulting in an optimal diabatization angle. The dynamical importance of the transverse term in the diabatic nuclear motion Schro ¨dinger equation is discussed on the basis of its magnitude not only in the vicinity of the conical intersection, but also over all of the energetically accessible regions of the full U domain. We also present and discuss the diabatic potential energy surfaces obtained by this optimal diabatization procedure.

We summarize here recent progress in predicting the 3-dimensional (3D) structure of G protein-coupled receptors (GPCR) and in predicting the binding sites for various agonists and antagonists. These receptors play a critical role in cell communications (dopamine, histamine, epinephrine, and serotonin) and in sensing the outside world (vision, smell, taste, and pain). There are no experimental 3D structures available for human GPCR despite their vital function and importance as therapeutic targets. Indeed, considering every form of life, there is an experimental structure for only 1 GPCR: bovine rhodopsin. Consequently, we developed the MembStruk method to predict the 3D structure without using homology. We then validated our predicted structures by using them to predict their binding sites and binding energies for strongly binding agonists and antagonists. The results were in excellent agreement with available binding and mutation experiments. We will summarize the results for adrenergic receptors, dopamine receptors, chemokine receptors, muscarinic acetylcholine receptors, and a tetrapeptide receptor (mas-related gene C11).

Accurate quantum mechanical reactive scattering calculations were performed for the collinear CϩNO→CNϩO reaction using a polynomial-modified London Eyring Polanyi Sato ͑PQLEPS͒ potential energy surface ͑PES͒, which has a 4.26 eV deep well in the strong interaction region, and a reference LEPS PES, which has no well in that region. The reaction probabilities obtained for both PESs show signatures for resonances. These resonances were characterized by calculating the eigenvalues and eigenvectors of the collision lifetime matrix as a function of energy. Many resonances were found for scattering on both PESs, indicating that the potential well in the PQLEPS PES does not play the sole role in producing resonances in this relatively heavy atom system and that Feshbach processes occur for both PESs. However, the well in the PQLEPS PES is responsible for the differences in the energies, lifetimes, and compositions of the corresponding resonance states. These resonances are also interpreted in terms of simple periodic orbits supported by both PESs ͑using the WKB formalism͒, to further illustrate the role played by that potential well on the dynamics of this reaction. The existence of the resonances is associated with the dynamics of the long-lived CNO complex, which is much different than that of systems having an activation barrier. Although these results were obtained for a collinear model of the reaction, its collinearly-dominated nature suggests that related resonant behavior may occur in the real world.

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