An optimal adiabatic-to-diabatic transformation of the 1 2A[prime] and 2 2A[prime] states of H3

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 (removable) and transverse (nonremovable) 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 Schrödinger equation, leaving however the transverse part contribution. We report here the results of an accurate calculation of this transverse part for the 1 2A[prime] and 2 2A[prime] electronic states of H3 obtained by solving a three-dimensional Poisson equation over the entire domain [sans-serif U] of internal nuclear configuration space [script Q] of importance to reactive scattering. In addition to requiring a knowledge of the first-derivative coupling vector everywhere in [sans-serif U], the solution depends on an arbitrary choice of boundary conditions. These have been picked so as to minimize the average value over [sans-serif 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 Schrödinger 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 [sans-serif U] domain. We also present and discuss the diabatic potential energy surfaces obtained by this optimal diabatization procedure

Geometric phase effects in H3 predissociation

We model the predissociation of H3 in the electronic state corresponding to the upper sheet of the conically intersecting 1 2A[prime] and 2 2A[prime] states, and we show that product-state rovibrational distributions are strongly influenced by the geometric phase. Similarly, the differences in the product-state energy distributions in recent three-body dissociation experiments for the 2s,2A1[prime] and 2p,2A2[double-prime] states of H3 are shown to result from the presence of the geometric phase in this system, and thus provide experimental evidence of the influence of this phase in a molecular dynamical process

A quantum and semiclassical study of dynamical resonances in the C + NO-->CN + O reaction

Accurate quantum mechanical reactive scattering calculations were performed for the collinear C+NO-->CN+O reaction using a polynomial-modified London Eyring Polanyi Sato (PQLEPS) potential energy surface (PES), 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 formalism), 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

Accurate first-derivative nonadiabatic couplings for the H3 system

A conical intersection exists between the ground (1 2 A[prime]) and the first-excited (2 2A[prime]) electronic potential energy surfaces (PESs) of the H3 system for C3v geometries. This intersection induces a geometric phase effect, an important factor in accurate quantum mechanical reactive scattering calculations, which at low energies can be performed using the ground PES only, together with appropriate nuclear motion boundary conditions. At higher energies, however, such calculations require the inclusion of both the 1 2A[prime] and 2 2A[prime] electronic PESs and the corresponding nuclear derivative couplings. Here we present ab initio first-derivative couplings for these states obtained by analytic gradient techniques and a fit to these results. We also present a fit to the corresponding 1 2A[prime] and 2 2A[prime] adiabatic electronic PESs, obtained from the ab initio electronic energies. The first-derivative couplings are compared with their approximate analytical counterparts obtained by Varandas et al. [J. Chem. Phys. 86, 6258 (1987)] using the double many-body expansion method. As expected, the latter are accurate close to conical intersection configurations but not elsewhere. We also present the contour integrals of the ab initio couplings along closed loops around the above-mentioned conical intersection, which contain information about possible interactions between the 2 2A[prime] and 3 2A[prime] states

G Protein-Coupled Receptors: Conformational “Gatekeepers” of Transmembrane Signal Transduction and Diversification

Proteins in the cellular signaling machinery accomplish an amazing spectrum of functions necessary for the growth and survival of life by a network of signaling events separated in both space and time. Membrane proteins enable signal transduction across the cell membrane, which results in these signaling events inside the cell leading to a physiological response. G protein-coupled receptors (GPCRs) form the largest family of membrane proteins that process a very diverse set of extracellular signals and are capable of transducing multiple intracellular signaling pathways, mediated by G proteins and/or Arrestins, each with potentially different functional consequences. This “pleiotropic” nature of GPCRs is enabled by a high conformational flexibility of GPCRs, which allows for a unique ensemble of possible conformations depending on the state of the GPCR, whether it is in the apo form, or interacting with a ligand/antibody, or interacting with another protein. Each ligand can induce a different set of conformations in a GPCR, which can interact with G protein and Arrestin pathways in different ways, resulting in different physiological outcomes. This chapter provides an overview of how GPCRs use their conformational flexibility to perform a complex array of functions and how this can be used advantageously to bias signaling within the cell. A detailed understanding of the signaling pathways that are turned on by GPCRs, combined with the development of biased agonists and allosteric modulators to select specific outcomes, provides a promising avenue for developing therapeutics with minimal side-effects

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms

Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions.' We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5 HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo [2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist-and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region

Predicted structures of agonist and antagonist bound complexes of adenosine A_3 receptor

We used the GEnSeMBLE Monte Carlo method to predict ensemble of the 20 best packings (helix rotations and tilts) based on the neutral total energy (E) from a vast number (10 trillion) of potential packings for each of the four subtypes of the adenosine G protein-coupled receptors (GPCRs), which are involved in many cytoprotective functions. We then used the DarwinDock Monte Carlo methods to predict the binding pose for the human A_3 adenosine receptor (hAA_3R) for subtype selective agonists and antagonists. We found that all four A_3 agonists stabilize the 15th lowest conformation of apo-hAA_3R while also binding strongly to the 1st and 3rd. In contrast the four A_3 antagonists stabilize the 2nd or 3rd lowest conformation. These results show that different ligands can stabilize different GPCR conformations, which will likely affect function, complicating the design of functionally unique ligands. Interestingly all agonists lead to a trans χ1 angle for W6.48 that experiments on other GPCRs associate with G-protein activation while all 20 apo-AA_3R conformations have a W6.48 gauche+ χ1 angle associated experimentally with inactive GPCRs for other systems. Thus docking calculations have identified critical ligand-GPCR structures involved with activation. We found that the predicted binding site for selective agonist Cl-IB-MECA to the predicted structure of hAA_3R shows favorable interactions to three subtype variable residues, I253^(6.58), V169^(EL2), and Q167^(EL2), while the predicted structure for hAA_(2A)R shows weakened to the corresponding amino acids: T256^(6.58), E169^(EL2), and L167^(EL2), explaining the observed subtype selectivity