RESUMO
The complex absorbing potential (CAP) approach offers a practical tool for characterization of energies and lifetimes of metastable electronic states, such as temporary anions and core ionized states. Here, we present an implementation of the smooth Voronoi CAP combined with the equation-of-motion coupled cluster with single and double substitutions method for metastable states. The performances of the smooth Voronoi CAP and box CAP are compared for different classes of systems: resonances in isolated molecules and localized and delocalized resonances in molecular clusters. The benchmark calculations show that the Voronoi CAP is generally more robust when applied to molecular clusters, but box CAPs are equally reliable for localized resonances or in the cases when the resonance does not exhibit significant electron density delocalization into the intramolecular region. As such, the choice of the CAP shape and onset should be guided by the character of the metastable states.
RESUMO
The complex absorbing potential equation-of-motion coupled-cluster (CAP-EOM-CC) method is routinely used to investigate metastable electronic states in small molecules. However, the requirement of evaluating eigenvalue trajectories presents a barrier to larger simulations, as each point corresponding to a different value of the CAP strength parameter requires a unique eigenvalue calculation. Here, we present a new implementation of CAP-EOM-CCSD that uses a subspace projection scheme to evaluate resonance positions and widths at the overall cost of a single electronic structure calculation. We analyze the performance of the projected CAP-EOM-CC scheme against the conventional scheme, where the CAP is incorporated starting from the Hartree-Fock level, for various small and medium sized molecules, and investigate its sensitivity to various parameters. Finally, we report resonance parameters for a set of molecules commonly used for benchmarking CAP-based methods, and we report estimates of resonance energies and widths for 1- and 2-cyanonaphtalene, molecules that were recently detected in the interstellar medium.
RESUMO
eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or the user-specified target. The identified pathways are ranked according to their effective length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu .
