Parsonsrosen5537

Along the way, we mention directions in which additional modeling could provide more clarity and yet more interesting developments in the future.Using a polymer-masking approach, we have developed metal-free 2D carbon electrocatalysts based on single-layer graphene with and without punched holes and/or N-doping. A combined experimental and theoretical study on the resultant 2D graphene electrodes revealed that a single-layer graphene sheet exhibited a significantly higher electrocatalytic activity at its edge than that over the surface of its basal plane. Furthermore, the electrocatalytic activity of a single-layer 2D graphene sheet was significantly enhanced by simply punching microholes through the graphene electrode due to the increased edge population for the hole-punched graphene electrode. In a good consistency with the experimental observations, our density function theory calculations confirmed that the introduction of holes into a graphene sheet generated additional positive charge along the edge of the punched holes and hence the creation of more highly active sites for the oxygen reduction reaction. The demonstrated concept for less graphene material to be more electrocatalytically active shed light on the rational design of low-cost, but efficient electrocatalysts from 2D graphene for various potential applications ranging from electrochemical sensing to energy conversion and storage.We develop a density matrix formalism to describe coupled electron-nuclear dynamics. To this end, we introduce an effective Hamiltonian formalism that describes electronic transitions and small (quantum) nuclear fluctuations along a classical trajectory of the nuclei. Using this Hamiltonian, we derive equations of motion for the electronic occupation numbers and for the nuclear coordinates and momenta. We show that, in the limit, when the number of nuclear degrees of freedom coupled to a given electronic transition is sufficiently high (i.e., the strong decoherence limit), the equations of motion for the electronic occupation numbers become Markovian. Furthermore, the transition rates in these (rate) equations are asymmetric with respect to the lower-to-higher energy transitions and vice versa. In thermal equilibrium, such asymmetry corresponds to the detailed balance condition. We also study the equations for the electronic occupations in the non-Markovian regime and develop a surface hopping algorithm based on our formalism. To treat the decoherence effects, we introduce additional "virtual" nuclear wave packets whose interference with the "real" (physical) wave packets leads to the reduction in coupling between the electronic states (i.e., decoherence) as well as to the phase shifts that improve the accuracy of the numerical approach. Remarkably, the same phase shifts lead to the detailed balance condition in the strong decoherence limit.We develop a range-separated stochastic resolution of identity (RS-SRI) approach for the four-index electron repulsion integrals, where the larger terms (above a predefined threshold) are treated using a deterministic RI and the remaining terms are treated using a SRI. The approach is implemented within a second-order Green's function formalism with an improved O(N3) scaling with the size of the basis set, N. Moreover, the RS approach greatly reduces the statistical error compared to the full stochastic version [T. Y. this website Takeshita et al., J. Chem. Phys. 151, 044114 (2019)], resulting in computational speedups of ground and excited state energies of nearly two orders of magnitude, as demonstrated for hydrogen dimer chains and water clusters.The use of projection-after-variation double-hybrid density functional theory is proposed and examined as a difference method for the calculation of excited states. The strengths and weaknesses of the proposed method are discussed with particular reference to connections with linear response coupled-cluster theory. Vertical excitation energies are computed for the 28 molecule benchmark of Schreiber and co-workers in order to compare how the model performs with linear response coupled-cluster theories and multireference perturbation theory. The findings of this study show that the proposed method can achieve standard deviations in the error of computed vertical excitation energies compared to complete active space second-order perturbation theory of similar size to linear response coupled-cluster theories.In 2020, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people worldwide and caused the coronavirus disease 2019 (COVID-19). Spike (S) glycoproteins on the viral membrane bind to ACE2 receptors on the host cell membrane and initiate fusion, and S protein is currently among the primary drug target to inhibit viral entry. The S protein can be in a receptor inaccessible (closed) or accessible (open) state based on down and up positions of its receptor-binding domain (RBD), respectively. However, conformational dynamics and the transition pathway between closed to open states remain unexplored. Here, we performed all-atom molecular dynamics (MD) simulations starting from closed and open states of the S protein trimer in the presence of explicit water and ions. MD simulations showed that RBD forms a higher number of interdomain interactions and exhibits lower mobility in its down position than its up position. MD simulations starting from intermediate conformations between the open and closed states indicated that RBD switches to the up position through a semi-open intermediate that potentially reduces the free energy barrier between the closed and open states. Free energy landscapes were constructed, and a minimum energy pathway connecting the closed and open states was proposed. Because RBD-ACE2 binding is compatible with the semi-open state, but not with the closed state of the S protein, we propose that the formation of the intermediate state is a prerequisite for the host cell recognition.Arrays of hydroporphyrins with boron complexes of dipyrromethene (BODIPY) are a promising platform for biomedical imaging or solar energy conversion, but their photophysical properties have been relatively unexplored. In this paper, we use time-resolved fluorescence, femtosecond transient absorption spectroscopy, and density-functional-theory calculations to elucidate solvent-dependent energy and electron-transfer processes in a series of chlorin- and bacteriochlorin-BODIPY arrays. Excitation of the BODIPY moiety results in ultrafast energy transfer to the hydroporphyrin moiety, regardless of the solvent. In toluene, energy is most likely transferred via the through-space Förster mechanism from the S1 state of BODIPY to the S2 state of hydroporphyrin. In DMF, substantially faster energy transfer is observed, which implies a contribution of the through-bond Dexter mechanism. In toluene, excited hydroporphyrin components show bright fluorescence, with quantum yield and fluorescence lifetime comparable to those of the benchmark monomer, whereas in DMF, moderate to significant reduction of both quantum yield and fluorescence lifetime are observed.