Cummingskay5816

The ability of the F atom of HC≡CF, H2C=CHF and H3CCH2F to serve as an electron donor to the triel (Tr) atom of TrR3 in the context of a triel bond is assessed by ab initio calculations. The triel bond formed by Csp3-F is strongest, as high as 30 kcal/mol, followed by Csp2-F, and then by Csp-F whose triel bonds can be as small as 1 kcal/mol. The noncovalent bond strength diminishes in the order Tr = Al > Ga > B, consistent with the intensity of the π-hole above the Tr atom in the monomer. The triel bond strength of the Al and Ga complexes increases along with the electronegativity of the R substituent but is largest for R=H when Tr=B. Electrostatics play the largest role in the stronger triel bonds, but dispersion makes an outsized contribution for the weakest such bonds.We study the dependence of kinetic energy densities (KEDs) on density-dependent variables that have been suggested in previous works on kinetic energy functionals for orbital-free density functional theory. We focus on the role of data distribution and on data and regressor selection. We compare unweighted and weighted linear and Gaussian process regressions of KEDs for light metals and a semiconductor. We find that good quality linear regression resulting in good energy-volume dependence is possible over density-dependent variables suggested in previous literature studies. This is achieved with weighted fitting based on the KED histogram. With Gaussian process regressions, excellent KED fit quality well exceeding that of linear regressions is obtained as well as a good energy-volume dependence, which was somewhat better than that of best linear regressions. We find that while the use of the effective potential as a descriptor improves linear KED fitting, it does not improve the quality of the energy-volume dependence with linear regressions but substantially improves it with Gaussian process regression. Gaussian process regression is also able to perform well without data weighting.This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide explosion of computation of today. We contrast the past and present in atomistic simulations, emphasizing those simple models that best achieve reproducibility and promote understanding. Few-body models with pair forces have led to today's "realistic" simulations with billions of atoms and molecules. Rapid advances in computer technology have led to change. Theoretical formalisms have largely been replaced by simulations incorporating ingenious algorithm development. We choose to study particularly simple, yet relevant, models directed toward understanding general principles. Simplicity remains a worthy goal, as does relevance. We discuss hard-particle virial series, melting, thermostatted oscillators with and without heat conduction, chaotic dynamics, fractals, the connection of Lyapunov spectra to thermodynamics, and finally simple linear maps. 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. 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. Olaparib 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. We attribute this quenching to photoinduced charge transfer from hydroporphyrin to BODIPY. No direct spectral signature of the charge-separated state is observed, which suggests that either (1) the charge-separated state decays very quickly to the ground state or (2) virtual charge-separated states, close in energy to S1 of hydroporphyrin, promote ultrafast internal conversion.Dyson orbitals, their electron-binding energies, and probability factors provide descriptions of electrons in molecules that are experimentally verifiable and that generalize qualitatively useful concepts of uncorrelated, molecular-orbital theory to the exact limit of Schrödinger's time-independent equation. Dyson orbitals are defined as overlaps between initial, N-electron states and final states with N ± 1 electrons and therefore are useful in the prediction and interpretation of many kinds of spectroscopic and scattering experiments. They also are characteristic of N-electron initial states and may be used to construct electron densities, one-electron properties, and total energies with correlated Aufbau procedures that include probability factors between zero and unity. Relationships with natural orbitals, Kohn-Sham orbitals, and Hartree-Fock orbitals facilitate insights into the descriptive capabilities of Dyson orbitals. Electron-propagator approximations that employ the Dyson quasiparticle equation or super-operator secular equations enable direct determination of Dyson orbitals and obviate the need for many-electron wavefunctions of initial or final states.