Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Energetic photons applied to COVID-19 Coronavirus S2 subunit of spike glycoprotein for host cell entry inhabitation: An alternative approach for conventional vaccination

We have investigated numerically the ability to inhibit spike protein from SARS-CoV-2 to attach and inter the host cell when exposed to energetic photons. The Geometric Progression fitting method have been adopted to calculate the equivalent atomic number for photon energy absorption (Zeq), exposure and absorption buildup factors in the energy range E∈ [15–300] keV for the S2-subunit in the spike protein. The buildup factors have shown a peak value at adsorption resonance energy between 36–60 eV per amino acid of the S2-subunit which depends on the mean free path of the photon within the protein structure and the type of mutation. The resonance energies (between UV and X-ray range) have been found to depend on the protein molecular composition. This opens the possibility of using energetic photons to break up the S2-subunit into small fragments. Our results may contribute to the continues racing for finding noninvasive technique for medical trials using radiotherapy treatment for the COVID-19 virus.

Role of the Binding Motifs in the Energy Level Alignment and Conductance of Amine-Gold Linked Molecular Junctions within DFT and DFT + Σ

We investigate, using density functional theory (DFT), the electronic and conducting properties of benzenediamine connected to gold electrodes via different tip structures. We examine a series of binding motifs to the electrodes and calculate the junction spectral properties. We consider corrections to the position of molecular resonances at the junction and discuss different approaches to the calculation of these shifts. We relate the magnitude of these corrections to resonance energies to the atomistic structure of the tip. Benzenediamine DFT-based transmission spectra can be well approximated by a Lorentzian model involving only the highest occupied molecular orbital (HOMO). We show how benzenediamine calculated conductance values in quantitative agreement with previous experiments can be achieved from the combination of DFT-based spectra and corrections to the DFT-based HOMO energy and an accessible Lorentzian model.

Density Functional Prediction of Quasiparticle, Excitation, and Resonance Energies of Molecules With a Global Scaling Correction Approach

Molecular quasiparticle and excitation energies determine essentially the spectral characteristics measured in various spectroscopic experiments. Accurate prediction of these energies has been rather challenging for ground-state density functional methods, because the commonly adopted density function approximations suffer from delocalization error. In this work, by presuming a quantitative correspondence between the quasiparticle energies and the generalized Kohn–Sham orbital energies, and employing a previously developed global scaling correction approach, we achieve substantially improved prediction of molecular quasiparticle and excitation energies. In addition, we also extend our previous study on temporary anions in resonant states, which are associated with negative molecular electron affinities. The proposed approach does not require any explicit self-consistent field calculation on the excited-state species, and is thus highly efficient and convenient for practical purposes.

Correlated energy uncertainties in reaction rate calculations

Context. Monte Carlo methods can be used to evaluate the uncertainty of a reaction rate that arises from many uncertain nuclear inputs. However, until now no attempt has been made to find the effect of correlated energy uncertainties in input resonance parameters. Aims. Our goal is to investigate the impact of correlated resonance energy uncertainties on reaction rates. Methods. Using a combination of numerical and Monte Carlo variation of resonance energies, the effect of correlations are investigated. Five reactions are considered: two fictional, illustrative cases and three reactions whose rates are of current interest. Results. The effect of correlations in resonance energies depends on the specific reaction cross section and temperatures considered. When several resonances contribute equally to a reaction rate, and when they are located on either side of the Gamow peak, correlations between their energies dilute their effect on reaction rate uncertainties. If they are both located above or below the maximum of the Gamow peak, however, correlations between their resonance energies can increase the reaction rate uncertainties. This effect can be hard to predict for complex reactions with wide and narrow resonances contributing to the reaction rate.

Combinatorics of Edge Symmetry: Chiral and Achiral Edge Colorings of Icosahedral Giant Fullerenes: C80, C180, and C240

We develop the combinatorics of edge symmetry and edge colorings under the action of the edge group for icosahedral giant fullerenes from C80 to C240. We use computational symmetry techniques that employ Sheehan’s modification of Pόlya’s theorem and the Möbius inversion method together with generalized character cycle indices. These techniques are applied to generate edge group symmetry comprised of induced edge permutations and thus colorings of giant fullerenes under the edge symmetry action for all irreducible representations. We primarily consider high-symmetry icosahedral fullerenes such as C80 with a chamfered dodecahedron structure, icosahedral C180, and C240 with a chamfered truncated icosahedron geometry. These symmetry-based combinatorial techniques enumerate both achiral and chiral edge colorings of such giant fullerenes with or without constraints. Our computed results show that there are several equivalence classes of edge colorings for giant fullerenes, most of which are chiral. The techniques can be applied to superaromaticity, sextet polynomials, the rapid computation of conjugated circuits and resonance energies, chirality measures, etc., through the enumeration of equivalence classes of edge colorings.