Evaluating the appropriateness of γ-graphyne derivatives as electrode materials for supercapacitors.

DFT calculations were used to study the quantum capacitance of pure, B/Al/Si/N/P-doped, and defective γ-graphyne. Due to the direct relationship between capacitance and electronic states around the Fermi level, structures' electronic properties were evaluated by DOS plots. The results of integrated specific quantum capacitance in the range of water stability potential show an improvement of capacity in each p and n-type doping. The calculated cohesive energies of doped structures reflect the stability enhancement. Also, the stability/capacitance of single and double vacancies in two distinct positions (sp and sp2) were examined. The results illustrate stability retention and quantum capacitance improvement of these defective structures. Among the doped structures, the maximum quantum capacitance is 2251.10 F/gr belonging to the aluminum doped structure (in the sp position). For the defective structures, the maximum quantum capacitance is 4221.69 F/gr belonging to removing two sp carbon atoms. These quantum capacitances significantly improved compared to the pristine structure (1216.87 F/gr) and many other structures. These stunning results can contribute to the design of appropriate structures as electrode materials for high-efficiency supercapacitors.

Spherical PEG/SiO2 promising agents for Lamivudine antiviral drug delivery, a molecular dynamics simulation study.

Spherical nanocarriers can lead to a bright future to lessen problems of virus infected people. Spherical polyethylene glycol (PEG) and spherical silica (SiO2) are novel attractive nanocarriers as drug delivery agents, especially they are recently noticed to be reliable for antiviral drugs like anti-HIV, anti-covid-19, etc. Lamivudine (3TC) is used as a first line drug for antiviral therapy and the atomic view of 3TC-PEG/SiO2 complexes enable scientist to help improve treatment of patients with viral diseases. This study investigates the interactions of 3TC with Spherical PEG/SiO2, using molecular dynamics simulations. The mechanism of adsorption, the stability of systems and the drug concentration effect are evaluated by analyzing the root mean square deviation, the solvent accessible surface area, the radius of gyration, the number of hydrogen bonds, the radial distribution function, and Van der Waals energy. Analyzed data show that the compression of 3TC is less on PEG and so the stability is higher than SiO2; the position and intensity of the RDF peaks approve this stronger binding of 3TC to PEG as well. Our studies show that PEG and also SiO2 are suitable for loading high drug concentrations and maintaining their stability; therefore, spherical PEG/SiO2 can reduce drug dosage efficiently.

Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs.

Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.

High-order harmonic generation by static coherent states method in single-electron atomic and molecular systems.

We solve the time-dependent Schrodinger equation using the coherent states as basis sets for computing high harmonic generation (HHG) in a full-dimensional single-electron "realistic" system. We apply the static coherent states (SCS) method to investigate HHG in the hydrogen molecular ion induced by a linearly polarized laser field. We show that SCS gives reasonable agreement compared to the three dimensional unitary split-operator approach. Next, we study isolated attosecond pulse generation in H 2 + . To do so, we employ the well-known polarization gating technique, which combines two delayed counter-rotating circular laser pulses, and opens up a gate at the central portion of the superposed pulse. Our results suggest that the SCS method can be used for full-dimensional quantum simulation of higher dimensional systems such as the hydrogen molecule in the presence of an external laser field.

Investigation of Boron-Doped Graphdiyne as a Promising Anode Material for Sodium-Ion Batteries: A Computational Study.

In this work, by density functional theory (DFT) calculations, sp-sp2-hybridized boron-doped graphdiyne (BGDY) nanosheets have been investigated as an anode material for sodium storage. The density of states (DOS) and band structure plots show that substituting a boron atom with a carbon atom in an 18-atom unit cell converts the semiconductor pristine graphdiyne (GDY) to metallic BGDY. Also, our calculations indicate that, due to the presence of boron atoms, the adsorption energy of BGDY is more than that of GDY. The diffusion energy barrier calculations show that the boron atom in BGDY creates a more suitable path with a low energy barrier for sodium movement. This parameter is important in the rate of charge/discharge process. On the other hand, the projected density of states (PDOS) plots show that sodium is ionized when adsorbed on the electrode surface and so Na-BGDY interaction has an electrostatic character. This type of interaction is necessary for the reversibility of adsorption in the discharge mechanism. Finally, the calculation of the theoretical capacity shows an increase in BGDY (872.68 mAh g-1) in comparison with that in GDY (744 mAh g-1). Thus, from comparison of different evaluated parameters, it can be concluded that BGDY is a suitable anode material for sodium-ion batteries.

Ab initio study of sodium diffusion and adsorption on boron-doped graphyne as promising anode material in sodium-ion batteries.

The electronic properties, adsorption energies and energy barrier of sodium ion diffusion in B-doped graphyne (BGY) are studied by density functional theory (DFT) method. If some carbon atoms in pristine graphyne (GY) are substituted by boron atoms (one substitution per unit cell in this work), BGY is obtained, and the band structure and density of state (DOS) plots indicate a transition from a semiconductive state for GY to a metallic state for BGY. The calculated adsorption energy shows an improvement in the trigonal-like pore (T site) and hexagonal ring (H site) adsorption of BGY compared to the corresponding analog sites in GY. The comparison of projected density of state (PDOS) plots before and after adsorption reveals charge transfer from sodium to nanosheets. Therefore, the interaction between adsorbed sodium atom and BGY/GY has ionic character and not covalent. This phenomenon is important for the reversible sodium adsorption in secondary batteries. Moreover, PDOS plots show that the electron transfer from sodium atom to host structure in BGY is more than in GY, which is in agreement with adsorption energies. According to diffusion energy barrier calculations, boron atoms in BGY structure provide low energy paths for sodium ions diffusion. We estimate a theoretical capacity of 751 mA h g-1 for the maximum sodium adsorption on BGY (without cluster formation). Therefore, BGY is a promising anode material for sodium ion batteries (SIBs).

Complementary version of fermion coupled coherent states method and gram-schmidt algorithm: Theory and applications for electronic states of H2 and H2.

In our previous report, we introduced a new version of Fermion coupled coherent states method (FCCS) which was especially suited for simulating the first symmetric spatial electronic state of two-electron systems. In this manuscript, we report a complementary version for FCCS method to simulate both of the first symmetric and antisymmetric spatial electronic states of two-electron systems. Moreover, the Gram-Schmidt orthogonalization process is employed to reach the excited states of the system. We apply this FCCS method and the original coupled coherent state method to simulate the energy of different electronic states of H2 and H2+, respectively. The results for the energy of computed electronic states of H2 and H2+ show a pretty good consistency with the exact values. © 2017 Wiley Periodicals, Inc.

Precise description of single and double ionization of hydrogen molecule in intense laser pulses.

A new simulation box setup is introduced for the precise description of the wavepacket evolution of two electronic systems in intense laser pulses. In this box, the regions of the hydrogen molecule H(2), and singly and doubly ionized species, H(2) (+) and H(2) (+2), are well discernible and their time-dependent populations are calculated at different laser field intensities. In addition, some new regions are introduced and characterized as quasi-double ionization and their time-dependencies on the laser field intensity are calculated and analyzed. The adopted simulation box setup is special in that it assures proper evaluation of the second ionization. In this study, the dynamics of the electrons and nuclei of the hydrogen molecule are separated based on the adiabatic approximation. The time-dependent Schrödinger and Newton equations are solved simultaneously for the electrons and the nuclei, respectively. Laser pulses of 390 nm wavelength at four different intensities (i.e., 1 × 10(14), 5 × 10(14), 1 × 10(15), and 5 × 10(15) W cm(-2)) are used in these simulations. Details of the central H(2) region are also presented and discussed. This region is divided into four sub-regions related to the ionic state H(+)H(-) and covalent (natural) state HH. The effect of the motion of nuclei on the enhanced ionization is discussed. Finally, some different time-dependent properties are calculated, their dependencies on the intensity of the laser pulse are studied, and their correlations with the populations of different regions are analyzed.