Pressure-induced superconductivity of Ac-B-H hydrides.

The search for room-temperature superconductors among high-pressure hydrides is a hot research topic. In this study, the structures, stabilities and superconducting properties of ternary Ac-B-H hydrides were studied using a genetic algorithm (GA) combined with density functional theory (DFT) calculations. It was shown that the R3̄m-AcBH8 and I4/mmm-AcB2H8 structures were thermodynamically and dynamically stable above 70 and 125 GPa, respectively. In the R3̄m-AcBH8 structure, the BH6 unit and the dispersed H atoms were bonded to form a corrugated structure. The I4/mmm-AcB2H8 structure contained a cage and the Ac atom located at the cage center. The calculations of the electron-phonon coupling showed that the R3̄m-AcBH8 and I4/mmm-AcB2H8 structures had Tc values of 140 K (70 GPa) and 99 K (125 GPa), respectively. The analyses of the phonon dispersion curves revealed that electron-phonon coupling was closely related to the vibrations of the B-H bonds.

Identification of Dual-Target Inhibitors for Epidermal Growth Factor Receptor and AKT: Virtual Screening Based on Structure and Molecular Dynamics Study.

Epidermal growth factor EGFR is an important target for non-small cell lung (NSCL) cancer, and inhibitors of the AKT protein have been used in many cancer treatments, including those for NSCL cancer. Therefore, searching small molecular inhibitors which can target both EGFR and AKT may help cancer treatment. In this study, we applied a ligand-based pharmacophore model, molecular docking, and MD simulation methods to search for potential inhibitors of EGFR and then studied dual-target inhibitors of EGFR and AKT by screening the immune-oncology Chinese medicine (TCMIO) database and the human endogenous database (HMDB). It was found that TCMIO89212, TCMIO90156, and TCMIO98874 had large binding free energies with EGFR and AKT, and HMDB0012243 also has the ability to bind to EGFR and AKT. These results may provide valuable information for further experimental study.

Energy decomposition analysis of cationic carbene analogues with group 13 and 16 elements as a central atom: a comparative study.

Decomposition of the molecular interaction energies into physically intuitive components provides insight to the chemical bonding between fragments. Extended transition state-natural orbital for chemical valence (ETS-NOCV) and natural energy decomposition analysis (NEDA) are methodologically different schemes to partition the interaction energies into physically similar components. To answer the question if the two energy decomposition analysis (EDA) schemes render the same interpretations of reactions, both schemes are employed to study the reactions of two cationic carbene analogues: (1) bis(tri-tert-butylphosphane) group-13-element monocations [(PtBu3)2M+ (M = B, Al, Ga, In, and Tl)] and (2) N-heterocyclic carbene (NHC) dications with a group 16 element as the central atom [(Dipp2DAB)M2+, M = O, S, Se, and Te; Dipp2DAB = 1,4-(2,6-diisopropyl)phenyl-1,4-diaza-1,3-butadiene]. Comparison of the EDA components obtained using the ETS-NOCV and NEDA schemes suggests that, for each individual reaction, the two EDA schemes may not necessarily lead to a consensus about the interpretation or "understanding" of the reaction. However, if the whole families of the studied cationic carbene analogue reactions with simple hydrocarbons are considered, the ETS-NOCV and NEDA schemes agree that the most dominant effects on the interaction energies are the orbital interactions, with the second most dominant being electrostatics, and Pauli exclusions being the least effective.

Structures and localized vibrational states of defects in graphite by tight-binding calculations.

The structural and vibrational properties of pristine graphite and point defects in graphite are studied by tight-binding (TB) calculations using a three-center TB potential model. We showed that the three-center TB potential without "ad hoc" van der Waals interaction corrections can accurately describe the inter-layer distance of graphite and the lowest-energy structures and stabilities of typical point defects in graphite. The results from our TB calculations are in good agreement with those from density-functional theory calculations with van der Waals interaction corrections. We also investigated the vibrational properties to gain better understanding on the localization of vibrational states induced by the point defects. Our calculation results show that although localized or quasi-localized vibrational modes can be found in all defected graphite, the localization induced by Frenkel pair, dual-vacancy, and dual-interstitial defects is much stronger. Atomic displacements associated with the localized vibrational modes induced by these three point defects are also analyzed.

Study on superconducting Li-Se-H hydrides.

The structures, stabilities and superconducting properties of LiSeHn (n = 4-10) hydrides at 150-300 GPa were studied by the genetic algorithm (GA) and DFT calculation method. Three stable stoichiometries of LiSeH4, LiSeH6 and LiSeH10 were uncovered under high pressure. Four other metastable stoichiometries of LiSeH5, LiSeH7, LiSeH8, and LiSeH9 were also studied. By analyzing the electronic band structure and electronic density of states, C2 LiSeH4, Pmm2 LiSeH6 and C2 LiSeH10 were all found to be metal phases above 150 GPa. Electron-phonon coupling calculations showed that C2 LiSeH4 and Pmm2 LiSeH6 were promising superconductors. The predicted Tc values of C2 LiSeH4 and Pmm2 LiSeH6 were 77 K at 200 GPa and 111 K at 250 GPa, respectively.

Localized electronic and vibrational states in amorphous diamond.

Amorphous diamond structures are generated by quenching high-density high-temperature liquid carbon using tight-binding molecular-dynamics simulations. We show that the generated amorphous diamond structures are predominated by strong tetrahedral bonds with the sp3 bonding fraction as high as 97%, thus exhibit an ultra-high incompressibility and a wide band gap close to those of crystalline diamond. A small amount of sp2 bonding defects in the amorphous sample contributes to localized electronic states in the band gap while large local strain gives rise to localization of vibrational modes at both high and low frequency regimes.

Ultra-coarse-graining modeling of liquid water.

It is a great challenge to develop ultra-coarse-grained models in simulations of biological macromolecules. In this study, the original coarse-graining strategy proposed in our previous work [M. Li and J. Z. H. Zhang, Phys. Chem. Chem. Phys. 23, 8926 (2021)] is first extended to the ultra-coarse-graining (UCG) modeling of liquid water, with the NC increasing from 4-10 to 20-500. The UCG force field is parameterized by the top-down strategy and subsequently refined on important properties of liquid water by the trial-and-error scheme. The optimal cutoffs for non-bonded interactions in the NC = 20/100/500 UCG simulations are, respectively, determined on energy convergence. The results show that the average density at 300 K can be accurately reproduced from the well-refined UCG models while it is largely different in describing compressibility, self-diffusion coefficient, etc. The density-temperature relationships predicted by these UCG models are in good agreement with the experiment result. Besides, two polarizable states of the UCG molecules are observed after simulated systems are equilibrated. The ion-water RDFs from the ion-involved NC = 100 UCG simulation are nearly in accord with the scaled AA ones. Furthermore, the concentration of ions can influence the ratio of two polarizable states in the NC = 100 simulation. Finally, it is illustrated that the proposed UCG models can accelerate liquid water simulation by 114-135 times, compared with the TIP3P force field. The proposed UCG force field is simple, generic, and transferable, potentially providing valuable information for UCG simulations of large biomolecules.

Transcriptome analysis revealed that multiple genes were related to the cyflumetofen resistance of Tetranychus cinnabarinus (Boisduval).

Metabolic resistance is one of the main causes of acaricide resistance. Many previous studies focused on the function of specific genes in insecticides/acaricides resistance. However, during the development of resistance, the overall dynamic of expression levels of detoxification enzyme genes in mites is still unclear. Tetranychus cinnabarinus, a major agricultural pest, which is notorious for developing resistance to acaricides rapidly. In this study, a field susceptible strain (YS) was continuously selected for 16, 25 and 32 generations, and developed to low resistance (7.83-fold, L), medium resistance (17.23-fold, M) and high resistance (86.05-fold, H), respectively. Transcriptome sequencing was performed in YS, L, M and H strains. Overall, compared with YS strain, the number of differential expression genes increased slightly with the development of cyflumetofen-resistance. As for detoxification genes, the median of fold change of up-regulated P450、CCE and GST genes was higher than those of all up-regulated genes in three resistance level, but only the number and the median of fold change of up-regulated P450 genes was increased slightly with the development of resistance. In addition, synergism experiments also proved that P450 and GST genes were the major contributors to the metabolic resistance of cyflumetofen of T. cinnabarinus. These results showed that the resistance of T. cinnabarinus to cyflumetofen was related to many resistant genes, among which P450 genes could play crucial roles in cyflumefen resistance.

A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles.

As coarse-grained (CG) studies of large biomolecules increase, developments of reliable CG solvent models become particularly important. In this work, we reduce five water molecules into a three-point CG model with permanent dipole and quadrupole moments. In the CG force field, the modified Morse potential is utilized and an ideal three-water cluster is designed to derive CG-level permanent multipoles. The new CG model is parametrized on the AMOEBA polarizable force field. Various important properties of liquid water are examined to validate the new CG model. Results show that the new CG model can correctly reproduce certain important experimental properties such as density, isothermal compressibility and relative static dielectric permittivity, even better than the existing AA models. Additionally, the CPU tests reveal that the CG model can accelerate molecular dynamics simulations by a factor of 19 compared to the popular AA force field. Compared with the fix-point-charge model widely used in other CG models, the permanent-multipole-based CG model describes more rigid electrostatic attractions. This study also illustrates that the permanent multipole moments contribute a lot to the electrostatic calculations in CG simulation.

Characterization of three phases of liquid carbon by tight-binding molecular dynamics simulations.

We have performed systematic molecular dynamics simulations to study the structures of liquid carbon at 5000 K with the weight density ranging from 1.4 to 3.5 g cm-3, using a three-center tight-binding potential of carbon. The simulation results show that the bonding characteristics of the liquid changes predominately from twofold to threefold, and then to fourfold coordination as the density increases. Signals of two structural changes at the densities of about 1.9 and 3.0 g cm-3 respectively are revealed by the slope changes in the density dependence of structural, electronic and dynamical properties. Our simulation results suggest that there are three distinct liquid carbon phases in this density range. However, further thermodynamics calculations, e.g., free energy calculations, would be required to clarify the possible liquid-liquid transitions.

Novel superconducting structures of BH2 under high pressure.

The crystal structures of boron hydrides in a pressure range of 50-400 GPa were studied using the genetic algorithm (GA) method combined with first-principles density functional theory calculations. BH4 and BH5 are predicted to be thermodynamically unstable. Two new BH2 structures with Cmcm and C2/c space group symmetries, respectively, were predicted, in which the B atoms tend to form two-dimensional sheets. The calculated band structures showed that in the pressure range of 50-150 GPa, the Cmcm-BH2 phase has very small gaps, while the C2/c-BH2 phase at 200-400 GPa is metallic. The superconductivity of the C2/c-BH2 structure was also investigated, and electron-phonon coupling calculations revealed that the estimated Tc values of C2/c-BH2 are about 28.18-37.31 K at 250 GPa.

Theoretical investigation of real-time charge dynamics in open systems coupled to bulk materials.

Environmental effects play an important role on the electron dynamics of open systems, which provide channels for dissipation of electrons and energy in the systems. However, accurate description of the environment of quantum systems is still challenging. The environment is usually assumed to be a quasi-one-dimensional reservoir in previous theoretical studies. In this work, we focus on systems that are adsorbed on bulk surfaces. Two different approaches to describe the spectral details of the environment are adopted and compared: the Lorentzian decomposition approach and the complex absorbing potential (CAP) approach. To achieve similar accuracy for the spectral density of the environment, it is shown that the Lorentzian decomposition approach is computationally more efficient than the CAP approach, especially for bulk systems. The electron dynamics is then followed using the nonequilibrium Green's function method for two systems: a modeling bulk surface system and a scanning tunneling microscope junction. Dissipation paths of excited charge carriers can be analyzed, which provide insights into the understanding of excitation dynamics in bulk materials.

Theoretical Prediction of Si2-Si33 Absorption Spectra.

The optical absorption spectra of Si2-Si33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ∼12 eV, it is noted that all the clusters have remarkable absorption in deep ultraviolet region of 100-200 nm, and the maximum absorption intensity is ∼100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.

Si78 double cage structure and special optical properties.

We performed first-principles calculations to study the structural stability of Si78 clusters with or without hydrogen passivation. The calculations reveal that an endohedral double cage isomer is more stable than the diamond-like structure, whereas the opposite is found for the hydrogen passivated isomers. In particular, the hydrogenated double cage and diamond-like structure may display blue shifts to the visible and UV regions, respectively. The IR vibration spectra, ionization potential (IP) and electronic density-of-states of the clusters were calculated and discussed.

Geometric and electronic structures of potassium-adsorbed rubrene complexes.

The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K1RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D2- and C2h-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K1RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules, the structures of D2- and C2h-like K1RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D2-like complexes show minimum-energy basins, whereas the C2h-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D2-like complexes is most likely along the backbone in contrast to the C2h-like ones. Although the electronic structures of the minimum-energy structures of D2- and C2h-like K1RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced resemblance of the simulated to the experimental spectra. Fourth, the HOMO and LUMO are mainly the α and ß components of the 2p orbitals of the backbone carbons, respectively.

Structures and electronic properties of the SiAu(n) (n = 17-20) clusters.

The structures and electronic properties of the SiAu(n) (n = 17-20) clusters are systematically investigated using DFT calculations. The result shows that doping with silicon would significantly change the structures of the gold clusters. For the SiAu(n) (n = 17-20) clusters, the lowest-energy structures exhibit shell-like cage configuration in which the dopant Si atom binds to the cage surface and one Au atom skips to the top of the Si atom forming a SiAu5 or SiAu6 subunit except SiAu19, which is a tetrahedron-like structure with a protruding Au atom. The Au atoms of the SiAu(n) (n = 17-20) clusters carry different partial charges due to their different locations.

AmberMDrun: A Scripting Tool for Running Amber MD in an Easy Way.

MD simulations have been widely applied and become a powerful tool in the field of biomacromolecule simulations and computer-aided drug design, etc., which can estimate binding free energy between receptor and ligand. However, the inputs and force field preparation for performing Amber MD is somewhat complicated, and challenging for beginners. To address this issue, we have developed a script for automatically preparing Amber MD input files, balancing the system, performing Amber MD for production, and predicting receptor-ligand binding free energy. This script is open-source, extensible and can support customization. The core code is written in C++ and has a Python interface, providing both efficient performance and convenience.

Study of fusion peptide release for the spike protein of SARS-CoV-2.

The spike protein of SARS-CoV-2 can recognize the ACE2 membrane protein on the host cell and plays a key role in the membrane fusion process between the virus envelope and the host cell membrane. However, to date, the mechanism for the spike protein recognizing host cells and initiating membrane fusion remains unknown. In this study, based on the general assumption that all three S1/S2 junctions of the spike protein are cleaved, structures with different forms of S1 subunit stripping and S2' site cleavage were constructed. Then, the minimum requirement for the release of the fusion peptide was studied by all-atom structure-based MD simulations. The results from simulations showed that stripping an S1 subunit from the A-, B- or C-chain of the spike protein and cleaving the specific S2' site on the B-chain (C-chain or A-chain) may result in the release of the fusion peptide, suggesting that the requirement for the release of FP may be more relaxed than previously expected.

Ground and excited states of even-numbered Hubbard ring at half-filling: comparison of the extended Gutzwiller approach with exact diagonalization.

It remains a great challenge in condensed matter physics to develop a method to treat strongly correlated many-body systems with balanced accuracy and efficiency. We introduce an extended Gutzwiller (EG) method incorporating a manifold technique, which builds an effective manifold of the many-body Hilbert space, to describe the ground-state (GS) and excited-state (ES) properties of strongly correlated electrons. We systematically apply an EG projector onto the GS and ES of a non-interacting system. Diagonalization of the true Hamiltonian within the manifold formed by the resulting EG wavefunctions gives the approximate GS and ES of the correlated system. To validate this technique, we implement it on even-numbered fermionic Hubbard rings at half-filling with periodic boundary conditions, and compare the results with the exact diagonalization (ED) method. The EG method is capable of generating high-quality GS and low-lying ES wavefunctions, as evidenced by the high overlaps of wavefunctions between the EG and ED methods. Favorable comparisons are also achieved for other quantities including the total energy, the double occupancy, the total spin and the staggered magnetization. With the capability of accessing the ESs, the EG method can capture the essential features of the one-electron removal spectral function that contains contributions from states deep in the excited spectrum. Finally, we provide an outlook on the application of this method on large extended systems.

High island densities and long range repulsive interactions: Fe on epitaxial graphene.

The understanding of metal nucleation on graphene is essential for promising future applications, especially of magnetic metals which can be used in spintronics or computer storage media. A common method to study the grown morphology is to measure the nucleated island density n as a function of growth parameters. Surprisingly, the growth of Fe on graphene is found to be unusual because it does not follow classical nucleation: n is unexpectedtly high, it increases continuously with the deposited amount θ and shows no temperature dependence. These unusual results indicate the presence of long range repulsive interactions. Kinetic Monte Carlo simulations and density functional theory calculations support this conclusion. In addition to answering an outstanding question in epitaxial growth, i.e., to find systems where long range interactions are present, the high density of magnetic islands, tunable with θ, is of interest for nanomagnetism applications.