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Epidermal growth factor EGFR is an important target for non-small cell lung (NSCL) cancer, and inhibitors of AKT protein has been used in many cancer treatments including NSCL cancer. Therefore, screening small molecular inhibitors targeting both EGFR and AKT can help for cancer treatment. In this study, we screened Traditional Chinese Medicine on Immune-Oncology (TCMIO) database for potential natural product inhibitors that can target both EGFR and AKT using ligand-based pharmacophore model, molecular docking, and MD simulations methods. The human endogenous database HMDB was also screened. It was found that TCMIO89212, TCMIO90156 and TCMIO98874 from the TCMIO database had large binding free energies with EGFR and AKT. In the HMDB database, kinetin-7-N-glucoside was found to have ability to bind to EGFR and AKT. These results may provide valuable information for further experimental studies.

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 "

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.

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

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.

As nanoelectronic synapses, memristive ferroelectric tunnel junctions (FTJs) have triggered great interest due to the potential applications in neuromorphic computing for emulating biological brains. Here, we demonstrate multiferroic FTJ synapses based on the ferroelectric modulation of spin-filtering BaTiO

Si nanostructures (Si-NSs) epitaxially grown or adsorbed on Si (111) surface, with various shapes including pit-like, bars, islands, hill-like, diamond-like and double cage, were studied theoretically using density-functional theory (DFT) calculations. The electronic and optical properties of these Si-NSs were calculated, showing that the designed Si-NSs modifications can enhance the optical absorption for Si surface.

Interactions between defects in graphene and the lattice distortion and electronic charge localization induced by the defect interactions are studied by tight-binding (TB) calculations using the recently developed three-center TB potential model. The interaction between two 5–7 Stone–Wales defects gliding along the zig-zag (ZZ) direction of graphene, which has been observed by experiment, is studied at first to validate the TB calculations. Reconstructed divacancy defect pairs and di-adatom defect pairs separated along the glide ZZ and armchair (AC) directions in graphene, respectively, are then studied. We show that the characteristics (i.e., attractive or repulsive) and the strength of interactions between these defects are dependent on the type of defects and on the direction and distance of the defect separation on graphene. Although elastic interaction due to graphene lattice distortion induced by the defect has significant contribution to the total interaction energy, redistribution of electron char...

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.

Iron hydrides can be formed under high pressure and have special physical and chemical properties. Structures and stabilities of FeXSeHY (X = 1–2, Y = 1–6) hydrides under high pressure were studied using a genetic algorithm method combined with DFT calculations. Further, using triangular phase diagrams, we found that the C2/m-FeSeH is most stable among FeSeH1–6 at 150 GPa. Among Fe2SeH1–6, the enthalpy values of Amm2- and I4/mmm-Fe2SeH2 phases are the lowest at 150 and 200 GPa, respectively, and the Immm-Fe2SeH phase is the lowest in enthalpy at 250–300 GPa. The predicted superconducting transition temperatures (Tc) show that C2/m-FeSeH and Amm2-Fe2SeH2 have almost no superconductivity, while the predicted Tc values of I4/mmm-Fe2SeH2 and Immm-Fe2SeH at 150 GPa are 8.6 and 1.1 K, respectively, and that of Pm-FeSeH6 at 150 GPa is 34.4 K.

In this work, the photoemission spectroscopy (PES) of rubrene thin films deposited with heavy alkali metal (cesium, rubidium, and potassium) at the alkali/rubrene stoichiometric ratio of 1:1 are studied with density functional theory (DFT) and compared with experiments available in the literature. The common characteristics of PES observed in the rubrene thin films doped with heavy alkali metal are explicable with the DFT simulations. Detailed analysis on the geometric and electronic structures of cesium-, rubidium-, and potassium-rubrene complexes reveals two fundamental reasons for the commonness of their photoemission spectra. First, the electronic structures demonstrated with the energy density-of-states analysis are not much affected by the different adsorption sites of the alkali atom on the tetracene-like backbone of rubrene. Second, the minimum-energy structures of the three (heavy-alkali)-rubrene complexes are similar. The (heavy-alkali)-rubrene complexes differ from the (light-alkali)-rubrene complexes (lithium- and sodium-rubrene) in minimum-energy geometries and the orbital constituents of the highest occupied molecular orbital (HOMO) level.

The crystal structures of $\mathrm{CaB}\text{\ensuremath{-}}{\mathrm{H}}_{n}$ compounds with $n=1--12$ in a pressure range of 50--300 GPa were studied using the genetic algorithm method and first-principles density-function theory calculations. Stable structures with stoichiometry of $\mathrm{CaB}{\mathrm{H}}_{6}$ and $\mathrm{CaB}{\mathrm{H}}_{7}$ were predicted in different pressure range. $\mathrm{B}{\mathrm{H}}_{4}$, $\mathrm{B}{\mathrm{H}}_{5}$, and $\mathrm{B}{\mathrm{H}}_{6}$ units were found to be the main motifs in these compounds. Moreover, metastable $Imm2$ $\mathrm{CaB}{\mathrm{H}}_{7}$ is dynamically stable above 180 GPa, with the formation of tetrahedral $\mathrm{B}{\mathrm{H}}_{4}$ unit surrounded by Ca atom and ${\mathrm{H}}_{3}$ unit. Electron-phonon coupling (EPC) calculations reveal that the superconducting properties are closely related to the strong hydrogen-boron bonding of the $\mathrm{B}{\mathrm{H}}_{4}$ unit in $Imm2$, and ${T}_{c}$ can reach \ensuremath{\sim}200 K at 200 GPa. As the major units, $\mathrm{B}{\mathrm{H}}_{4}$, $\mathrm{B}{\mathrm{H}}_{5}$, and $\mathrm{B}{\mathrm{H}}_{6}$ units exist in the $Imm2$, ${P}_{2}$, and $P{2}_{1}/m$ phases of $\mathrm{CaB}{\mathrm{H}}_{7}$ at 300 GPa, respectively; the corresponding EPC parameter \ensuremath{\lambda} decreases with the increase of hydrogen content in $\mathrm{CaB}{\mathrm{H}}_{7}$.

We introduce a rotationally invariant approach combined with the Gutzwiller conjugate gradient minimization method to study correlated electron systems. In the approach, the Gutzwiller projector is parametrized based on the number of electrons occupying the onsite orbitals instead of the onsite configurations. The approach efficiently groups the onsite orbitals according to their symmetry and greatly reduces the computational complexity, which yields a speedup of 20 ∼ 50 × in the minimal basis energy calculation of dimers. The computationally efficient approach promotes more accurate calculations beyond the minimal basis that is inapplicable in the original approach. A large-basis energy calculation of F2 demonstrates favorable agreements with standard quantum-chemical calculations Bytautas et al (2007 J. Chem. Phys. 127 164317)

The structures and interaction energies of water clusters with ring stacking motifs are studied by using ab initio calculations. The structures of the water clusters are constructed by stacking either single rings or multi‐rings of tetramer, pentamer, and hexamer. We found that, in the single‐ring‐stacking motif, the most stable isomers exhibit an alternative clockwise‐anticlockwise stacking pattern. We also show that four‐layer single‐ring‐stacking isomers are not energetically favorable in comparison with those of two‐layer multi‐ring‐stacking isomers. The relative stability of the isomers is also analyzed in terms of H‐bond strength and elastic distortions of the water molecules.

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.

We review our recent work on the Gutzwiller conjugate gradient minimization method, an ab initio approach developed for correlated electron systems. The complete formalism has been outlined that allows for a systematic understanding of the method, followed by a discussion of benchmark studies of dimers, one- and two-dimensional single-band Hubbard models. In the end, we present some preliminary results of multi-band Hubbard models and large-basis calculations of F2 to illustrate our efforts to further reduce the computational complexity.

The search for high-Tc superconductors under high pressure has been a hot research topic. In this work, the structures under high pressure of ternary hydrogen-rich compounds KYHn (n = 3-8, 10, 12 and 14) were searched by genetic algorithm method combined with the density function theory (DFT) method. The results showed that KYH8 and KYH14 demonstrate good stability and possess superconductivity. The KYH8-C2/m structure has buckled “H3” units and heavy atom with layered arrangement. For the KYH14-Cmmm structure, the rich H atoms form a cage-like structure with the K atom at the center. The electron-phonon coupling (EPC) calculations indicated that the Tc's of KYH8-C2m are 111.3, 122.0 and 163.7 K at 200, 250 and 300 GPa, respectively. The KYH14-Cmmm was predicted to have a Tc of 167.1 K at 300 GPa, and the strong EPC might be resulted mainly from the high-frequency vibrations of the H atoms.

Coarse-grained (CG) model has been a powerful tool in bridging the gap between theoretical studies and experimental phenomena in biological computing field. The reconstruction from a CG model to an atomic-detail structure is especially important in CG studies of biological systems. In this work, a rigid-fragment- and local-frame-based (RF-LF) backmapping method was proposed to achieve reverse mapping from CG models to atomic-level structures. The initial atomic-level structures were further refined to yield the final backmapping ones. With the popular Martini force field, the performance of the RF-LF method was extensively examined in the CG → AA (CG to AA) backmapping of protein/DNA/RNA systems. Besides, the RF-LF method was also extended to the backmapping of the TMFF model. Numerical results illustrate that the RF-LF backmapping method is generic and parameter-free and can provide a promising way to tackle atomic-level studies in CG models.

Interaction between two hydrogen adatoms on graphene was studied by first-principles calculations. We showed that there is an attraction between two H adatoms on graphene. However, the strength of interaction between two hydrogen adatoms and magnetic properties of graphene are strongly dependent on the residence of the two adatoms on the graphene sublattices. Hydrogen adatoms introduce lattice distortion and electron localization in graphene which mediate the attractive interaction between the two H adatoms.

The optical absorption properties of non-crystalline and crystalline Ge nanoparticles with the sizes from ∼2.5 to 15 A have been studied at the B3LYP/6-31G level using time-dependent density functional theory. Hydrogen passivation and phosphorus doping on some selected Ge nanoparticles were also calculated. With the increase of cluster size, the optical absorption spectra of the non-crystalline Ge nanoparticles change from many peaks to a continuous broad band and at the same time exhibit a systematic red-shift. Doping phosphorus also causes the absorption spectra to shift toward the lower energy region for both non-crystalline and crystalline Ge nanoparticles. The non-crystalline Ge nanoparticles are found to have stronger absorption in the visible region in comparison with the crystalline ones, regardless phosphorus doping.

Using genetic algorithm (GA) method combined with first-principles calculations, the structures, dynamical and thermodynamic stabilities of GaH 5 were studied. The calculated results suggested that at the pressure range 150–400 GPa, the P2 1 /m phase of GaH 5 is the most favorable phase and dynamically stable, but thermodynamically it is unstable and can decompose into GaH 3 and H 2 . The superconducting property of GaH 5 was further calculated, and the predicted superconducting transformation temperature T c of GaH 5 P2 1 /m phase is about 35.63 K at 250 GPa. Besides, we compared the GaH 5 and GaH 3 superconducting properties, and found that GaH 3 -Pm-3n structure has a larger DOS near Fermi level than GaH 5 -P2 1 /m structure, which may be the main reason causing higher T c of GaH 3 than GaH 5 .

Neuromorphic computing is a promising candidate for next-generation information technologies. In the present work, we report the realization of long-term plasticity and synapse emulations in Ag/SrTiO3/(La,Sr)MnO3 memristors with the SrTiO3 active layers down to 3 unit cells (u.c.) in thickness. In the 3 u.c.-thick SrTiO3 device, efficient control of Ag+-ion migration gives rise to enhanced memristive properties with the conductance continuously modulated within a large memory window of ∼26 000% between an Ohmic low resistance state (LRS) and an electron-tunneling high resistance state (HRS). In addition, long-term plasticity of the Ag/SrTiO3/(La,Sr)MnO3 memristors is found to be dependent upon the resistance state. In the HRS, the devices exhibit excellent spike-timing-dependent plasticity characteristics with a large modulation of synaptic weight of ∼3500% and sensitive response to electrical stimuli of as low as ∼1.0 V and as fast as ∼0.01 ms. Adopting the spike-timing-dependent plasticity results as database, supervised learning simulations are demonstrated in the Ag/SrTiO3/(La,Sr)MnO3-based neural networks and a high accuracy rate of 95.5% is achieved for recognizing handwritten digits. These results provide more insights into the ionic migration at nanoscale for continuous resistance modulation and facilitate the design of ultrathin memristors for high-density 3D stacking artificial neural networks.

Effects of alkaline earth metal atoms doping in boron hydrides at high pressure are investigated by first-principles calculations. The calculated results showed that doping with Mg, Ca, Ba, and Sr in B8H16 at 50 GPa is thermodynamically favorable and dynamically stable. The doping changes the B8H16 from a semiconductor to a metal with substantial electronic density-of-state around the Fermi level. The superconductivity of the alkaline earth metal doped B8H16 is studied based on electron-phonon coupling mechanism. The calculated critical superconducting transition temperatures (Tc) range from 10 to 25 K at 50 GPa upon doping. These results suggest that doping metal atoms in boron hydrides is an efficient way in designing superconducting materials.

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.

Proper design of nanomaterials for broadband light absorption is a key factor for improving the conversion efficiency of solar cells. Here we present a hybrid design of silicon–carbon nanostructures with silicon clusters coated by carbon cages, i.e., Sim@C2n for potential solar cell application. The optical properties of these hybrid nanostructures were calculated based on time dependent density function theory (TDDFT). The results show that the optical spectra of Sim@C2n are very different from those of pure Sim and C2n clusters. While the absorption spectra of pure carbon cages and Sim clusters exhibit peaks in the UV region, those of the Sim@C2n nanostructures exhibit a significant red shift. Superposition of the optical spectra of various Sim@C2n nanostructures forms a broad-band absorption, which extends to the visible light and infrared regions. The broadband adsorption of the assembled Sim@C2n nanoclusters may provide a new approach for the design of high efficiency solar cell nanomaterials.

Lattice distortion and electronic charge localization induced by vacancy and embedded-atom defects in graphene were studied by tight-binding (TB) calculations using the recently developed three-center TB potential model. We showed that the formation energies of the defects are strongly correlated with the number of dangling bonds and number of embedded atoms, as well as the magnitude of the graphene lattice distortion induced by the defects. We also showed that the defects introduce localized electronic states in the graphene which would affect the electron transport properties of graphene.

The geometric and electronic structures of neutral monolithium- and monosodium-rubrene (Li 1 Rub and Na 1 Rub) isomers are investigated and compared with monopotassium-rubrene (K 1 Rub). Based on the alkali binding site, all isomers of these alkali-rubrene complexes can be subdivided into two types: intramolecularly intercalated and extramolecularly adsorbed. The minimum-energy Li 1 Rub and Na 1 Rub are intercalated structures, whereas the minimum-energy K 1 Rub is adsorbed. The fact that the intercalated Li 1 Rub and Na 1 Rub structures are energetically favorable over the adsorbed ones can be explained by two energy rules. First, “double” proximity of the intercalating alkali element to a pair of phenyl side groups enormously reduces the total energy. Second, accommodation of a minuscule intercalant does not significantly deform the carbon frame and, thus, increases the energy only by a small amount. Additionally, the peculiar effects of intramolecular intercalation on the electronic structures of molecules are also studied in this simulation of monoalkali intercalation. In the monoalkali-intercalated rubrene complex, only one of the two pairs of phenyl groups of rubrene is intercalated, intentionally leaving another pair pristine, which facilitates the comparison of electronic structures between the intercalated and pristine pairs of phenyl side groups in a single molecule. The uniformity of chemical environments of the phenyl groups of the intercalated Li 1 Rub/Na 1 Rub is deteriorated by the incorporation of the intercalant, and leads to their spectral characteristics in contrast to K 1 Rub. In particular, the introduction of the intercalant promotes the carbon 2 p orbitals of the intercalated phenyl pair to take part in the electronic structures of the HOMO and LUMO peaks of Li 1 Rub/Na 1 Rub. The unpaired electron in the HOMO is delocalized over the backbone with higher probability of distributing over the central two fused rings than over the outer two.

It has been a hot issue to search for hydrides at high pressure with high superconducting transition temperature (Tc). In this work, we studied YBaHn (n = 2∼12) at 50 - 200 GPa and found that most of YBaH2−12 are thermodynamically stable with respect to the elementary YBa and H systems at this pressure range. The most stable phases of YBaH4, YBaH5 and YBaH8 from genetic algorithm (GA) search have C2/m, P3m1 and P4/mmm symmetries at 50 GPa, and P6/mmm, R3m and P4/mmm at 150 GPa, respectively. The P4/mmm-YBaH8 was suggested to be formed by BaH2 + YH6 → YBaH8. In addition, the electric properties, phonon spectra and the superconductivity of the YBaH8 and BaH2 were calculated and discussed. The Tc of P4/mmm-YBaH8 was predicted to be 49.6 K at 50 GPa and 89.4 K at 150 GPa.

We present numerical results of ground-state energies of 9 molecules in the well-established G2 molecule set given by the Gutzwiller conjugate gradient minimization (GCGM) method. The method, beyond the commonly used Gutzwiller approximation, was recently developed based on Gutzwiller variational wave functions. We find that compared to benchmark data given by full configuration interaction, GCGM total energies are reasonably well reproduced with the minimum basis set. To include the dynamical correlation beyond the minimal basis calculations, we adopt the local density approximation for the dynamical correlation energy E c . By comparing the results with benchmark data given by experiments and large-basis configuration interaction, the GCGM total energies with E c are in general better reproduced, but discrepancies are still observed for some dimers.

Low-energy structures of silicon nanoclusters (NCs) at the size about 220 atoms were studied using tight-binding and first-principles calculations. The structures including bulk-like, icosahedral, bucky–diamond, and onion-like structures have been extensively investigated. The results showed that the bulk-like structures are energetically favorable for the Si220 NCs. Our calculations also showed that although the icosahedral structure is energetically competitive with the bulk-like structures at the special size of 220 atoms, the bulk-like structures are more robust as the number of atoms varies. We also studied the structure-energy trend for Si NCs as the function of cluster size and the structural transition to bulk-like motif occur at the size range of 173–215 atoms.

The CO adsorption on the In-doped SnO2 (1 1 0) surface has been studied by the first-principles calculations based on density functional theory. The study reveals that CO can be chemically adsorbed on the bridge site of the In-doped SnO2 (1 1 0) surface transforming into CO2. The favorable oxidization of CO on the surface occurs with a small reaction barrier of 1.03 eV and is exothermic by 1.72 eV. These results suggest that the In-doping can contribute to the improvement of gas sensing properties of the SnO2-based sensors for CO gas.

The structures and optical properties of silicon nanoclusters (Si NCs) have attracted continuous interest in the last few decades. However, it is a great challenge to determine the structures of Si NCs for accurate property calculation due to the complication and competition of various structural motifs. In this work, a Si172 NC with a size of about 1.8 nm was investigated using a genetic algorithm combined with tight-binding and DFT calculations. We found that a diamond crystalline core with 50 atoms (1.2 nm) was formed in the Si172 NC. It can be expected that at a size of about 172 atoms, a diamond crystalline structure can nucleate from the center of the Si NCs. The optical properties of the pure and hydrogenated Si172 NC structures also have been studied using the TDDFT method. Compared with the pure Si172 NC, the absorption peaks of the hydrogenated Si172 NC are obviously blue-shifted.

Tri-layer Au/Pd/Ni(P) films have been widely used as surface finish over the Cu pads in high-end packaging applications. It was found that a thin (Cu,Pd)6Sn5 IMC layer was beneficial in effective reducing inter-diffusion between a Cu substrate and a solder, and therefore the growth of the IMC layer and the EM (electromigration) processes. In this study, the structural properties and phase stability of monoclinic Cu6Sn5-based structures with Pd substitutions were studied by using the first-principles method. The (Cu,Pd)6Sn5 structure with the 4e site substituted by Pd has the lowest heat of formation and is the most stable among (Cu,Pd)6Sn5 structures. Hybridization of Pd-d and Sn-p states is a dominant factor for stability improvement. Moreover, Pd atoms concentration corresponding to the most stable structure of (Cu,Pd)6Sn5 was found to be 1.69 %, which is consistent with the experimental results.

The optical absorption spectra of Si

We performed a global search for possible Au-Si crystal structures using a genetic algorithm (GA) combined with density functional theory (DFT) calculations. Two Au-Si structures, $\mathrm{A}{\mathrm{u}}_{8}\mathrm{S}{\mathrm{i}}_{8}$ and $\mathrm{A}{\mathrm{u}}_{16}\mathrm{S}{\mathrm{i}}_{8}$, were found to be energetically stable and have no imaginary frequencies by phonon calculations. The formation energies of all the studied structures gave a convex hull of the Au-Si system, showing that the most stable composition was $\mathrm{Au}\ensuremath{-}\mathrm{Si}=1:1$ and that the Si-rich structures were much less stable than the Au-rich ones.

The complexes formed by calcium ion and 12 common amino acids were investigated systematically in the gas phase at the level of MP2/6-311++G(d,p)//MP2/6-31G(d,p). The results show that the salt-bridge structure is the most preferred motif for Ca2+ binding aliphatic amino acids without heteroatom in the side chain, while charge-solvated(CS) structure is the most preferred motif for Ca2+ binding other amino acids except for glutamine and lysine. IR spectra of Gln-Ca2+ and Asn-Ca2+ complexes were calculated and compared well with the available experiments. From the study in aqueous solution, the bidentate salt-bridge structure was determined to be the most favorable for all the twenty kinds of amino acids to chelate Ca2+ to both the oxygen atoms of the negatively carboxylate group in the backbone.

Modified Si(111) surface with designed nanostructural modifications including grown pits, nanobars and nanoislands as well as deposited hill-, diamond- and cage-like nanoclusters were studied using density-functional theory (DFT) calculations. The thermal stabilities, electronic structures and optical properties of these various nanostructural modifications of the Si(111) surface were calculated and discussed. The results indicate that the optical absorption of the modified Si(111) surface can be enhanced by these surface modifications especially when depositing diamond-like nanoclusters on the surface.

The hydrated clusters of complexes formed by calcium ion and three different zwitterionic amino acids, glycine (Gly), threonine (Thr) and phenylalanine (Phe) have been studied in the gas phase at MP2/6-311++G(d,p), considering the coordination numbers 6–8 for Ca 2+ . The clusters with the first hydration shell around calcium ion exhibiting the 8-coordination configuration were found to be most preferred for all the three hydrated systems. The relative stabilities of Gly-, Thr- and Phe-Ca 2+ decrease in the order Thr-Ca 2+ (H 2 O) n > Phe-Ca 2+ (H 2 O) n > Gly-Ca 2+ (H 2 O) n upon hydration in contrast to the order without water Phe-Ca 2+ > Thr-Ca 2+ > Gly-Ca 2+ . It may demonstrate that the nature of side chain has remarkable influence on the stability of hydrated calcium–amino acid clusters. The NBO charges were analyzed to understand the bonding characteristics between the calcium ion and the amino acids. Spectroscopic characters of the most stable hydrated clusters can be assigned based on researching the calculated spectra.

Triangular graphene nanoflakes (GNFs) embedded in fluorinated graphene are systematically investigated using first-principles density functional theory (DFT) calculations. The electronic and magnetic properties of such nanoflakes depend sensitively on the topology (armchair or zigzag) and the length of the edge of nanofakes. All embedded armchair triangular GNFs are semiconducting with size-dependent band gaps. The embedded zigzag triangular GNFs are magnetic with a ferrimagnetic ground state due to topological frustration of the π bonds. The magnetic moment scales linear with the size of the triangular GNF.