2012年2月-Materials Studio文献参考

时间:2014-01-07

 


 

[2012年1月30日] 
CASTEP


First principle study of the elastic properties of InGaAs with different doping concentrations of indium
   The electronic structure and elastic properties of the InGaAs crystal with different doping concentrations of indium are studied by the plane-wave pseudopotential method based on density functional theory with Cambridge Serial Total Energy Package programme. The density of states and the elastic constants of the InGaAs crystal with different doping concentrations of indium are obtained. The elastic modulus is also calculated from the theoretical elastic constants by Voigt?Reuss?Hill averaging scheme. The band gaps of the InGaAs crystal decrease monotonically with increasing indium concentration. Similarly, the elastic constants of the InGaAs crystal with the symmetry of cubic crystal system decrease monotonically with increasing indium concentration. With increasing indium concentration, the brittleness of the InGaAs crystal decreases and the ductility of the InGaAs crystal increases monotonically, resulting in the tangential deformation of the supercells which is more prone to occur. The values of the elastic constants obtained will be helpful in analysing the elastic properties of InGaAs/GaAs semiconductor saturable absorber mirror and in guiding the application of InGaAs/GaAs as a saturable absorber in passively Q-switched laser.

http://dx.doi.org/10.1080/08927022.2011.602975

CASTEP + DMol3

   First-principle calculations of structural stabilities and elastic properties of Al2Sr and Mg2Sr phases
   Structural stabilities, elastic properties and electronic structures of Mg17Al12, Al2Sr and Mg2Sr phases have been determined from first?principle calculations by using CASTEP and DMOL programs based on the density functional theory. The calculated formation heats and cohesive energies indicated that Al2Sr has the strongest alloying ability as well as the highest structural stability. The calculated Gibbs free energy showed that the structural stabilities of Mg17Al12, Al2Sr andMg2Sr change with elevated temperature, when the temperature is above 423 K, Al2Sr is more stable than Mg17Al12phase, and Sr addition to the Mg?Al base alloys can improve the creep properties. The calculated bulk modulus (B), anisotropy values (A), Young’s modulus (E), shear modulus (G) and Poisson ratio (ν) showed that Mg2Sr is ductile, on the contrary, Mg17Al12and Al2Sr are both brittle, and among the three phases Mg2Sr is a phase with the best plasticity. The calculations of the density of states (DOS) and Mulliken electronic populations showed that the reason of Al2Sr having the highest structural stability attributes to Al2Sr phase having the more covalent bonds compared with Mg17Al12 and Mg2Sr phases, while Mg17Al12 phase having more stable structure is the result of co?action of ionicand covalent bonds.

http://www.ams.org.cn/EN/abstract/abstract19702.shtml

CASTEP + GULP

Computer simulation of Na-bearing majoritic garnet 
http://dx.doi.org/10.1134/S1028334X11110092

DMol3

   On the difference in cycling behaviors of lithium-ion battery cell between the ethylene carbonate- and propylene carbonate-based electrolytes
   Density functional theory (DFT) calculations and classical molecular dynamics (MD) simulations have been performed to gain insight into the difference in cycling behaviors between the ethylene carbonate (EC)-based and the propylene carbonate (PC)-based electrolytes in lithium-ion battery cells. DFT calculations of the lithium solvation, Li+(S)i (S = EC or PC; i = 1?4) with and without the presence of the counter anion showed that the desolvation energy to remove one solvent molecule from the first solvation shell of the lithium ion was significantly reduced by as much as 70 kcal mol?1 (293.08 kJ mol?1) in the presence of the counter anion, suggesting the lithium ion is more likely to be desolvated at high salt concentrations. The thermodynamic stability of the ternary graphite intercalation compounds, Li+(S)iC72, in which Li+(S)i was inserted into a graphite cell, was also examined by DFT calculations. The results suggested that Li+(EC)iC72 was more stable than Li+(PC)iC72 for a given i. Furthermore, some of Li+(PC)iC72 were found to be energetically unfavorable, while all of Li+(EC)i=1?4C72 were stable, relative to their corresponding Li+(S)i in the bulk electrolyte. In addition, the interlayer distances of Li+(PC)iC72 were more than 0.1 nm longer than those of Li+(EC)iC72. MD simulations were also carried out to examine the solvation structures at a high salt concentration of LiPF6: 2.45 mol kg?1. The results showed that the solvation structure was significantly interrupted by the counter anions, having a smaller solvation number than that at a lower salt concentration (0.83 mol kg?1). We propose that at high salt concentrations, the lithium desolvation may be facilitated due to the increased contact ion pairs so as to form a stable ternary GIC with less solvent molecules without destruction of graphite particles, followed by solid?electrolyte-interface film formation reactions. The results from both DFT calculations and MD simulations are consistent with the recent experimental observations.

http://dx.doi.org/10.1016/j.electacta.2011.05.112

   A density functional theory study on the Ti/P binary cluster ions
   Under the framework of density functional theory, an all-electron calculation on the geometrical structures and dissociation channels of Ti/P binary cluster ions has been carried out. The P2, P3 and P4 structures are found to be the relatively stable units in these cluster ions. The lowest energy geometries of these Ti/P binary cluster ions may be constructed by bonding Ti, Ti2, Ti3 or Ti4 unit with one or two relatively stable P2, P3 and P4 units. The most possible dissociation channels of these Ti/P binary cluster ions are the detachment of P2, P3 or P4 fragment. It is well consistent with the photodissociation experimental results.

http://dx.doi.org/10.1080/08927022.2011.604855

DMol3 + Forcite + Adsorption locator + QSAR

   Quantitative Structure and Activity Relationship Modeling Study of Corrosion Inhibitors: Genetic Function Approximation and Molecular Dynamics Simulation Methods
   QSAR studies on the inhibition corrosion efficiencies of twenty three organic compounds on steel surface in hydrochloric acid solutions using several physicochemical descriptors and investigation of the adsorption of these compounds on the steel surface by Monte Carlo simulation method were studied. Topological indices as well as several structural descriptors are used in the development of quantitative structure-activity relationships (QSARs) using genetic function approximation statistical analysis method. From our studies it is clear that quantum descriptors are a better choice when predictivity is the main issue. Among the descriptors with major contribution we should point out that lowest unoccupied molecular orbital energy (E(LUMO)) and molecular volume are important predictive descriptors. Computational studies have been used to find the most stable adsorption sites for tributlyamine inhibitor on steel surface.

http://www.electrochemsci.org/papers/vol6/6094077.pdf

[2012年3月2日]

CASTEP

   New insights into the lattice dynamics of α-quartz
   The lattice dynamics of α-quartz has been studied in great details by combining inelastic X-ray scattering (IXS) from single- and polycrystalline samples, 3D mapping of thermal diffuse scattering (TDS) and ab initio calculations. Pronounced features in TDS patterns have been identified and the origin of first peak in vibrational density of states is unambiguously revealed.

http://dx.doi.org/10.1524/zkri.2012.1432

   Mapping application performance to HPC architecture
   A suite of application benchmarks, designed to be broadly representative of UK HPC usage, has been developed to stress a broad range of architectural features of large scale parallel HPC resources. A generic methodology to investigate application performance and scaling characteristics has been defined, resulting in a detailed understanding of the performance of these applications. This methodology is transferable to other applications and systems: it is of practical value to developers and users who are aiming for optimal utilisation of HPC resources. An understanding of the performance characteristics of a range of large-scale HPC resources has been obtained using low-level synthetic benchmarks. A relatively simple, qualitative mechanism to assess and predict application performance on current and future architectures using synthetic benchmark results together with application performance analysis results is explored.

http://dx.doi.org/10.1016/j.cpc.2011.11.013

   Potential-Dependent Structural Memory Effects in Au?Pd Nanoalloys
   Alloying of metals offers great opportunities for directing reactivity of catalytic reactions. For nanoalloys, this is critically dependent on near-surface composition, which is determined by the segregation energies of alloy components. Here Au?Pd surface composition and distribution of Pd within a Au0.7Pd0.3 nanoalloy were investigated by monitoring the electrocatalytic behavior for the oxygen reduction reaction used as a sensitive surface ensemble probe. A time-dependent selectivity toward the formation of H2O2 as the main oxygen reduction product has been observed, demonstrating that the applied potential history determines surface composition. DFT modeling suggests that these changes can result both from Pd surface diffusion and from exchange of Pd between the shell and the core. Importantly, it is shown that these reorganizations are controlled by surface adsorbate population, which results in a potential-dependent Au?Pd surface composition and in remarkable structural memory effects.

http://dx.doi.org/10.1021/jz201660t

   Defect configurations of high-k cations in germanium
   At germanium/high-k interfaces cations and oxygen interstitials can diffuse into the germanium substrate. Here we employ density functional theory calculations to investigate the interaction of a range of such cations (Al, Y, Zr, Nb, La, and Hf) with intrinsic defects and oxygen in germanium. It is predicted that high-k cations strongly bind with lattice vacancies, oxygen interstitials, and A-centers. The implications for microelectronic device performance are discussed.

http://dx.doi.org/10.1063/1.3679089

   The photocatalytical activities for water decomposition of K4R2M10O30 (R = Y, La, Ce, Nd, Sm; M = Ta, Nb) and their photophysical properties based on the first principle calculation
   Series of photocatalysts K4R2M10O30 (R = Y, La, Ce, Nd, Sm; M = Ta, Nb) were presented as iso-structural compounds by solid-state reaction method. These photocatalysts showed water decomposition activities under λ > 300 nm irradiation with Na2SO3 and AgNO3 solution acting as hole and electron scavenges respectively. Among them, R = Ce demonstrated water decomposition activities under visible light irradiation (λ > 420 nm) and R = La showed overall water splitting activities under λ > 300 nm irradiation. The first principle calculation based on density functional theory with Plane-wave pseudo potential method and Generalized Gradient Approximation was conducted on M = Nb as representatives to investigate their electronic structure closely, so did on their precursor oxides. Combined with the electronic structures and absorption properties, the band structures of K4R2M10O30 (R = Y, La, Ce, Nd, Sm; M = Ta, Nb) were proposed and this model of band structure is in good agreement with their photocatalytical activities. Furthermore, the visible light responsive ability of R = Ce, as the only one among them, is regarded as the hybridization and overlap of partial occupied and unoccupied Ce 4f with O 2p and Nb 4d (Ta 5d), while in other cases, the band gap transition from O 2p to Nb 4d Ta (5d), which mainly consist their valence band and conduction band respectively, is dominant. Furthermore, there showed obvious inherent relationship between K4R2M10O30 (R = Y, La, Ce, Nd, Sm; M = Ta, Nb) and their precursor rare earth oxides in terms of electronic structure and photophysical properties.

http://dx.doi.org/10.1016/j.molcata.2011.10.019

   Single crystal titanate?zirconate nanoleaf: Synthesis, growth mechanism and enhanced photocatalytic hydrogen evolution properties
   A novel titanate?zirconate solid solution with controllable nanoleaf/microsisal-like three-dimensional morphology, Na2(Ti0.75Zr0.25)4O9, grows on the surface of a Ti-based bulk metallic glass by a combination of hydrothermal and dealloying processes. A single sisal-like bundle consists of a number of nano-sized leaves and each nanoleaf has a thickness, width and length of 20?30 nm, 200?300 nm and 15?20 μm, respectively. A modified dipole driving Ostwald ripening mechanism for the interesting architectures has been proposed based on a series of time-dependent experiments and the structure feature of titanate. Moreover, the as-synthesized nanoleaf/microsisal-like material exhibits extraordinary ability to produce hydrogen from a methanol/water solution that is higher than that of a commercial TiO2 (Degussa P25) film, undoping titanate nanotube film and titanate?zirconate one-dimensional nanoleaf film. Possible origins of the high performance of the as-synthesized three-dimensional nanomaterials were discussed based on theoretical and experimental results.

http://dx.doi.org/10.1039/C1CE06088K

CASTEP + DMol3

   Calculation of Infrared/Raman Spectra and Dielectric Properties of Various Crystalline Poly(lactic acid)s by Density Functional Perturbation Theory (DFPT) Method
   We calculated infrared (IR) and Raman spectra of poly(lactic acid) (PLA) polymorphs by employing density functional perturbation theory (DFPT) and a plane wavebasis set. Significant different characteristics are found in the calculated spectra of poly(l-lactic acid) (PLLA) α-form and PLLA/poly(d-lactic acid) (PDLA) stereocomplex (sc) form. Particularly in the carbonyl stretching region, there is only one sharp peak in the sc-form while there are five peaks in the PLLA α-form. A low wavenumber (65 cm?1) vibration band of α-PLLA observed in a previous terahertz time-domain spectroscopy study was reproduced in the calculated solid-state PLLA spectra. This band could not be obtained by using DFT (B3LYP/6-31G*) simulation on a single PLA oligomer chain and had been attributed to lattice vibrations in the crystal. The permittivity and polarizability tensors of PLA single crystals were also obtained using the DFPT method and were found to be anisotropic.

http://dx.doi.org/10.1021/jp210123q

DMol3

   Theory Structure, Synthesis, and Spectroscopic Characterization, in Vitro Antitumor Activity, and DNA Docking Studies of (p-Cymene)Ru(curcuminato)chloro
   The in vitro antiproliferative activity of the title compound on five tumor cell lines shows preference for the colon?rectal tumor HCT116, IC50 = 13.98 μM, followed by breast MCF7 (19.58 μM) and ovarian A2780 (23.38 μM) cell lines; human glioblastoma U-87 and lung carcinoma A549 are less sensitive. A commercial curcumin reagent, also containing demethoxy and bis-demethoxy curcumin, was used to synthesize the title compound, and so (p-cymene)Ru(demethoxy-curcuminato)chloro was also isolated and chemically characterized. The crystal structure of the title compound shows (1) the chlorine atom linking two neighboring complexes through H-bonds with two O(hydroxyl), forming an infinite two-step network; (2) significant twist in the curcuminato, 20° between the planes of the two phenyl rings. This was also seen in the docking of the Ru-complex onto a rich guanine B-DNA decamer, where a Ru?N7(guanine) interaction is detected. This Ru?N7(guanine) interaction is also seen with ESI-MS on a Ru-complex-guanosine derivative.

http://dx.doi.org/10.1021/jm200912j

   Nonphotochemical Base-Catalyzed Hydroxylation of 2,6-Dichloroquinone by H2O2 Occurs by a Radical Mechanism
   Kinetic and structural studies have shown that peroxidases are capable of the oxidation of 2,4,6-trichlorophenol (2,4,6-TCP) to 2,6-dichloro-1,4-benzoquinone (2,6-DCQ). Further reactions of 2,6-DCQ in the presence of H2O2 and OH? yield 2,6-dichloro-3-hydroxy-1,4-benzoquinone (2,6-DCQOH). The reactions of 2,6-DCQ have been monitored spectroscopically [UV?visible and electron spin resonance (ESR)] and chromatographically. The hydroxylation product, 2,6-DCQOH, has been observed by UV?visible and characterized structurally by 1H and 13C NMR spectroscopy. The results are consistent with a nonphotochemical base-catalyzed oxidation of 2,6-DCQ at pH > 7. Because H2O2 is present in peroxidase reaction mixtures, there is also a potential role for the hydrogen peroxide anion (HOO?). However, in agreement with previous work, we observe that the nonphotochemical epoxidation by H2O2 at pH < 7 is immeasurably slow. Both room-temperature ESR and rapid-freeze-quench ESR methods were used to establish that the dominant nonphotochemical mechanism involves formation of a semiquinone radical (base -catalyzed pathway), rather than epoxidation (direct attack by H2O2 at low pH). Analysis of the kinetics using an Arrhenius model permits determination of the activation energy of hydroxylation (Ea = 36 kJ/mol), which is significantly lower than the activation energy of the peroxidase-catalyzed oxidation of 2,4,6-TCP (Ea = 56 kJ/mol). However, the reaction is second order in both 2,6-DCQ and OH? so that its rate becomes significant above 25 °C due to the increased rate of formation of 2,6-DCQ that feeds the second-order process. The peroxidase used in this study is the dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata, which is used to study the effect of a catalyst on the reactions. The control experiments and precedents in studies of other peroxidases lead to the conclusion that hydroxylation will be observed following any process that leads to the formation of the 2,6-DCQ at pH > 7, regardless of the catalyst used in the 2,4,6-TCP oxidation reaction.

http://dx.doi.org/10.1021/jp208536x

   Strong Interaction between Gold and Anatase TiO2(001) Predicted by First Principle Studies
   The adsorption of gold clusters (Aun, n = 1?10) on the minority surface, (001), of anatase titanium dioxide (TiO2) has been studied in the framework of density functional theory. Various adsorption geometries of gold (Au) clusters on clean, unreconstructed TiO2(001) have been investigated. It is found the adsorption of gold on TiO2(001) is much stronger than that on the majority surface, (101). Due to the strong interfacial bonding, the valence electrons of gold have been highly delocalized and dominate the highest occupied frontier orbitals of Au/TiO2(001). Consequently, it is predicted that the support of TiO2(001) may offer better catalysis performance than conventionally used TiO2(101).

http://dx.doi.org/10.1021/jp208948x

   Anti-Kubas Type Interaction in Hydrogen Storage on a Li Decorated BHNH Sheet: A First-Principles Based Study
   We have performed first-principles DFT calculations to explore the possibility of using a metal-functionalized hydrogenated BN sheet for storage of molecular hydrogen. The chair BHNH conformer is ideally suited for adsorption of metal adatoms on the surface of the sheet. The Li metal, in particular, binds to the sheet with a binding energy (~0.88 eV/Li atom) and becomes cationic, which thereby attracts hydrogen molecules. However, the interaction of the BHNH sheet and the absorbed H2 molecules with Li+ is different from the conventionally known Dewar coordination or Kubas-type interaction for hydrogen storage. Each Li+ can adsorb up to four H2 molecules, and the hydrogen binding energy is in the desired energy window for effective storage of molecular hydrogen. The fully Li-functionalized BHNH sheet yields a reasonably high gravimetric density, which is more than 7 wt %.

http://dx.doi.org/10.1021/jp210355n

   Lowest-energy structures of (MgO)n (n = 2?7) clusters from a topological method and first-principles calculations
   A topological method combined with first-principles calculations is used to generate isomer structures and to globally search on the potential energy surface of (MgO)n clusters with n = 2?7. In addition to the previously reported ground-state configurations, our approach has located many new metastable isomer structures. The growth pattern of MgO clusters can be classified into three motifs: the expansion of two-dimensional ring-like structures, the combination of basic units like quadrangle and hexagon, and the addition of atoms to smaller-sized clusters. The size-dependent stability and electronic properties of MgO clusters are analyzed. Hexagonal ring-like unit is found highly stable for (MgO)n clusters, while the (MgO)5 cluster is not as stable as the clusters of other sizes.

http://dx.doi.org/10.1016/j.comptc.2011.11.015

   A Co-Crystal Composed of the Paramagnetic Endohedral Metallofullerene La@C82 and a Nickel Porphyrin with High Electron Mobility
   The structure of 
La@C82 was clarified by single-crystal X-ray diffraction of samples co-crystallized with [NiII(OEP)] (OEP=octaethylporphyrin; see structure La?red, N?blue, Ni?yellow, H?pink). The charge-carrier mobility of the co-crystal was determined using flash-photolysis time-resolved microwave conductivity measurements. The material exhibited an anisotropic and high electron mobility of up to 0.9?cm2?V?1?s?1.
http://dx.doi.org/10.1002/anie.201106912

   Hydrogen Storage on Scandium-Coated Toroidal Carbon Nanostructure C120  modeled with Density Functional Theory
   Ab initio density functional calculations were performed on a toroidal carbon C120 nanostructure doped from one to ten Sc atoms bonded to its outer surface. These calculations are based on DFT with the generalized gradient approximation PW91 (Perdew and Wang) as implemented in the Materials Studio v.4.3 code. The Dmol3 module was used to calculate, among others, total energies, charge density, HOMO-LUMO and Mulliken population analysis. On the basis of these results, it is possible to propose that a single Sc atom is able to adsorb up to 6 H2 molecules. Therefore the study was extended for a system with 10 Sc atoms, which can adsorb up to 60 H2 molecules. This leads to 6.01 wt %, which fulfils the current requirement (6 wt %, at 2010, specified by US Department of Energy (DOE)). Accordingly, the scandium-coated toroidal carbon C120 nanostructure is a good candidate for H2 storage with moderate adsorption energy.

GULP

   Dependence of volume changes during solid solution formation and of volume size factor on solute volume, group number and crystalline structure
   This paper describes the dependence of both volume change during primary solid solution formation and that of volume size factor, Vsf on solute mean atomic volume. Our research findings demonstrate a direct relationship between Vsf or volume change and solute atomic volume. For twenty solvent elements, the average linear correlation coefficient between Vsf and solute atomic volume is 0.659. The average correlation coefficient for volume changes is 0.592. Forty-seven systems solute?solvents with the same crystalline structure indicate that the average linear correlation coefficient between Vsf and solute atomic volume is 0.780. The average correlation coefficient between Vsf and solute atomic volume is 0.907 for solute elements from the same group in the Periodic Table. The average correlation coefficient for volume changes is 0.775. Forty-eight systems were analyzed. For fourteen elements, it was found that elements with the same crystalline structure have an average correlation coefficient between Vsf and solvents atomic volume of 0.934. The relationship between volume changes and solvent atomic volume can be expressed with a quadratic model. Then, volume change during primary solid solution depends upon solute volume, group number and crystalline structure.

http://dx.doi.org/10.1016/j.intermet.2011.11.004

   Incorporation of Yb3+ ions in multicomponent phase-separated fibre glass performs
   The local environment around Yb3+ ions in silica-based optic fibre preforms has been studied in specimens with different composition and submitted to different annealing processes. The formation upon annealing of nano-sized particles of YbPO4 has been evidenced by X-ray Absorption Spectroscopy whereas optical luminescence present Stark-split states in the anti-Stokes lines, typical of a structurally ordered phase. This evidences the preferential location of Yb in highly coordinated phosphate environment, with remarkable effects of such ordered phase on the optical response of the system. This study confirms and extends analogous observations done in previous literature on Erbium in similar glasses.

http://dx.doi.org/10.1016/j.optmat.2011.09.010

   The 4:5 Si-to-SiC atomic lattice matching interfaces in the system of Si(111) heteroepitaxially grown on 6H-SiC(001) substrates
   Corresponding lattice planes of 4:5 Si-to-SiC atomic matching structures are observed at the Si(111)/6H-SiC(001) interface. The periodical Si/SiC interface structure is further illustrated and characterized by an atomic model derived from experiment results. It is discovered that there is a minor lattice mismatch of 0.26% in the structure. Moreover, the atomic structure of the interface and its stability are energetically investigated by molecular dynamics simulations. The results demonstrate that the atomic relaxations caused by lattice mismatch are slight to the growth of a perfect crystalline Si film and the interfaces are quite stable with the formation energy of ?22.452 eV.

http://dx.doi.org/10.1016/j.ssc.2011.10.037