Atomic Sphere Research Articles

Noncollinear magnetism of Mn nanowires on Fe(1 1 0)

Magnetic properties of Mn linear nanochains on a bcc Fe(1 1 0) surface have been studied using the first-principles real space-linear muffin-tin orbital atomic sphere approximation (RS–LMTO–ASA) method. We have considered up to nine Mn atoms deposited on bcc Fe(1 1 0). Our ab initio calculations reveal the competition between the antiferromagnetic Mn–Mn and Mn–Fe couplings, presenting a behavior which is very different from Mn nanowires on Fe(0 0 1), as shown in a previous publication. Due to this competition and non-negligible Dzyaloshinskii–Moriya interaction, noncollinear magnetic structures are stabilized as ground states for the Mn nanochains on Fe(1 1 0).

Li4Ge2B as a new derivative of the Mo2B5 and Li5Sn2 structure types.

Binary and multicomponent intermetallic compounds based on lithium and p-elements of Groups III-V of the Periodic Table are useful as modern electrode materials in lithium-ion batteries. However, the interactions between the components in the Li-Ge-B ternary system have not been reported. The structure of tetralithium digermanium boride, Li4Ge2B, exhibits a new structure type, in the noncentrosymmetric space group R3m, in which all the Li, Ge and B atoms occupy sites with 3m symmetry. The title structure is closely related to the Mo2B5 and Li5Sn2 structure types, which crystallize in the centrosymmetric space group R-3m. All the atoms in the title structure are coordinated by rhombic dodecahedra (coordination number = 14), similar to the atoms in related structures. According to electronic structure calculations using the tight-binding-linear muffin-tin orbital-atomic spheres approximation (TB-LMTO-ASA) method, strong covalent Ge-Ge and Ge-B interactions were established.

Quantum crystallographic charge density of urea.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.

Molecular thermodynamic modeling of ionic liquids using the perturbation-based linear Yukawa isotherm regularity

In this paper, we present the results of an extensive study on a novel approach to the molecular modeling of pure ionic liquids (ILs) that incorporates the perturbed thermodynamic linear Yukawa isotherm regularity (LYIR), which is derived based on an effective nearest neighboring pair attractive interaction of the Yukawa potential. The LYIR was used to model the densities of ILs up to high pressures (35 MPa) and in the temperature range 293.15 to 393.15 K. To use the LYIR for ILs, a simple molecular model was proposed to describe their molecular structure, in which they were considered as a liquid consisting of the ion pairs moving together in the fluid, and each ion pair was assumed to be a one-center spherical united atom. The ILs under consideration contained one of the IL cations [C2mim]+, [C4mim]+, [C7mim]+, [C8mim]+, [C3mpy]+, [C3mpip]+, [C3mpyr]+ or [C4mpyr]+, and one of the IL anions [BF4]−, [C(CN)3]−, [CF3SO4]− or [NTf2]−. The reliability and physical significance of the parameters as well as the proposed molecular model were tested by calculating the densities of pure imidazolium-, pyridinium-, piperidinium- and pyrrolidimium-based ILs. The results showed that the LYIR can be used to predict and reproduce the density of ILs in good agreement with the experimental data. In addition, the LYIR enabled us to determine the physical quantities, such as an effective Yukawa screening length, λeff, the product of the effective energy well depth and the effective coordination number, (εeff/k)zeff, the contribution of the non-reference thermal pressure and also the influence of the anionic and cationic structure on the λeff parameter. The standard deviation of the IL densities predicted in this work is lower than those calculated by the one other important equation of state reported in the literature.

Electronic Band Structures of the Highly Desirable III–V Semiconductors: TB-mBJ DFT Studies

The correct band gaps of semiconductors are highly desirable for their effective use in optoelectronic and other photonic devices. However, the experimental and theoretical results of the exact band gaps are quite challenging and sometimes tricky. In this article, we explore the electronic band structures of the highly desirable optical materials, III–V semiconductors. The main reason of the ineffectiveness of the theoretical band gaps of these compounds is their mixed bonding character, where large proportions of electrons reside outside atomic spheres in the intestinal regions, which are challenging for proper theoretical treatment. In this article, the band gaps of the compounds are revisited and successfully reproduced by properly treating the density of electrons using the recently developed non-regular Tran and Blaha’s modified Becke–Johnson (nTB-mBJ) approach. This study additionally suggests that this theoretical scheme could also be useful for the band gap engineering of the III–V semiconductors. Furthermore, the optical properties of these compounds are also calculated and compared with the experimental results.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement.

Excess of manganese in an iron-based superconductor: a first-principles study of its electronic, magnetic and superconducting properties

Alloying and doping have always been an effective way of improving the properties of materials—be it electronic, magnetic or superconducting. In this direction, we present a first-principles investigation of the electronic, magnetic and superconducting properties of the systems (where x = 0.0, 0.01, 0.02 and 0.03). The calculations were performed using the Korringa–Kohn–Rostoker (KKR) atomic sphere approximation (ASA). In order to treat the disorder, we employed the coherent-potential approximation (CPA) into the KKR method. We performed both unpolarized and spin-polarized calculations and found that these systems are close to being magnetic. The results have been analyzed in terms of the density of states (DOS), electronic band structures, Fermi surfaces and the superconducting transition temperature Tc. We find that there are no significant changes in the shape of the Fermi surfaces in unpolarized calculations with respect to pure FeSe, but in spin-polarized calculations, the excess of the transition-metal Mn atoms substantially modifies the Fermi surface compared with the parent FeSe and compounds. We have also estimated the value of electron–phonon mass enhancement factor λ which is the sum of the electron–phonon coupling constant as well as the electron–electron interaction. Using λ, we have calculated the superconducting transition temperature Tc for the Mn doped superconductor. The calculated Tc are in good agreement with the experimental results. Additionally, Hopfield parameters are also calculated from the charge self-consistent potential using the KKR–ASA–CPA method for understanding the trend of Tc and DOS at Fermi energy.

First-principles Study of Electronic Properties of FeCrxSe Alloys

ABSTRACTWe performed first-principles study of electronic properties of FeCrxSe (x=0.0, 0.01, 0.02, 0.04) alloys using the Green’s function-based Korringa-Kohn-Rostoker Atomic Sphere Approximation method within the coherent potential approximation (KKR-ASA-CPA). The KKR-ASA-CPA method is implemented with density function theory (DFT). We find that the excess of Cr into FeSe significantly affects the electronic structure with respect to the parent FeSe. The results have been analyzed in terms of changes in the density of states (DOS), partial DOS, band structures, Fermi surface, bare Sommerfeld constant and the superconducting transition temperature of FeCr0.01Se, FeCr0.02Se and FeCr0.04Se alloys respectively. Our calculations show that calculated Tc for these alloys are close to experimental values, given the nature of approximations used in our calculations.

Derivation of the Spherical Atom Model for Dispersion Forces

Derivation of the Spherical Atom Model for Dispersion Forces

First-principles study of electronic properties of B and C doped CuNNi3

We have performed ab initio electronic structure calculations for and () alloys using the Green's-function-based Korringa–Kohn–Rostoker method, formulated within atomic sphere approximation. The disorder in sub-lattice is treated within single-site coherent potential approximation. The spin-polarized calculations predict CuNNi3 and its alloys and to be non-magnetic for the entire doping range. For ordered phase, the density of states (DOS) at Fermi energy is mainly composed of Ni 3d states with small contributions from N 2p and Cu 3d states as well. Additionally, we observe a high DOS peak at which arises from Ni and Cu 3d states. For both and alloys, the DOS at Fermi energy decreases monotonically with concentration. This is in sharp contrast to what is expected for a hole doped system with high DOS peak below Fermi energy. The decrease in DOS at Fermi energy is more prominent in alloys. Hence the doping is found to be more deteriorating to superconductivity than . Moreover, the doping induced effects are not entirely rigid-band like, rather a moderate redistribution of electronic states is observed.

Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model.

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

First-principle studies of half-metallicities and magnetisms of the semi-Heusler alloys CoCrTe and CoCrSb

Half-metallic ferromagnet, in which the electrons with one spin band are metallic and the electrons with another spin band are semiconducting, is believed to be the most promising spin-injector material for spintronic devices, such as spin valves, spin filters, spin diodes, and magnetic tunnel junctions. The main advantages of half-metallic Heusler alloy over other half-metallic systems are their relatively high Curie temperatures and structural similarity to important binary semiconductors that are widely utilized in the industry. Thus far, half-metallicity has been predicted theoretically or confirmed experimentally in a limited number of Heusler alloys. Exploring new half-metallic Heusler alloys is necessary. In this study, the full-potential linearized augmented plane wave (FP_LAPW) method under density functional theory is utilized to investigate the electronic structures and magnetisms of semi-Heusler alloys CoCrTe and CoCrSb. In the calculations, the generalized gradient approximation (GGA) in the scheme of Perdew-Bueke-Ernzerhof is adopted to treat the exchange-correlation potential. The cutoff parameter is set to be Rmt Kmax =9, where Rmt is the smallest atomic sphere radius and Kmax is the maximum value of the reciprocal lattice vector. Meshes (131313 k-points) are used in the first Brillouin zone integration. Self-consistent calculations are considered to be convergent only when the integrated charge difference between the last two iterations is less than 110-4 e/cell. Spin-polarized calculations of the electronic structure for the semi-Heusler alloys CoCrTe and CoCrSb are performed. The calculations reveal that CoCrTe and CoCrSb at their equilibrium lattice constants are half-metallic ferromagnets with half-metallic gaps of 0.28 and 0.22 eV and total magnetic moments of 3.00 and 2.00 B per formula unit, respectively. The calculated integer total magnetic moments (in B) are consistent with the Slater-Pauling rule, Mt = Zt-18, where Zt denotes the total number of valence electrons and Mt means the total magnetic moment (in B) per formula unit. Moreover, the spin moment of the Cr atom is obviously larger than those of the Co, Te, and Sb atoms. Co, Te and Sb are all antiferromagnetically coupled to Cr for CoCrTe and CoCrSb. The electronic structures of CoCrTe and CoCrSb are also calculated as their lattice constants change from -13% to +13% relative to the equilibrium lattice constant. The calculated results indicate that CoCrTe and CoCrSb can maintain their half-metallicities and retain their total magnetic moments of 3.00 and 2.00 B per formula unit even as their lattice constants change from -11.4% to 9.0% and from -11.2% to 2.0%, respectively. The semi-Heusler alloys CoCrTe and CoCrSb should be useful in spintronics and other applications.

First-principles study of electronic and magnetic properties of Fe1−xTMxSe0.5Te0.5 alloys (TM ≡ Cr, Mn, Co, Ni)

We have studied the effects of transition metal (TM) substitution on Fe sub-lattice in Fe1−xTMxSe0.5Te0.5 (TM ≡ Cr, Mn, Co, Ni and x = 0, 0.01, 0.05, 0.10) in terms of changes in its electronic and magnetic properties. The calculations were performed with the Korringa-Kohn-Rostoker (KKR) Atomic Sphere Approximation (ASA) method within the coherent-potential approximation (CPA). Our spin-polarized calculations show these alloys to be magnetic in nature. We discuss the calculated density of states (DOS), band structures and Fermi surfaces (FS) in terms of the contributions of Fe3d64s2, Cr3d54s1, Mn3d54s2, Co3d74s2, Ni3d84s2 and Se4s24p4 outer most electrons. Our results indicate that the effects of doping on the electronic properties are significant with respect to parent FeSe and FeSe0.5Te0.5 superconductor. We have also estimated the value of electron-phonon mass enhancement factor λ (which is the sum of electron–phonon coupling constant and the electron–electron interaction present in the material) to calculate the superconducting transition temperature Tc for the TM-doped FeSe0.5Te0.5. Hopfield parameters are also calculated from the charge self-consistent potentials obtained from KKR-ASA CPA method.

Aesthetics of assembly of giant molecules under precision synthesis

The problems to efficiently and robustly pack the objects together have been studied for centuries due to their mathematic aesthetics and direct applications to understand the myriad phase structures compacted from spherical metallic atoms to other polyhedral building blocks. For the simplest polyhedron, rigid tetrahedra were shown to form crystalline and quasi-crystalline phases by analytical calculations or computer simulations if only packing or shape entropy dominates the free energy. However, related experimental observations of the structures or their formation mechanisms are remained largely unexplored, possibly mainly due to two reasons: firstly, enthalpy interaction in real system cannot be ruled out as in modeling, and secondly, precise control of the shape and tuning of the enthalpy interaction of the building blocks are so far extremely challenging experimentally. Recently, Prof. Stephen Z. D. Cheng from University of Akron and his collaborators including Dr. Wen-Bin Zhang from Peking University have represented a rigorous work to show how to control the selective assembly of a class of nanosized giant tetrahedra by precisely mediating the interactions between the tetrahedra and the overall molecular geometry.

Study of Electronic and Magnetic Properties of CuPd, CuPt, Cu<sub>3</sub>Pd and Cu<sub>3</sub>Pt: Tight Binding Linear Muffin-Tin Orbitals Approach

Electronic structure of ordered alloys CuPd, CuPt, Cu3Pd and Cu3Pt have been studied using Tight Binding Linear Muffin-Tin Orbitals Atomic Sphere Approximation (TB-LMTO-ASA). For the electronic properties, we have performed band structure calculations. Our findings show that all the systems considered are metallic in nature. To know the contribution of the orbitals in the bands, the system is analyzed via fat bands which reveal most of the contributions on valence band for CuPd, CuPt, Cu3Pd and Cu3Pt is from d-orbital and on conduction band is from s and p-orbitals. We have also checked the magnetic properties of the alloys. The density of states for spin up and spin down electrons have found to be same in each and every steps, showing non-magnetic nature of CuPd, CuPt, Cu3Pd and Cu3Pt.Journal of Institute of Science and Technology, 2014, 19(1): 137-144

Theoretical study of electronic structure and superconductivity in FeSe0.9−x(Si/Sb)x alloys

We have studied the effects of doping Si and Sb at the Se site in FeSe0.9 (i.e., FeSe0.9−x(Si/Sb)x for x = 0, 0.05, 0.10,0.15 and 0.20) using the Korringa-Kohn-Rostoker Atomic Sphere Approximation method within the coherent-potential approximation. Our calculations show that the ground state of FeSe0.9 is nonmagnetic while FeSe0.9−x(Si/Sb)x alloys tend to be magnetic. We present the results of unpolarized and spin-polarized, charge self-consistent, calculations for FeSe0.9−x(Si/Sb)x alloys in terms of density of states (DOS), band structure and Fermi surface (FS). In particular, we find that the doped FeSe0.9 exhibits the same topology of the FS as that of FeSe, differing only in subtle FS nesting features in case of unpolarized calculations but in case of spin-polarized calculations, the topology of the FS is very different from that of FeSe. We have also estimated the values of electron–phonon mass enhancement factor λ (which is the sum of electron–phonon coupling constant as well as the electron–electron interaction) to calculate the superconducting transition temperature Tc for the FeSe0.9−x(Si/Sb)x alloys. We find that the calculated Tc are in good agreement with experimental results.

Amendment of the Li-Bi Phase Diagram Crystal and Electronic Structure of Li2Bi

The phase diagram of the Li-Bi binary system was amended by x-ray analysis and differential scanning calorimetry. The formation of the binary compound Li2Bi was confirmed and its structure determined by x-ray single crystal diffraction. The Li2Bi compound crystallizes with the Mg2Ga structure type (space group P-62c, hP18, a = 8.0712(4) A, c = 6.8352(3) A). The analysis of the interatomic distances together with electronic structure calculations using the tight-binding linear muffin-tin orbital atomic spheres approximations (TB-LMTO-ASA) indicate the dominance of a metallic type of bonding, although there is a weak partially ionic bonding, caused by charge transfer from Li to Bi.

Electronic properties of excess Cr in FeCrxSe alloy

Abstract We have studied the effects of transition-metal Cr in excess on the electronic and magnetic properties of FeCr x Se (x = 0.0, 0.01, 0.02, 0.03, 0.04, 0.05, 0.10) alloys. We have used density functional based method Korringa–Kohn–Rostoker atomic sphere approximation within the coherent potential approximation to calculate the densities of states (DOS), band structures and Fermi surfaces (FS) of these alloys. Our calculations show that these alloys ( FeCr x Se ) are non-magnetic. Our unpolarized calculations show a subtle change in terms of density of states, band structure and Fermi surface with respect to the pure FeSe. We have also estimated bare Sommerfeld constant, electron–phonon coupling constant and the superconducting transition temperature T c for these alloys, which were found to be in good agreement with experiments.

Synthesis and Crystal Structures of Lithium, Sodium, and ­Potassium Derivatives of 2‐(Methylthio)aniline and 2‐(Phenylthio)aniline

Abstract2‐(Methylthio)aniline (H2L1) and 2‐(phenylthio)aniline (H2L2) were treated with n‐butyllithium to yield the corresponding anilides [LiHL1] and [LiHL2]. Recrystallization from diethyl ether and THF afforded the solvates [LiHL1(Et2O)] and [LiHL2(THF)2]. The X‐ray crystal structure determination revealed dimeric molecules which exhibit a centrosymmetric Li2N2 ring. In the case of [LiHL1(Et2O)] the SMe group is involved in Li coordination and in the case of [LiHL2(THF)2] the SPh group is part of an intramolecular N–H···S hydrogen bridge. The sodium anilides [NaHL1(DME)] and [NaHL2(DME)] were obtained from the reaction of H2L1 and H2L2 with sodium amide in DME as solvent. Like in the case of the lithium amides the sodium derivatives [NaHL1(DME)] and [NaHL2(DME)] display centrosymmetric Na2N2 cores. The coordination sphere of the sodium atoms is completed by DME molecules, which act as chelating ligands. In the case of [NaHL1(DME)] the DME molecules enable additionally a linkage of the dimeric subunits to give a chain structure. The potassium derivatives [KNHL1] and [KNHL2(DME)] were obtained from H2L1 and H2L2 and potassium hydride in DME as solvent. [KNHL1] displays a distinct structure based on [(KNHL1)2] dimers, which are linked by additional [KNHL1] units to give a 3D coordination polymer with {4.8.16(3)} topology. [KNHL2(DME)] forms dimers linked by bridging DME molecules to give a chain‐like coordination polymer.

Electronic band structures of binary skutterudites

The electronic properties of complex binary skutterudites, MX3 (M = Co, Rh, Ir; X = P, As, Sb) are explored, using various density functional theory (DFT) based theoretical approaches including Green's Function (GW) as well as regular and non-regular Tran Blaha modified Becke Jhonson (TB-mBJ) methods. The wide range of calculated bandgap values for each compound of this skutterudites family confirm that they are theoretically as challenging as their experimental studies. The computationally expensive GW method, which is generally assume to be efficient in the reproduction of the experimental bandgaps, is also not very successful in the calculation of bandgaps. In this article, the issue of the theoretical bandgaps of these compounds is resolved by reproducing the accurate experimental bandgaps, using the recently developed non-regular TB-mBJ approach, based on DFT. The effectiveness of this technique is due to the fact that a large volume of the binary skutterudite crystal is empty and hence quite large proportion of electrons lie outside of the atomic spheres, where unlike LDA and GGA which are poor in the treatment of these electrons, this technique properly treats these electrons and hence reproduces the clear electronic picture of these compounds.