DFT Program Research Articles

Study of Electronic Properties of GaAs Semiconductor Using Density Functional Theory

The properties of GaAs material in zinc blende type was calculated using Hiroshima Linear Plane Wave program based on the Density Functional Theory. This calculation aims to determine electronic properties of GaAs material are based on Density of States and energy band structure. This simulation’s results are DOS shows that hybridization of s orbital of Ga with s orbital of As provides covalent properties. The simulation of energy band structure from GaAs material indicates that semiconductor properties of GaAs is direct band gap. The energy band gap results obtained for GaAs is 0.80 eV. The computational result of the energy band gap calculation form HiLAPW has better accuracy and prediction with good agreement within reasonable acceptable errors when compared to some other DFT programs and the results of the experimental obtained.

Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT.

In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401,624 COCONUT compounds. The introduced drug repurposing pipeline consists of compound similarity with C3 fungicides and molecular docking (MD) simulations with final QM/MM binding energy determination, while aiming for potential novel chromophores and perserving at least an amide (R1HN(C=O)R2) or ester functional group of almost all up to date C3 fungicides. 3D descriptors used for a similarity test were based on the 280 most stable Padel descriptors. Hit compounds that passed fingerprint and 3D descriptor similarity condition and had either an amide or an ester group were submitted to docking where they further had to satisfy both Chemscore fitness and specific conformation constraints. This rigorous selection resulted in a very limited number of candidates that were forwarded to MD simulations and QM/MM binding affinity estimations by the ORCA DFT program. In this final step, stringent criteria based on (a) sufficiently high frequency of H-bonds; (b) high interaction energy between protein and ligand through the whole MD trajectory; and (c) high enough QM/MM binding energy scores were applied to further filter candidate inhibitors. This elaborate search pipeline led finaly to four Drugbank synthetic lead compounds (DrugBank) and seven natural (COCONUT database) lead compounds—tentative new inhibitors of cytochrome bc1. These eleven lead compounds were additionally validated through a comparison of MM/PBSA free binding energy for new leads against those obtatined for 19 QoIs.

Combined experimental and theoretical study, characterization, and nonlinear optical properties of doped-poly (p-nitroaniline -co- o-aminophenol) thin films

Hydrochloric acid doped poly (p-nitroaniline -co- o-aminophenol) [PpNAoAP] is synthesized via oxidative polymerization method using ferric chloride as an initiator and PEG200 as a soft template. By using PVD technique, the resulting doped [PpNAoAP]TF thin film was fabricated by evaporation of a thin layer (thickness ≈ 200 ± 5 nm) on a freshly cleaved mica substrate at a low deposition rate. Different techniques including FT-IR, 1HNMR, XRD, and SEM were used to characterize the resulting copolymer thin film. CATSTEP and DMol3 techniques were used to optimize the samples using DFT program. The optical constant values for the resulted [PpNAoAP]TF films are measured and comparable with experimental and CATSTEP processes. The computed structure and optical properties resulted from CATSTEP method are in good agreement with the obtained experimental data. The combined experimental of thin films and computed theoretical data of isolated molecules of [PpNAoAP]TF produce a promising outcome to be a good candidate for optoelectronic devices and polymer-solar cell applications.

Exploring the Reliability of DFT Calculations of the Infrared and Terahertz Spectra of Sodium Peroxodisulfate

A number of DFT programs with various combinations of pseudo-potentials and van der Waals’ dispersive corrections have been used to optimize the structure of sodium peroxodisulfate, Na2(SO4)2, and to calculate the infrared, attenuated total reflectance and terahertz absorption spectra of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles of Na2(SO4)2 is also considered using the Mie method. The results of the calculations are compared with experimental measurements of the transmission and attenuated total reflection spectra.

Relativistic four-component linear damped response TDDFT for electronic absorption and circular dichroism calculations.

We present a detailed theory, implementation, and a benchmark study of a linear damped response time-dependent density functional theory (TDDFT) based on the relativistic four-component (4c) Dirac-Kohn-Sham formalism using the restricted kinetic balance condition for the small-component basis and a noncollinear exchange-correlation kernel. The damped response equations are solved by means of a multifrequency iterative subspace solver utilizing decomposition of the equations according to Hermitian and time-reversal symmetry. This partitioning leads to robust convergence, and the detailed algorithm of the solver for relativistic multicomponent wavefunctions is also presented. The solutions are then used to calculate the linear electric- and magnetic-dipole responses of molecular systems to an electric perturbation, leading to frequency-dependent dipole polarizabilities, electronic absorption, circular dichroism (ECD), and optical rotatory dispersion (ORD) spectra. The methodology has been implemented in the relativistic spectroscopy DFT program ReSpect, and its performance was assessed on a model series of dimethylchalcogeniranes, C4H8X (X = O, S, Se, Te, Po, Lv), and on larger transition metal complexes that had been studied experimentally, [M(phen)3]3+ (M = Fe, Ru, Os). These are the first 4c damped linear response TDDFT calculations of ECD and ORD presented in the literature.

First principles study of Ag absorption mechanism in amorphous large silica clusters

Ag nanoparticles cause interesting modifications to the electronic and optical properties of amorphous silica scaffold that is used in optical fibers. The present study is first of its kind to implement first principles based calculation of large amorphous dielectric host with metal inclusions in it. Ground state structural parameters and equilibrium geometries of amorphous (SiO2)n clusters (n = 8,16,24,32,40) with Ag atoms doped inside the interstitial space of the scaffold have been calculated using DMol3 DFT program. We have shown that the configuration of small Ag clusters depend strongly on the structural characteristics of the scaffold. This creates a unique opportunity to control the microscopic properties of small metal clusters via Ag impregnation. Our study reveals that small sized silica clusters have lower level of absorption due to self-purification effect and Ag absorption efficiency depends on the nature of amorphicity of clusters having different geometries but same number of atoms. The nature of amorphicity of two different geometries of equal sized silica clusters has been verified via two independent approaches viz. (a) pair correlation and bond length/angle distributions plot of Si atoms and (b) the quasi-entropy calculated using USPEX code. More amorphous network of host leads to incorporation of more number of Ag atoms. The effect of host silica matrix on the structures of Ag nanoclusters are evaluated and the results show that bond distances in Ag clusters increase when encapsulated in silica matrix. The effect of doped Ag atoms on the structural characteristics of silica clusters are also evaluated and correlated with the shift in frequencies and change in Raman spectral intensities.

Large-Scale First-Principles Simulation on Li-Intercalated Graphite

Lithium-ion batteries (LIBs) have attracted considerable attention for use in larger power sources like electric vehicles and energy storage system because of their high energy densities. In the LIB, carbon materials, such as highly oriented pyrolytic graphite (HOPG), are used as negative electrode. During the charge and discharge cycle, Li-ions are intercalated to the graphite. For the Li- ions intercalation into the layered graphite, phase transition between different staging structures occurs. At first, Li-ions are intercalated randomly to whole layers, called dilute stage1. Next, stage transformation between dilute stage 1 and stage 4, stage 4 and stage 2, stage 2 and stage 1 proceed. This stage transformation plays an important role for the LIB performance, especially the maximum capacity and charge discharge rate of batteries. Regarding atomic scale mechanism of the stage transformation, Daumas and Hérold model was proposed. In the model, fully occupied and empty region of Li-ions in the layers exist, but the layers can be distorted to localize the Li-ion occupied region. This layer distortion is the key for the stage transformation. To clarify this mechanism from the view point of the first-principles study, large-scale calculations is required. In this study, we investigate the atomic and electronic structures of Li-intercalated graphite by using our large-scale DFT program CONQUEST [1]. The CONQUEST code uses real-space local orbital functions to express density matrices instead of the plane-wave basis. Especially, recently-developed “multi-site method” [2] reduces the number of local orbital basis functions to be minimal size keeping high accuracy, which reduces the computational cost dramatically and enables us to treat large systems containing 10,000+ atoms. The comparison of the geometries and electronic structures of Li-intercalated graphite at several stage structures with several thousand atoms (as in figure 1) will be discussed in the presentation. [1] http://www.order-n.org/ [2] A. Nakata, D. R. Bowler, T. Miyazaki, Phys. Chem. Chem. Phys. 17, 31427 (2015). Figure 1. Large-scale simulation model of Li-intercalated graphite (stage1). Figure 1

Photoluminescent-dielectric duple switch in a perovskite-type high-temperature phase transition compound: [(CH3)3PCH2OCH3][PbBr3

A bistable optical-electrical duple switch belongs to a class of highly satisfying intelligent materials that can transform optical and electrical responses simultaneously in one device. A perovskite-type high-temperature phase transition compound with one-dimensional chain-like crystal structure, ([(CH3)3PCH2OCH3][PbBr3], 1), displays remarkable bistable photoluminescent-dielectric duple switching behaviors. The noteworthy order-disorder transition of the phosphonium cation and the motions of anions contribute to the phase transition, leading to the space group P21/c at a low temperature phase to C2/c at a high temperature phase. 1 exhibits a prominent step-like dielectric anomaly at 401.0 K and demonstrates novel optical properties with a band gap of 3.54 eV. The photoluminescence intensity suddenly declines from 398 K to 408 K, which may be attributed to the occurrence of phase transition. The electron cloud distributions of the frontier orbital in compound 1 have been calculated using a DFT program.

Hydrogen atom chemisorption and diffusion on neutral and charged polycyclic aromatic hydrocarbon (PAH) flakes in the interstellar media

Hydrogen atoms diffusion on a hydrocarbon flake is studied using PM6 and DFT programs using as models neutral and positive charged coronene. Chemisorption and potential energy surfaces and diffusion paths were calculated. Results show that diffusion occurs through CC bonds. Edge effects are very important because the most stable adsorptions occur on hydrogenated border sites, so the diffusion is biased toward edge sites. Charged coronene has stronger adsorption energies than neutral systems. A large difference between barriers in neutral and charged systems was not observed in most of the cases. A discussion of modeling diffusion processes is presented.

Optimized multi-site local orbitals in the large-scale DFT program CONQUEST.

We introduce numerical optimization of multi-site support functions in the linear-scaling DFT code CONQUEST. Multi-site support functions, which are linear combinations of pseudo-atomic orbitals on a target atom and those neighbours within a cutoff, have been recently proposed to reduce the number of support functions to the minimal basis while keeping the accuracy of a large basis [J. Chem. Theory Comput., 2014, 10, 4813]. The coefficients were determined by using the local filter diagonalization (LFD) method [Phys. Rev. B: Condens. Matter Mater. Phys., 2009, 80, 205104]. We analyse the effect of numerical optimization of the coefficients produced by the LFD method. Tests on crystalline silicon, a benzene molecule and hydrated DNA systems show that the optimization improves the accuracy of the multi-site support functions with small cutoffs. It is also confirmed that the optimization guarantees the variational energy minimizations with multi-site support functions.

Syntheses and Characterization of Six Quaternary Uranium Chalcogenides A2M4U6Q17 (A = Rb or Cs; M = Pd or Pt; Q = S or Se)

The A(2)M(4)U(6)Q(17) compounds Rb(2)Pd(4)U(6)S(17), Rb(2)Pd(4)U(6)Se(17), Rb(2)Pt(4)U(6)Se(17), Cs(2)Pd(4)U(6)S(17), Cs(2)Pd(4)U(6)Se(17), and Cs(2)Pt(4)U(6)Se(17) were synthesized by the high-temperature solid-state reactions of U, M, and Q in a flux of ACl or Rb(2)S(3). These isostructural compounds crystallize in a new structure type, with two formula units in the tetragonal space group P4/mnc. This structure consists of a network of square-planar MQ(4), monocapped trigonal-prismatic UQ(7), and square-antiprismatic UQ(8) polyhedra with A atoms in the voids. Rb(2)Pd(4)U(6)S(17) is a typical semiconductor, as deduced from electrical resistivity measurements. Magnetic susceptibility and specific heat measurements on single crystals of Rb(2)Pd(4)U(6)S(17) show a phase transition at 13 K, the result either of antiferromagnetic ordering or of a structural phase transition. Periodic spin-polarized band structure calculations were performed on Rb(2)Pd(4)U(6)S(17) with the use of the first principles DFT program VASP. Magnetic calculations included spin-orbit coupling. With U f-f correlations taken into account within the GGA+U formalism in calculating partial densities of states, the compound is predicted to be a narrow-band semiconductor with the smallest indirect and direct band gaps being 0.79 and 0.91 eV, respectively.

Solvothermal Syntheses and Physical Properties of Noncentrosymmetric Olefin–Copper(I) Coordination Compounds

Solvothermal reactions of CuX (X = Cl, Br) and the organic olefin ligand 1,3,5-tris(diallylaminomethyl)-2,4,6-trimethylbenzene (TTB) in the presence of acid offered two novel olefin–copper(I) coordination compounds with unprecedented CuX cluster structures. The C3 symmetry of TTB leads to the formation of a novel C3-symmetric CuX cluster in oligomer compound 1 (H3TTB[Cu4Cl3]) and CuX framework in the two-dimensional compound 2 (H3TTB[Cu8Br11]). However, the flexibility and kink of H3TTB induce olefin–copper(I) coordination compounds to crystallize in noncentrosymmetric space groups R3c and R3 for compounds 1 and 2, respectively. In addition to the bowl-like structure of the olefin ligand and C3-symmetric CuX cluster found in compound 1, such bowl-like moieties are connected by another kind of C3-symmetric CuX cluster to form a novel two-dimensional framework in compound 2. The electron cloud distributions and energy levels of the frontier orbitals in both compounds have been calculated by a DFT program. Nonlinear optical property measurement results show that both compounds are second-harmonic generation (SHG) active. Compounds 1 and 2 display no phase transition according to the measurement of the temperature dependence of dielectric properties in the temperature range 100–300 K. The close packing and large density from the high CuX/ligand ratio in compound 2 correspond to the higher dielectric constant.

Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling.

Constrained density functional theory (cDFT) is a powerful tool to investigate the dynamics of the electrons accompanying various physical-chemical processes. In this article we present our recent progresses in the implementation of the method in the parallelized version of the DFT program deMon2k. We take advantage of the possibility to express atomic densities in terms of linear combination of Hermite Gaussian functions to improve the computation of the cDFT integration weights within the Hirshfeld and Voronoi deformation density electronic population approaches. The efficiency of the method is illustrated on the computation of the average electronic coupling for an electron transfer (ET) through a glycine polypeptide of increasing length. The sampling is based on cDFT and hybrid cDFT/molecular mechanics molecular dynamics simulations. We also report the first estimations of quantum decoherence times from cDFT-based simulations for an ET reaction.

Wannier functions approach to van der Waals interactions in ABINIT

The method to calculate van der Waals interactions based on maximally localized Wannier functions (MLWFs), proposed by Silvestrelli [Phys. Rev. Lett. 100 (2008) 053002], has been implemented within the ab initio DFT program ABINIT. In addition to a brief review of the theoretical background behind this methodology, we present the details of the implementation, which will help users to assess van der Waals corrections in both molecular and periodic systems with a negligible additional computational cost. Some tests on argon dimer, argon FCC solid, benzene dimer and bilayer of graphene are presented. A discussion about the reliability of the method is also included.

Theoretical Study on Photochromism and Spectrum Properties of Spiropyran

In order to elucidate the mechanism of photochromism and spectrum properties observed for spiropyran, the model complexes of spiropyran, in which different substituent and structure are key factors, have been optimized by using ab initio and hybrid DFT programs. The primary relationship between the substituent species and structure and photochromism was given by simulation calculation.

Phonons calculated from first-principles

First-principle phonon calculations can be performed using standard DFT program and the direct method. For that the supercell of studied crystal must be optimized, the Hellmann-Feynman forces derived, the dynamical matrix constructed and diagonalized, and hence all phonon modes calculated. The method has already been applied to large number of crystals, including crystals with defects and surfaces.

The object-oriented DFT program library S/PHI/nX

In order to simplify the development and implementation process of quantum mechanical algorithms, we developed a set of object-oriented C + + libraries which can exploit modern computer architectures. The libraries are characterized as follows: (i) State-of-the-art computer science techniques have been applied or developed in this work to provide language elements to express algebraic expressions efficiently on modern computer platforms. (ii) Quantum mechanical algorithms are crucial in the field of materials research. The new libraries support the Dirac notation to implement such algorithms in the native language of physicists. (iii) The libraries are completed by elements to express equations of motions efficiently which is required for implementing structural algorithms such as molecular dynamics. Based on these libraries we introduce the DFT program package S/PHI/nX.

Molecular Modeling, Multinuclear NMR, and Diffraction Studies in the Templated Synthesis and Characterization of the Aluminophosphate Molecular Sieve STA-2

Molecular modeling has been used to assist in the design of a new structure directing agent (SDA) for the synthesis of the AlPO(4) form of STA-2, bis-cliazabicyclooctane-butane (BDAB). This is incorporated as a divalent cation within the large cages of STA-2, as determined via a combination of solid-state (13)C and (15)N MAS NMR, supported by (14)N and (1)H-(15)N HMQC solution NMR and density functional calculations. As prepared AlPO4 STA-2 containing cationic SDA molecules achieves neutrality by the inclusion of hydroxide ions bridging between 5-fold coordinated framework Al atoms. Synchrotron X-ray powder diffraction data of the dehydrated as-prepared form indicates triclinic symmetry (Al(12)P(12)O(48)(OH)(2)center dot BDAB, P1, a = 12.3821(2) angstrom, b = 12.3795(2) angstrom, c = 12.3797(3) angstrom, alpha = 63.3585(8)degrees, 63.4830(7)degrees, gamma = 63.4218(7)) with the distortion from rhombohedral R (3) over bar symmetry resulting from the partial order of hydroxide ions in bridging Al-OH-Al sites within cancrinite cages. Upon calcination in oxygen, the organic SDA is removed, leaving AlPO(4) STA-2 with a pore volume of 0.22 cm(3) g(-1) (R (3) over bar, Al(36)P(36)O(144), a = 12.9270(2) angstrom, c = 30.7976(4) angstrom). Dehydrated calcined AlPO(4) STA-2 has two crystallographically distinct P and Al sites: (31)P MAS NMR resolves the two distinct P sites, and although 27AI MAS NMR only partially resolves the two Al sites, they are separated by MQMAS. Furthermore, 2D (27)Al -> (31)P MQ-J-HETCOR correlation spectroscopy confirms that each framework Al is linked to the two different P sites via AI-O-P connections in a 3:1 ratio (and vice versa for P linked to different Al). The (27)Al and (31)P resonances are assigned to the crystallographic Al and P sites by calculation of the NMR parameters using the CASTEP DFT program for an energy-minimized AlPO(4)(SAT) framework.

A theoretical study of an amorphous aluminium oxide layer used as a tunnel barrier in a magnetic tunnel junction

AbstractAn amorphous aluminium oxide layer is assumed to be a condensed gas phase composed of (AlOx)N molecules. The total energy and the electron affinity of (AlOx)N molecules is calculated by using a DFT program. The effective tunnel barrier height in the MTJ is presumed from a difference between the work function of the ferromagnetic metal and the electron affinity of (AlOx)N molecules. By using a quantum‐mechanical free electron model the TMR and the R×A product are calculated as a function of the thickness of an amorphous aluminium oxide layer in the F/I/F tunnel junction. It is inferred that the tunnel barrier width determined by subtracting 6 Å from the thickness of an amorphous aluminium oxide layer is more suitable to explain an experimental report qualitatively than the tunnel barrier width equivalent to the thickness of an amorphous aluminium oxide layer. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

First-principle lattice dynamics and thermodynamics of crystals

Recent first-principle phonon calculations make use of the standard DFT program, and the direct method. The procedure requires to optimize the structure, calculate the Hellmann-Feynman forces, construct the dynamical matrix, and hence all interesting phonon properties. The method has been already applied to a large number of crystal, crystal with defects, multilayers and surfaces to calculate the phonon dispersion curves, phonon density of states, and thermodynamical functions.