Ab Initio Simulation Methods Research Articles

Prediction of threshold displacement energies in TiC by ab initio molecular dynamics simulation method

Prediction of threshold displacement energies in TiC by ab initio molecular dynamics simulation method

Semiconducting Characteristic of Antiferromagnetic Al4X3Mn (X = P, As and Sb) Compounds with Ab Initio Simulation Methods

This research reports the electronic characteristics of ternary aluminium-based Al4X3Mn (X=P, As and Sb) compounds for the most stable magnetic order which is A-type antiferromagnetic. The related systems are comforming 215 space number with P-43m space group which is simple cubic crystal structure. The computations in this research have been done within the framework of Density Functional Theory. The calculations utilized Perdew-Burke-Ernzerhof type correlation functionals within the meta-generalized gradient approximation. For considered four different type magnetic orders, the visualized volume-energy plots and the calculated formation energy values imply that the magnetic nature of these compositions is A-type antiferromagnetic. Besides, the investigated electronic natures in the detected stable magnetic phase of these systems are semiconductor since the band gaps were observed in their electronic band structures and density of states (Eg = 0.36 eV for Al4P3Mn, Eg = 0.33 eV for Al4As3Mn, and Eg = 0.18 eV for Al4Sb3Mn).

Family behavior and Dirac bands in armchair nanoribbons with 4–8 defect lines

Bottom-up synthesis from molecular precursors is a powerful route for the creation of novel synthetic carbon-based low-dimensional materials, such as planar carbon lattices. The wealth of conceivable precursor molecules introduces a significant number of degrees-of-freedom for the design of materials with defined physical properties. In this context, a priori knowledge of the electronic, vibrational and optical properties provided by modern ab initio simulation methods can act as a valuable guide for the design of novel synthetic carbon-based building blocks. Using density functional theory, we performed simulations of the electronic properties of armchair-edged graphene nanoribbons (AGNR) with a bisecting 4–8 ring defect line. We show that the electronic structures of the defective nanoribbons of increasing width can be classified into three distinct families of semiconductors, similar to the case of pristine AGNR. In contrast to the latter, we find that every third nanoribbon is a zero-gap semiconductor with Dirac-type crossing of linear bands at the Fermi energy. By employing tight-binding models including interactions up to third-nearest neighbors, we show that the family behavior, the formation of direct and indirect band gaps and of linear band crossings in the defective nanoribbons is rooted in the electronic properties of the individual nanoribbon halves on either side of the defect lines, and can be effectively through introduction of additional ‘interhalf’ coupling terms.

Nonadiabatic Dynamics Simulations for Photoinduced Processes in Molecules and Semiconductors: Methodologies and Applications.

Nonadiabatic dynamics (NAMD) simulations have become powerful tools for elucidating complicated photoinduced processes in various systems from molecules to semiconductor materials. In this review, we present an overview of our recent research on photophysics of molecular systems and periodic semiconductor materials with the aid of ab initio NAMD simulation methods implemented in the generalized trajectory surface-hopping (GTSH) package. Both theoretical backgrounds and applications of the developed NAMD methods are presented in detail. For molecular systems, the linear-response time-dependent density functional theory (LR-TDDFT) method is primarily used to model electronic structures in NAMD simulations owing to its balanced efficiency and accuracy. Moreover, the efficient algorithms for calculating nonadiabatic coupling terms (NACTs) and spin-orbit couplings (SOCs) have been coded into the package to increase the simulation efficiency. In combination with various analysis techniques, we can explore the mechanistic details of the photoinduced dynamics of a range of molecular systems, including charge separation and energy transfer processes in organic donor-acceptor structures, ultrafast intersystem crossing (ISC) processes in transition metal complexes (TMCs), and exciton dynamics in molecular aggregates. For semiconductor materials, we developed the NAMD methods for simulating the photoinduced carrier dynamics within the framework of the Kohn-Sham density functional theory (KS-DFT), in which SOC effects are explicitly accounted for using the two-component, noncollinear DFT method. Using this method, we have investigated the photoinduced carrier dynamics at the interface of a variety of van der Waals (vdW) heterojunctions, such as two-dimensional transition metal dichalcogenides (TMDs), carbon nanotubes (CNTs), and perovskites-related systems. Recently, we extended the LR-TDDFT-based NAMD method for semiconductor materials, allowing us to study the excitonic effects in the photoinduced energy transfer process. These results demonstrate that the NAMD simulations are powerful tools for exploring the photodynamics of molecular systems and semiconductor materials. In future studies, the NAMD simulation methods can be employed to elucidate experimental phenomena and reveal microscopic details as well as rationally design novel photofunctional materials with desired properties.

An ab initio study on half-metallicity and lattice dynamics stability of ternary half-Heusler vanadium antimonides: VXSb (X = Co, Rh, and Ir)

Ternary half-Heusler VXSb (X = Co, Rh, and Ir) antimonides having C1b cubic crystal structure and conforming to F4‾3m space group with 216 space number, have been investigated in α, β, and γ structural phases with ab initio simulation methods. First, the gamma phase was found to be the most favorable atomic arrangement from the enthalpies of formation and energy-volume curves calculated for these materials. Then, the electronic nature, some mechanical properties, and lattice dynamical stability were investigated in the most stable γ phase. While examining the electronic behavior of these compounds, both GGA + PBE and mBJ approaches have been used to observe the band gaps. As a result of the electronic band structure calculations, it is understood that these compounds have a half-metallic nature with 100% spin polarization. In addition, the total magnetic moments of these half-metallic ferromagnets are found to have an integer value of 1 μB per formula, which is consistent with the Slater-Pauling rule. These crystal systems have mechanical stability because the elastic constants satisfy the Born-Huang stability criteria. Besides, it has been observed that the materials exhibit ductile and anisotropic behavior. Finally, phonon dispersion curves and some thermodynamic properties for these systems were obtained and it was seen that they have lattice dynamics stability. The results obtained in this study show that these compounds are suitable candidates for spintronic applications at room temperature.

Structural transitions at high pressure and metastable phase in Si0.8Ge0.2

The high-pressure behaviour of Si0.8Ge0.2 alloy is explored using in situ Raman spectroscopy, X-ray diffraction techniques and density functional theory (DFT) simulations. High pressure experiments revealed a pressure-induced transition from the stable cubic semiconducting phase (dc- Si0.8Ge0.2) to the tetragonal β-tin metallic phase (β-Si0.8Ge0.2) during compression. This sluggish transition is significantly accelerated at moderate temperature (<300 °C). Upon decompression, successive transitions towards metastable phases are observed. A first transition from the metallic β-Si0.8Ge0.2 toward the rhombohedral r8-Si0.8Ge0.2 phase is observed at 10.3 GPa followed by a partial transition to the body-centered cubic bc8-Si0.8Ge0.2 phase at 2.2 GPa. After releasing the pressure, r8 and bc8 phases coexist at ambient conditions. This transition pathway is similar to that followed by pure silicon and is consistent with the ab initio enthalpy calculations. This phase transition sequence is confirmed by in situ Raman spectroscopy, where signatures of r8 and bc8 phases are observed in the Raman spectra at decompression. An ab initio simulation method is proposed to assign the Raman spectrum of Si0.8Ge0.2 alloy using group theory and projection operators. The exploration of metastable states in these alloys is of major interest both in terms of applications (e.g. optoelectronics) and from a fundamental point of view to better understand the effects of alloying on the physical properties (e.g. vibrational).

Ga4X3Mn (X = P and As)’in Manyetik ve Elektronik Özelliklerinin İncelenmesi Üzerine İlk İlkeler Çalışması

In this study, the magnetic nature and also, electronic characteristics of Ga4X3Mn (X=P and As) systems, which have simple cubic structure confirming P4 ̅3m space group and 215 space number, have been reported. All calculations realized within the framework of ab initio simulation methods have been performed using the meta-generalized gradient (META-GGA) approach within the Density Functional Theory (DFT). In view of the energy-volume curves and the calculated cohesive and formation energies for considering four different types of magnetic orders, it has been detected that these compounds have A-type antiferromagnetic nature. Also, the examined electronic behaviors in the A-type antiferromagnetic order of the related systems show that all two compounds are semiconductors due to having small band gaps in their electronic band structures (Eg = 0.23 eV for Ga4P3Mn and Eg = 0.16 eV for Ga4As3Mn).

First-principles calculations to investigate new ferromagnetic quaternary Heusler alloys FeZrTiZ(Z=Si, Sn, Pb): Compatible for spin polarized device and waste heat recovery applications

In this article, we have studied the structural, electronic, magnetic, mechanical and thermoelectric properties of new quaternary Heusler alloys FeZrTiZ (Z = Si, Sn, Pb), using ab-initio simulation methods. Our structural phase stability studies show that all these compounds stabilize in Y1-type structure and showing ferromagnetic ground state. From the calculation based on Generalized Gradient Approximation method we found that all these alloys are having half metallic behavior with the band gap value of around 1eV in one of the spin channels. The half metallic nature of these alloys is a precursor for high spin polarization. These alloys also satisfy the Slater-Pauling rule with magnetic moment of MT = NV − 18 for half metallicity and as a result they have a total magnetic moment of 2μB. The calculated elastic constants convey the mechanical stability of these alloys and though they have a cubic structure they exhibit strong mechanical anisotropy with ductile behavior. The Seebeck coefficient and the thermoelectric figure of merit were calculated using semi-classical Boltzmann transport theory. The highest Seebeck coefficient value for FeZrTiZ (Z = Si, Sn, Pb) is 110.5 μV/K, 121.8 μV/K and 100.6 μV/K respectively at the temperature 900 K, 600 K and 750 K and the corresponding figure of merit is 0.85, 0.9 and 0.59. The observation of half metallicity indicates that these materials can be used in spintronic devices and the observation of substantial thermoelectric figure of merit suggests that these materials can be used in waste heat recovery.

Density Functional Theory Calculation of Electronic Structure of Fe-N-C, Fe-O-C, Fe-P-C, Fe-S-C Single-atom Catalysts Systems

Single atom catalysts (SACs) have emerged as a novel class of heterogeneous catalysts which exhibit superior catalytic performance in various reaction, CO oxidation, CO2 conversion, oxygen reduction reaction (ORR), etc. It is challenging to explore electronic structure and catalytic mechanics of SACs when the single metal atom is bonding with different dopants via experimental methods, which influence the catalytic efficiency directly. In this paper, Density Functional Theory (DFT) calculations, an ab initio simulation methods, have been carried out to investigate the properties of Fe-N-C, Fe-O-C, Fe-P-C, and Fe-S-C with oxo or hydroxyl group, four common SACs models. Geometry structure of Fe-N-C, Fe-O-C, Fe-P-C, Fe-S-C, and after each has bonded with oxo or hydroxyl group are studied. Formation energy of the Single Atom Catalyst (SAC), oxygen formation energy, and hydrogen atom transfer energy of the four SACs models are also calculated. In order to investigate the electronic structure of the four SACs, we examined the HOMO LUMO gap values for each system. In addition, we plotted the corresponding HOMO and LUMO orbitals of each SACs models and with oxo or hydroxyl group. Through analyzing the data, I anticipated that Fe-N-C model is the easiest to synthesis and the most stable among the four models. Our work discloses the microscopic property of SACs and provides valuable suggestions to experimental scientists.

Excited state deactivation mechanisms of protonated adenine: a theoretical study.

The quantum chemical computational method and Born-Oppenheimer (BO) dynamics simulation were employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We located three conical intersections (CIs) between the first 1ππ* excite state and the S0 ground state potential energy surfaces for the two most stable protonated isomers of adenine. It was predicted that the barrier-free potential energy profile along the out-of-plane deformation coordinates of the six-member ring plays the most prominent role in the deactivation of the excited AH+ from 1ππ* to the ground state via ultrafast internal conversions. This ring deformation was predicted to provide a common deactivation pathway in protonated DNA/RNA bases, describing their high level of photostability, and corresponding neutral homologues.

Theoretical insights on the excited-state-deactivation mechanisms of protonated thymine and cytosine.

Ab initio and surface-hopping nonadiabatic dynamics simulation methods were employed to investigate relaxation mechanisms in protonated thymine (TH+) and cytosine (CH+). A few conical intersections were located between 1ππ* and S0 states for each system with the CASSCF (8,8) theoretical model and relevant contributions to the deactivation mechanism of titled systems were addressed by the determination of potential energy profiles at the CASPT2 (12,10) theoretical level. It was revealed that the relaxation of the 1ππ* state of the most stable conformer of both systems to the ground state is mostly governed by the accessible S1/S0 conical intersection resulting from the barrier-free out-of-plane deformation. Interestingly, it was exhibited that the ring puckering coordinate driven from the C6 position of the heterocycle ring in TH+ and CH+ plays the most prominent role in the deactivation mechanism of considered systems. Our ab initio results are also supported by excited-state nonadiabatic dynamics simulations based on ADC(2), describing the ultrashort S1 lifetime of TH+/CH+ by analyzing trajectories leading excited systems to the ground. It was confirmed that the excited-state population mostly relaxes to the ground via the ring puckering coordinate from the C6 moiety. Overall, the theoretical results of this study shed light on the deactivation mechanism of protonated DNA bases.

Large-scale first-principles quantum transport simulations using plane wave basis set on high performance computing platforms

As the characteristic lengths of advanced electronic devices are approaching the atomic scale, ab initio simulation method, with full consideration of quantum mechanical effects, becomes essential to study the quantum transport phenomenon in them. The widely used non-equilibrium Green’s function (NEGF) combined with the density functional theory (DFT) approach prefers a localized basis set. As many states of the art DFT calculations for solid state systems are carried out in plane waves, it is thus worth to investigate the feasibility of using the plane wave basis set for large-scale quantum transport calculations. Here we present a plane wave method for large-scale transport calculations based on a previously developed scattering state calculation approach (Wang, 2005). We address the unique computational challenges of applying that approach for large-scale systems where it is too expensive to calculate all the occupied eigenstates of the system as in conventional DFT calculations. By applying several high-efficiency parallel algorithms, including linear-scaling DFT algorithm, folded spectrum method, and Chebyshev filter technique, we demonstrate that it is possible to use this approach to simulate a system with several thousand atoms on high performance computing platforms. This method is not only used to study nanowire interconnects, showing how the shape and point defect affects their transport properties, but also used to study nanoscale Si transistor. Such quantum transport simulation method will be useful for investigating and designing nanoscale devices.

Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.

Atomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existing ab initio simulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions. Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein's folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, with unfolding simulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation. Our algorithm, which is available online, can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease.

Revealing the Magnesium-Storage Mechanism in Mesoporous Bismuth via Spectroscopy and Ab-Initio Simulations.

We present mesoporous bismuth nanosheets as a model to study the charge-storage mechanism of Mg/Bi systems in magnesium-ion batteries (MIBs). Using a systematic spectroscopy investigation of combined synchrotron-based operando X-ray diffraction, near-edge X-ray absorption fine structure and Raman, we demonstrate a reversible two-step alloying reaction mechanism Bi↔MgBi↔Mg3 Bi2 . Ab-initio simulation methods disclose the formation of a MgBi intermediate and confirm its high electronic conductivity. This intermediate serves as a buffer for the significant volume expansion (204 %) and acts to regulate Mg storage kinetics. The mesoporous bismuth nanosheets, as an ideal material for the investigation of the Mg charge-storage mechanism, effectively alleviate volume expansion and enable significant electrochemical performance in a lithium-free electrolyte. These findings will benefit mechanistic understandings and advance material designs for MIBs.

Silica surface states and their wetting characteristics

The wetting characteristics of silica (SiO2) surfaces can be described by molecular dynamics (MD) and ab initio simulations, including comparison of silica surfaces (talc (001), siloxanated quartz, tridymite (001) and quartz (001)), some of which have not been considered previously in the literature. Classic MD and ab initio simulation methods have been used to determine the contact angle, interfacial water structure, hydroxylation reaction and hydration energy, the results of which are compared with experimental results reported in the literature. Wetting of silica surfaces depends on surface polarity and extent of hydroxylation. The non-polar siloxane surfaces are characterized by a contact angle of about 80°, an MD ‘water exclusion zone’ of about 3 Å, a relaxed interfacial water orientation, inertness to hydroxylation and minimal hydration energy. The polar silica surfaces can be wetted by water and have a more ordered interfacial water structure. Silanol groups form at the polar silica surface during hydroxylation reactions, and the calculated hydration energy of −1·2 and −1·6 eV matches the experimental heat of immersion measurements reported in the literature, which correspond to hydrogen (H) bonding with interfacial water. Fundamental understanding of silica surfaces is important for understanding flotation phenomena and fluid flow in silica nanopores.

Ab Initio Simulation of Position-Dependent Electron Energy Loss and Its Application to the Plasmon Excitation of Nanographene

We present a newly developed ab initio simulation method of the position-dependent electron energy loss and employ it to study the plasmon excitation of the zigzag-edged nanographene. This method e...

Spin-dependent electron scattering in cobalt interconnects

We use state-of-the-art ab initio simulation methods to study fundamental electron scattering mechanisms in cobalt conductors for applications in advanced interconnect technology. In particular, we consider electron scattering at intrinsic defect sites, twin grain boundaries, and at the Co/metal/Co interfaces present in vertical interconnects. Effective resistivity values and reflection coefficients are calculated in each case. The explicit treatment of electron spin results in distinct majority and minority spin behavior, with majority spin states exhibiting less scattering than minority states. Our results indicate that grain boundary scattering dominates over scattering at intrinsic point defect sites. Vertical resistance calculations indicate that Co vias can have substantially lower resistance than corresponding Cu vias at comparable dimensions. These results help build a fundamental understanding of electron scattering mechanisms in non-Cu conductors for advanced interconnect applications.

Adsorption of N2 and H2 at AlN(0001) Surface: Ab Initio Assessment of the Initial Stage of Ammonia Catalytic Synthesis

Adsorption of molecular nitrogen and molecular hydrogen at an Al-terminated AlN(0001) surface was investigated using ab initio simulation methods. It was shown that both species undergo dissociatio...

Metallic atomic hydrogen at a pressure of 300-500 GPa

Atomic metallic hydrogen with a symmetry FDDD of a lattice cell is shown to have a stable crystalline structure under hydrostatic compression in the pressure range of 350-500 GPa. The resulting phase is shown to have a stable structure regarding the collapse of the phonon spectrum. Ab-initio simulation method has been used to calculate the structural, electronic, phonon and other characteristics of the normal FDDD metallic phase of hydrogen at a pressure of 350-500 GPA.

Bi-Axial Growth Mode of Au–TTF Nanowires Induced by Tilted Molecular Column Stacking

In this study, to understand the molecular self-organization in metal–organic charge-transfer nanowires, single gold-tetrathiafulvalene (Au–TTF) nanowires were analyzed using polarized Raman spectroscopy, combined with density functional theory (DFT) calculations. To verify the methodology, an investigation was done for neutral tetrathiafulvalene (TTF) bulk crystals with well-known structure. On the basis of the DFT calculation of the molecular Raman tensor and simulation of the angular-dependent depolarization ratio, the molecular orientation in single TTF crystals was verified. Thereon, the combined experimental and ab initio-simulation method was applied to study single Au–TTF nanowires. Our results clearly demonstrate, in contrast to the commonly accepted parallel molecular stacking model, that at least two molecules with different orientations are located in the unit cell of the nanowire’s crystal structure. The new tilted molecular column stacking wire model explains also the axial and radial growth...