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We report APW+lo (augmented plane wave plus local orbital) density functional theory (DFT) calculations of large molecular systems using the domain specific SIRIUS multi-functional DFT package. The APW and FLAPW (full potential linearized APW) task and data parallelism options and the advanced eigen-system solver provided by SIRIUS can be exploited for performance gains in ground state Kohn–Sham calculations on large systems. This approach is distinct from our prior use of SIRIUS as a library backend to another APW+lo or FLAPW code. We benchmark the code and demonstrate performance on several magnetic molecule and metal organic framework systems. We show that the SIRIUS package in itself is capable of handling systems as large as a several hundred atoms in the unit cell without having to make technical choices that result in the loss of accuracy with respect to that needed for the study of magnetic systems. [ABSTRACT FROM AUTHOR]

The factorized form of the unitary coupled cluster Ansatz is a popular state preparation Ansatz for electronic structure calculations of molecules on quantum computers. It is often viewed as an approximation (based on the Trotter product formula) for the conventional unitary coupled cluster operator. In this work, we show that the factorized form is quite flexible, allowing one to range from a conventional configuration interaction, to conventional unitary coupled cluster, to efficient approximations that lie in between these two. The variational minimization of the energy often allows simpler factorized unitary coupled cluster approximations to achieve high accuracy, even if they do not accurately approximate the Trotter product formula. This is similar to how quantum approximate optimization algorithms can achieve high accuracy with a small number of levels. [ABSTRACT FROM AUTHOR]

The energy landscape of ZrO2-doped amorphous Ta2O5 is explored in this work. With models corresponding to experimental concentrations of 50% Zr and 50% Ta cations, we search for, gather, and analyze two-level systems (TLSs) from molecular dynamic simulations. The mechanical loss function is calculated for each TLS individually. The results show that TLS with low asymmetry and large elastic coupling constants contribute the most to mechanical loss. We identify these as "bad actors." The higher barriers relate to the mechanical loss at higher temperatures. The concept of the oxygen cage that describes the local structural environment surrounding a metal ion is introduced. The existence of a drastic change in local environment, or a cage-breaking process, enables us to understand the double peaks present in the asymmetry distribution and provides a pictorial interpretation to distinguish two types of TLS. Quantitatively, a cage-breaking event is related to at least one large distance change in an atom–atom pair, and non-cage-breaking transitions have only small rearrangements. The majority of TLSs are cage-breaking transitions, but non-cage-breaking TLS transitions show higher average mechanical loss in ZrO2-doped Ta2O5. By decomposing the contributions to mechanical loss, we find that the low temperature loss peak near 40 K mainly comes from non-cage-breaking TLS transitions and the second loss peak near 120 K originates from cage-breaking TLS transitions. This finding is important for understanding the interplay between the atomic structure of TLS and mechanical loss. [ABSTRACT FROM AUTHOR]

The glass transition temperatures of common binary oxides, including those with low glass-forming ability, are estimated using pair distribution functions (PDFs) from ab initio molecular dynamics simulations. The computed glass transition temperatures for good glass-formers such as silica (SiO2), germania (GeO2), and boron oxide (B2O3) are in agreement with measured values. These calculations are then used to compute the glass transition temperatures of alumina (Al2O3), tantala (Ta2O5), and telluria (TeO2), which are known to exhibit low glass-forming ability. For Al2O3 and Ta2O5, we also compute the simulated caloric curve from molecular dynamics simulations using two-body empirical force fields. Finally, we discuss the possibility of extracting the glass transition temperature by measuring the thermal broadening of the PDFs from scattering measurements. [ABSTRACT FROM AUTHOR]

Exchange coupling constants (J) are fundamental to the understanding of spin spectra of magnetic systems. Here, we investigate the broken-symmetry (BS) approaches of Noodleman and Yamaguchi in conjunction with coupled cluster (CC) methods to obtain exchange couplings. J values calculated from CC in this fashion converge smoothly toward the full configuration interaction result with increasing level of CC excitation. We compare this BS-CC scheme to the complementary equation-of-motion CC approach on a selection of bridged molecular cases and give results from a few other methodologies for context. [ABSTRACT FROM AUTHOR]

Amorphous tantala, titania, and hafnia are important oxides for biomedical implants, optics, and gate insulators. Understanding the effects of oxide doping is crucial to optimize performance in these applications. However, no molecular dynamics potentials have been created to date that combine these and other oxides that would allow computational analyses of doping-dependent structural and mechanical properties. We report a novel set of computationally efficient, two-body potentials modeling van der Waals and covalent interactions that reproduce the structural and elastic properties of both pure and doped amorphous oxides. In addition, we demonstrate that the potential accurately produces energy barrier distributions for pure and doped samples. The distributions can be directly compared to experiment and used to calculate physical quantities such as internal friction to understand how doping affects material properties. Future analyses using these potentials will be of great value to determine optimal doping concentrations and material combinations for myriad material science applications. [ABSTRACT FROM AUTHOR]

To understand the role of chlorine in the stability and the observed fragmentation of Ag dendritic nanostructures, we have studied computationally two model systems using density functional theory. The first one relates to diffusion of Agn and AgnClm (n = 1-4) clusters on an Ag(111) surface, and the second demonstrates interaction strength of (Ag55)2 dimers with and without chloridation. Based on our calculated energy barriers, AgnClm clusters are more mobile than Agn clusters for n = 1-4. The binding energy between two Ag55 clusters is significantly reduced by surface chloridation. Bond weakening and enhanced mobility are two important mechanisms underlying corrosion and fragmentation processes. [ABSTRACT FROM AUTHOR]

Interfaces between two topological insulators are of fundamental interest in condensed matter physics. Inspired by experimental efforts, we study interfacial processes between two slabs of BiSbTeSe 2 (BSTS) via first principles calculations. Topological surface states are absent for the BSTS interface in its equilibrium separation, but our calculations show that they appear if the inter-slab distance is greater than 6 Å. More importantly, we find that topological interface states can be preserved by inserting two or more layers of hexagonal boron nitride between the two BSTS slabs. In experiments, the electric current tunneling through the interface is insensitive to back gate voltage when the bias voltage is small. Using a first-principles based method that allows us to simulate the gate field, we show that at low bias, the extra charge induced by a gate voltage resides on the surface that is closest to the gate electrode, leaving the interface almost undoped. This provides clues to understand the origin of the observed insensitivity of transport properties to back voltage at low bias. Our study resolves a few questions raised in experiment, which does not yet offer a clear correlation between microscopic physics and transport data. We provide a road map for the design of vertical tunneling junctions involving the interface between two topological insulators. [ABSTRACT FROM AUTHOR]

We report investigations of adsorption of N2 and O2 molecules on silver cluster cations. We have first revisited structures of small silver clusters based on first-principles calculations within the framework of density functional theory with hybrid functional. The 2D to 3D transition for the neutral clusters occurs from n = 6 to 7 and for cations, in agreement with experiments, from n = 4 to 5. With the refined structures, adsorption energies of N2 and O2 molecules have been calculated. We have identified characteristic drops in the adsorption energies of N2 that further link our calculations and experiments, and confirm the reported 2D-3D transition for cations. We have found that perturbations caused by physisorbed molecules are small enough that the structures of most Ag clusters remain unchanged, even though physisorption stabilizes the 3D Ag7+ structure slightly more than the 2D counterpart. Results for pure O2 adsorption indicate that charge transfer from Agn+ to O2 occurs when n > 3. Below that size oxygen essentially physisorbes such as nitrogen to the cluster. We interpret the experimentally observed mutually cooperative co-adsorption of oxygen and nitrogen using results from density functional theory with generalized gradient approximations. The key to the enhancement is N2-induced increase in charge transfer from Agn+ cations to O2. [ABSTRACT FROM AUTHOR]

We use the density functional theory method to study dry (1 × 1) α-quartz (0001) surfaces that have Frenkel-like defects such as oxygen vacancy and oxygen displacement. These defects have distinctively different effects on the water-silica interface depending on whether the adsorbent is a single water molecule, a cluster, or a thin film. The adsorption energies, bonding energies, and charge transfer or redistributions are analyzed, from which we find that the existence of a defect enhances the water molecule and cluster surface interaction by a large amount, but has little or even negative effect on water thin film-silica surface interaction. The origin of the weakening in film-surface systems is the collective hydrogen bonding that compromises the water-surface interaction in the process of optimizing the total energy. For clusters on surfaces, the lowest total energy states lower both the bonding energy and the adsorption energy. [ABSTRACT FROM AUTHOR]

The approximate representation of a quantum solid as an equivalent composite semiclassical solid is considered for insulating materials. The composite is comprised of point ions moving on a potential energy surface. In the classical bulk domain this potential energy is represented by potentials constructed to give the same structure and elastic properties as the underlying quantum solid. In a small local quantum domain the potential is determined from a detailed quantum calculation of the electronic structure. The new features of this well-studied problem are (1) a clearly stated theoretical context in which approximations leading to the model are introduced, (2) the representation of the classical domain by potentials focused on reproducing the specific quantum response being studied, (3) development of “pseudoatoms” for a realistic treatment of charge densities where bonds have been broken to define the environment of the quantum domain, and (4) inclusion of polarization effects on the quantum domain due to its distant bulk environment. This formal structure is illustrated in detail for a SiO2 nanorod. More importantly, each component of the proposed modeling is tested quantitatively for this case, verifying its accuracy as a faithful multiscale model of the original quantum solid. To do so, the charge density of the entire nanorod is calculated quantum mechanically to provide the reference by which to judge the accuracy of the modeling. The construction of the classical potentials, the rod, the pseudoatoms, and the multipoles is discussed and tested in detail. It is then shown that the quantum rod, the rod constructed from the classical potentials, and the composite classical/quantum rod all have the same equilibrium structure and response to elastic strain. In more detail, the charge density and forces in the quantum subdomain are accurately reproduced by the proposed modeling of the environmental effects even for strains beyond the linear domain. The accuracy of the modeling is shown to apply for two quite different choices for the underlying quantum chemical method: transfer Hamiltonian and density functional methods. [ABSTRACT FROM AUTHOR]

We have combined density functional theory (DFT) with classical interatomic potential functions to model hydrolysis of amorphous silica surfaces. The water–silica interaction is described by DFT with incorporation of a long-range elastic field described by classical interatomic potentials. Both physisorption and chemisorption of water on a surface site, known as the two-membered silica ring, are studied in detail. The hybrid quantum-mechanical and classical mechanical method enables more realistic treatment of chemical processes on an extended surface than previous methods. We have studied cooperative events in the hydrolytic reactions and discovered a new reaction pathway that involves a double proton transfer process. In addition, the evaluation of the total energy in a hybrid quantum-mechanical and classical mechanical system is discussed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The stability and the structure of small silver and silver-oxide particles are investigated by a comparison between experimentally deduced intensity relations in the evaporative ensemble limit and theoretical results of a Born--Oppenheimer local spin density molecular dynamics calculation. We have found two-dimensional (2D) structures for pure small silver particles up to seven atoms and three-dimensional (3D) above. In contrast, we found 3D structures for all oxidized clusters even the small ones. Small silver cluster therefore undergo a 2D-to-3D structural transition by oxidation. The electronic shell structure of the metallic part still persists, when the oxygen atoms are added, taking into account that each oxygen atom reduces the number of valence electrons by 2. The enhanced stability at electronic shell closings presents some unusual evaporation channels like the ejection of a single oxygen atom from Ag[SUB3]O[SUP+] leading to Ag[SUB3]O[SUP+]→Ag[SUP+,SUB3]+O as the preferential decay channel. [ABSTRACT FROM AUTHOR]

SiO[sub 2]-water clusters are studied using first-principles Born-Oppenheimer molecular dynamics based on density functional theory and generalized gradient approximations. Systematic investigations of structure and energetics as functions of cluster size demonstrate the roles of water molecules in chemical reactions. The water-assisted formation of a Si(OH)[sub 4] molecule from a single SiO[sub 2] molecule is revealed at the atomic level. The dynamics of dissociation of water molecules and formation of Si-OH bonds is investigated via simulations at finite temperature. A complex process that involves double and triple hydrogen atom transfer is discovered to be the reaction path. [ABSTRACT FROM AUTHOR]

The dynamics of clusters (H2O)nH+ (n=1,2,3,4) interacting with an NH3 molecule has been studied by first-principles Born–Oppenheimer molecular dynamics (BOMD) simulations. These small clusters are chosen as prototype systems for studying the mechanisms of proton transfer at atomistic level. We focus on the fundamental steps of proton motion in molecular clusters, the dynamical consequences of proton affinities, and the interplay between proton motion and proton affinity in these systems. A characteristic feature of the motion, the forming and breaking of O–H bonds in H3O+ is analyzed in detail. The transfer process is found to be consecutive along a quasi-one-dimensional channel. The umbrella mode in NH3 can easily be excited to direct the lone pair of the ammonia molecule to the water clusters. The hydronium ion, however, reorients mainly via rotation. When NH3 reaches one terminal water molecule of a protonated water cluster, the system undergoes a series of intermediate states in which the mobile protons travel within the water clusters, H3O+ transients are formed as protons approach individual water molecules. The lifetime of the H3O+ transient is 8–20 fs, or 1–3 vibrational periods of the O–H stretch mode. Proton transfer is observed for n=1, 2, 3, although for n=3 NH+4(H2O)3 is in existence with NH3(H2O)2H+. For n=4, NH3(H2O)4H+ is the dominant statistical configuration. Vibrational spectrum of NH3(H2O)4H+ is analyzed in detail. The features of the spectrum can be used, in principle, to probe the proton motion in the transition state region reactions. In these calculations, the electronic charge distribution is calculated concurrently with the nuclear dynamics. An analysis of isocharge density surfaces gives qualitative and quantitative descriptions of the dynamics of electronic redistribution. The BOMD is performed in the framework of density functional theory with local spin density and generalized gradient... [ABSTRACT FROM AUTHOR]

We investigated thin water films on quartz (0001) surfaces using first-principles density functional theory calculations. Interfacial structure and energetics were studied through a layer-by-layer deposition. From monolayer to multilayer, the low energy state configurations and adsorption sites show a transition due to formation of a highly stable bilayer membranelike structure. The water adsorption energy on a quartz surface coated by this membrane is of typical hydrogen bond strength for both dry and fully hydroxylated surfaces. The interactions between the surface and the water films are short-ranged due to shielding of the bilayer. [ABSTRACT FROM AUTHOR]

Reconstruction of α-quartz (0001) surfaces is studied using combined classical molecular dynamics and density functional theory. Five reconstruction patterns are identified, including three (2×1) patterns and two (1×1) patterns. The energetically most stable surface structure is found to be a (2×1) reconstruction pattern, and several patterns can coexist in a large-scale surface. A combination of structures can explain the experimentally observed (2×2) diffraction pattern. [ABSTRACT FROM AUTHOR]

The energy landscape of ZrO 2 -doped amorphous Ta 2 O 5 is explored in this work. With models corresponding to experimental concentrations of 50% Zr and 50% Ta cations, we search for, gather, and analyze two-level systems (TLSs) from molecular dynamic simulations. The mechanical loss function is calculated for each TLS individually. The results show that TLS with low asymmetry and large elastic coupling constants contribute the most to mechanical loss. We identify these as "bad actors." The higher barriers relate to the mechanical loss at higher temperatures. The concept of the oxygen cage that describes the local structural environment surrounding a metal ion is introduced. The existence of a drastic change in local environment, or a cage-breaking process, enables us to understand the double peaks present in the asymmetry distribution and provides a pictorial interpretation to distinguish two types of TLS. Quantitatively, a cage-breaking event is related to at least one large distance change in an atom-atom pair, and non-cage-breaking transitions have only small rearrangements. The majority of TLSs are cage-breaking transitions, but non-cage-breaking TLS transitions show higher average mechanical loss in ZrO 2 -doped Ta 2 O 5 . By decomposing the contributions to mechanical loss, we find that the low temperature loss peak near 40 K mainly comes from non-cage-breaking TLS transitions and the second loss peak near 120 K originates from cage-breaking TLS transitions. This finding is important for understanding the interplay between the atomic structure of TLS and mechanical loss.

Studying the adsorption of water on the metallic LaMnO3 surface can provide insight into this complicated surface-adsorbate interaction. Using density functional theory, we investigated the adsorption of a water monomer, dimer, trimer, and a monolayer on the surface. The electronic structure of ground state configurations is explored using analysis of density of states, charge density, and crystal orbital overlap populations. We found that the interaction between the surface and water molecules is stronger than hydrogen bonding between molecules, which facilitates wetting of the surface. Adsorbed water molecules form very strong hydrogen bonds, with substantially shifted OH stretch modes. For the monolayer of adsorbed water, a hint of a bilayer is observed with a height separation of only 0.2 A. However, simulated scanning tunneling microscopy images and vibrational spectra suggest a significant difference between the two layers due to intermolecular bonding and interaction with the substrate.

We have investigated the group 14 nitrides (M3N4) in the spinel phase (γ-M3N4 with M = C, Si, Ge, and Sn) and β phase (β-M3N4 with M = Si, Ge, and Sn) using density functional theory with the local density approximation and the GW approximation. The Kohn-Sham energies of these systems have been first calculated within the framework of full-potential linearized augmented plane waves (LAPW) and then corrected using single-shot G0W0 calculations, which we have implemented in the modified version of the Elk full-potential LAPW code. Direct band gaps at the Γ point have been found for spinel-type nitrides γ-M3N4 with M = Si, Ge, and Sn. The corresponding GW-corrected band gaps agree with experiment. We have also found that the GW calculations with and without the plasmon-pole approximation give very similar results, even when the system contains semi-core d electrons. These spinel-type nitrides are novel materials for potential optoelectronic applications because of their direct and tunable band gaps.

We have used large-scale first-principles calculations based on density functional theory to investigate the structure, energetics, electronic, and magnetic structures of Fe(n)-doped C(60) monolayers supported by h-BN monolayer-covered Ni(111) surfaces. A systematic study of n-dependent physical properties has been performed (n=1-4,15). Binding energies on Fe atoms to the Fe(n-1)-C(60) complex have been calculated for n=1-4 after a thorough configuration search and structural optimization. The binding energy, electron charge transfer (from Fe(n) to C(60)), and magnetic moment all increase monotonically as functions of n. The electron charge transfer, ranging from approximately 1e(-) to 5e(-), is from the spin minority population. This leads to a situation in which the net spin of the C(60) molecule aligns with the spin minority and the magnetic moment in C(60) is opposite to the total magnetic moment of the system. For n=2, a competing antiferromagnetic state has been found. In this state, the net spin of the system as well as the C(60) is zero. Density of states and projected density of states analysis indicate that the system becomes metallic upon metal doping regardless its magnetic state. In addition, we have also performed calculations with the Hubbard U term (DFT+U) for two systems, n=4 and 15, to investigate possible gap opening near the Fermi surface.

Via ab initio simulation, we study the behavior of interfaces of water with silica nanotubes. We find profound differences between zero and finite tensile strains and between unconfined (exterior) versus confined (interior) water. For these distinct cases, we characterize the fracture dynamics of the silica nanotube and the underlying physical mechanisms.

A basic issue in nanoscale systems is whether large-scale behavior occurs or not. At and above the mesoscale, the water-silica interaction is known to have large effects, e.g., the geological importance of hydrolytic weakening. Here, we show that water not only substantially weakens a silica nanochain that has been the focus of much recent research but also leads to novel proton conduction. The SiO2 chain consists of a string of orthogonal (planes alternating vertically and horizontally) two-membered rings. We treat two cases of adjacent water to understand both local and collective motion in the system. The first is two water molecules, the second is a water monolayer film that coats the entire chain. Structure, charge separation, stress dependent bond breaking and formation, and proton conduction are discussed based on results obtained at the room temperature. The simulations have been performed using both first-principles molecular dynamics and a novel multiscale quantum-classical software system.

A temperature controlled source for protonated water clusters has been combined with high-resolution mass spectroscopy to study the stability pattern of ice clusters and compounds with ammonia and hydrogen peroxide depending on temperature. The stability pattern of pure protonated ice shows the two well known peaks at 21 and 28 molecules and also less pronounced structure up to n=55. Ammonia and hydrogen peroxide do not destroy this pattern but shift it by a number of water molecules. The additives are therefore integrated in the persisting crystalline structure of the pure protonated ice. Based on this structural information, density functional theory calculations reveal that hydrogen peroxide and ammonia occupy surface positions on a dodecahedral 21-molecule cluster and are not caged in the center.

We present our computational investigations on the energetics of clusters that consist of H2O and SiO2 using first-principles Born-Oppenheimer molecular dynamics method. Cohesive energy and hydration energy of both pure (or dry) and hydroxylated (or wet) ring-structured clusters have been investigated as functions of system size. We have found clear trends of energy as the cluster size increases. Energetics of a small silica nano-rod that contains 108 atoms is also obtained as a middle reference point for size evolution. Results from cluster and nano-rod calculations are compared with values from bulk quartz calculations using the same level of theoretical treatments.