Electronic structure of C60 semiconductors under controlled doping with B,N, and Co atoms

We present our recent studies of ab initio density functional theory (DFT) calculations of the electronic structures of several selected n- and p-type doped C₆₀ semiconductors. A super-cell approach was used. We performed a series of ab initio density functional computations to systematically study the changes of the electronic structure of C₆₀ semiconductors doped with boron, nitrogen and cobalt atoms. We found that boron and cobalt doped, face-centered cubic (FCC) C₆₀ solids have the electronic structures of n-type semiconductors. Nitrogen doped FCC C₆₀ solid has an electronic structure similar to those of a p-type semiconductor, with shallow impurity energy levels near the top of the valence bands of the host material.     

The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in “Brugia Rapid”. However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.     

A scheme for fabricating single wall carbon nanocones standing on metal surfaces and an evaluation of their stability

A scheme is proposed for fabricating single wall carbon nanocones standing on metal surfaces with controlled sizes and cone angles by tailoring graphene sheets. A statistical model to examine the feasibility and stability of the cones has been developed. Combined with classical molecular dynamics simulations and ab initio calculations, the results show that cones with five different cone angles can be obtained, and the cone consisting of only 70 atoms can exist for 10¹¹ years at room temperature.     

Phase formation of Nb2AlC investigated by combinatorial thin film synthesis and ab initio calculations

The phase formation of Nb₂AlC was studied by combinatorial thin film synthesis and ab initio calculations. Thin films with lateral chemical composition gradients were synthesized by DC magnetron sputtering at substrate temperatures of 710–870 °C. The lowest formation temperature for Nb₂AlC is between 710 and 750 °C. A predominantly single phase Nb₂AlC region where 99% of the X-ray diffraction intensity originate from Nb₂AlC was identified. Furthermore, selected area electron diffraction analysis reveals the local formation of single phase Nb₂AlC. The limited Al solubility in Nb₂AlC compared with Cr₂AlC can be understood by comparing the defect formation energy of Al substituting Nb and Cr in Nb₂AlC and Cr₂AlC, respectively. This methodology may serve as indicator for the magnitude of the A-element homogeneity range in M_n+1AX_n phases. The structural and elastic properties of Nb₂AlC determined experimentally are in very good agreement with the ab initio calculated data.     

New structural insight for antimony(III)-tartrate

Theoretical calculations (density functional theory and ab initio (MP2)) and nuclear magnetic resonance experiments reveal a new metal-oxygen-bridged isomeric form for antimony(III)-l-tartrate that co-exists in solution and in the gas phase with its crystallographically-determined structure.     

Study of O2 and OH adsorption energies on Pd-Cu alloys surface with a quantum chemistry approach

Variation of the intrinsic metal surface properties (lattice parameter, binding energy, work function (W_f), d-band filling and d-band center ?_d) and O₂ and OH adsorption energies of on (1 1 1) Pd-Cu surface alloys were determined using ab initio program. Calculations of these parameters were based on plane waves approach on slab system with density functional theory (DFT) using the Vienna ab initio simulation program (VASP). It was shown that insertion of Cu atoms in Pd lattice affects geometric and electronic properties of Pd. These changes influence significantly O₂ and OH adsorption. Indeed, the highest OH adsorption energy and the lowest O₂ adsorption energy were found with 30 at.% in Cu. The volcano shape of the O₂ and OH adsorption with composition in Cu was explained, respectively, by firstly the highest bond distance that reduces adsorption energy of oxygen and the compromise between low DOS(E_f) and secondly, low band width (W) reach for Pd₃Cu which leads to the highest OH adsorption energy. O₂ and OH adsorption energies tendency could explain effect of the transition metal (TM) on kinetic current of the oxygen reduction reaction.     

First-principles, UV Raman, X-ray diffraction and TEM study of the structure and lattice dynamics of the diamond-lonsdaleite system

We report the results of the study of the polycrystalline powder of the diamond-lonsdaleite system by X-ray diffractometry, transmission electron microscopy and UV Raman spectroscopy. The measured data of structural parameters are in good agreement with ab initio calculations. We show that the Raman spectrum is proportional to the phonon density of states of the diamond-lonsdaleite system.     

Some crystallographic considerations on the novel orthorhombic ZrO2 stabilized with Ta doping

Some crystallographic considerations on the novel orthorhombic ZrO₂ (o-ZrO₂) stabilized at ambient conditions by Ta substitutional doping are presented. Specifically, how the Ta-doped o-ZrO₂ was observed for the first time by conventional X-ray diffractometry (XRD) is reported, after which the ab initio and non-ab initio procedures used to resolve its crystal structure are detailed. The crystal structure is then explicitly reported (i.e., space group and cell parameters, as well as atomic positions of the asymmetric unit). It is also shown that this novel Ta-doped o-ZrO₂ has a crystal structure similar, but not identical, to the high-pressure o-ZrO₂. Additionally, given that the crystal structure of the Ta-doped o-ZrO₂ is identified as being a symmetry-breaking distortion of the typical tetragonal ZrO₂ (t-ZrO₂) stabilized with the commonest dopants, a complete analysis is also made of the structural distortions relating both the Ta-doped o-ZrO₂ and the high-pressure o-ZrO₂ to the t-ZrO₂. Finally, a justification for the apparent greater immunity of the Ta-doped o-ZrO₂ to aging is provided.     

Conformational Analysis of Thioether Musks Using Density Functional Theory

A conformational analysis of nine macrocyclic thioether musks has been carried out using molecular mechanics (MMFF), density functional theory (DFT) using both B3LYP and M06 functionals, as well as Hartree-Fock and post-Hartree-Fock (MP2) ab initio methods. 6-Thia-, 10-thia- and 4-methyl-5-thia-14-tetradecananolide, 4-thia-, 7-thia-, 11-thia- and 12-thia-15-pentadecanolide and 6-thia- and 12-thia-16-hexadecanolide were modeled. Unfortunately, there was little agreement between the computational methods at the levels of theory used in this study.     

Crystal and electronic structure of PbTe/CdTe nanostructures

In this article, the authors reported a theoretical study of structural and electronic properties of PbTe inclusions in CdTe matrix as well as CdTe nano-clusters in PbTe matrix. The structural properties are studied by ab initio methods. A tight-binding model is constructed to calculate the electron density of states (DOS) of the systems. In contrast to the ab initio methods, the latter allows studying nanostructures with diameters comparable to the real ones. The calculations show that both kinds of inclusions lead to changes of the DOS of the carriers near the Fermi level, which may affect optical, electrical and thermoelectric properties of the material. These changes depend on the size, shape, and concentration of inclusions.     

An ab initio study of the electronic properties of carbon nanotubes activated by hydrogen-passivated vacancies

The effect of multi-vacancies on the electronic structure of semiconducting carbon nanotubes is studied using the ab initio pseudopotential density-functional method. The di-vacancy is found particularly effective in changing the band gap of the semiconducting nanotubes, while mono-, tri-, or tetra-vacancies introduce gap-states. A significant modulation of band gap is observed for a certain type of zigzag nanotube upon varying concentration of di-vacancy. The hydrogen passivation is found critical for stabilizing the vacancies. Based on present calculations, a conceptual model is proposed for semiconductor-semiconductor junctions that do not involve the chirality change of the tube.     

A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.     

Raman spectroscopy and band structure of Pd-hybridized multilayer graphene

Graphene sheets prepared through liquid exfoliation of expanded graphite were hybridized with Pd nanoparticles. The impact of these particles on the electronic and physical structure of the graphene is determined through transmission electron microscopy and Raman spectroscopy using 532 and 325 nm excitation wavelengths. Based on the changes to the Raman D and G peaks, insights are provided concerning the deposition mechanism at pristine and defective lattice sites, as well as electronic scattering. These data are compared to ab initio band structure computations. For purposes of the model, the graphene/Pd hybrid was approximated by a charged graphene sheet. The resulting structure exhibited π–π¹ expansion approaching the Γ point of the Brillouin zone which was validated by tracking the Raman D band dispersion.     

In Situ EXAFS Study on the Chemical State of Arsenic Deposited on a NiMoP/Al2O3 Hydrotreating Catalyst

The chemical state of arsenic deposited on a NiMoP/Al₂O₃ hydrotreating catalyst exposed to ppb levels of arsenic over several years in a refinery reactor has been studied by in situ EXAFS. In the as-received As-NiMoP catalyst, arsenic is exclusively coordinated to oxygen atoms. Upon sulfiding the sample in 2%H₂S/2%H₂/96%He, the As atoms become surrounded by approximately two sulfur atoms. No evidence was found for Ni–As bond formation. A possible model for the As local environment is suggested on the basis of combined EXAFS results, STM data and FEFF8.0 simulations (program for ab initio calculations on multiple scattering XAFS and XANES). The FEFF8.0 simulations of the proposed model are in accord with the experimental data measured at the As K edge. In this model, an As atom is located at the edge of a hexagonally truncated Ni-MoS₂ slab and is blocking the active NiMoS site.     

Cobalt in diamond: An ab initio investigation

We carried out an ab initio investigation on the structural and electronic properties of cobalt impurities in diamond. The calculations provided the stable configurations, symmetries, spins, energetics and hyperfine parameters of cobalt in diamond in substitutional, interstitial, and divacancy sites. The results were compared to available experimental data on active centers in diamond.     

In situ observations of the nucleation and growth of atomically sharp graphene bilayer edges

Using in situ transmission electron microscopy, we observed the nucleation and growth of graphene bilayer edges (BLE) with “fractional nanotube”-like structure from the reaction of graphene monolayer edges (MLEs). Most BLEs showed atomically sharp zigzag or armchair crystallographic facets in contrast to the atomically rough MLEs with irregular shapes, suggesting that the BLEs are much more stable and crystallographically anisotropic. Our direct observations and theoretical studies (geometric models and ab initio calculations) provide important clues for tailoring the edge structure and transport properties of multi-layer graphene.     

Theoretical Investigation of the NO3 Radical Addition to Double Bonds of Limonene

The addition reactions of NO₃ to limonene have been investigated using ab initio methods. Six different possibilities for NO₃ addition to the double bonds, which correspond to the two C–C double bonds (endocyclic or exocyclic) have been considered. The negative activation energies for the addition of NO₃ to limonene are calculated and the energies of NO₃-limonene radical adducts are found to be 14.55 to 20.17 kcal mol-1 more stable than the separated NO₃ and limonene at the CCSD(T)/6–31G(d) + CF level. The results also indicate that the endocyclic addition reaction is more energetically favorable than the exocyclic one.     

Germacrene D Cyclization: An Ab Initio Investigation

Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G^*) and post Hartree-Fock (MP2/6-31G^{* *}) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils.