Theoretical search for characteristic atoms in supported gold nanoparticles: a large-scale DFT study.

The size and site dependences of atomic and electronic structures in isolated and supported gold nanoparticles have been investigated using large-scale density functional theory (DFT) calculations using multi-site support functions. The effects of the substrate on nanoparticles with diameters of 2 nm and several different shapes have been examined. First, isolated gold nanoparticles with diameters of 0.6 nm (13 atoms) to 4.5 nm (2057 atoms), which have comparable sizes to nanoparticles used in experiments, were considered. To analyse huge amounts of data obtained from large-scale DFT calculations, we performed principal component analysis (PCA), which helps systematically and efficiently clarify the electronic structures of large nanoparticles. The PCA results reveal the site dependence of the electronic structures. Notably, the atoms in the surface and subsurface have different electronic structures to those located in the inner layers, especially at the vertexes of the particles. The convergence of local electronic structures with respect to the particle size has also been demonstrated. For supported nanoparticles, PCA helps indicate which atoms are affected, and how much, by the substrate. The correlation between the PCA results and site dependence of reaction activity is also discussed herein.

Supported Anionic Gold Nanoparticle Catalysts Modified Using Highly Negatively Charged Multivacant Polyoxometalates.

Although supported anionic gold nanoparticle catalysts have been theoretically investigated for their efficacy in activating O2 in aerobic oxidation reactions, limited studies have been reported due to the difficulty of designing these catalysts. Herein, we developed a feasible method for preparing supported anionic gold nanoparticle catalysts using multivacant lacunary polyoxometalates with high negative charges. We confirmed the strong and robust electronic interaction between gold nanoparticles and multivacant lacunary polyoxometalates, and the electronic states of the supported gold nanoparticle catalysts can be sequentially modulated. Particularly, the catalyst prepared using [SiW9 O34 ]10- acted as an efficient reusable heterogeneous catalyst, showing superior catalytic performance for the oxidative dehydrogenation of piperidone derivatives to the corresponding enaminones and remarkably higher stability than supported gold nanoparticle catalysts without this modification.

Large scale and linear scaling DFT with the CONQUEST code.

We survey the underlying theory behind the large-scale and linear scaling density functional theory code, conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with diagonalization and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focusing in particular on the parallel scaling, and provide examples of recent developments and applications.

On low-lying excited states of extended nanographenes.

Low-lying excited states of planarly extended nanographenes are investigated using the long-range corrected (LC) density functional theory (DFT) and the spin-flip (SF) time-dependent density functional theory (TDDFT) by exploring the long-range exchange and double-excitation correlation effects on the excitation energies, band gaps, and exciton binding energies. Optimizing the geometries of the nanographenes indicates that the long-range exchange interaction significantly improves the CC bond lengths and amplify their bond length alternations with overall shortening the bond lengths. The calculated TDDFT excitation energies show that long-range exchange interaction is crucial to provide accurate excitation energies of small nanographenes and dominate the exciton binding energies in the excited states of nanographenes. It is, however, also found that the present long-range correction may cause the overestimation of the excitation energy for the infinitely wide graphene due to the discrepancy between the calculated band gaps and vertical ionization potential (IP) minus electron affinity (EA) values. Contrasting to the long-range exchange effects, the SF-TDDFT calculations show that the double-excitation correlation effects are negligible in the low-lying excitations of nanographenes, although this effect is large in the lowest excitation of benzene molecule. It is, therefore, concluded that long-range exchange interactions should be incorporated in TDDFT calculations to quantitatively investigate the excited states of graphenes, although TDDFT using a present LC functional may provide a considerable excitation energy for the infinitely wide graphene mainly due to the discrepancy between the calculated band gaps and IP-EA values. © 2017 Wiley Periodicals, Inc.

Relationship between orbital energy gaps and excitation energies for long-chain systems.

The difference between the excitation energies and corresponding orbital energy gaps, the exciton binding energy, is investigated based on time-dependent (TD) density functional theory (DFT) for long-chain systems: all-trans polyacetylenes and linear oligoacenes. The optimized geometries of these systems indicate that bond length alternations significantly depend on long-range exchange interactions. In TDDFT formalism, the exciton binding energy comes from the two-electron interactions between occupied and unoccupied orbitals through the Coulomb-exchange-correlation integral kernels. TDDFT calculations show that the exciton binding energy is significant when long-range exchange interactions are involved. Spin-flip (SF) TDDFT calculations are then carried out to clarify double-excitation effects in these excitation energies. The calculated SF-TDDFT results indicate that double-excitation effects significantly contribute to the excitations of long-chain systems. The discrepancies between the vertical ionization potential minus electron affinity (IP-EA) values and the HOMO-LUMO excitation energies are also evaluated for the infinitely long polyacetylene and oligoacene using the least-square fits to estimate the exciton binding energy of infinitely long systems. It is found that long-range exchange interactions are required to give the exciton binding energy of the infinitely long systems. Consequently, it is concluded that long-range exchange interactions neglected in many DFT calculations play a crucial role in the exciton binding energies of long-chain systems, while double-excitation correlation effects are also significant to hold the energy balance of the excitations. © 2016 Wiley Periodicals, Inc.

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.

Ultra-stable and highly reactive colloidal gold nanoparticle catalysts protected using multi-dentate metal oxide nanoclusters.

Owing to their remarkable properties, gold nanoparticles are applied in diverse fields, including catalysis, electronics, energy conversion and sensors. However, for catalytic applications of colloidal gold nanoparticles, the trade-off between their reactivity and stability is a significant concern. Here we report a universal approach for preparing stable and reactive colloidal small (~3 nm) gold nanoparticles by using multi-dentate polyoxometalates as protecting agents in non-polar solvents. These nanoparticles exhibit exceptional stability even under conditions of high concentration, long-term storage, heating and addition of bases. Moreover, they display excellent catalytic performance in various oxidation reactions of organic substrates using molecular oxygen as the sole oxidant. Our findings highlight the ability of inorganic multi-dentate ligands with structural stability and robust steric and electronic effects to confer stability and reactivity upon gold nanoparticles. This approach can be extended to prepare metal nanoparticles other than gold, enabling the design of novel nanomaterials with promising applications.

Density functional theory for comprehensive orbital energy calculations.

This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.

Prenatal exposure to perfluorinated chemicals and relationship with allergies and infectious diseases in infants.

BACKGROUND: Recent studies have shown effects of prenatal exposure to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) on infants in the general environmental levels. Laboratory animal studies have shown that exposure to PFOS and PFOA is associated with immunotoxic effects. OBJECTIVES: To investigate the relationship between maternal PFOS and PFOA levels and infant allergies and infectious diseases during the first 18 months of life. Cord blood immunoglobulin (Ig) E levels were also evaluated. METHODS: We conducted a prospective cohort study of pregnant women from 2002 to 2005 in Sapporo, Japan. Maternal PFOS and PFOA levels were measured in relation to cord blood IgE concentrations (n=231) and infant allergies and infectious diseases (n=343). Characteristics of mothers and their infants were obtained from self-administered questionnaires and medical records. Development of infant allergies and infectious diseases was determined from self-administered questionnaires at 18 months of age. Concentrations of PFOS and PFOA in maternal serum and concentrations of IgE in umbilical cord serum at birth were measured. RESULTS: Cord blood IgE levels decreased significantly with high maternal PFOA concentration among female infants. However, there were no significant associations among maternal PFOS and PFOA levels and food allergy, eczema, wheezing, or otitis media in the 18 month-old infants (adjusted for confounders). CONCLUSIONS: Although cord blood IgE level decreased significantly with high maternal PFOA levels among female infants, no relationship was found between maternal PFOS and PFOA levels and infant allergies and infectious diseases at age in 18 months.

Phosphorus-Alloying as a Powerful Method for Designing Highly Active and Durable Metal Nanoparticle Catalysts for the Deoxygenation of Sulfoxides: Ligand and Ensemble Effects of Phosphorus.

The modification of metal nanoparticles (NPs) by incorporating additional metals is a key technique for developing novel catalysts. However, the effects of incorporating nonmetals into metal NPs have not been widely explored, particularly in the field of organic synthesis. In this study, we demonstrate that phosphorus (P)-alloying significantly increases the activity of precious metal NPs for the deoxygenation of sulfoxides into sulfides. In particular, ruthenium phosphide NPs exhibit an excellent catalytic activity and high durability against sulfur-poisoning, outperforming conventional catalysts. Various sulfoxides, including drug intermediates, were deoxygenated to sulfides with excellent yields. Detailed investigations into the structure-activity relationship revealed that P-alloying plays a dual role: it establishes a ligand effect on the electron transfer from Ru to P, facilitating the production of active hydrogen species, and has an ensemble effect on the formation of the Ru-P bond, preventing strong coordination with sulfide products. These effects combine to increase the catalytic performance of ruthenium phosphide NPs. These results demonstrate that P-alloying is an efficient method to improve the metal NP catalysis for diverse organic synthesis.

Spin-orbit relativistic long-range corrected time-dependent density functional theory for investigating spin-forbidden transitions in photochemical reactions.

A long-range corrected (LC) time-dependent density functional theory (TDDFT) incorporating relativistic effects with spin-orbit couplings is presented. The relativistic effects are based on the two-component zeroth-order regular approximation Hamiltonian. Before calculating the electronic excitations, we calculated the ionization potentials (IPs) of alkaline metal, alkaline-earth metal, group 12 transition metal, and rare gas atoms as the minus orbital (spinor) energies on the basis of Koopmans' theorem. We found that both long-range exchange and spin-orbit coupling effects are required to obtain Koopmans' IPs, i.e., the orbital (spinor) energies, quantitatively in DFT calculations even for first-row transition metals and systems containing large short-range exchange effects. We then calculated the valence excitations of group 12 transition metal atoms and the Rydberg excitations of rare gas atoms using spin-orbit relativistic LC-TDDFT. We found that the long-range exchange and spin-orbit coupling effects significantly contribute to the electronic spectra of even light atoms if the atoms have low-lying excitations between orbital spinors of quite different electron distributions.

Modified regional self-interaction correction method based on the pseudospectral method.

A modification of the regional self-interaction correction (RSIC) scheme (Tsuneda et al., J. Comput. Chem. 2003, 24, 1592), pseudospectral RSIC (PSRSIC), is proposed to eliminate the self-interaction errors (SIEs) especially in core regions. PSRSIC reduces the SIEs by substituting the HF exchange energy density calculated with the use of the pseudospectral technique for the exchange energy in the SI-domain region. PSRSIC is combined with the long-range correction (LC) scheme. TDDFT calculations with LC-PSRSIC yield all of the core-, valence-, Rydberg-, and charge-transfer-excitation energies with reasonable accuracy. Core-ionization energies are also well-reproduced by LC-PSRSIC.

A cobalt phosphide catalyst for the hydrogenation of nitriles.

The study of metal phosphide catalysts for organic synthesis is rare. We present, for the first time, a well-defined nano-cobalt phosphide (nano-Co2P) that can serve as a new class of catalysts for the hydrogenation of nitriles to primary amines. While earth-abundant metal catalysts for nitrile hydrogenation generally suffer from air-instability (pyrophoricity), low activity and the need for harsh reaction conditions, nano-Co2P shows both air-stability and remarkably high activity for the hydrogenation of valeronitrile with an excellent turnover number exceeding 58000, which is over 20- to 500-fold greater than that of those previously reported. Moreover, nano-Co2P efficiently promotes the hydrogenation of a wide range of nitriles, which include di- and tetra-nitriles, to the corresponding primary amines even under just 1 bar of H2 pressure, far milder than the conventional reaction conditions. Detailed spectroscopic studies reveal that the high performance of nano-Co2P is attributed to its air-stable metallic nature and the increase of the d-electron density of Co near the Fermi level by the phosphidation of Co, which thus leads to the accelerated activation of both nitrile and H2. Such a phosphidation provides a promising method for the design of an advanced catalyst with high activity and stability in highly efficient and environmentally benign hydrogenations.

Modified regional self-interaction corrected time-dependent density functional theory for core excited-state calculations.

A modified regional self-interaction correction (mRSIC) method is proposed for obtaining accurate core-excitation energies in time-dependent density functional theory (TDDFT) calculations. The mRSIC method is an improvement of the RSIC method (Tsuneda et al. J Comput Chem 2003, 24, 1592). It takes into account the energy contributions from 2s and higher atomic orbitals that the RSIC method neglects. Furthermore, mRSIC improves the poor description for the nuclear-electron cusp of Gaussian basis functions. The mRSIC method was combined with a long-range correction (LC) scheme, which has been proved to give accurate valence-, Rydberg-, and charge transfer (CT)-excitation energies. In so doing, it dramatically improved the accuracy of the calculated core-excitation energies and did not affect the already accurate values of valence-, Rydberg-, and CT-excitation energies produced by the LC functionals. These results mean that the combined scheme is accurate for all excitation energy forms.

Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory.

The Sakurai-Sugiura projection (SS) method was implemented and numerically assessed for diagonalization of the Hamiltonian in time-dependent density functional theory (TDDFT). Since the SS method can be used to specify the range in which the eigenvalues are computed, it may be an efficient tool for use with eigenvalues in a particular range. In this article, the SS method is applied to core excited calculations for which the eigenvalues are located within a particular range, since the eigenvalues are unique to atomic species in molecules. The numerical assessment of formaldehyde molecule by TDDFT with core-valence Becke's three-parameter exchange (B3) plus Lee-Yang-Parr (LYP) correlation (CV-B3LYP) functional demonstrates that the SS method can be used to selectively obtain highly accurate eigenvalues and eigenvectors. Thus, the SS method is a new and powerful alternative for calculating core-excitation energies without high computation costs.

Core-excitation energy calculations with a long-range corrected hybrid exchange-correlation functional including a short-range Gaussian attenuation (LCgau-BOP).

We report the calculations of core-excitation energies of first-row atoms using the time-dependent density functional theory (DFT) and the long-range correction (LC) scheme for exchange-correlation functionals, including LC-BOP, Coulomb-attenuated method BLYP, and our recently developed LCgau-BOP method, which includes a flexible portion of short-range Hartree-Fock (HF) exchange through the inclusion of a Gaussian function in the LC scheme. We show that the LC scheme completely fails to improve the poor accuracy of conventional generalized gradient approximation functionals, while the LCgau scheme gives an accuracy which is an order of magnitude better than BLYP and significantly better than B3LYP. A reoptimization of the two parameters controlling the inclusion of short-range HF exchange in the LCgau method enables the errors to be reduced to the order of 0.1 eV which is competitive with the best DFT methods we are aware of. This reparametrization does not affect the LC scheme and therefore maintains the high accuracy of predicted reaction barrier heights. Moreover, while there is some loss in accuracy in thermochemical predictions compared to the previously optimized LCgau-BOP, rms errors in the atomization energies over the G2 test set are found to be comparable to B3LYP. Finally, we attempt to rationalize the success of the LC and LCgau schemes in terms of the well-known self-interaction error (SIE) of conventional functionals. To estimate the role of the SIE, we examine the total energy calculations for systems with a fractional number of electrons, not only in the highest occupied molecular orbital but also in the 1s-characterized core orbital. Our conclusion is that the inclusion of short-range HF exchange in LC-type functionals can significantly alleviate the problems of the SIE in the core region. In particular, we confirm that the absence of the SIE diagnostics in the core orbital energies correlates with the accurate prediction of core-excitation energies using the newly optimized LCgau approach.

High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: the case of graphene-metal interfaces.

Over many years, computational simulations based on density functional theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy. For this task we use a localised basis set with the Conquest code, both in their primitive, pseudo-atomic orbital form, and using a recent multi-site approach. This multi-site scheme allows us to maintain accuracy while saving computational time and memory requirements, even in our exemplar complex system of graphene grown on Rh(1 1 1) with and without intercalated atomic oxygen. This system offers a rich scenario that will serve as a benchmark, demonstrating that highly accurate simulations in cells with over 3000 atoms are feasible with modest computational resources.

Efficient Calculation of Electronic Structure Using O(N) Density Functional Theory.

We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by Conquest, and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.

Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST.

Multisite local orbitals, which are formed from linear combinations of pseudoatomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [ Phys. Rev. B 2009 , 80 , 205104 ]. Two new methods, the double cutoff method and the smoothing method, are introduced to the LFD method to improve efficiency and stability. The Hamiltonian and overlap matrices with multisite local orbitals are constructed by efficient sparse-matrix multiplications in CONQUEST. The investigation of the calculated energetic and geometrical properties and band structures of bulk Si, Al, and DNA systems demonstrate the accuracy and the computational efficiency of the present method. The representability of both occupied and unoccupied band structures with the present method has been also confirmed.

Correlations between prenatal exposure to perfluorinated chemicals and reduced fetal growth.

BACKGROUND: Perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are man-made, ubiquitous, and persistent contaminants in the environment, wildlife, and humans. Although recent studies have shown that these chemicals interfere with fetal growth in humans, the results are inconsistent. OBJECTIVES: Our goal was to investigate the correlation between relatively low levels of PFOS and PFOA in maternal serum and birth weight and birth size. METHODS: We conducted a hospital-based prospective cohort study between July 2002 and October 2005 in Sapporo, Japan. A total of 428 women and their infants were involved in the study. We obtained characteristics of the mothers and infants from self-administered questionnaire surveys and from medical records. We analyzed maternal serum samples for PFOS and PFOA by liquid chromatography-tandem mass spectrometry (LC/MS/MS). RESULTS: After adjusting for confounding factors, PFOS levels negatively correlated with birth weight [per log10 unit: beta = -148.8 g; 95% confidence interval (CI), -297.0 to -0.5 g]. In addition, analyses stratified by sex revealed that PFOS levels negatively correlated with birth weight only in female infants (per log10 unit: beta = -269.4 g; 95% CI, -465.7 to -73.0 g). However, we observed no correlation between PFOA levels and birth weight. CONCLUSION: Our results indicate that in utero exposure to relatively low levels of PFOS was negatively correlated with birth weight.