Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

Gaussian-Approximated Poisson Preconditioner for Iterative Diagonalization in Real-Space Density Functional Theory

Various real-space methods optimized on massive parallel computers have been developed for efficient large-scale density functional theory (DFT) calculations of materials and biomolecules. The iterative diagonalization of the Hamiltonian matrix is a computational bottleneck in real-space DFT calculations. Despite the development of various iterative eigensolvers, the absence of efficient real-space preconditioners has hindered their overall efficiency. An efficient preconditioner must satisfy two conditions: appropriate acceleration of the convergence of the iterative process and inexpensive computation. This study proposed a Gaussian-approximated Poisson preconditioner (GAPP) that satisfied both conditions and was suitable for real-space methods. A low computational cost was realized through the Gaussian approximation of a Poisson Green's function. Fast convergence was achieved through the proper determination of Gaussian coefficients to fit the Coulomb energies. The performance of GAPP was evaluated for several molecular and extended systems, and it showed the highest efficiency among the existing preconditioners adopted in real-space codes.

Molecular modification approach on kojic acid derivatives as antioxidants related to ascorbic acid

A hypothetical study by using molecular modeling for antioxidant capacity of kojic acid derivatives was performed using quantum chemistry calculations by DFT/B3LYP/6-311++G(3d,2p). Four modification approaches were considered namely simplification, functional modifications, ring regioisomerism, and hydroxylation. Molecular orbitals, single-electron transfers, hydrogen atom transfers, and spin density distributions were used for antioxidant prediction. In accordance with HOMO, LUMO, Gap, ionization potential, bond dissociation energy, and stabilization energy, the molecular simplifications of kojic acid show that enol moiety is more important for antioxidant capacity than alcohol group. Few molecular modifications on alcohol or enol position were more potent than kojic acid. The π conjugation system among ether, alkene, and hydroxyl moieties can be involved on resonance effects of better compounds. A different performance was observed on alcohol molecular modifications when compared to enol position. All lactone derivatives were more potent than kojic acid on both mechanisms, and their hydroxylated derivatives were more potent than ascorbic acid. In conclusion, the ring regioisomers and its hydroxylated derivatives have better antioxidant capacity than kojic acid. Graphical Abstract The theoretical study using molecular modeling for antioxidant capacity prediction of kojic acid was more related to enol moiety than alcohol. The regioisomerism and hybrid derivatives show that the lactone derivatives increase antioxidant capacity more than the pyrone derivatives.

Study of Li Adsorption on Graphdiyne Using Hybrid DFT Calculations

Promising applications of graphdiyne have often been initiated by theoretical predictions especially using DFT known as the most powerful first-principles electronic structure calculation method. However, there is no systematic study on the reliability of DFT for the prediction of the electronic properties of the graphdiyne. Here, we performed a study of Li adsorption on the graphdiyne using hybrid DFT with LC-ωPBE and compared the results with those of PBE, because accurate prediction of the Li adsorption is important for performance as a Li storage that was first theoretically suggested and then experimentally realized. Our results show that PBE overestimates the adsorption energy inside a pore and the barrier height at the transition state of in-plane diffusion compared to the those of LC-ωPBE. In particular, LC-ωPBE predicted almost barrier-less in-plane diffusion of Li on the graphdiyne because of the presence of both in-plane and out-of-plane π orbitals. Also, LC-ωPBE favors a high spin state due to the exact exchange energy when several Li atoms are adsorbed on the graphdiyne, whereas PBE favors a low spin state. Thus, the use of the hybrid DFT is critical for reliable predictions on the electronic properties of the graphdiyne.

Fragment-orbital tunneling currents and electronic couplings for analysis of molecular charge-transfer systems

In theoretical charge-transfer research, calculation of the electronic coupling element is crucial for examining the degree of the electronic donor-acceptor interaction. The tunneling current (TC), representing the magnitudes and directions of electron flow, provides a way of evaluating electronic couplings, along with the ability of visualizing how electrons flow in systems. Here, we applied the TC theory to π-conjugated organic dimer systems, in the form of our fragment-orbital tunneling current (FOTC) method, which uses the frontier molecular-orbitals of system fragments as diabatic states. For a comprehensive test of FOTC, we assessed how reasonable the computed electronic couplings and the corresponding TC densities are for the hole- and electron-transfer databases HAB11 and HAB7. FOTC gave 12.5% mean relative unsigned error with regard to the high-level ab initio reference. The shown performance is comparable with that of fragment-orbital density functional theory, which gave the same error by 20.6% or 13.9% depending on the formulation. In the test of a set of nucleobase π stacks, we showed that the original TC expression is also applicable to nondegenerate cases under the condition that the overlap between the charge distributions of diabatic states is small enough to offset the energy difference. Lastly, we carried out visual analysis on the FOTC densities of thiophene dimers with different intermolecular alignments. The result depicts an intimate topological connection between the system geometry and electron flow. Our work provides quantitative and qualitative grounds for FOTC, showing it to be a versatile tool in characterization of molecular charge-transfer systems.

Non-empirical atomistic dipole-interaction-model for quantum plasmon simulation of nanoparticles

Plasmonic nanoparticles in the quantum regime exhibit characteristic optical properties that cannot be described by classical theories. Time-dependent density functional theory (TDDFT) is rising as a versatile tool for study on such systems, but its application has been limited to very small clusters due to rapidly growing computational costs. We propose an atomistic dipole-interaction-model for quantum plasmon simulations as a practical alternative. Namely the atomic dipole approximation represents induced dipoles with atomic polarizabilities obtained from TDDFT without empirical parameters. It showed very good agreement with TDDFT for plasmonic spectra of small silver clusters at much lower computational cost, though it is not appropriate for molecular-like excitations. It could also reproduce the plasmonic band shift experimentally observed in sub-10 nm silver particles.

Effects of the locality of a potential derived from hybrid density functionals on Kohn-Sham orbitals and excited states

Density functional theory (DFT) has been an essential tool for electronic structure calculations in various fields. In particular, its hybrid method including the Hartree-Fock (HF) exchange term remarkably improves the reliability of DFT for chemical applications and computational material design. There are two different types of exchange-correlation potential that can be derived from hybrid functionals. The conventional approach adopts a non-multiplicative potential including the non-local HF exchange operator. Herein, we propose to use a local multiplicative potential as an alternative for accurate excited state calculations. We show that such a local potential can be derived from existing global hybrid functionals using the optimized effective potential method. As a proof-of-concept, we chose PBE0 and investigated its performance for the Caricato benchmark set. Unlike the conventional one, the local potential produced orbital energy gaps with no strong dependence on the mixing ratio as a good approximation for optical excitations. Furthermore, its time-dependent DFT resulted in a surprisingly small mean absolute error even with a local density approximation kernel, surpassing all reported values with various popular functionals. In particular, most excitations were dictated by single orbital transitions due to physically meaningful virtual orbitals, which is beneficial to clear interpretations in the molecular orbital picture.

Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid

We investigated the performance of heterogeneous computing with graphics processing units (GPUs) and many integrated core (MIC) with 20 CPU cores (20×CPU). As a practical example toward large scale electronic structure calculations using grid-based methods, we evaluated the Hartree potentials of silver nanoparticles with various sizes (3.1, 3.7, 4.9, 6.1, and 6.9 nm) via a direct integral method supported by the sinc basis set. The so-called work stealing scheduler was used for efficient heterogeneous computing via the balanced dynamic distribution of workloads between all processors on a given architecture without any prior information on their individual performances. 20×CPU + 1GPU was up to ∼1.5 and ∼3.1 times faster than 1GPU and 20×CPU, respectively. 20×CPU + 2GPU was ∼4.3 times faster than 20×CPU. The performance enhancement by CPU + MIC was considerably lower than expected because of the large initialization overhead of MIC, although its theoretical performance is similar with that of CPU + GPU. © 2016 Wiley Periodicals, Inc.

Configuration interaction singles based on the real-space numerical grid method: Kohn–Sham versus Hartree–Fock orbitals

We developed a program code of CIS based on a numerical grid method and showed that Kohn–Sham orbitals from the Krieger–Li–Iafrate (KLI) approximation provide better reference configurations for CIS than the standard Hartree–Fock and Kohn–Sham orbitals.