Ultrafine Spatial Modulation of Diazapyrene-Based Two-Dimensional Conjugated Covalent Organic Frameworks.

Tailormade bottom-up synthesis of covalent organic frameworks (COFs) from various functional building blocks offer not only tunable topology and pore size but also multidimensional properties. High crystallinity is one of the prerequisites for their structures and associated physicochemical properties. Among different π-conjugated motifs for constructing COFs, pyrene-based tetragonal structures are effective in achieving highly ordered and crystalline states. In the present research, we demonstrated that the substitution of pyrene with 2,7-diazapyrene produces nearly "flat" structures of two-dimensional (2D) COF layers by controlling the torsional angle of linker molecules. Featuring finite pore diameters and excellent thermodynamic stability of ∼500 °C, ordered face-to-face (slipped AA) stacking arrangements were produced. Extended electrical conjugation spanning 2D frames with modest optical bandgaps (Eg) of ∼2.1 eV shows the planar character of diazapyrene-based COFs. The stacking of the conjugated 2D frames with small Eg values is also beneficial for the formation of highly stable conducting pathways in the crystalline state, which was confirmed by the results of the microwave conductivity measurements. Nitrogen centers in diazapyrene units also play a key role as the active sites for proton transfer, and the maximum proton conductivity of σ = 10-2 S cm-1 was achieved along the cocontinuous nanopore structures surrounded by the active sites. Results show that tetragonal COFs based on diazapyrene can be used as a highly crystalline two-dimensional material with special electrical and proton-conducting capabilities.

Theoretical study of short-range exchange interaction based on semiconductor dielectric function model toward time-dependent dielectric density functional theory.

This study explores various models of semiconductor dielectric functions, with a specific emphasis on the large wavenumber spectrum and the derivation of the screened exchange interaction. Particularly, we discuss the short-range effect of the screened exchange potential. Our investigation reveals that the short-range effect originating from the high wavenumber spectrum is contingent upon the dielectric constant of the targeted system. To incorporate dielectric-dependent behaviors concerning the short-range aspect into the dielectric density functional theory (DFT) framework, we utilize the local Slater term and the Yukawa-type term, adjusting the ratio between these terms based on the dielectric constant. Additionally, we demonstrate the efficacy of the time-dependent dielectric DFT method in accurately characterizing the electronic structure of excited states in dyes and functional molecules. Several theoretical approaches have incorporated parameters dependent on the system to elucidate short-range exchange interactions. Our theoretical analysis and discussions will be useful for those studies.

Stability and bonding nature of positronic lithium molecular dianion.

We studied the stability of a system consisting of a positron (e+) and two lithium anions, [Li-; e+; Li-], using first-principles quantum Monte Carlo calculations combined with the multi-component molecular orbital method. While diatomic lithium molecular dianions Li22- are unstable, we found that its positronic complex can form a bound state with respect to the lowest energy decay into the dissociation channel Li2- and a positronium (Ps). The [Li-; e+; Li-] system has the minimum energy at the internuclear distance of ∼3 Å, which is close to the equilibrium internuclear distance of Li2-. At the minimum energy structure both an excess electron and a positron are delocalized as orbiting around the Li2- molecular anion core. A dominant feature of such a positron bonding structure is described as the Ps fraction bound to Li2-, unlike the covalent positron bonding scheme for the electronically isovalent [H-; e+; H-] complex.

A comprehensive theoretical study of positron binding and annihilation properties of hydrogen bonded binary molecular clusters.

We studied the positron binding and annihilation of hydrogen bonded binary molecular clusters containing small inorganic molecules such as water, hydrogen fluoride, ammonia, hydrogen sulfide, hydrogen chloride, and phosphine, using first-principles calculation. While unimolecular systems of these species mostly exhibit no or very small positron binding energies (positron affinities), we found that all of their hydrogen bonding clusters have greater positive positron affinities. The permanent dipole moment enhanced by the formation of the intermolecular hydrogen bond acts as a dominant parameter to bind a positron for a given proton donor, whereas it is insufficient for reproducing the dependence of the positron affinity on substitutions of the proton donor. By multiple regression analyses with inherent properties of the clusters, we found a reasonable model with additional effective parameters represented by, particularly, the number of hydrogen atoms free from the hydrogen bond. By density analyses for the single-particle and electron-positron collision probabilities, we revealed that these effective parameters are associated with the electronic structure changes induced by the hydrogen bond and positron binding, which have important roles to enhance the electron-positron contact densities due to the proton-screening effect.

Theoretical investigations of positron affinities and their structure-dependent properties of carbon dioxide clusters (CO2)n (n = 1-5).

Although positron binding to van der Waals intermolecularly bonded clusters of non-polar carbon dioxide (CO2) molecules was experimentally suggested, the positron binding feature has been poorly understood. We investigated positron affinities (PAs) by means of multi-component configuration interaction calculations for various structures of (CO2)n (n = 1-5) obtained by the single-component artificial force induced reaction (SC-AFIR) method. Our calculations showed that CO2 monomers do not bind a positron, whereas positron affinities for clusters tend to increase with an increase in the cluster size. Our regression analyses for determining PAs with electrostatic and structural properties of conformations revealed a significant conformer effect due to which structural characteristics such as flatness may have a strong influence on PA for loosely bound positronic complexes of (CO2)n.

Hydrogen/Deuterium Transfer from Anisole to Methoxy Radicals: A Theoretical Study of a Deuterium-Labeled Drug Model.

Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of deuterium-labeled drugs is crucial, both fundamentally and for real applications. To understand the mechanisms of H- and D-transfer reactions, in this study, we used deuterated anisole as a deutetrabenazine model and computationally considered the nuclear quantum effects of protons, deuterons, and electrons. We demonstrated that geometrical differences exist in the partially and fully deuterated methoxy groups and hydrogen-bonded structures of intermediates and transition states due to the H/D isotope effect. The observed geometrical features and electronic structures are ascribable to the different nuclear quantum effects of protons and deuterons. Primary and secondary kinetic isotope effects (KIEs) were calculated for H- and D-transfer reactions from deuterated and undeuterated anisole, with the calculated primary KIEs in good agreement with the corresponding experimental data. These results reveal that the nuclear quantum effects of protons and deuterons need to be considered when analyzing the reaction mechanisms of H- and D-transfer reactions and that a theoretical approach that directly includes nuclear quantum effects is a powerful tool for the analysis of H/D isotope effects in H- and D-transfer reactions.

Role of OH Termination in Mitigating Friction of Diamond-like Carbon under High Load: A Joint Simulation and Experimental Study.

Diamond-like carbon (DLC) has recently attracted much attention as a promising solid-state lubricant because it exhibits low friction, low abrasion, and high wear resistance. Although we previously reported the reason why H-terminated DLC exhibits low friction based on a tight-binding quantum chemical molecular dynamics (TB-QCMD) simulation, experimentally, the low-friction state of H-terminated DLC is not stable, limiting its application. In the present work, our TB-QCMD simulations suggest that H/OH-terminated DLC could give low friction even under high loads, whereas H-terminated DLC could not. By using gas-phase friction experiments, we confirm that OH termination can indeed provide much more stable lubricity than H termination, validating the predictions from simulations. We conclude that H/OH-terminated DLC is a new low-friction material with high load capacity and high stable lubricity that may be suitable for practical use in industrial applications.

A theoretical study on solvatofluorochromic asymmetric thiazolothiazole (TTz) dyes using dielectric-dependent density functional theory.

In this work, the excitation energies of asymmetric thiazolothizaole (TTz) dye molecules have been theoretically studied using dielectric-dependent density functional theory (DFT). In the dielectric-dependent DFT approach, the ratio (fraction) of the nonlocal Hartree exchange term incorporated into the DFT exchange-correlation functional is a system-dependent parameter, which is inversely proportional to the dielectric constant of the target material. The dielectric-dependent DFT method is closely related to the Coulomb hole and screened exchange (COHSEX) approximation in the GW method and therefore has been applied to crystalline systems with periodic boundary conditions, such as semiconductors and inorganic materials. By focusing on the solvatofluorochromic phenomena of asymmetric TTz dyes, we show that excitation energy calculations obtained from the dielectric-dependent DFT method can reproduce the corresponding experimental UV-vis absorption and emission spectra of dyes in solvents.

Theoretical investigation of the enhancement of positron affinity by the vibration and dimerization of non-polar carbon disulfide.

The positronic bound state for the non-polar carbon disulfide (CS2) has been experimentally identified, although previous theoretical investigations, which were dedicated to studying the positronic CS2 monomer, could not reasonably reproduce the experimentally measured positron affinity. In the present study, we performed analysis of the vibrational averaged positron affinity for the positronic CS2 dimer, [C2S4; e+], using the Hartree-Fock and configuration interaction levels of the multi-component molecular orbital method combined with the self-consistent field level of the vibrational variational Monte Carlo method. We demonstrated that the equilibrium structure of the non-polar C2S4 can have the positronic bound state with a positron affinity of about 46.18 meV in the configuration interaction level, while this is 0 meV in the Hartree-Fock level. Furthermore, by taking into account the vibrational effect, we succeeded in reproducing the resonant positron kinetic energies lying close to the experimental value, where the vibrational averaged positron affinity becomes greater with an increased dipole moment and dipole polarizability. We also showed possible mechanisms to effectively enhance the resonant positron capture for [C2S4; e+], associated with both the infrared active and infrared inactive vibrational modes.

PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties.

We report on optimized molecular geometries and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to neutral states, we also calculated those for cationic, anionic, and spin flipped electronic states of 56.2%, 49.7%, and 41.3% of the molecules, respectively. Thus, the grand total of the PM6 calculations amounted to 221 million. We compared the resulting molecular geometries with B3LYP/6-31G* optimized geometries for 2.6 million molecules. The root-mean-square deviations in bond length and bond angle were approximately 0.016 Å and 1.7°, respectively. Then, using linear regression to examine the HOMO energy levels E(HOMO) in the B3LYP and PM6 calculations, we found that EB3LYP(HOMO) = 0.876EPM6(HOMO) + 1.975 (eV) and calculated the coefficient of determination to be 0.803. Likewise, we examined the LUMO energy levels and found EB3LYP(LUMO) = 1.069EPM6(LUMO) - 0.420 (eV); the coefficient of determination was 0.842. We also generated four subdata sets, each of which was composed of molecules with molecular weights less than 500. Subdata set i contained C, H, O and N, ii contained C, H, N, O, P, and S, iii contained C, H, N, O, P, S, F, and Cl, and iv contained C, H, N, O, P, S, F, Cl, Na, K, Mg, and Ca. The data sets are available at http://pubchemqc.riken.jp/pm6_datasets.html under a Creative Commons Attribution 4.0 International license.

Theoretical study on mesoscopic-size impurity effects in the charge separation process of organic photocells.

A bulk-heterojunction structure is often employed to develop high-performance organic photocells, in which the donor and acceptor regions are complexly intertwined. In such situations, mesoscopic-scale islands and peninsulas that compose the donor materials may be formed in the acceptor region. Alternatively, the donor region may extend deeply into the acceptor region. This yields mesoscopic-size impurities that can create obstacles in the charge separation (exciton dissociation) process of organic photocells and prevents the dissociation of excitons (electron-hole pairs). We previously reported on the effect of the cooperative behavior between the hot charge transfer (CT) state and the dimensional (entropy) effect on the charge separation process. In this paper, we discuss the mesoscopic-scale impurity effect on the charge separation process in PCBM acceptor models by considering the hot CT state and dimensional effects. In addition, we discuss atomic-scale effects such as molecular distortions and conformation changes using molecular dynamics (MD) simulations.

PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry.

Large-scale molecular databases play an essential role in the investigation of various subjects such as the development of organic materials, in silico drug design, and data-driven studies with machine learning. We have developed a large-scale quantum chemistry database based on first-principles methods. Our database currently contains the ground-state electronic structures of 3 million molecules based on density functional theory (DFT) at the B3LYP/6-31G* level, and we successively calculated 10 low-lying excited states of over 2 million molecules via time-dependent DFT with the B3LYP functional and the 6-31+G* basis set. To select the molecules calculated in our project, we referred to the PubChem Project, which was used as the source of the molecular structures in short strings using the InChI and SMILES representations. Accordingly, we have named our quantum chemistry database project "PubChemQC" ( http://pubchemqc.riken.jp/ ) and placed it in the public domain. In this paper, we show the fundamental features of the PubChemQC database and discuss the techniques used to construct the data set for large-scale quantum chemistry calculations. We also present a machine learning approach to predict the electronic structure of molecules as an example to demonstrate the suitability of the large-scale quantum chemistry database.

A theoretical study on hot charge-transfer states and dimensional effects of organic photocells based on an ideal diode model.

This paper discusses an ideal diode model with hot charge-transfer (CT) states to analyze the power conversion efficiency of an organic photocell. A free carrier generation mechanism via sunlight in an organic photocell consists of four microscopic processes: photon absorption, exciton dissociation, CT, and charge separation. The hot CT state effect has been actively investigated to understand the charge separation process. We previously reported a theoretical method to calculate the efficiency of the charge separation process via a hot CT state (T. Shimazaki et al., Phys. Chem. Chem. Phys., 2015, 17, 12538 and J. Chem. Phys., 2016, 144, 234906). In this paper, we integrate the simulation method into the ideal photocell diode model and calculate several properties such as short circuit current, open circuit voltage, and power conversion efficiency. Our results highlight that utilizing the dimensional (entropy) effect together with the hot CT state can play an essential role in developing more efficient organic photocell devices.

Group molecular orbital approach to solve the Huzinaga subsystem self-consistent-field equations.

An algorithm to solve the Huzinaga subsystem self-consistent field equations is proposed using two approximations: a local expansion of subsystem molecular orbitals and a truncation of the projection operator. Test calculations are performed on water and ammonia clusters, and n-alkane and poly-glycine. The errors were 2.2 and -0.6 kcal/mol for (H2O)40 and C40H82, respectively, at the Hartree-Fock level with the 6-31G basis set.

Application of the dielectric-dependent screened exchange potential approach to organic photocell materials.

This paper discusses the fundamental features of the dielectric-dependent screened exchange potential approach for organic molecules and photocell materials. The energy difference (gap) between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) is a key factor when designing organic photocell materials. The magnitude of this energy gap strongly depends on the ratio of the Hartree-Fock (HF) exchange term combined with hybrid density functional theory (DFT) functionals. In ordinary hybrid DFT functionals, the HF exchange term ratio is often determined empirically and a constant value is employed for all materials. Conversely, the dielectric-dependent exchange potential approach employs a system-dependent value for this parameter, which is proportional to the inverse of the dielectric constant. The organic materials examined in this paper take different dielectric constant values according to their material types and unit lengths; therefore, their HF exchange ratios are also different. This paper discusses the relationship between the energy gaps, the dielectric constants, and the HF exchange ratios in the dielectric-dependent screened exchange potential approach. For a series of acene-type compounds, it was found that the HOMO-LUMO gap decreased when their conjugation systems are extended. The dielectric-dependent screened exchange potential approach demonstrated that the values of the dielectric constants of the compounds increased; consequently, the HF exchange ratio decreased. Similar results were obtained for a series of thiophene-based donor molecules. The calculated values were compared with those obtained via experimental measurements. We found that although the theoretical calculations of the HOMO-LUMO gap usually overestimate experimental optical gaps, a better agreement between the experimental and calculated values can be obtained if we correct for the exciton binding energy.

Theoretical study on the cooperative exciton dissociation process based on dimensional and hot charge-transfer state effects in an organic photocell.

This paper discusses the exciton dissociation process at the donor-acceptor interface in organic photocells. In our previous study, we introduced a local temperature to handle the hot charge-transfer (CT) state and calculated the exciton dissociation probability based on the 1D organic semiconductor model [T. Shimazaki and T. Nakajima, Phys. Chem. Chem. Phys. 17, 12538 (2015)]. Although the hot CT state plays an essential role in exciton dissociations, the probabilities calculated are not high enough to efficiently separate bound electron-hole pairs. This paper focuses on the dimensional (entropy) effect together with the hot CT state effect and shows that cooperative behavior between both effects can improve the exciton dissociation process. In addition, we discuss cooperative effects with site-disorders and external-electric-fields.

Theoretical study of exciton dissociation through hot states at donor-acceptor interface in organic photocell.

We theoretically study the dissociation of geminate electron-hole pairs (i.e., excitons) through vibrational hot states at the donor-acceptor interface of organic photocells. To conduct this, we modify the formalism of Rubel et al. [Phys. Rev. Lett., 2008, 100, 196602], and use the theoretical concepts of Arkhipov et al. [Phys. Rev. Lett., 1999, 82, 1321] and Knights et al. [J. Phys. Chem. Sol., 1974, 35, 543] to consider vibrational hot states. The effects of band-offset energy and the dissipation of excess energy are discussed on the basis of calculations of the escape probability for hot electrons. Furthermore, we show that vibrational hot state and delocalization of excitons lead to an increased probability to separate geminate electron-hole pairs.

Theoretical study of a screened Hartree-Fock exchange potential using position-dependent atomic dielectric constants.

Dielectric-dependent screened Hartree-Fock (HF) exchange potential and Slater-formula have been reported, where the ratio of the HF exchange term mixed into potentials is inversely proportional to the dielectric constant of the target semiconductor. This study introduces a position-dependent dielectric constant method in which the dielectric constant is partitioned between the atoms in a semiconductor. These partitioned values differ depending on the electrostatic environment surrounding the atoms and lead to position-dependent atomic dielectric constants. These atomic dielectric constants provide atomic orbital-based matrix elements for the screened exchange potentials. Energy band structures of several semiconductors and insulators are also presented to validate this approach.

Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations.

We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step.

Communication: different behavior of Young's modulus and fracture strength of CeO2: density functional theory calculations.

In this Communication, we use density functional theory (DFT) to examine the fracture properties of ceria (CeO2), which is a promising electrolyte material for lowering the working temperature of solid oxide fuel cells. We estimate the stress-strain curve by fitting the energy density calculated by DFT. The calculated Young's modulus of 221.8 GPa is of the same order as the experimental value, whereas the fracture strength of 22.7 GPa is two orders of magnitude larger than the experimental value. Next, we combine DFT and Griffith theory to estimate the fracture strength as a function of a crack length. This method produces an estimated fracture strength of 0.467 GPa, which is of the same order as the experimental value. Therefore, the fracture strength is very sensitive to the crack length, whereas the Young's modulus is not.