Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.chemphys.2024.112478

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jacs.4c07091

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Language：English   Publishing type：Research paper (scientific journal)  

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.

DOI： 10.1063/5.0207751

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcc.4c01525

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

The radical reaction of acrylate (ACR) and/or methacrylate (MA) is necessary for producing synthetic acrylic polymers. However, this synthesis requires sophisticated and precise control of employed radical reactions. As a...

DOI： 10.1039/d4cp04656k

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Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

We analyzed the difference in the structural H/D isotope effect between an excess proton in light water (H-body) and an excess deuteron in heavy water (D-body), including the nuclear quantum effect, using path integral molecular dynamics simulations. We found that the second peak of the H-body is shorter than that of the D-body in the radial distribution function of O*–O, where O* is the oxygen atom of the H3O+/D3O+ fragment. The main reason for this would be the difference in the ratio of the Zundel structure with the sp3-like configuration, where the Zundel structure in the H-body (14.0%) is greater than that in the D-body (12.0%). We also found rare occurrences of double H3O+/D3O+ configurations, mainly including Zundel–Zundel-like structures such as H7O3+/D7O3+ and H9O4+/D9O4+. The ratios of such configurations appearing in our simulations are 0.89% and 0.20% for the H-body and the D-body, respectively.

DOI： 10.1093/bulcsj/uoad009

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Other Link： https://academic.oup.com/bcsj/article-pdf/97/1/uoad009/56616043/uoad009.pdf

Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.cplett.2023.140744

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.3c01450

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Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20230085

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Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

To understand the mechanism of the H–D exchange reaction for synthesizing various deuterium-labeled molecules on heterogeneous metal catalysts as a first step, we analyzed the effects of H/D isotopes on the adsorption of H2O/D2O and their dissociated OH/OD and H/D species on the Pt(111) surface. We applied the combined plane-wave and localized basis set method developed by us to directly treat the electronic structures of the surface and the localized adsorbed region and the nuclear quantum effect of H and D. The results showed that the adsorption energies for the D-compounds on the Pt surface were larger than those for the H-compounds. This is in keeping with the experimental observations. The difference in the distance between the adsorbates and the Pt surface induced by the H/D isotope effect depends on the bonding characteristics. While the distance between D2O and the Pt surface was longer than that in the H2O case, the distance between the D atom and the Pt surface was shorter than that for the H atom. This is the first report on the geometrical differences between H and D based on a systematic analysis of water and its dissociated species.

DOI： 10.1063/5.0151660

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Language：English   Publishing type：Research paper (scientific journal)  

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.

DOI： 10.1063/5.0150246

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/adfm.202303321

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (1612+, 2612+, and 3612+) of GSAs (12+, 22+, and 32+, respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 12+, 22+, and 32+ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3612+ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1612+ and 3612+, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2612+ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.

DOI： 10.1021/acs.jpcb.2c07444

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

This study demonstrated that nickel-nanocluster catalysts exhibit 2.3 times higher electrocatalytic oxygen evolution reaction activity compared with nickel-oxide catalysts prepared using a general impregnation method on carbon black.

DOI： 10.1039/D2NR06952K

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Decomposition analysis shows that the solvent reorientation effect causes solvatofluorochromism of TTz dyes.

DOI： 10.1039/d2ra06454e

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.cplett.2021.139263

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

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.

DOI： 10.1021/acs.jpca.1c08514

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

DOI： 10.1246/cl.210760

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acsomega.1c06976

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

The one-dimensional porphyrin chains in the cocrystal play a very important role in the hole transport properties of C₇₀/porphyrin nanoribbons.

DOI： 10.1039/d2ra02669d

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.cplett.2022.139740

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Small hydrogen inorganic molecules such as water have no positron binding ability. We revealed that their hydrogen bonded binary molecular clusters exhibit greater positron affinities due to the increased dipole moments and polarization effect.

DOI： 10.1039/d2cp03813g

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

Clusters of CO₂ can have positron binding states. Besides, they have various kinds of binding origins depending on the nuclear configurations.

DOI： 10.1039/d2cp03788b

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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.

DOI： 10.1039/d1cp02047a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

Despite the fact that the positron annihilation has been used in biomedical applications, the detailed mechanism of the positron annihilation on biological molecules remains poorly understood so far. In this work, we investigated the positron binding and positron annihilation properties for both global minimum and hydrogen-bonded structures of 20 amino acid molecules using the multicomponent molecular orbital method. By regression analysis, we confirmed that positron affinity can increase with an increase of the permanent dipole moment of the parent amino acids as reported in previous studies, while the annihilation rate linearly increases with respect to the square root of positron affinity. By the one-particle property analyses for probabilities of electron-positron contacts, we found that delocalization characteristics of both electrons and positrons play key roles to enhance the positron annihilation rate arising from both the valence electrons in σ- and π-type molecular orbitals from 2p atomic orbitals but not from the highest occupied molecular orbital electrons, particularly for comparatively weakly bound positronic amino acid systems.

DOI： 10.1021/acsomega.1c03409

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

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.

DOI： 10.1021/acs.langmuir.1c00727

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

We found that CS₂ obtains positron binding ability by dimerization with vibrational Feshbach resonance.

DOI： 10.1039/d1cp02808a

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jcim.0c00740

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Terahertz (THz) absorption spectra of cross-linked polyurethane films were observed at 30-180 degrees C. The obtained spectra displayed characteristic absorption bands. A band observed at 2.6 THz was assigned to the C=O center dot center dot center dot N-H hydrogen bond vibration using previously reported data. DFT calculation results confirmed that a band at 7.5 THz arises owing to the torsional vibration of cross-linked molecules containing urethane bonds. The slight changes in the temperature-dependent spectra were analyzed by the first derivative of absorption intensity with temperature. The thermal behavior of absorption intensities indicates the dynamics of hydrogen bonds and cross-linked structures in polyurethane films.

DOI： 10.1007/s10762-019-00667-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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.

DOI： 10.1039/c7cp08125a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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.

DOI： 10.1039/c7cp01455d

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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. (C) 2017 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

DOI： 10.1063/1.4976646

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

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://pubchemqcsiken.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.

DOI： 10.1021/acs.jcim.7b00083

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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. (C) 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

DOI： 10.1063/1.4953905

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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.

DOI： 10.1039/c6cp04863c

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

A Gaussian-based range-separation approach is applied to the Hartree-Fock exchange interaction and the second-order perturbation theory, comparing the results with those provided through the erfc short-range potential approach. The Gaussian short-range potential's behavior resembles more that of the bare 1/r potential than that of the erfc short-range potential around the origin. Thus, the Gaussian-based range-separation of the exchange term agrees better with the ordinary HF method and the Moller-Plesset perturbation theory. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.12.069

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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. (C) 2015 AIP Publishing LLC.

DOI： 10.1063/1.4908061

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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.

DOI： 10.1039/c5cp00740b

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Publishing type：Research paper (international conference proceedings)   Publisher：ACM Press  

DOI： 10.1145/2830168.2830170

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

A Gaussian-based cutoff scheme in the dielectric-dependent Hartree-Fock (HF) exchange potential under periodic boundary conditions is discussed. The scheme is applied to HF and hybrid density functional theory methods. For comparison, we examine short-range potentials based on the complementary error function. To investigate the behaviors of these short-range exchange potentials, we study several polymers, such as polyethylene and polytetrafluoroethylene. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.06.001

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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. (C) 2014 AIP Publishing LLC.

DOI： 10.1063/1.4869515

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

The methanation reaction of CO2 on a Ru nanoparticle supported on TiO2 catalyst has been investigated by density functional theory (DFT) using the generalized gradient approximation with periodic boundary conditions. Two plausible reaction paths were found for the transformation of CO2 to CH4 on TiO2-supported Ru nanoparticles. The origin of the high activity of the catalyst is discussed based on the overall reaction energy diagram obtained from DFT calculations. The CO2 is readily and stably adsorbed on Ru cluster at moderate temperature as compared with that on bulk Ru surface. It is due to the difference of the Ru structure between the Ru nanoparticle and the bulk Ru surface. The elementary reactions of the hydrogenation of adsorbed CO and of the production of CH4 are possible to become the rate-determining steps over the methanation reaction, because these two reactions have a higher potential energy barrier than that of other elementary reactions in the overall reaction path. These potential energy barriers for the hydrogenation of CO and the production of CH4 on TiO2-supported Ru nanoparticles were lower than those on bulk Ru surface, which explains the high activity of the Ru nanoparticle-loaded TiO2 catalyst. The lowering of these potential energy barriers can be caused by weak charge transfer between Ru atoms and adsorbed species on the TiO2-supported Ru nanoparticles. As the results, the catalytic activity of the Ru nanoparticles supported on TiO2 catalyst is characterized by the structure of Ru nanoparticles and by the weak charge transfer between Ru atoms and adsorbed species. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.apcata.2013.11.016

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

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); 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. (C) 2014 AIP Publishing LLC.

DOI： 10.1063/1.4895623

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

In this paper, we discuss a range-separation density-fitting method for obtaining the electronic band structure. The formalism is based on Gaussian orbital basis functions. The Hartree term and the nuclear attractive term are divided into long-and short-range contributions by using the error and complementary error functions, respectively. The long-range Hartree term is evaluated through a density-fitting procedure based on Gaussian auxiliary functions, where the net charge neutrality of electrons and atomic nuclei in the unit cell is ensured by Lagrange multipliers. We implemented a first-principles program code based on the methodology, and demonstrate calculation results, using semi-local density functional theory (DFT) functionals, the Hartree-Fock, and hybrid DFT methods. We also discuss the efficiency and accuracy of the methodology.

DOI： 10.7566/JPSJ.83.054702

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

DOI： 10.1021/ja3106434

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

We have recently developed an efficient theoretical methodology that takes into account the weak nuclear quantum effect of hydrogen. In our methodology the differences between the weak hydrogen (nuclear) quantum effect and the Born-Oppenheimer approximation are described by a short-range Coulomb-like one-electron potential. Here, we focus on density functional theory (DFT) with the weak hydrogen quantum effect, and show that there is no strong DFT-functional dependence of the weak hydrogen quantum effect. In addition, we show an electron density analysis to investigate complex calculation results from different DFT functionals considering the hydrogen quantum effect. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2011.12.059

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

Recently, much attention has been given to diamond-like carbon (DLC) as a solid-state lubricant, because it exhibits high resistance to wear, low friction and low abrasion. Experimentally it is reported that gas environments are very important for improving the tribological characteristics of DLC films. Recently one of the authors in the present paper, J.-M. Martin, experimentally observed that the low friction of DLC films is realized under alcohol environments. In the present paper, we aim to clarify the low-friction mechanism of the DLC films under methanol environments by using our tight-binding quantum chemical molecular dynamics method. We constructed the simulation model in which one methanol molecule is sandwiched between two hydrogen-terminated DLC films. Then, we performed sliding simulations of the DLC films. We observed the chemical reaction of the methanol molecule under sliding conditions. The methanol molecule decomposed and then OH-termination of the DLC was realized and the CH3 species was incorporated into the DLC film. We already reported that the OH-terminated DLC film is very effective to achieve good low-friction properties under high pressure conditions, compared to H-terminated DLC films. Here, we suggest that methanol environments are very effective to realize the OH-termination of DLC films which leads to the good low-friction properties.

DOI： 10.1039/c2fd00125j

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

We investigate the oxidation process of a platinum surface by using the density functional theory approach under the periodic boundary condition. This oxidation process has received much attention because it is an initial step in the dissolution of platinum catalysts in polymer electrolyte fuel cells. In this research, we determine the optimized structure of alpha -PtO2-like and beta-PtO2-like oxidized platinum surfaces, which have recently been proposed on the basis of in situ X-ray diffraction analysis, at the Kohn Sham density functional theory (KS-DFT) generalized gradient approximation (GGA) level of theory. We discuss the phase transition from the alpha-PtO2-like surface to the beta-PtO2-like surface, including the place-exchange reaction between oxygen and platinum atoms. We propose an intermediate structure in the phase transition, and show that the beta-PtO2-like structure can be formed directly from this intermediate structure.

DOI： 10.1007/s00214-011-1012-y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Diamond-like carbon (DLC) has recently attracted much attention as a solid-state lubricant, because of its resistance to wear, low friction, and low abrasion. Several factors, such as the hydrogen atoms in DLC and transfer film formation are important for improving the tribological characteristics of DLC. In this paper, we discuss the low-friction mechanism of DLC by using our tight-binding quantum chemical molecular dynamics method. The method employs a DLC film sliding simulation in order to explore the effect of hydrogen atoms on the carbon-based transfer film. The formation of C-C bonds between DLC films increases friction, while surface hydrogen atoms suppress C-C bond formation, which results in the low-friction state. Moreover, the steric effect of hydrogen molecule generation was found to remove the load from the substrate, inhibiting C-C bond formation. In addition, we determined that surface hydrogen atoms play a key role in the cleavage of C-C bonds formed during sliding of DLC films.

DOI： 10.1021/jp207065n

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

We have proposed the Gaussian and Fourier transform (GFT) method as an efficient calculation technique for the Hartree term under the periodic boundary condition (PBC), and discuss its analytical energy-gradient formalism in this Letter. We also discuss a Fourier transform technique to estimate the matrix element of the density functional theory (DFT) exchange correlation term. A first-principles molecular dynamics (MD) simulation of water at ambient conditions is executed using those methodologies. (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2010.12.089

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

It has been experimentally shown that an O(-c)-polar ZnO surface is more stable than a Zn(+c)-polar surface in H(2) ambient. We applied first-principles calculations to investigating the polarity dependence on the stability at the electronic level. The calculations revealed that the -c surface terminated with H atom was stable maintaining a wurtzite structure, whereas the +c surface was unstable due to the change of coordination numbers of Zn at the topmost surface from four ( wurtzite) to six ( rock salt). This causes the generation of O(2) molecules, resulting in instability at the +c surface. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3675680]

DOI： 10.1063/1.3675680

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

The screening effect on the Hartree-Fock (HF) exchange term plays a key role in the investigation of solid-state materials by first-principles electronic structure calculations. We recently proposed a novel screened HF exchange potential, in which the inverse of the dielectric constant represents the fraction of the HF exchange term incorporated into the potential. We demonstrated that this approach can be used to reproduce the energy band structure of diamond well [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009)]. In the present paper, we report that the screened HF exchange method is applicable to other semiconductors such as silicon, AlP, AlAs, GaP, and GaAs. (C) 2010 American Institute of Physics. [doi:10.1063/1.3431293]

DOI： 10.1063/1.3431293

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

The validity and accuracy of various ways of drastically reducing the number of k-points in the Brillouin zone integrations Occurring in second-order many-body perturbation calculations of one-dimensional solids has been investigated. The most promising approximation can recover correlation energies of polyethylene and polyacetylene within 1% of converged values at less than a tenth of usual computational cost. The quasi-particle energy bands have also been reproduced quantitatively with the same approximation. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 2953-2959, 2009

DOI： 10.1002/qua.22176

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

An application of second-order many-body perturbation theory to energies and energy bands of polymers is often hindered by the steep polynomial dependence of its computational cost on the number of wave vector sampling points (K) in the Brillouin zone (BZ). It is shown that a Hartree-Fock (HF) calculation with a large value of K (120 in the first BZ) followed by a second-order many-body perturbation calculation with a much smaller value (K=6) can lead to reliable, interpolated correlated energy bands and density of states of a polymer at less than 1% of the computational cost of the conventional approach. Quantitative simulations on photoelectron spectra of trans- and cis-polyacetylenes and polyethylene show that the correlated energy bands and densities of states thus obtained agree quantitatively with the observed and are significant (sometimes qualitative) improvements over the HF results. The energy bands and photoelectron spectra of polydiacetylene are predicted by this method to assist in the interpretation of future high-resolution measurements.

DOI： 10.1103/PhysRevB.80.085118

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

The conductivity of single molecules has received much attention, because achieving it is a fundamental requirement for developing molecular-scale electronics. On the other hand, electron correlation is very important to investigate various features of molecules. We report on a nonequilibrium Green's function (NEGF)-based second-order Moller-Plesset (MP2) approach to accommodate the effect of electron correlation. The NEGF-based MP2 method reduces to an ordinary MP2 method for an isolated molecule, if the molecule does not interact with semi-infinite electrodes. Moreover, we calculate the theoretical current and the conductance of benzenedithiol and fluoro-benzenedithiol molecules using this technique. (c) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 1834-1840, 2009

DOI： 10.1002/qua.21994

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

A screened Hartree-Fock (HF) exchange potential with the dielectric constant was previously reported by Shimazaki and Asai [Chem. Phys. Lett. 466, 91 (2008)], in which the inverse of the dielectric constant was used to represent a fraction of the HF exchange term. In that report, the experimentally obtained value for the dielectric constant was employed. Herein, we discuss a self-consistent technique, in which the value of the dielectric constant can be automatically determined. This technique enables the energy band structure to be determined without using the experimental value. The band energy structure of diamond is calculated, a self-consistent procedure is determined to give closer bandgaps compared with the local density approximation and the generalized gradient approximation. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3119259]

DOI： 10.1063/1.3119259

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Unique taurine-containing Uridine derivatives, 5-taurinomethyluridine (tau m(5)U) and 5-taurinomethyl-2-thiouridine (tau m(5)s(2)U), which were discovered in mammalian mitochondrial tRNAs, exist at the first position of the anticodon. In this paper, we report the first efficient synthesis of tau m(5)U and tau m(5)s(2)U and describe their physicochemical properties. These modified ribonucleosides were synthesized by the reaction of 5-substituted uridine derivatives with a tetrabutylammonium salt of taurine that is highly reactive and well-soluble in common organic solvents. UV and H-1 NMR spectrometric studies revealed the structural properties of the taurine-containing base moieties and the Sugar conformations of these modified ribonucleosides.

DOI： 10.1021/jo802697r

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

We developed the Gaussian and Fourier transform method for crystalline systems. In this method, the Hartree (Coulomb) term of valence electron contribution is taken into account by solving the Poisson equation based on Fourier transform technique. We compared the band structures obtained by the Hartee-Fock (HF) approximation and the density functional theory (DFT). We used three different types of density functional approximations such as the local density approximation (LDA), generalized gradient approximation (GGA), and hybrid density functional. In this paper, we confirm that our calculation technique yields similar results to previous studies.

DOI： 10.1021/ct800329m

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

We investigated the screening effect on the Fock exchange and argued that the effect strongly improves the bandgap description. In this Letter, we propose a screened Fock potential, and the screened Fock exchange method yields diamond's bandgap values which are very close to the experimentally obtained values. We also compared the band structures obtained by using the Hartee-Fock (HF) approximation and the density functional theory (DFT). (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2008.10.012

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

Post-transcriptional modifications at the first ( wobble) position of the tRNA anticodon participate in precise decoding of the genetic code. To decode codons that end in a purine (R) (i.e. NNR), tRNAs frequently utilize 5-methyluridine derivatives (xm(5)U) at the wobble position. However, the functional properties of the C5-substituents of xm(5)U in codon recognition remain elusive. We previously found that mitochondrial tRNAs(Leu(UUR)) with pathogenic point mutations isolated from MELAS ( mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) patients lacked the 5-taurinomethyluridine (tau m(5)U) modification and caused a decoding defect. Here, we constructed Escherichia coli tRNAs(Leu(UUR)) with or without xm(5)U modifications at the wobble position and measured their decoding activities in an in vitro translation as well as by A-site tRNA binding. In addition, the decoding properties of tRNA(Arg) lacking mnm(5)U modification in a knock-out strain of the modifying enzyme (Delta mnmE) were examined by pulse labeling using reporter constructs with consecutive AGR codons. Our results demonstrate that the xm(5)U modification plays a critical role in decoding NNG codons by stabilizing U center dot G pairing at the wobble position. Crystal structures of an anticodon stem-loop containing tau m(5)U interacting with a UUA or UUG codon at the ribosomal A-site revealed that the m(5)U center dot G base pair does not have classical U center dot G wobble geometry. These structures provide help to explain how the tau m(5)U modification enables efficient decoding of UUG codons.

DOI： 10.1074/jbc.M800233200

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

We have studied the lineshape of the inelastic electron tunneling spectroscopy (IETS) theoretically. In order to calculate vibronic currents including the inelastic effect, we have adopted the Keldysh Green's function method and the self-consistent Born approximation, which is applied to the electron-intramolecular-vibration couplings. The second derivative of the vibronic current taken against the bias voltage has peak and dip structures in the IETS. In this paper, we discuss intrinsic and extrinsic mechanisms which control and modify the lineshape of the IETS. The effect of the intrinsic physical parameters, i.e., the contact transfer integral between the molecule and the electrode and the energy gap between the molecular orbital energy and the Fermi level of the electrode, on the lineshape will be discussed first. Next, we will discuss an extrinsic factor, i.e., the effect of the macroscopic shape of the electrode. In order to take into account the shape effect, we use the envelope function method. Our theoretical study will be useful as a guideline to understand various lineshapes of the IETS observed in various experimental situations.

DOI： 10.1103/PhysRevB.77.115428

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

We discuss bias voltage effects on the elastic and the inelastic currents in the tunneling region. We have derived and solved two self-consistent loops: one for electron-electron interaction within the Hartree-Fock approximation, and another for the electron-intramolecular vibration coupling within the Born approximation. The formalism is based on Keldysh Green's function theory; numerical calculations were made in terms of ab initio quantum chemistry techniques augmented with a model for the electrodes. While no remarkable voltage effect on the vibronic currents was found in the low-bias voltage region, we found significant bias voltage effect in the high-bias voltage region. The suppressive correlation between the elastic and the inelastic components of the current is reduced because of the molecular orbital energy shift in the latter region.

DOI： 10.1103/PhysRevB.77.075110

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP PUBLISHING LTD  

We discuss the features of a three-terminal molecular device and the control of electric current using a gate terminal. We introduce a capacitance model to investigate the effect of the gate terminal that could reduce to a two-terminal molecule for a very small gate capacitance. Therefore, this capacitance model can be used in the framework of ordinary ab initio quantum chemical methods. We show the effect of the gate terminal analytically using a simple Huckel method. Moreover, we used our capacitance model with a nonequilibrium Green's function (NEGF)-based Hartree-Fock (HF) approach to study the gate control features of the benzenedithiolate molecule, and we show that the current through the molecule can be modulated by the gate voltage in the case of a high gate control parameter. We also discuss the molecule's response to the applied bias voltage. It is found that the molecular charging effect has a strong influence on the behavior of molecular-based electronic devices.

DOI： 10.1088/0957-4484/18/42/424012

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Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.2177652

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/qua.20819

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Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.2074127

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jp047456d

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