Review
Chemistry, Multidisciplinary
Egbert Zojer, Andreas Terfort, Michael Zharnikov
Summary: Controlling the physical and chemical properties of surfaces and interfaces is crucial in physical chemistry and nanotechnology. Self-assembled monolayers (SAMs) offer a promising strategy for this control. SAMs are commonly used in organic electronics for electrostatic engineering of interfaces. Embedding polar groups into the backbone of SAM-forming molecules allows independent optimization of electronic interface engineering and the nucleation of further layers. This concept has been demonstrated successfully on different substrates, resulting in significant work-function changes.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Egbert Zojer, Andreas Terfort, Michael Zharnikov
Summary: Controlling the physical and chemical properties of surfaces and interfaces is crucial in physical chemistry and nanotechnology. Embedding polar groups into self-assembled monolayers (SAMs) allows for independent optimization of electronic interface engineering and further layer nucleation, promising advancements in organic electronics and semiconductor devices.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Hari Padmanabhan, Maxwell Poore, Peter K. Kim, Nathan Z. Koocher, Vladimir A. Stoica, Danilo Puggioni, Huaiyu (Hugo) Wang, Xiaozhe Shen, Alexander H. Reid, Mingqiang Gu, Maxwell Wetherington, Seng Huat Lee, Richard D. Schaller, Zhiqiang Mao, Aaron M. Lindenberg, Xijie Wang, James M. Rondinelli, Richard D. Averitt, Venkatraman Gopalan
Summary: This study provides evidence for interlayer magnetophononic coupling in layered magnetic topological insulator MnBi2Te4. The anomalies in phonon scattering intensities across magnetic field-driven phase transitions are observed using magneto-Raman spectroscopy, which is attributed to phonons modulating the interlayer exchange coupling. The signatures of magnetophononic coupling are also observed in the time domain through ultrafast excitation and detection of coherent phonons.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Miguel Gallegos, Jose Manuel Guevara-Vela, angel Martin Pendas
Summary: This article introduces a neural network model for calculating atomic charges using machine learning techniques. The model has been trained and tested in various scenarios, showing good reliability and performance while significantly accelerating the calculation process and achieving low prediction errors.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Max Bramberger, Jernej Mravlje, Martin Grundner, Ulrich Schollwock, Manuel Zingl
Summary: The study reveals that BaOsO3 is a moderately correlated oxide with moderate quasiparticle renormalization. Spin-orbit coupling leads to a splitting of van Hove singularity near the Fermi energy and a reduction in electronic correlations.
Article
Chemistry, Physical
Irena Efremenko, Jan M. L. Martin
Summary: This study evaluated accurate canonical CCSD(T) energies for reactions between benzene and methyl acrylate catalyzed by Ru(II, III) chloride carbonyl, and compared the performance of different methods and density functionals. The results showed that some new density functionals exhibit superior performance in both closed- and open-shell calculations, and most tested (meta)-GGA and hybrid density functionals perform better for open-shell complexes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Physics, Applied
Su-Hyun Yoo, Mira Todorova, Jorg Neugebauer, Chris G. Van de Walle
Summary: GaN/(Al, Ga)N heterojunctions are crucial for high-electron-mobility transistors. The density of the two-dimensional electron gas (2DEG) on the GaN side is significantly enhanced by the strong polarization fields at the interface. The source of the electrons in the 2DEG is intrinsic to the overall structure and the negative charge is balanced by fixed charge on the surface, rather than surface states.
PHYSICAL REVIEW APPLIED
(2023)
Article
Chemistry, Physical
Zheng Pei, Yuezhi Mao, Yihan Shao, WanZhen Liang
Summary: This work focuses on deriving and implementing analytic energy derivatives with respect to nuclear coordinates and an external electric field within the framework of the QM/DIM method. These derivatives are used to efficiently calculate vibrational frequencies, infrared and Raman spectra of molecules near noble metal clusters/nanoparticles. The results demonstrate the validity and accuracy of the analytic approach, especially when considering the hyperpolarizability of the metal cluster to improve the prediction of Raman spectral intensities. Additionally, the potential impact of charge migration between the adsorbate and MNPs is addressed.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Michal Janecek, Petra Kuhrova, Vojtech Mlynsky, Michal Otyepka, Jiri Sponer, Pavel Banas
Summary: The study proposed improvements to the RESP charge derivation model, including reoptimizing atomic radii, redesigning the restraining scheme, and adding extra point charges, to enhance the description of the electrostatic potential around molecules. The suggested W-RESP(-EP) charge derivation model shows potential for improving nucleic acid force fields, especially for enhancing RESP fitting in aromatic heterocyclic molecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Dong Li, Hongguang Wang, Kaifeng Li, Bonan Zhu, Kai Jiang, Dirk Backes, Larissa S. I. Veiga, Jueli Shi, Pinku Roy, Ming Xiao, Aiping Chen, Quanxi Jia, Tien-Lin Lee, Sarnjeet S. Dhesi, David O. Scanlon, Judith L. MacManus-Driscoll, Peter A. van Aken, Kelvin H. L. Zhang, Weiwei Li
Summary: Transition metal oxides are considered promising candidates for the next generation of spintronic devices due to their controllable properties by strain, defects, and microstructure. In this study, the authors reveal the formation of ordered oxygen vacancies and suppression of CoO6 octahedral rotations in LaCoO3 films, explaining the origin of their ferromagnetic-insulating state. The findings provide valuable insights into the mechanisms of this state and suggest potential applications in low-power spintronic devices.
NATURE COMMUNICATIONS
(2023)
Article
Spectroscopy
Haiying Zhao, Xin Xu, Shenghan Wang, Shuo Li, Chenglin Sun, Zhiwei Men
Summary: Resonance Raman and absorption spectra of lutein were studied in different solvent polarizabilities and temperatures, revealing the influence of temperature and solvent on the Raman scattering cross-section, electron-phonon coupling, and electronic transition wavenumber of linear polyene molecules.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Physical
Brandon C. C. Bukowski, Stephen C. C. Purdy, Evan C. C. Wegener, Zhenwei Wu, A. Jeremy Kropf, Guanghui Zhang, Jeffrey T. T. Miller, Jeffrey Greeley
Summary: Synchrotron spectroscopy and Density Functional Theory (DFT) are combined to develop a new descriptor for the stability of adsorbed chemical intermediates on metal alloy surfaces. The descriptor is related to shifts in Resonant Inelastic X-ray Scattering (RIXS) signals and provides a connection to traditional descriptions of chemisorption. The accessibility of this descriptor to both DFT calculations and experimental spectroscopy allows for deeper connections between theory and characterization in the discovery of new catalysts.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Payal Saha, Bhargab Kakati, Purbajyoti Bhagowati, Munima B. Sahariah
Summary: This study investigates the impact of spin-orbit coupling (SOC) on the electronic and magnetic properties of Mn1.5PtSn compound using density functional theory. Regardless of SOC, ferrimagnetic configuration is found to be more stable at the ground state compared to ferromagnetic and antiferromagnetic configurations. The SOC affects the ground state energy of the compounds, and various analysis methods provide insights into the magnetic and electronic properties of the system. The stable ferrimagnetic configuration shows high spin polarization and low magnetocrystalline anisotropy energy, making it suitable for spin-transfer-torque-based device applications like magnetic recording heads.
Article
Quantum Science & Technology
Masaki Hattori, Giovanni Tomassucci, Genki Hayashi, Mario Okawa, Marek Kopciuszynski, Alexey Barinov, Yangfan Lu, Hidenori Takagi, Naurang L. Saini, Takashi Mizokawa
Summary: The electronic properties of insulators can be controlled by chemical substitution, which has been used to obtain exotic superconducting phases in Mott insulators. However, the impact of chemical substitution on excitonic insulators is not well studied. In this study, space-resolved angle-resolved photoemission spectroscopy of Ta2Ni(Se1-xSx)(5) was conducted to explore the effect of S substitution on the excitonic behavior. The results showed that the substitution introduced electronic inhomogeneity, but the excitonic coupling in Ta2NiSe5 remained robust against this inhomogeneity.
ADVANCED QUANTUM TECHNOLOGIES
(2023)
Article
Materials Science, Multidisciplinary
Shiang Fang, Linda Ye, Madhav Prasad Ghimire, Mingu Kang, Junwei Liu, Minyong Han, Liang Fu, Manuel Richter, Jeroen van den Brink, Efthimios Kaxiras, Riccardo Comin, Joseph G. Checkelsky
Summary: In this study, we investigated the electronic structure of the ferromagnetic kagome metal Fe3Sn2 without spin-orbit coupling. We found two energetically split helical nodal lines near K and K' in the Brillouin zone, resulting from the trigonal stacking of the kagome layers. The hopping across A-A stacking introduced energy splitting, while that across A-B stacking controlled the momentum space amplitude of the helical nodal lines. Our findings have important implications for the design of topological materials.
Article
Chemistry, Multidisciplinary
Shuhei Kusano, Yuma Ichikura, Kazuhiro J. Fujimoto, Sae Konishi, Yuji Yamada, Osamu Hayashida
Article
Chemistry, Physical
Kazuhiro J. Fujimoto, Keiichi Inoue
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Kazuhiro J. Fujimoto, Takumi Minoda, Takeshi Yanai
Summary: This study theoretically investigates excited states of two types of bacteriochlorophyll aggregates in photosynthetic light-harvesting complexes, revealing that the spectral redshift of B800 is mainly due to electrostatic interaction while that of B850 is attributed to excitonic coupling. Additionally, interchromophore charge transfer plays a crucial role in the spectral redshift of B850.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Biochemistry & Molecular Biology
Kazuhiro J. Fujimoto
Summary: The photo-functional chromophore retinal demonstrates diverse optical absorption properties depending on its interactions with proteins and other chromophores. Quantum chemical calculations have revealed molecular mechanisms underlying light absorption in rhodopsins, providing insights into unique optical properties and strategies for artificial design.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Plant Sciences
Takahiro N. Uehara, Takashi Nonoyama, Kyomi Taki, Keiko Kuwata, Ayato Sato, Kazuhiro J. Fujimoto, Tsuyoshi Hirota, Hiromi Matsuo, Akari E. Maeda, Azusa Ono, Tomoaki T. Takahara, Hiroki Tsutsui, Takamasa Suzuki, Takeshi Yanai, Steve A. Kay, Kenichiro Itami, Toshinori Kinoshita, Junichiro Yamaguchi, Norihito Nakamichi
Summary: This study demonstrates the necessity of CDKC;2 in maintaining the circadian period in Arabidopsis. Through chemical biology and genetic approaches, it was found that CDKC;2 maintains transcriptional activity by phosphorylating the C-terminal domain of RNA polymerase II, affecting clock gene expression and period length.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Virology
Kazuhiro J. Fujimoto, Daniel C. F. Hobbs, Miki Umeda, Akihiro Nagata, Rie Yamaguchi, Yoshitaka Sato, Ayato Sato, Kohsuke Ohmatsu, Takashi Ooi, Takeshi Yanai, Hiroshi Kimura, Takayuki Murata
Summary: This study investigates the crucial elements that cause the difference in anti-SARS-CoV-2 activity of nafamostat and camostat, and indicates that the ease of covalent bond formation with Ser441 in TMPRSS2 possibly plays a major role in the anti-SARS-CoV-2 effect of nafamostat and its derivatives.
Article
Chemistry, Multidisciplinary
Masato Ito, Shusuke Shirai, Yongfa Xie, Tomokatsu Kushida, Naoki Ando, Hiroki Soutome, Kazuhiro J. Fujimoto, Takeshi Yanai, Kenichi Tabata, Yasuo Miyata, Hiroshi Kita, Shigehiro Yamaguchi
Summary: We report on a new class of emissive and stable pi-radicals containing a boron atom, which exhibit unique fluorescence properties and potential applications in organic light-emitting diodes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Kazuhiro J. Fujimoto, Shota Minami, Takeshi Yanai
Summary: We propose a novel machine-learning-based scoring function that incorporates ligand and protein structural information into drug discovery. It accurately predicts binding affinity, surpassing conventional scoring functions. The findings provide chemical insights and are useful for rational drug discovery.
Review
Plant Sciences
Norihito Nakamichi, Junichiro Yamaguchi, Ayato Sato, Kazuhiro J. Fujimoto, Eisuke Ota
Summary: Recent advances in chemical biology have revealed the function and regulation of plant circadian clocks through small molecules, including post-translational modifications and metabolites.
Article
Plant Sciences
Ami N. Saito, Akari E. Maeda, Tomoaki T. Takahara, Hiromi Matsuo, Michiya Nishina, Azusa Ono, Katsuhiro Shiratake, Michitaka Notaguchi, Takeshi Yanai, Toshinori Kinoshita, Eisuke Ota, Kazuhiro J. Fujimoto, Junichiro Yamaguchi, Norihito Nakamichi
Summary: The circadian clock, an internal time-keeping system, coordinates physiological processes. BML-259, a small molecule with CDK5/CDK2 inhibition activity, lengthens Arabidopsis circadian clock periods.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ayaka Ueda, Yusuke Aihara, Shinya Sato, Keiko Kano, Emi Mishiro-Sato, Hiroyuki Kitano, Ayato Sato, Kazuhiro J. Fujimoto, Takeshi Yanai, Kazuma Amaike, Toshinori Kinoshita, Kenichiro Itami
Summary: This study discovered 2,6-dihalopurines as a new inhibitor of stomatal opening and investigated its mechanism. Biological assays suggested that the pathway related to plasma membrane H+-ATPase phosphorylation may be involved. Through affinity-based pull down assay and molecular dynamics simulation, Leucine-rich repeat extensin proteins (LRXs), LRX3, LRX4, LRX5, and RALF were identified as target protein candidates for 2,6-dihalopurines. The mechanism of stomatal movement related to LRXs-RALF is an unexplored pathway, and further studies may uncover new signaling pathways and regulatory factors in stomatal movement.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Natsumi Fukaya, Soichiro Ogi, Hikaru Sotome, Kazuhiro J. Fujimoto, Takeshi Yanai, Nils Baeumer, Gustavo Fernandez, Hiroshi Miyasaka, Shigehiro Yamaguchi
Summary: This study reports the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles. The hydrophobic/hydrophilic balance plays a crucial role in controlling the assembly of these molecules into two-dimensional nanostructures in aqueous media.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Kazuhiro J. Fujimoto, Fumika Minowa, Michiya Nishina, Shunta Nakamura, Sayaka Ohashi, Kota Katayama, Hideki Kandori, Takeshi Yanai
Summary: The relationship between the unique Cl- binding site of monkey green (MG) pigment and the spectral tuning in green pigments is still unknown. This study presents computational structural modeling and quantum-chemical simulation of MG pigments, investigating the spectral redshift and physicochemical relevance when Cl- is present. The modeled protein structures are consistent with the experimental observations, and the red-shifted absorption energies are successfully reproduced by excited-state calculations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Akihiro Kondo, Kazuhiro J. Fujimoto, Takeshi Yanai
Summary: Nafamostat and camostat inhibit the fusion of SARS-CoV-2 by forming a covalent bond with TMPRSS2. Nafamostat exhibits stronger inhibitory activity compared to camostat, and the molecular mechanism of TMPRSS2 inhibition remains unclear.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Kazuhiro J. Fujimoto, Tomoya Miyashita, Takehisa Dewa, Takeshi Yanai
Summary: This study theoretically investigated the orientation factor of fluorescence resonance energy transfer (FRET) between LH2 and A647. Molecular dynamics simulations and electronic coupling calculations were performed, and the results showed that A647 was approximately 26 angstrom away from the BChl assembly in LH2. The average orientation factor was predicted to be 1.55, significantly different from the isotropic mean value.
SCIENTIFIC REPORTS
(2022)