Call for Application: RCCS Computational Resources FY2026
Application Types: Categories (A), (B), (I), and Library Development
Application Open: Monday, Dec 1, 2025.
Application Close (Category (B)): Thursday, Jan 15, 2026 at 24:00.
Application Close (Categories (A) and (I), Library Development): Friday, Mar 19, 2027 at 24:00.
Resource Available Period: Wednesday, Apr 8, 2026 at 17:00 to Monday, Apr 5, 2027 at 9:00.
NOTE : For Category (A)/(I) applicants who want to use resources from Apr 8, 2026, please submit your application until Jan 15, 2026 at 24:00.

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Scientific results using RCCS

Electrochemical cascade access to hetero[8]circulenes as potent organophotocatalysts for diverse C–X bond formations

The chemistry of hetero[8]circulenes has been limited to three types due to challenges in making unsymmetrical variants. We introduce an electrochemical approach to a hetero[8]circulene bearing five hexagons and three pentagons. Exploiting electrochemistry’s selectivity, differential oxidation enables selective inter- and intramolecular couplings, giving dioxaza[8]circulenes in up to 83% yield with good functional-group tolerance. A one-pot protocol from commercially available substrates forges six new bonds. Structural, optical, and electrochemical characterizations (X-ray crystallography, spectrophotometric analysis) with DFT calculations elucidate properties. Motivated by these features, we demonstrate transition-metal-free organophotocatalysis under 365-nm LED irradiation, effecting diverse C–X (X = C, B, P) bond formations in up to 97% yield.

A. S. Gabr, M. S. H. Salem*, M. I. Khalid, R. Takahashi, Y. Nishimoto, M. Yasuda, S. Takizawa*, Nat. Commun., 16, 5682 (2025).

Electrochemical cascade access to hetero[8]circulenes as potent organophotocatalysts for diverse C–X bond formations

A. S. Gabr, M. S. H. Salem*, M. I. Khalid, R. Takahashi, Y. Nishimoto, M. Yasuda, S. Takizawa*, Nat. Commun., 16, 5682 (2025).

Molecular Simulation × AI Reveals Structural Changes of Transporter Proteins

Transporter proteins exist in the plasma membrane and transport various substrates into and out of the cell. It is believed that substrates are transported by a mechanism involving conformational changes called alternating access. Therefore, it is necessary to elucidate the structural changes in order to understand the mechanism. We have elucidated the conformational changes of the oxalate transporter, which transports oxalic acid, a substance contained in vegetables and nuts that causes urinary tract stones, by combining molecular dynamics (MD) simulations and the structure prediction AI AlphaFold. MD simulations predicted the inward-open conformation, which is experimentally difficult to analyze, and AlphaFold successfully predicted mutations that stabilize the inward-open conformation.

Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT
J. Ohnuki, T. Jaunet-Lahary, A. Yamashita, and K. Okazaki, J. Phys. Chem. Lett. 15, 725–732 (2024).

Electronic structure informatics to search for hightly efficient photovoltaic materials using singlet fission

The transition from fossil fuels to environment-friendly and renewable sources of energy has become one of the central challenges for today’s society and across scientific disciplines. Though global energy studies report that there has been record-breaking growth in sustainable energy production, further improvements are desirable. Solar energy is a promising solution for the near future, owing to its availability and potentially high output.

In this study, an "electronic structure informatics" approach combining the semiempirical molecular orbital method, time-dependent density functional theory, and machine learning has been applied to rapidly search for materials that can be used as photovoltaic cell materials with high efficiency by multiple exciton generation using singlet fission from over 4 million derivatives based on indigo, a famous dye of natural origin. The obtained promising candidate molecules and their possible candidates were identified and compared with those not. Random forest classification of the chemical structures of the obtained promising and non-promising candidate molecules led to the discovery of chemical structure rules that effectively show singlet fission and the identification of candidate materials with symmetric chemical structures and sufficient synthesizability in the order of several hundred.

Weber F., Mori H., npj Comput. Mater., 8, 176 (2022).

Electronic structure informatics to search for hightly efficient photovoltaic materials using singlet fission

Weber F., Mori H., npj Comput. Mater., 8, 176 (2022).

The mechanism of divalent cation block of ion channel activity

Nervous activity is subjected to complex regulation by ion channels. In this study, we reproduced the divalent cations block in molecular dynamics simulation and elucidated the blocking mechanism. It was observed that introducing a hydrophilic environment into the channel lumen allows the stable existence of divalent cations. This retention of divalent cations makes it difficult for ions to permeate the ion channel. This result also provides new knowledge about the reproduction of polyvalent ions in molecular dynamics simulations.

K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi, Nat. Commun., 14, 4236 (2023).

The mechanism of divalent cation block of ion channel activity

K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi, Nat. Commun., 14, 4236 (2023).

Au-Ag nanoclusters showing intense phosphorescence in cells

Luminescent metal nanoclusters are expected to exhibit unique physical properties in the cluster structure depending on the ligand structure, metal type, number of nuclei and arrangement. In this study, carbon-centered gold-silver (CAu₆Ag₂) clusters with N-heterocyclic carbene (NHC) ligands were designed and synthesized, and it was found that these clusters emit strong phosphorescence in solution, and the contribution of NHC ligands to phosphorescence emission was revealed by theoretical calculation. The luminescence rate constant was calculated by an analysis including spin-orbit interactions, and the quantum yield was discussed in terms of the energy barrier to the minimum energy crossing point. Furthermore, the phosphorescent gold-silver clusters with long luminescence lifetime were used for cellular imaging, which revealed the pathway of uptake into the cell and selective localization to specific organelles, confirming their superior functionality, which is different from the non-selective uptake of conventional phosphine ligands.
Z. Lei, M. Endo, H. Ube, T. Shiraogawa, P. Zhao, K. Nagata, X.-L. Pei, T. Eguchi, T. Kamachi, M. Ehara, T. Ozawa, M. Shionoya Nature Commun. 13, 4288-1-9 (2022).

Au-Ag nanoclusters showing intense phosphorescence in cells

“Bucket brigade” of remdesivir in RNA-dependent RNA polymerase of SARS-CoV-2

　The process of remdesivir uptake into the protein (RNA-dependent RNA polymerase) that replicates the gene of SARS-CoV-2 was revealed by molecular dynamics simulations. Remdesivir has a phosphate group with a negative charge, and the binding site of RNA polymerase has Mg²⁺ ions. In addition, RNA polymerase has lysine residues, which are positively charged, in a line toward the binding site. It was found that the lysine residue attracts the phosphate group of remdesivir and passes it to the next lysine residue sequentially, transporting the drug to the binding site like a bucket brigade.

S. Tanimoto, S. G. Itoh, and H. Okumura: Biophys. J. (2021), DOI: 10.1016/j.bpj.2021.07.026, “Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

“Bucket brigade” of remdesivir in RNA-dependent RNA polymerase of SARS-CoV-2

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Update Information

2025-12-03	Storage issues 3:20 PM to 11:20 PM on 12/3
(Dec 4 9:10 AM) The storage response degradation after recovery was resolved by 4:30 AM on Dec 4. (Dec 3 11:55 PM) The storage failure has been resolved around 11:20 PM. We sincerely apologize for any inconvenience caused. In case you still experience some connectivity issues, you might need to wait a moment when logging in or try logging in again. Read more about Storage issues 3:20 PM to 11:20 PM on 12/3

2025-12-03

Storage issues 3:20 PM to 11:20 PM on 12/3

(Dec 4 9:10 AM) The storage response degradation after recovery was resolved by 4:30 AM on Dec 4. (Dec 3 11:55 PM) The storage failure has been resolved around 11:20 PM. We sincerely apologize for any inconvenience caused. In case you still experience some connectivity issues, you might need to wait a moment when logging in or try logging in again.

Read more about Storage issues 3:20 PM to 11:20 PM on 12/3

2025-11-25	Notice of recovery from access issues on the Sapporo Basis Functions website
Between October 24th and November 25th, the Sapporo Basis Functions website ( http://sapporo.center.ims.ac.jp/sapporo/ Read more about Notice of recovery from access issues on the Sapporo Basis Functions website

2025-10-22	Nov 13 (Thu) 9:00-17:00 NOUS scheduled maintenance
Due to maintenance, NOUS will be unavailable from 9:00 to 17:00 on Nov 13 (Thu). New applications cannot be submitted during the maintenance. The service is scheduled to be down for 8 hours, but will resume as soon as the maintenance work is completed. Read more about Nov 13 (Thu) 9:00-17:00 NOUS scheduled maintenance

2025-10-20	Issue Preventing Use of osub Script Resolved
An issue that began around 10:00 AM on Monday, October 20th prevented the osub script from being used. This issue has now been resolved, and osub is working normally again. We apologize for any inconvenience this may have caused. Read more about Issue Preventing Use of osub Script Resolved

2025-10-20	osub now supports external file references
We have implemented a feature that automatically detects external file references in ORCA input files and rewrites them as absolute paths in the edited input file .ap. Read more about osub now supports external file references

2025-09-17	osub External File Handling
To avoid calculation errors, note that osub does not automatically copy external files. When using external files, you must either use the -N option or specify absolute paths. Read more about osub External File Handling

2025-07-22	Aug 14 (Thu) 9:00-17:00: NOUS scheduled maintenance
NOUS will be unavailable from 9:00 to 17:00 on Aug 14 (Thu) due to the maintenance. New applications cannot be submitted during the maintenance. Read more about Aug 14 (Thu) 9:00-17:00: NOUS scheduled maintenance

2025-07-03	Introduction to the ORCA Job Submission Command: osub
(9/3) Fixed a bug where the local scratch directory wasn't used by default. The -N option is now required if you need to check intermediate files like .out during the calculation. Read more about Introduction to the ORCA Job Submission Command: osub

2025-06-18	ORCA 6.1.0 installed
We have installed the latest release, ORCA version 6.1.0. Please refer to the official website for details about the updates. Registration is required to use it. If you have already registered, you can continue using it without any changes. The software is available at /apl/orca/6.1.0, and sample files can be found under /apl/orca/6.1.0/samples. Read more about ORCA 6.1.0 installed

2025-06-03	Gaussian Job Submission Feature Added to Open OnDemand
We have newly added a Gaussian job submission feature using g16sub/g09sub to Open OnDemand's job submission functionality. Access Method Read more about Gaussian Job Submission Feature Added to Open OnDemand