Publications | Muraoka Lab

pymatgen: 15 years of community growth, new functionality, and future prospects

arXiv, 2026.

J. George, M.K. Horton, A.D. Kaplan, S.R. Kavanagh, J. Riebesell, A.S. Rosen, H. Yang, F. Adams, M. Amachraa, O. Andriuc, O.A. Ashour, S. Bajaj, E. Banyas, L. Barroso-Luque, K. Berket, N. Bernstein, A. Bhardwaj, A.H.U. Bhatti, S.M. Blau, B. Bocklund, A. Bonkowski, D. Broberg, G. Brunin, K. Bystrom, C.A. Cardot, R. Chang, C. Chen, W. Chen, X. Chen, Y. Chiang, K. Choudhary, O.A. Cohen, M.D. Costa, S.T. Dacek, M. de Jong, T. Demeyere, A.K. Dozier, A. Dunn, S. Dwaraknath, M.T. Dylla, K. Eimre, A.R. Epstein, C. Ertural, M. Esters, M.L. Evans, J. Falke, A. Fekete, B. Field, A. Fonari, N.C. Frey, D.W. Gaines, A.M. Ganose, M. Giantomassi, R.E.A. Goodall, P.-F. Gostin, A. Gupta, V.-A. Ha, G. Hautier, N. Heinsdorf, M.F. Herbst, T. Hou, P. Huck, Y. Ikeda, A.J. Jackson, S. Jayaraman, F.R. Kearns, S. Kim, R.S. Kingsbury, A.M. Krajewski, Y. Kumagai, M.C. Kuner, W.T. Laderer, W. Li, X.-G. Li, Y.H. Liang, H. Liu, K. Liu, M. Liu, A. Lutfi, O. Marchand, M.J. McDermott, B.K. Medasani, F. Meng, K.D. Miller, H. Miranda, R.S. Mohanakrishnan, J.H. Montoya, G.C. Moore, B.J. Morgan, J.M. Munro, K. Muraoka, A.A. Naik, W. O'Leary, A. Onwuli, J. Park, D.F. Parsons, K. Pei, G. Petretto, T.A.R. Purcell, J. Qi, X. Qu, I. Radchenko, N.N. Rajput, F. Ricci, B.S. Rich, W.D. Richards, G.-M. Rignanese, X. Ruan, G. Salvato Vallverdu, J. Schmidt, J.-X. Shen, R. Shimogawa, K. Shinohara, A.K. Singh, E. Sivonxay, S. Smeets, T.E. Smidt, A. Sobolev, E.W.C. Spotte-Smith, C. Stihl, W. Sun, J.D. Sundberg, Y. Suzuki, L. Talirz, H. Tang, E. Taw, C. Tezak, F. Therrien, S.D. Thiel, S.B. Torrisi, M.E. Turiansky, K. Ueltzen, M.J. van Setten, J. Vieten, S. Vijay, N. Wagner, F. Wan, A. Wang, J. Wang, Z. Wang, L. Ward, T. Warford, D. Waroquiers, M. Wen, O. Weser, N. Winner, D. Winston, M. Wolloch, B.M. Wood, R. Woods-Robinson, Y. Xiao, Y. Xie, F. Yalcin, R.X. Yang, W. Ye, P. Zarabadi-Poor, J. Zeng, H. Zhao, K. Zheng, H. Zhu, Z. Zhu, N.E.R. Zimmermann, D. Zügner, K.A. Persson, A. Jain, S.P. Ong

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Universal graph-based identifiers of chemical structures for linking large material databases

Nature Communications, 2026.

K. Muraoka, T. Tanimoto, T. Munekata, A. Nakayama

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Engineering Zeolite Synthesis for the Green Energy Transformation

JACS Au, 2026.

J. Zhu, K. Muraoka, T. Wakihara, T. Okubo

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Benchmarking Universal Interatomic Potentials on Zeolite

The Journal of Physical Chemistry C, 2026.

S. Ito, K. Muraoka+, A. Nakayama+

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Controlling Aluminum Siting in Low-Silica Zeolite Frameworks: A Post-Synthetic Approach Exemplified by MAZ-type Topology

Chemistry of Materials, 2026.

Y. Yoshida, K. Yamashita, K. Muraoka, M. Hasumi, R. Osuga, Y. Yanaba, K. Nakajima, A. Nakayama, T. Wakihara, T. Okubo, K. Iyoki

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Unveiling the Structural Factors Governing the Diffusion of Ethene in Small-Pore Zeolites through Machine Learning

The Journal of Physical Chemistry Letters, 2025.

J. Ping, K. Muraoka+, Z. Liu+, A. Nakayama+

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Drawing Boundaries between Feasible and Unfeasible Zeolite Intergrowths using High-Throughput Computational Screening with Synthesis Validation

Nature Materials, 2025.

K. Oishi, K. Muraoka+, S. Toyama, T. Iwata, T. Seki, N. Shibata, K. Iyoki, T. Wakihara, T. Okubo, A. Nakayama+

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Focused Thermal Energy at Atomic Microwave Antenna Sites for Eco-catalysis

Science Advances, 2025.

R. Ishibashi, F. Kishimoto, T. Yoshioka, H. Yamada, K. Muraoka, T. Ina, H. Taniguchi, A. Nakayama, T. Wakihara, K. Takanabe

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Reaction Mechanism of Silylation of C−O Bonds in Alkyl Ethers over Supported Gold Catalysts: Experimental and Theoretical Investigations

Physical Chemistry Chemical Physics, 2025.

Y. Tsunesada, T. Ikeda, K. Muraoka, M. Doi, H. Miura, T. Shishido, A. Nakayama

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Enabling Reliable Data-Driven Tafel Analysis

ChemRxiv, 2025.

K. Muraoka+, K. Sakaushi, A. Nakayama+

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Knowledge-Informed Molecular Design for Zeolite Synthesis Using General-Purpose Pretrained Large Language Models Towards Human-Machine Collaboration

Chemistry of Materials, 2025.

S. Ito, K. Muraoka+, A. Nakayama+

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Computational Insight into Selective Hydrogenolysis over Monomeric MoOx-Modified Rh Catalysts in the Aqueous Phase

The Journal of Physical Chemistry C, 2025.

K. Takei, T. Ikeda, K. Muraoka, Y. Nakagawa, K. Tomishige, A. Nakayama

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DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials

Journal of Chemical Theory and Computation, 2025.

J. Zeng, D. Zhang, A. Peng, X. Zhang, S. He, Y. Wang, X. Liu, H. Bi, Y. Li, C. Cai, C. Zhang, Y. Du, J.-X. Zhu, P. Mo, Z. Huang, Q. Zeng, S. Shi, X. Qin, Z. Yu, C. Luo, Y. Ding, Y.-P. Liu, R. Shi, Z. Wang, S.L. Bore, J. Chang, Z. Deng, Z. Ding, S. Han, W. Jiang, G. Ke, Z. Liu, D. Lu, K. Muraoka, H. Oliaei, A.K. Singh, H. Que, W. Xu, Z. Xu, Y.-B. Zhuang, J. Dai, T.J. Giese, W. Jia, B. Xu, D.M. York, L. Zhang, H. Wang

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Organic-Free Synthesis of High-Silica Zeolite Y with Aluminophosphate as the Aluminum Carrier

Angewandte Chemie International Edition, 2025.

Q. Zhao, J. Ling, J. Wang, Y. Gao, H. Liu, Z. Zhang, J. Jiang, A. Nakayama, J. Li+, K. Muraoka+, P. Wu+, L. Xu+

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Lattice oxygen insertion mechanism in CeO2 catalyzed reactions in water: nitrile hydration reaction

Chemical Science, 2024.

T. Endo, T. Ikeda, K. Muraoka, Y. Kita, M. Tamura, A. Nakayama

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Stress-Induced Martensitic Transformation in Na3YCl6

Journal of the American Chemical Society, 2024.

A. Miura+, K. Muraoka+ (1st author, corresponding author), K. Maki, S. Kawaguchi, K. Hikima, H. Muto, A. Matsuda, I. Yamane, T. Shimada, H. Ito, Y. Mizuguchi, C. Moriyoshi, H. Nakajima, S. Mori, H. Oike, A. Nakayama, W. Sun, N.C. Rosero-Navarro, K. Tadanaga

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Spontaneous-Spin-Polarized 2D π-d Conjugated Frameworks towards Enhanced Oxygen Evolution Kinetics

Small, 2024.

W.S. Lee, H. Maeda, Y.-T. Kuo, K. Muraoka, N. Fukui, K. Takada, S. Sasaki, H. Masunaga, A. Nakayama, H.-K. Tian, H. Nishihara, K. Sakaushi

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On-the-Fly Kinetic Monte Carlo Simulations with Neural Network Potentials for Surface Diffusion and Reaction

The Journal of Chemical Physics, 2024.

T. Yokaichiya, T. Ikeda, K. Muraoka, A. Nakayama

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High-pressure phase and pressure-induced phase transition of Ag3YCl6

CrystEngComm, 2024.

K. Maki, K. Muraoka, S. Kawaguchi, T. Tanimoto, A. Nakayama, S. Yokokura, T. Shimada, K. Tadanaga, A. Miura

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Synthesis and Structural Analysis of High-Silica ERI Zeolite with Spatially-Biased Al Distribution as a Promising NH3-SCR Catalyst

Advanced Science, 2024.

J. Zhu, K. Muraoka+, T. Ohnishi, Y. Yanaba, M. Ogura, A. Nakayama, T. Wakihara+, Z. Liu+, T. Okubo

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Direct microwave energy input on a single cation for outstanding selective catalysis

Science Advances, 2023.

F. Kishimoto, T. Yoshioka, R. Ishibashi, H. Yamada, K. Muraoka, H. Taniguchi, T. Wakihara, K. Takanabe

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DeePMD-kit v2: A software package for Deep Potential models

The Journal of Chemical Physics, 2023.

J. Zeng, D. Zhang, D. Lu, P. Mo, Z. Li, Y. Chen, M. Rynik, L. Huang, Z. Li, S. Shi, Y. Wang, H. Ye, P. Tuo, J. Yang, Y. Ding, Y. Li, D. Tisi, Q. Zeng, H. Bao, Y. Xia, J. Huang, K. Muraoka, Y. Wang, J. Chang, F. Yuan, S.L. Bore, C. Cai, Y. Lin, B. Wang, J. Xu, J.-X. Zhu, C. Luo, Y. Zhang, R.E.A. Goodall, W. Liang, A.K. Singh, S. Yao, J. Zhang, R. Wentzcovitch, J. Han, J. Liu, W. Jia, D.M. York, W. E, R. Car, L. Zhang, H. Wang

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Analysis of Al Site-Directing Ability of Organic Structure-Directing Agents in FER and CHA Zeolites: A Computational Exploration of Energetic Preferences

Chemical Communications, 2023.

K. Oishi, K. Muraoka+, A. Nakayama+

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Density Functional Theory Study of Deoxydehydration Reaction by TiO2-Supported Monomeric and Dimeric Molybdenum Oxide Catalysts

The Journal of Physical Chemistry C, 2022.

D. Asada, T. Ikeda, K. Muraoka, Y. Nakagawa, K. Tomishige, A. Nakayama

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Materials informatics-guided superior electrocatalyst: A case of pyrolysis-free single-atom coordinated with N-graphene nanomesh

Nano Energy, 2022.

W. Xia, Z. Hou, J. Tang, J. Li, W. Chaikittisilp, Y. Kim, K. Muraoka, H. Zhang, J. He, B. Han, Y. Yamauchi

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Multi-Objective De Novo Molecular Design of Organic Structure-Directing Agents for Zeolites Using Nature-Inspired Ant Colony Optimization

Chemical Science, 2020.

K. Muraoka, W. Chaikittisilp, T. Okubo

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Linking synthesis and structure descriptors from a large collection of synthetic records of zeolite materials

Nature Communications, 2019.

K. Muraoka, Y. Sada, D. Miyazaki, W. Chaikittisilp, T. Okubo

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Bridging the Gap between Structurally Distinct 2D Lamellar Zeolitic Precursors through a 3D Germanosilicate Intermediate

Angewandte Chemie International Edition, 2019.

L. Xu, M.K. Choudhary, K. Muraoka, W. Chaikittisilp, T. Wakihara, J.D. Rimer, T. Okubo

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Tracking Rearrangement of Atomic Configurations During the Conversion from FAU Zeolite to CHA Zeolite

Chemical Science, 2019.

K. Muraoka, Y. Sada, A. Shimojima, W. Chaikittisilp, T. Okubo

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Crucial Factors on Seed-Directed Synthesis of CON-type Aluminoborosilicate Zeolites using Tetraethylammonium

Crystal Growth & Design, 2019.

S. Sogukkanli, K. Muraoka, K. Iyoki, S.P. Elangovan, Y. Yanaba, W. Chaikittisilp, T. Wakihara, T. Okubo

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Designed Synthesis of Zeolite by the Integrated Experimental Chemistry, Computational Chemistry and Data Science Approach

Zeolite, 2019.

K. Muraoka, W. Chaikittisilp, T. Okubo

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Crystallization of a Novel Germanosilicate ECNU-16 Provides Insights into the Space-Filling Effect on Zeolite Crystal Symmetry

Chemistry – A European Journal, 2018.

L. Xu, L. Zhang, J. Li, K. Muraoka, F. Peng, H. Xu, C. Lin, Z. Gao, J.-G. Jiang, W. Chaikittisilp, J. Sun, T. Okubo, P. Wu

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Resolving the Framework Position Organic Structure-Directing Agents in Hierarchical Zeolites via Polarized Stimulated Raman Scattering

The Journal of Physical Chemistry Letters, 2018.

G. Fleury, J. Steele, I. Gerber, F. Jolibois, P. Puech, K. Muraoka, S.H. Keoh, W. Chaikittisilp, T. Okubo, M. Roeffaers

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Directing Aluminum Atoms into Energetically Favorable Tetrahedral Sites in a Zeolite Framework by Using Organic Structure‐Directing Agents

Angewandte Chemie International Edition, 2018.

K. Muraoka, Y. Yanaba, T. Yoshikawa, W. Chaikittisilp, T. Okubo

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Organic‐Free Synthesis of a Highly Siliceous Faujasite Zeolite with Spatially Biased Q4(nAl) Si Speciation

Angewandte Chemie International Edition, 2017.

M.D. Oleksiak*, K. Muraoka (*: 1st author)*, M.‐F. Hsieh, M.T. Conato, A. Shimojima, T. Okubo, W. Chaikittisilp, J.D. Rimer

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Factors Governing the Formation of Hierarchically and Sequentially Intergrown MFI Zeolites by Using Simple Diquaternary Ammonium Structure-Directing Agents

Chemistry of Materials, 2016.

S.H. Keoh, W. Chaikittisilp, K. Muraoka, R.R. Mukti, A. Shimojima, P. Kumar, M. Tsapatsis, T. Okubo

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Energy Analysis of Aluminosilicate Zeolites with Comprehensive Ranges of Framework Topologies, Chemical Compositions, and Aluminum Distributions

Journal of the American Chemical Society, 2016.

K. Muraoka, W. Chaikittisilp, T. Okubo

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Organic structure-directing agent-free synthesis of NES-type zeolites using EU-1 seed crystals

Microporous and Mesoporous Materials, 2015.

K. Iyoki, M. Takase, K. Itabashi, K. Muraoka, W. Chaikittisilp, T. Okubo

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Highly nanoporous silicas with pore apertures near the boundary between micro- and mesopores through an orthogonal self-assembly approach

Chemical Communications, 2015.

K. Muraoka, W. Chaikittisilp, Y. Yanaba, T. Yoshikawa, T. Okubo

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Mesoporous Architectures with Highly Crystallized Frameworks

Journal of Materials Chemistry A, 2014.

W. Chaikittisilp, K. Muraoka, Q. Ji, K. Ariga, Y. Yamauchi

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