.. ZHANG Jun website documentation master file

Welcome to ZHANG Jun's (张鋆) website!
========================================

**Quick links:**

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   :target: abcluster.html

.. image:: /_images/a2.png
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   :target: abcrystal.html

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.. toctree::
   :numbered: 0
   :maxdepth: 1
   :caption: Research

   topics.rst
   publications.rst
   teaching.rst

.. toctree::
   :numbered: 0
   :maxdepth: 1
   :caption: Software

   abcluster.rst
   abcluster-applications.rst
   abcrystal.rst
   abpolymer.rst

.. toctree::
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   :maxdepth: 1
   :caption: Apps

   apps.rst   

Topics
===================================================

I focus on the development of methods and algorithms for theoretical chemistry and high-performance scientific computing.

Structure Prediction
----------------------------------

:doc:`abcluster`: The most popular software for molecular conformation search and cluster global optimization:

- |:fire:| To download ABCluster, please visit: :doc:`abcluster`
- |:fire:| To learn how to use ABCluster, please visit: `ABCluster Manual <http://zhjun-sci.com/abcluster/doc>`_
- `Phys. Chem. Chem. Phys. 2016, 18, 3003-3010. <http://dx.doi.org/10.1039/C5CP06313B>`_
- `Phys. Chem. Chem. Phys. 2015, 17, 24173-24181. <http://dx.doi.org/10.1039/C5CP04060D>`_

An invited **review** for the theory of cluster structure prediction:

- `Int. J. Quantum Chem. 2021, 121, e26553. <http://dx.doi.org/10.1002/qua.26553>`_

Some applications of ABCluster (For 700+ applications: :doc:`abcluster-applications`):

- `Results Phys. 2023, 52, 106852. <https://www.sciencedirect.com/science/article/pii/S2211379723006459>`_
- `Phys. Chem. Chem. Phys. 2017, 19, 10676-10684. <http://dx.doi.org/10.1039/C6CP08834A>`_
- `J. Am. Chem. Soc. 2016, 138, 11368-11377. <https://pubs.acs.org/doi/10.1021/jacs.6b07246>`_
- `J. Am. Chem. Soc. 2016, 138, 7973-7981. <http://dx.doi.org/10.1021/jacs.6b03798>`_

NWPEsSe (`GitHub <https://github.com/pnnl/NWPEsSE>`_): Global optimization for nano-sized clusters:

- `J. Chem. Theory Comput. 2020, 16, 3947-3958. <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01107>`_

Electronic Structure Theory
-----------------------------------

Projected hybrid orbital (PHO): A powerful QM/MM method to treat QM/MM systems with covalent bonds across QM/MM boundary:

- |:fire:| To use PHO-QM/MM, please download `Qbics <http://www.qbics.info>`_ and see `QM/MM method in Qbics <http://www.qbics.info/doc/keywords/qmmm.html>`_.
- `J. Chem. Theory Comput. 2024, 20, 10574-10587. <https://pubs.acs.org/doi/10.1021/acs.jctc.4c01326>`_

Target state optimization (TSO): Powerful DFT for excited and diabatic states:

- |:fire:| To use TSO-DFT, please download `Qbics <http://www.qbics.info>`_ and see tutorials for `excited states <http://www.qbics.info/doc/tutorials/tso1.html>`_ and `diabatic states <http://www.qbics.info/doc/tutorials/tso2.html>`_.
- `J. Chem. Theory Comput. 2023, 19, 1777-1789. <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.2c01317>`_
- `J. Phys. Chem. A 2023, 127, 8473-8485. <https://doi.org/10.1021/acs.jpca.3c04799>`_

Using TSO-DFT to predict K-edge X-Ray Absorption Spectra (XAS):

- |:fire:| To compute K-edge XAS or core ionization energies using `Qbics <http://www.qbics.info>`_, see `this tutorial <http://www.qbics.info/doc/tutorials/msdft2.html>`_.
- `J. Chem. Theory Comput. 2026, 22, 2390-2404. <https://doi.org/10.1021/acs.jctc.5c01819>`_

Many-body energy decomposition analysis (MB-EDA):

- |:fire:| To use MB-EDA, please download `Qbics <http://www.qbics.info>`_ and see `MB-EDA tutorial <http://www.qbics.info/doc/tutorials/eda.html>`_.
- `Phys. Chem. Chem. Phys. 2024, 26, 17549-17560. <https://pubs.rsc.org/en/content/articlelanding/2024/cp/d4cp01259c>`_

Excited energy decomposition analysis:

- `JACS Au 2023, 3, 1800-1819. <https://pubs.acs.org/doi/10.1021/jacsau.3c00186>`_
- `J. Phys. Chem. Lett. 2023, 14, 2917-2926. <https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.3c00545>`_

Multi-state density functional theory (MS-DFT):

- `J. Chem. Theory Comput. 2022, 18, 6407-6420. <https://pubs.acs.org/doi/10.1021/acs.jctc.2c00908>`_

Molecular Integrals: Automatic code generation and optimization:

- |:fire:| The source code of these papers has been integrated into `Qbics <http://www.qbics.info>`_.
- `Phys. Chem. Chem. Phys. 2021, 23, 20323-20328. <https://pubs.rsc.org/en/content/articlelanding/2021/cp/d1cp02805g>`_
- `J. Chem. Theory Comput. 2018, 14, 572-587. <http://dx.doi.org/10.1021/acs.jctc.7b00788>`_

Incremental coupled cluster: For accurate calculations of large molecules:

- `Mol. Phys. 2026, 124, e2553619. <https://www.tandfonline.com/doi/full/10.1080/00268976.2025.2553619>`_
- `J. Chem. Theory Comput. 2015, 11, 962-968. <http://dx.doi.org/10.1021/ct501052e>`_
- `J. Chem. Phys. 2014, 140, 044114. <http://dx.doi.org/10.1063/1.4862826>`_
- `J. Chem. Theory Comput. 2013, 9, 2992-3003. <http://dx.doi.org/10.1021/ct400284d>`_

AI for Chemistry
-------------------------

`CPPCGM <https://github.com/QiufenChen/CPPCGM>`_: Identification and generation of cell-penetrating peptides using a protein language model:

- `J. Chem. Inf. Model. 2025, 65, 3357-3369. <https://pubs.acs.org/doi/10.1021/acs.jcim.5c00199>`_

SOGCN: Prediction of key properties of MR-TADF materials:

- `Chem. Eng. J. 2024, 501, 157676. <https://www.sciencedirect.com/science/article/pii/S1385894724091678>`_

`AtomTyping <https://zhjun-sci.com/abcluster/doc/eg-pincer.html>`_: A lightweight tool for atom typing, which has been integrated into :doc:`abcluster` source code:

- `J. Chem. Phys. 2022, 156, 204108. <https://aip.scitation.org/doi/10.1063/5.0095008>`_

`SolubNet <https://github.com/QiufenChen/SolubNet>`_: A model to predict molecular solubility:

- `Artif. Intell. Chem. 2023, 1, 100010. <https://www.sciencedirect.com/science/article/pii/S2949747723000106>`_

Prediction of molecular properties using machine learning:

- `J. Chem. Inf. Model. 2020, 60, 3746-3754. <https://pubs.acs.org/doi/10.1021/acs.jcim.0c00388>`_

Materials Chemistry
---------------------------------------------

Inverted perovskite CsPbI\ :sub:`2`\ Br solar cell surface passivation treatment:

- `Org. Electron. 2024, 132, 107097. <https://www.sciencedirect.com/science/article/pii/S1566119924001083>`_
- `Mater. Today Chem. 2024, 36, 101980. <https://www.sciencedirect.com/science/article/pii/S2468519424000867>`_
- `J. Chem. Phys. 2024, 160, 094705. <https://doi.org/10.1063/5.0192041>`_

Ionic liquid clusters as separation materials (All clusters were searched by :doc:`abcluster`):

- `Chem. Mater. 2022, 34, 2612-2623. <https://pubs.acs.org/doi/10.1021/acs.chemmater.1c03836>`_
- `J. Phys. Chem. Lett. 2020, 11, 6844-6851. <https://pubs.acs.org/doi/10.1021/acs.jpclett.0c01671>`_

MOF as hydrogen storage materials:

- `Int. J. Hydrog. Energy 2022, 47, 41034-41045. <https://www.sciencedirect.com/science/article/abs/pii/S0360319922043294>`_

Graphene oxide as separation materials:

- `JACS Au 2021, 1, 766-776. <https://pubs.acs.org/doi/10.1021/jacsau.0c00075>`_

Selective catalysis of nitro-oxo compounds:

- `J. Phys. Chem. C 2022, 126, 8720-8733. <https://pubs.acs.org/doi/10.1021/acs.jpcc.2c01268>`_

Catalytic thermal conversion of ethanol:

- `J. Catal. 2020, 386, 30-38. <https://www.sciencedirect.com/science/article/pii/S0021951720301147>`_

Biochemistry and Biophysics
-------------------------------------

The allosteric regulation in light harvesting complex LHCII:

- `Nat. Plants 2023, 9, 1547-1557. <https://www.nature.com/articles/s41477-023-01500-2>`_

Antimicrobial peptides from marine organisms:

- `Pharmaceutics 2022, 14, 413-430. <https://www.mdpi.com/1999-4923/14/2/413>`_

Auxins:

- `Acta Chim. Sin. 2010, 68, 2500-2508. <http://sioc-journal.cn/Jwk_hxxb/CN/abstract/abstract339631.shtml>`_

Inorganic Chemistry
----------------------------------------------

The first observation of **labile capping bonds**, confirmed by an experiment in 2017 (`Chem. Eur. J. 2017, 23, 1110. <http://dx.doi.org/10.1002/chem.201604390>`_):

- `J. Phys. Chem. A 2015, 119, 774-780. <http://dx.doi.org/10.1021/jp511043c>`_

The solution and coordination chemistry of lanthanides, actinides, and transition metals:

- `Dalton Trans. 2021, 50, 5342-5350. <https://pubs.rsc.org/en/Content/ArticleLanding/2021/DT/D1DT00066G>`_
- `J. Comput. Chem. 2020, 41, 305-316. <http://dx.doi.org/10.1002/jcc.26103>`_
- `Phys. Chem. Chem. Phys. 2017, 19, 20160-20171. <http://dx.doi.org/10.1039/C7CP02861J>`_
- `Phys. Chem. Chem. Phys. 2015, 17, 20605-20616. <http://dx.doi.org/10.1039/C5CP03100A>`_
- `Inorg. Chem. 2014, 53, 7700-7708. <http://dx.doi.org/10.1021/ic500991x>`_
- `J. Chem. Theory Comput. 2014, 10, 5593-5598. <http://dx.doi.org/10.1021/ct5007339>`_

Organic Chemistry
----------------------------------------------------------

Dispersion interactions determine the conformation of a large organic molecule:

- `Chem. Eur. J. 2014, 20, 13909-13912. <http://dx.doi.org/10.1002/chem.201404106>`_

Mechanisms for C-H bond activation by metallic clusters or complexes:

- `Org. Biomol. Chem. 2018, 16, 8064-8071. <http://dx.doi.org/10.1039/c8ob02271b>`_
- `J. Phys. Chem. A 2017, 121, 3501-3514. <http://dx.doi.org/10.1021/acs.jpca.6b13113>`_

Polymer Chemistry
--------------------------------------

Collaborations with polymer chemists:

- `Angew. Chem. Int. Ed. 2025, 64, e202514768. <https://doi.org/10.1002/anie.202514768>`_
- `J. CO2 Util. 2019, 32, 196-201. <https://www.sciencedirect.com/science/article/pii/S2212982018309594?via%3Dihub>`_
- `Polymer 2015, 60, 215-220. <http://dx.doi.org/10.1016/j.polymer.2015.01.035>`_
- `Polym. Chem. 2014, 5, 646-652. <http://dx.doi.org/10.1039/C3PY01101A>`_


Publications
===================================================

|:link:| `ZHANG Jun's Google Scholar <https://scholar.google.com/citations?user=XBVuJXoAAAAJ&hl=zh-CN>`_

..
 - **Zhang, J.***; Yang, J.; Liu, M.; Gao, J.* *XX* **2025**, *XX*, XX-XX. `Diabatic Minimum Energy Crossing Point (dMECP): A Transition State Search Method using Energetic Coordinates. <XX>`_
 - Zhang, J. PIM Building. 
 - Zhang, X.; Pan, Z.; Hou, X.; Zhao, R.; **Zhang, J.***; Gao, J.* *XX* **2025**, *XX*, XX-XX. `Realistic Modeling of Condensed-Phase Electron Transfer: The Failure of Geometric Reaction Coordinate <XX>`_

2026
-----------------

- Zhu, H.; Lu, Y.; Gao, J.*; **Zhang, J.*** *J. Chem. Theory Comput.* **2026**, *22*, 2390-2404. `Target State Optimization with Density Functional Theory for Computing K-edge X-Ray Absorption Spectra <https://doi.org/10.1021/acs.jctc.5c01819>`_
- **Zhang, J.**; Cao, X.; Dolg, M.* *Mol. Phys.* **2026**, *124*, e2553619. `Incremental Scheme for High Level Electronic Correlation Calculations of Large Molecular Clusters <https://www.tandfonline.com/doi/full/10.1080/00268976.2025.2553619>`_

2025
-----------------

- Chen, Q.; Zhang, Y.; Gao, J.*; **Zhang, J.*** *J. Chem. Inf. Model.* **2025**, *65*, 3357-3369. `CPPCGM: A Highly Efficient Sequence-based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides <https://pubs.acs.org/doi/10.1021/acs.jcim.5c00199>`_
- Chen, Z.; Li, R.*; Jia, Q., Deng, J.; Liang, D.; Cao, L.; **Zhang, J.**; Wang, C.; Shi, Y.*; Zhang, H.* *Angew. Chem. Int. Ed.* **2025**, *64*, e202514768. `Dual-Engineered DPP Polymers: Synergistic Hydrogen Bonding and Ring-Fusion for High-Mobility Organic Field-Effect Transistors <https://doi.org/10.1002/anie.202514768>`_

2024
-------------------

- Li, Y.; Zhang, B.; Ren, A.-M.; Wang, D.; **Zhang, J.***; Nie, C.*; Su, Z.; Zou, L.* *Chem. Eng. J.* **2024**, *501*, 157676. `SOGCN: Prediction of Key Properties of MR-TADF Materials Using Graph Convolutional Neural Networks <https://www.sciencedirect.com/science/article/pii/S1385894724091678>`_
- Zhao, R.; Wang, Y.; Gao, J.*; **Zhang, J.*** *J. Chem. Theory Comput.* **2024**, *20*, 10574-10587. `Method and Implementation of Projected Hybrid Orbitals for Treating Multiple Covalent Bonds in Combined QM/MM Calculations <https://pubs.acs.org/doi/10.1021/acs.jctc.4c01326>`_
- Gong, Q.; Huang, S.; Wang, H.; Wang, L.; Cao, S.; She, X.; **Zhang, J.***; Wang, Z.; Li, J.; Liu, H.; Liu, Y.; Sun, H.; Yang, D.*; Liu, X.* *Org. Electron.* **2024**, *132*, 107097. `Effective Surface Treatment for Efficient and Stable Inverted Inorganic CsPbI2Br Perovskite Solar Cells. <https://www.sciencedirect.com/science/article/pii/S1566119924001083>`_
- Tang, Z.; Zhu, H.; Pan, Z.; Gao, J.*; **Zhang, J.*** *Phys. Chem. Chem. Phys.* **2024**, *26*, 17549-17560. `A Many-Body Energy Decomposition Analysis (MB-EDA) Scheme based on a Target State Optimization Self-Consistent Field (TSO-SCF) Method. <https://pubs.rsc.org/en/content/articlelanding/2024/cp/d4cp01259c>`_
- Wang, L.; She, X.; Li, W.; Cao, S.; Gong, Q.; Zhong, Z.; Wang, Z.; Li, J.; Liu, H.; Wang, X.; Sun, H.; Yang, D.; **Zhang, J.***; Liu, X.* *Mater. Today Chem.* **2024**, *36*, 101980. `Effective Surface Passivation for Stable and High-Performance Inverted CsPbI2Br Perovskite Solar Cells with Efficiency over 15%. <https://www.sciencedirect.com/science/article/pii/S2468519424000867>`_
- Liu, X.*; She, X.; Wang, L.; Li, W.; Zhang, W.; Wang, S.; Wangyang, P.; Wang, Z.; Li, J.; Cui, X.; Lan, M.; Liu, L.*; Sun, H.*; **Zhang, J.***; Yang, D.* *J. Chem. Phys.* **2024**, *160*, 094705. `Fluorinated Organic Ammonium Salt Passivation for High-Efficiency and Stable Inverted CsPbI2Br Perovskite Solar Cells. <https://doi.org/10.1063/5.0192041>`_

2023
--------

- Zhu, H.; Zhao, R.; Lu, Y.; Liu, M.*; **Zhang, J.***; Gao, J.* *J. Phys. Chem. A* **2023**, *127*, 8473-8485. `Leveling the Mountain Range of Excited-State Benchmarking through Multistate Density Functional Theory. <https://doi.org/10.1021/acs.jpca.3c04799>`_
- Zhu, B.-C.; Liu, C.-J.; Deng, P.-J.; Zhao, J.; **Zhang, J.***; Zeng, L.*; Liao, Y.-H.; Bao, L.; Bao, J. *Results Phys.* **2023**, *52*, 106852. `DFT-based Study on the Differences between Odd and Even Cn (n = 6-31) Ring Clusters. <https://www.sciencedirect.com/science/article/pii/S2211379723006459>`_
- Chen, Q.; Zhang, Y.; Gao, P.; **Zhang, J.*** *Artif. Intell. Chem.* **2023**, *1*, 100010. `An Interpretable Graph Representation Learning Model for Accurate Predictions of Drugs Aqueous Solubility. <https://www.sciencedirect.com/science/article/pii/S2949747723000106>`_
- Hettich, C.; Zhang, X.; Kemper, D.; Zhao, R.; Zhou, S.; Lu, Y.; Gao, J.*; **Zhang, J.***; Liu, M.* *JACS Au* **2023**, *3*, 1800-1819. `Multistate Energy Decomposition Analysis of Molecular Excited States. <https://pubs.acs.org/doi/10.1021/jacsau.3c00186>`_
- Zhao, R.; Christian, H.; **Zhang, J.***; Liu, M.*; Gao, J.* *J. Phys. Chem. Lett.* **2023**, *14*, 2917-2926. `Excimer Energies. <https://pubs.acs.org/doi/10.1021/acs.jpclett.3c00545>`_
- **Zhang, J.***; Tang, Z.; Zhang, X.; Zhu, H.; Zhao, R.; Lu, Y.; Gao, J.* *J. Chem. Theory Comput.* **2023**, *19*, 1777-1789. `Target State Optimized Density Functional Theory for Electronic Excited and Diabatic States. <https://doi.org/10.1021/acs.jctc.2c01317>`_
- Ruan, M.; Li, H.; Zhang, Y.; Zhao, R.; **Zhang, J.**; Wang, Y.; Gao, J.*; Wang, Z.; Wang, Y.; Sun, D.; Ding, W.*; Weng, Y.* *Nat. Plants* **2023**, *9*, 1547-1557. `Cryo-EM Structures of LHCII in Photo-Active and Photo-Protecting States Reveal Allosteric Regulation of Light-Harvesting and Excess Energy-Dissipation. <https://www.nature.com/articles/s41477-023-01500-2>`_

2022
-------
- Gao, P.; **Zhang, J.***; Liu, Z.*; Hu, X. *Int. J. Hydrog. Energy* **2022**, *47*, 41034-41045. `Computational Insights into the Energy Storage of Ultraporous MOFs NU-1501-M (M = Al or Fe): Protonization Revealing and Performance Improving by Decoration of Superalkali Clusters. <https://www.sciencedirect.com/science/article/abs/pii/S0360319922043294>`_
- **Zhang, J.*** *J. Chem. Phys.* **2022**, *156*, 204108. `Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? <https://aip.scitation.org/doi/10.1063/5.0095008>`_
- Zhang, Y.; **Zhang, J.***; Wang, H.; Yang, W.; Wang, C.; Peng, Y.*; Chen, J.; Li, J.; Gao, F.* *J. Phys. Chem. C* **2022**, *126*, 8720-8733. `Selective Catalytic Reduction of NOx with NH3 over Cu/SSZ-13: Elucidating Dynamics of Cu Active Sites with <i>in situ</i> UV-Vis Spectroscopy and DFT Calculations. <https://pubs.acs.org/doi/10.1021/acs.jpcc.2c01268>`_
- Lu, Y.*; Zhao, R.; **Zhang, J.**; Liu, M.*; Gao, J.* *J. Chem. Theory Comput.* **2022**, *18*, 6407-6420. `Minimal Active Space: NOSCF and NOSI Methods in Multistate Density Functional Theory. <https://pubs.acs.org/doi/10.1021/acs.jctc.2c00908>`_
- Baxter, E.; **Zhang, J.**; Tan, S.; Nguyen, M.-T.; Zhang, D.; Yuan, Q.; Cao, W.; Wang, X.-B; Prabhakaran, V.*; Glezakou, V.-A.*; Johnson, G. E.* *Chem. Mater.* **2022**, *34*, 2612-2623. `Functionalization of Electrodes with Tunable [EMIM]x[Cl]x+1- Ionic Liquid Clusters for Electrochemical Separations. <https://pubs.acs.org/doi/10.1021/acs.chemmater.1c03836>`_
- Zhang, W.; Xu, X.; **Zhang, J.**; Ye, T.; Zhou, Q.; Xu, Y.; Li, W.*; Hu, Z.; Shang, C.* *Pharmaceutics* **2022**, *14*, 413-430. `Discovery and Characterization of a New Crustin Antimicrobial Peptide from Amphibalanus amphitrite. <https://www.mdpi.com/1999-4923/14/2/413>`_

2021
------
- **Zhang, J.***; Tian, L. *Phys. Chem. Chem. Phys.* **2021**, *23*, 20323-20328. `Efficient Evaluation of Electrostatic Potential with Computerized Optimized Code. <https://pubs.rsc.org/en/content/articlelanding/2021/cp/d1cp02805g>`_
- **Zhang, J.***; Glezakou, V.-A. *Int. J. Quantum Chem.* **2021**, *121*, e26553. `Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges. <http://dx.doi.org/10.1002/qua.26553>`_
- Nguyen, M.-T.; **Zhang, J.**; Cantu, D. C.; Rousseau, R.; Glezakou, V.-A.* *Rare Earth Elements and Actinides: Progress in Computational Science Applications.* **2021**, *1388*, *11*, 219-245. `Tailored Computational Approaches to Interrogate Heavy Element Chemistry and Structure in Condensed Phase. <https://pubs.acs.org/doi/10.1021/bk-2021-1388.ch011>`_
- Nguyen, M.-T.; **Zhang, J.**; Prabhakaran, V.; Shuai, T.; Baxter, E.; Shutthanandan, V.; Johnson, G. E.*; Rousseau, R.; Glezakou, V.-A.* *JACS Au* **2021**, *1*, 766-776. `Graphene Oxide as Pb(II) Separations Medium: Has Part of the Story been Overlooked? <https://pubs.acs.org/doi/10.1021/jacsau.0c00075>`_
- Campanella, A. C.; Nguyen, M. T.; **Zhang, J.**; Ngendahimana, T.; Antholine, W. E.; Eaton, G. R.; Eaton, S. S.; Glezakou, V.-A.; Zadrozny, J. M.* *Dalton Trans.* **2021**, *50*, 5342-5350. `Ligand Control of Low-Frequency Electron Paramagnetic Resonance Linewidth in Cr(III) Complexes. <https://pubs.rsc.org/en/Content/ArticleLanding/2021/DT/D1DT00066G>`_

2020
------

- **Zhang, J.**; Baxter, E.; Nguyen, M.-T.; Prabhakaran, V.; Rousseau, R.; Johnson, G. E.*; Glezakou, V.-A.* *J. Phys. Chem. Lett.* **2020**, *11*, 6844-6851. `Structure and Stability of the Ionic Liquid Clusters [EMIM]n[BF4]n+1- (n = 1-9): Implications for Electrochemical Separations. <https://pubs.acs.org/doi/10.1021/acs.jpclett.0c01671>`_
- Gao, P.; **Zhang, J.***; Peng, Q.; Zhang, J.; Glezakou, V.-A. *J. Chem. Inf. Model.* **2020**, *60*, 3746-3754. `A General Protocol for the Accurate Predictions of Molecular 13C/1H NMR Chemical Shifts via Machine Learning-Augmented DFT. <https://pubs.acs.org/doi/10.1021/acs.jcim.0c00388>`_
- **Zhang, J.**; Glezakou, V.-A.*; Rousseau, R.; Nguyen, M.-T. *J. Chem. Theory Comput.* **2020**, *16*, 3947-3958. `NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems. <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01107>`_
- Akhade, S. A.; Winkelman, A.; Dagle, V. L.; Kovarik, L.; Yuk, S. F.; Lee, M.-S.; **Zhang, J.**; Padmaperuma, A. B.; Dagle, R. A.; Glezakou, V. A.; Wang, Y.; Rousseau, R.* *J. Catal.* **2020**, *386*, 30-38. `Influence of Ag Metal Dispersion on the Thermal Conversion of Ethanol to Butadiene over Ag-ZrO2/SiO2 Catalysts. <https://www.sciencedirect.com/science/article/pii/S0021951720301147>`_
- Cao, X.*; Wu, L.; **Zhang, J.**; Dolg, M. *J. Comput. Chem.* **2020**, *41*, 305-316. `Density Functional Studies of Coenzyme NADPH and its Oxidized Form NADP+. Structures, UV-Vis Spectra, and the Oxidation Mechanism of NADPH. <http://dx.doi.org/10.1002/jcc.26103>`_

2019
-------

- Kothandaraman, J.; **Zhang, J.**; Glezakou, V.-A.; Mock, M. T.; Heldebrant, D. J.* *J. CO*\ :sub:`2` *Util.* **2019**, *32*, 196-201. `Chemical Transformations of Captured CO2 into Cyclic and Polymeric Carbonates. <https://www.sciencedirect.com/science/article/pii/S2212982018309594>`_

2018
------

- **Zhang, J.*** *Org. Biomol. Chem.* **2018**, *16*, 8064-8071. `Origins of the Enantioselectivity of a Palladium Catalyst with BINOL-phosphoric Acid Ligands. <http://dx.doi.org/10.1039/c8ob02271b>`_
- **Zhang, J.*** *J. Chem. Theory Comput.* **2018**, *14*, 572-587. `LIBRETA: Computerized Optimization and Code Synthesis for Electron Repulsion Integral Evaluation. <http://dx.doi.org/10.1021/acs.jctc.7b00788>`_

2017
-----

- Wang, Y.; Sun, X.*; **Zhang, J.***; Li, J. *J. Phys. Chem. A* **2017**, *121*, 3501-3514. `A Theoretical Study on Methane C-H Bond Activation by Bare [FeO]+/0/-. <http://dx.doi.org/10.1021/acs.jpca.6b13113>`_
- Cao, X.*; Heinz, N.; **Zhang, J.**; Dolg, M. *Phys. Chem. Chem. Phys.* **2017**, *19*, 20160-20171. `The First Water Coordination Sphere of Lanthanide (III) Motexafins (Ln-Motex2+, Ln= La, Gd, Eu) and its Effects on Structures, Reduction Potentials and UV-vis Absorption Spectra. Theoretical Studies. <http://dx.doi.org/10.1039/C7CP02861J>`_
- Hou, G.-L.; **Zhang, J.**; Valiev, M.*; Wang, X.-B.* *Phys. Chem. Chem. Phys.* **2017**, *19*, 10676-10684. `Structures and Energetics of Hydrated Deprotonated cis-Pinonic Acid Anion Clusters and Their Atmospheric Relevance. <http://dx.doi.org/10.1039/C6CP08834A>`_

2016
------

- **Zhang, J.*** ; Dolg, M.* *Phys. Chem. Chem. Phys.* **2016**, *18*, 3003-3010. `Global Optimization of Clusters of Rigid Molecules Using the Artificial Bee Colony Algorithm. <http://dx.doi.org/10.1039/C5CP06313B>`_
- Li, J.; Zhou, S.; **Zhang, J.**; Schlangen, M.; Weiske, T.; Usharani, D.; Shaik, S.*; Helmut, S.* *J. Am. Chem. Soc.* **2016**, *138*, 11368-11377. `Mechanistic Variants in Gas-Phase Metal-Oxide Mediated Activation of Methane at Ambient Conditions. <https://pubs.acs.org/doi/10.1021/jacs.6b07246>`_
- Li, J.; Zhou, S.; **Zhang, J.**; Schlangen, M.; Weiske, T.; Usharani, D.; Shaik, S.*; Helmut, S.* *J. Am. Chem. Soc.* **2016**, *138*, 7973-7981. `Electronic Origins of the Variable Efficiency of Room-Temperature Methane Activation by Homo- and Heteronuclear Cluster Oxide Cations [XYO2]+ (X, Y = Al, Si, Mg): Competition between Proton-Coupled Electron Transfer versus Hydrogen-Atom Transfer. <http://dx.doi.org/10.1021/jacs.6b03798>`_

2015
------

- **Zhang, J.***; Dolg, M.* *Phys. Chem. Chem. Phys.* **2015**, *17*, 24173-24181. `ABCluster: the Artificial Bee Colony Algorithm for Cluster Global Optimization. <http://dx.doi.org/10.1039/C5CP04060D>`_
- **Zhang, J.***; Dolg, M.* *J. Chem. Theory Comput.* **2015**, *11*, 962-968. `Third-order Incremental Dual-basis Set Zero-buffer Approach for Large High-spin Open-shell Systems. <http://dx.doi.org/10.1021/ct501052e>`_
- **Zhang, J.***; Dolg, M.* *J. Phys. Chem. A* **2015**, *119*, 774-780. `Labile Capping Bonds in Lanthanide(III) Complexes: Shorter and Weaker. <http://dx.doi.org/10.1021/jp511043c>`_
- Cao, X.*; **Zhang, J.**; Weissmann, D.; Dolg, M; Chen, X. *Phys. Chem. Chem. Phys.* **2015**, *17*, 20605-20616. `Accurate Quantum Chemical Modelling of the Separation of Eu3+ from Am3+/Cm3+ by Liquid-liquid Extraction with Cyanex272. <http://dx.doi.org/10.1039/C5CP03100A>`_
- Zhang, H.; Ying, S.; Tieke, B.*; **Zhang, J.**; Yang, W. *Polymer* **2015**, *60*, 215-220. `1,6-Naphthodipyrrolidone-Based Donor-Acceptor Polymers with Low Bandgap. <http://dx.doi.org/10.1016/j.polymer.2015.01.035>`_

2014
--------

- **Zhang, J.***; Dolg, M.* *Chem. Eur. J.* **2014**, *20*, 13909-13912. `Dispersion Interaction Stabilizes Sterically Hindered Double Fullerences. <http://dx.doi.org/10.1002/chem.201404106>`_
- **Zhang, J.***; Heinz, N.; Dolg, M.* *Inorg. Chem.* **2014**, *53*, 7700-7708. `Understanding Lanthanoid(III) Hydration Structure and Kinetics by Insights from Energies and Wave Functions. <http://dx.doi.org/10.1021/ic500991x>`_
- **Zhang, J.***; Dolg, M.* *J. Chem. Phys.* **2014**, *140*, 044114. `Approaching the Complete Basis Set Limit of CCSD(T) for Large Systems by the Third-order Incremental Dual-basis Set Zero-buffer F12 Method. <http://dx.doi.org/10.1063/1.4862826>`_
- Heinz, N.; **Zhang, J.**; Dolg, M.* *J. Chem. Theory Comput.* **2014**, *10*, 5593-5598. `Actinoid(III) Hydration - First Principle Gibbs Energies of Hydration Using High Level Correlation Methods. <http://dx.doi.org/10.1021/ct5007339>`_
- Zhang, H.; **Zhang, J.**; Tieke, B.* *Polym. Chem.* **2014**, *5*, 646-652. `A Comparative Study of Polymers Containing Naphthodifuranone and Benzodifuranone Units in the Main Chain. <http://dx.doi.org/10.1039/C3PY01101A>`_

2013
------

- **Zhang, J.***; Dolg, M.* *J. Chem. Theory Comput.* **2013**, *9*, 2992-3003. `Third-order Incremental Dual-basis set Zero-buffer Approach: An Accurate and Efficient Way to Obtain CCSD and CCSD(T) Energies. <http://dx.doi.org/10.1021/ct400284d>`_

2010
-------

- Jia, X.; **Zhang, J.**; Sun, H.*; Chen, L.; Shen, R.; Lai, C. *Acta Chim. Sin.* **2010**, *68*, 2500-2508. `Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception. <http://sioc-journal.cn/Jwk_hxxb/CN/abstract/abstract339631.shtml>`_


Teaching
===================================================

Lecture Notes
----------------------------------

- `A Tutorial on Cluster Building for Computational Chemistry (in Chinese only) <http://zhjun-sci.com/teaching/books/computchemclusterbuilding.pdf>`_

I used to build and maintain a small computer cluster from 2009 to 2012. Based on that experience, I wrote a tutorial which is brief (only 50 pages) but sufficient for anyone to build a cluster with a network and a job queuing system in his/her own laboratory or home. Unfortunately, the contents in the book might be out of date and only a Chinese version is available. 

- `Understanding Quantum Chemistry from H2MODEL (English) <http://zhjun-sci.com/teaching/books/h2model_en.pdf>`_; `手算量子化学 (中文版) <http://zhjun-sci.com/teaching/books/h2model_zh.pdf>`_; `Source Code <http://zhjun-sci.com/teaching/books/h2model_source.tar.gz>`_

It is not straightforward for beginners in quantum chemistry to understand how to obtain numerical results from abstract theoretical formulae. Therefore I wrote this small tutorial from 2009 to 2012, discussing in detail how to carry out an actual Hartree-Fock, configuration interaction, coupled-cluster, time-dependent/independent density functional theory, geometry optimization or Hessian calculation using H2 as an example. It therefore was also known as "Understanding Quantum Chemistry from H2MODEL" several years ago.



ABCluster
===================================================

**Quick links:**

- |:fire:| :ref:`download-abcluster`
- |:park:| :doc:`abcluster-applications`
- |:books:| `ABCluster Manual <http://zhjun-sci.com/abcluster/doc>`_

.. image:: /_images/a1.png
   :align: center

Release Note 
-----------------

**Last update: Jan. 7, 2026**

|:fire:| **ABCluster 3.4 available! This is a bug-fixed version.** To download it, click :ref:`download-abcluster`.

- Fix the bug in ``isomer`` for I and I\ :sub:`h` symmetry cluster generation.

Introduction
--------------------------------------------

Briefly, ABCluster searches **the global as well as the local minima of flexible molecules and clusters.**

ABCluster searches the global minimum of a cluster by mimicking the foraging behavior of honey bee colonies. Don't worry if you are not familiar with it. Since ABCluster is a black-box program, you can perform a global optimization readily without any knowledge about heuristic algorithms. Therefore you can completely **focus on your chemical problem!**

Would like to download ABCluster? Click :ref:`download-abcluster`!

Would like to use ABCluster? Click `ABCluster Manual <http://zhjun-sci.com/abcluster/doc>`_!

Would like to see successful stories of ABCluster? Click :doc:`abcluster-applications`! 

.. _download-abcluster-source:

Download Current Source Code
--------------------------------------------

**Released on: Jan. 7, 2026**

Below is the source code of ABCluster. A simple registration is needed to download the source code. For compilation guidance, see `ABCluster Manual <http://zhjun-sci.com/abcluster/doc>`_.

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.. raw :: html

    <!-- Download Links -->
    <ul class="simple">
        <li><p>📦 <a class="download-link" data-file="abcluster-source.tar.gz">ABCluster Source Code (~ 19 MB)</a> This is the <strong>lean</strong> source code of ABCluster. To compile it, you may have to compile some libraries and set optimization and linking options yourself. The bonus is that you can optimize ABCluster at a better level on your machine.</p></li>
        <li><p>📦 <a class="download-link" data-file="abcluster-source-env.tar.gz">ABCluster Source Code with Environment (~ 180 MB)</a> This is the ABCluster source code with <strong>compilation environment</strong>. In principle, on most Linux and macOS systems, you can compile it with just one command <code class="docutils literal notranslate"><span class="pre">./build.sh</span></code>. This is recommended if you want to compile it rapidly.</p></li>
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Download ABCluster Skills
--------------------------------------------

A **Skill** is a small package of expert knowledge that you give to an AI coding agent. It is a folder containing a ``SKILL.md`` file that describes *when* the skill should be used and *how* to perform the task. When your request matches the skill, the agent reads the ``SKILL.md`` and follows its instructions, so you get answers from someone who already knows all the keywords, defaults, and pitfalls of the task.

ABCluster provides Skills that can be used to generate the input files using **AI coding agents** like `Cursor <https://cursor.com>`_ or `Claude <https://www.anthropic.com>`_ or `Codex <https://openai.com/api/codex/>`_, with **natural language** without learning any ABCluster keywords. See `<https://zhjun-sci.com/abcluster/doc/skill.html>`_ for more details.

- |:blue_book:| `ABCluster AI Skills <http://zhjun-sci.com/abcluster/teaching/ABCluster-Skills.zip>`_

.. _download-abcluster:

Download Current Release
--------------------------------------------

**Released on: Jan. 7, 2026**

- |:books:| `ABCluster Manual <http://zhjun-sci.com/abcluster/doc>`_
- |linuxlogo| `ABCluster 3.4 Executable (Linux) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-Linux.tar.gz>`_
- |winlogo| `ABCluster 3.4 Executable (Windows) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-Windows.zip>`_
- |maclogo| `ABCluster 3.4 Executable (macOS) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-macOS.tar.gz>`_
- |:video_camera:| 2022年6月16日ABCluster直播课程： `PDF课件 <http://zhjun-sci.com/abcluster/teaching/ABCluster-Tutorial-20220616.pdf>`_； `视频回放 <https://www.bilibili.com/video/BV1yW4y167Eb?spm_id_from=333.999.0.0&vd_source=7ffed8c11592e5ee99382e0798eb624e>`_

.. note::
    On Linux systems, error information like "**Segmentation fault**" or "**Illegal instruction**" means that the compiled executables are not compatible with your system, so you have to **compile ABCluster from source code**. This is very easy if you download `ABCluster Source Code with Environment (~ 180 MB) <http://zhjun-sci.com/abcluster/src/abcluster-source-env.tar.gz>`_ listed in :ref:`download-abcluster-source`.

**A GPU version of rigidmol**

- |gpulogo| `ABCluster 3.2 Executable (Linux, GPU70) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU70.tar.gz>`_
- |gpulogo| `ABCluster 3.2 Executable (Linux, GPU75) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU75.tar.gz>`_
- |gpulogo| `ABCluster 3.2 Executable (Linux, GPU80) <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU80.tar.gz>`_

.. |winlogo| image:: _static/figs/win-logo.png
    :width: 2ex

.. |linuxlogo| image:: _static/figs/linux-logo.png
    :width: 2ex

.. |maclogo| image:: _static/figs/mac-logo.png
    :width: 2ex

.. |gpulogo| image:: _static/figs/gpu-logo.png
    :width: 2ex    

Cite ABCluster
----------------------------------------

.. note::
    The best way to support the development of ABCluster is that in any published works using ABCluster, please **include the following references**:

    - Zhang, J.; Dolg, M. *Phys. Chem. Chem. Phys.* **2015**, *17*, 24173-24181. `ABCluster: The Artificial Bee Colony Algorithm for Cluster Global Optimization. <https://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/C5CP04060D>`_
    - Zhang, J.; Dolg, M. *Phys. Chem. Chem. Phys.* **2016**, *18*, 3003-3010. `Global Optimization of Clusters of Rigid Molecules Using the Artificial Bee Colony Algorithm. <https://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/C5CP06313B>`_

    Below is a **review of recent development of global optimization algorithms** for chemical clusters, including many applications of ABCluster:

    - Zhang, J.; Glezakou, V.-A. *Int. J. Quantum Chem.* **2021**, *121*, e26553. `Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges. <http://dx.doi.org/10.1002/qua.26553>`_

    Below is the **graph representation learning**-enabled automatic atom typing algorithm used in ABCluster:

    - Zhang, J. *J. Chem. Phys.* **2022**, *156*, 204108. `Atom Typing Using Graph Representation Learning: How Do Models Learn Chemistry? <https://aip.scitation.org/doi/10.1063/5.0095008>`_

Download Old Releases
----------------------------------------

- ABCluster 3.4 Executables: `Linux <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-Linux.tar.gz>`_; `Windows <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-Windows.zip>`_; `macOS <http://zhjun-sci.com/abcluster/exe/ABCluster-3.4-macOS.tar.gz>`_
- ABCluster 3.3 Executables: `Linux <http://zhjun-sci.com/abcluster/exe/ABCluster-3.3-Linux.tar.gz>`_; `Windows <http://zhjun-sci.com/abcluster/exe/ABCluster-3.3-Windows.zip>`_; `macOS <http://zhjun-sci.com/abcluster/exe/ABCluster-3.3-macOS.tar.gz>`_
- ABCluster 3.2 Executables: `Linux <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux.tar.gz>`_; `Windows <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Windows.zip>`_; 
- ABCluster rigidmol GPU: `Linux, GPU70 <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU70.tar.gz>`_; `Linux, GPU75 <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU75.tar.gz>`_; `Linux, GPU80 <http://zhjun-sci.com/abcluster/exe/ABCluster-3.2-Linux-GPU80.tar.gz>`_
- ABCluster 3.1 Executables and Manual: `Linux <http://zhjun-sci.com/abcluster/exe/ABCluster-3.1-Linux.tar.gz>`_; `Windows <http://zhjun-sci.com/abcluster/exe/ABCluster-3.1-Windows.zip>`_; `Manual <http://zhjun-sci.com/abcluster/exe/ABCluster-3.1-Manual.pdf>`_

About NWPEsSe
-----------------

NWPEsSe is a flexible and efficient program to search the global minimum of a potential energy surface in computational chemistry problems. Please refer to GitHub for details.

- Download: `GitHub <https://github.com/pnnl/NWPEsSE>`_

Reference:

- Zhang, J.; Glezakou, V.-A.; Rousseau, R.; Nguyen, M.-T. *J. Chem. Theory Comput.* **2020**, *16*, 3947-3958. `NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems. <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b01107>`_

Release History
---------------------

- Version 3.4 (Released on: Jan. 7, 2026): 1) Fix the bug in ``isomer`` for I and I\ :sub:`h` symmetry cluster generation.
- Version 3.3 (Released on: Dec. 4, 2024): 1) Add xTB-GFN0 and GFN-FF support in ``geom``. See Input File for ``geom`` and ``geom`` with xTB. 2) A bug in ``rigidmol`` has been fixed. Many thanks to Dr. Jakub Kubecka for reporting this bug. 3) A bug in ``geom`` has been fixed. Many thanks to Dr. Sungil Hong for reporting this bug.
- Version 3.2 (Released on: Dec. 4, 2023): 1) The stability and computational efficiency of ``rigidmol`` are improved significantly. 2) ``rigidmol`` can now be accelerated by single or multiple GPU cards! 3) For ``geom`` xTB engine, implicit solvation model can be used.
- Version 3.1 (Released on: May 25, 2022): 1) bee can be used to check if an update is available for ABCluster. 2) Calculations with geom can be restarted or continued. 3) New interfaces to third-party programs: VASP. 4) topgen can automatically type atoms without manual typing. 5) Some typos are fixed.
- Version 3.0 (Released on: Oct. 29, 2021): 1) ABCluster can perform conformation search for flexible molecules now! This is as easy as the global optimization of clusters! 2) ABCluster can manipulate clusters of both rigid and flexible molecules, i.e., doing global optimization and conformation search simultaneously. 3) ABCluster can generate atomic clusters with assigned point group symmetry! 4) ABCluster can treat complicated clusters more flexibly and easily at the nanometer scale: gas phase, ligated, surface-supported, and assemblies of clusters. 5) ABCluster has integrated xTB and CHARMM calculation engine internally. 6) Interfaces to third-party programs are provided officially: Gaussian, CP2K. 7) The manual is completely rewritten and is available both online and in a PDF version.
- Version 2.0 (Released on: Aug. 1, 2018): 1) For rigidmol-optimizer, ABCluster can study the molecular clusters in an external electric field. 2) For isomer and lego, the algorithm to generate initial guesses (thus the search efficiency) has been improved significantly (For example, clashes removing, coarse optimization)! 3) isomer and lego have been parallelized for both single and multi-nodes. 4) Official support for isomer and lego with DMol3 is provided (Courtesy of Prof. Dr. Lei Ma and Mr. Kai Wang, `Tianjin International Center for Nanoparticles and Nanosystems (TICNN) <http://ticnn.tju.edu.cn>`_).
- Version 1.5.1 (Released on: Dec. 18, 2017): 1) Official support for isomer and lego with ORCA, NWChem, and xTB-GFN is provided. 2) The evaluation codes have been optimized.
- Version 1.5 (Released on: Dec. 18, 2016): 1) A component cg-optimizer is added to support the anisotropic, coarse-grained particles, including electric multipole interaction and Paramonov-Yaliraki potential. 2) The component rigidmol-optimizer supports 1D, 2D and 3D periodic boundary conditions. 3) New modified Sutton-Chen and extended Lennard-Jones potential are supported. 4) A new keyword surface is added to lego for better supporting surface adsorption. 5) The output of isomer and lego is optimized.
- Version 1.4 (Released on: Apr. 5, 2016): 1) The new component lego has been added to support to search by third-party programs for both molecular and atomic clusters. 2) New Tersoff potential is supported.
- Version 1.3 (Released on: Jan. 22, 2016): New algorithm has been introduced. Now the efficiency of multi-component atomic clusters (e.g. Ag\ :sub:`14`\ Cu\ :sub:`24`) has been improved by 100 times!
- Version 1.2 (Released on: Nov. 6, 2015): The interfaces for third-party programs are available! Now ABCluster can do the global optimization with any quantum chemistry programs!
- Version 1.1 (Released on: Oct. 19, 2015): The optimization of Gupta and Sutton-Chen potential is significantly improved.
- Version 1.0 (Released on: Oct. 1, 2015): The first released version.



ABCluster Applications
===================================================

All clusters shown in the papers and images are built with ABCluster!

Atmospheric chemistry
--------------------------

.. comment
   https://chemrxiv.org/engage/chemrxiv/article-details/695f987fff1c4bced4f7f7d1 
   https://chemrxiv.org/doi/full/10.26434/chemrxiv.15001367/v1

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.. image:: /_images/abcluster-app18.png

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.. image:: /_images/abcluster-app9.png

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.. image:: /_images/abcluster-app4.png

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Lanthanide atomic cluster chemistry
------------------------------------

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.. image:: /_images/abcluster-app6.png

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Reaction mechanisms and design
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Molecular clusters
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Energy and materials chemistry
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Solution chemistry
---------------------

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.. image:: /_images/abcluster-app14.png

- `J. Mol. Liq. 2024, 415, 126343 <https://www.sciencedirect.com/science/article/abs/pii/S0167732224024024>`_

.. image:: /_images/abcluster-app1.png

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- `Data Brief 2022, 42, 108024 <https://www.sciencedirect.com/science/article/pii/S2352340922002359>`_
- `J. Mol. Liq. 2022, 350, 118522 <https://www.sciencedirect.com/science/article/abs/pii/S0167732222000575>`_
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- `Int. J. Quantum Chem. 2022, 122, e26840 <https://onlinelibrary.wiley.com/doi/full/10.1002/qua.26840>`_
- `J. Mol. Liq. 2021, 342, 117475 <https://www.sciencedirect.com/science/article/pii/S0167732221021991>`_
- `Phys. Chem. Chem. Phys. 2021, 23, 18990 <https://pubs.rsc.org/en/content/articlelanding/2021/CP/D1CP02524D>`_
- `Phys. Chem. Chem. Phys. 2021, 23, 14662 <https://pubs.rsc.org/en/Content/ArticleLanding/2021/CP/D1CP01609A>`_
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- `J. Mol. Liq. 2020, 318, 114300 <https://www.sciencedirect.com/science/article/abs/pii/S016773222033909X>`_
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Coordination chemistry
----------------------------

- `ChemPhysChem 2026, 27, e70434 <https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cphc.70434>`_
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- `J. Chem. Theory Comput. 2025, 21, 776 <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.4c01528>`_

.. image:: /_images/abcluster-app10.png

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.. image:: /_images/abcluster-app0.png

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- `Phys. Chem. Chem. Phys. 2017, 19, 20160 <http://dx.doi.org/10.1039/c7cp02861j>`_


ABCrystal (Preview)
===================================================

**Quick links:**

- |:fire:| :ref:`download-abcrystal`
- |:books:| `ABCrystal Manual <http://zhjun-sci.com/abcrystal/doc>`_

.. image:: /_images/a2.png
   :align: center

Introduction
--------------------------------------------

ABCrystal is a lightweight but powerful program for molecular crystal structure predictions. In short, given a molecular structure and its Z, ABCrystal will give you a set of possible crystal structures **(both atomic positions and crystal cell are optimized)** under specified pressure and crystal family in several seconds or hours by itself without any third-party software.

ABCrystal is very easy to use, as long as you have ever used ABCluster. However, it is **NOT** finished yet. So, below is a **PREVIEW** version. The official version will be released as soon as possible.

Would like to download ABCrystal? Click :ref:`download-abcrystal`!

Would like to use ABCrystal? Click `ABCrystal Manual <http://zhjun-sci.com/abcrystal/doc>`_!

.. _download-abcrystal:

Download Current Release
--------------------------------------------

**Released on: Jun. 6, 2024**

- |:books:| `ABCrystal Manual <http://zhjun-sci.com/abcrystal/doc>`_
- |linuxlogo| `ABCrystal 1.0Pre Executable (Linux) <http://zhjun-sci.com/abcrystal/exe/ABCrystal-1.0-Linux.tar.gz>`_
- |winlogo| `ABCrystal 1.0Pre Executable (Windows) <http://zhjun-sci.com/abcrystal/exe/ABCrystal-1.0-Windows.zip>`_

.. |winlogo| image:: _static/figs/win-logo.png
    :width: 2ex

.. |linuxlogo| image:: _static/figs/linux-logo.png
    :width: 2ex

.. |maclogo| image:: _static/figs/mac-logo.png
    :width: 2ex

.. |gpulogo| image:: _static/figs/gpu-logo.png
    :width: 2ex    


ABPolymer (Preview)
===================================================

**Quick links:**

- |:fire:| :ref:`download-abpolymer`
- |:books:| `ABPolymer Manual <http://zhjun-sci.com/abpolymer/doc>`_

.. image:: /_images/a6.png
   :align: center

Introduction
--------------------------------------------

ABPolymer is a lightweight but powerful program for amorphous covalent polymer structure predictions.

ABPolymer is very easy to use, as long as you have ever used ABCluster. However, it is **NOT** finished yet. So, below is a **PREVIEW** version. The official version will be released as soon as possible.

Would like to download ABPolymer? Click :ref:`download-abpolymer`!

Would like to use ABPolymer? Click `ABPolymer Manual <http://zhjun-sci.com/abpolymer/doc>`_!

.. _download-abpolymer:

Download Current Release
--------------------------------------------

**Released on: Nov. 8, 2025**

- |:books:| `ABPolymer Manual <http://zhjun-sci.com/abpolymer/doc>`_
- |linuxlogo| `ABPolymer 1.0Pre Executable (Linux) <http://zhjun-sci.com/abpolymer/exe/ABPolymer-1.0-Linux.tar.gz>`_
- |winlogo| `ABPolymer 1.0Pre Executable (Windows) <http://zhjun-sci.com/abpolymer/exe/ABPolymer-1.0-Windows.zip>`_

.. |winlogo| image:: _static/figs/win-logo.png
    :width: 2ex

.. |linuxlogo| image:: _static/figs/linux-logo.png
    :width: 2ex

.. |maclogo| image:: _static/figs/mac-logo.png
    :width: 2ex

.. |gpulogo| image:: _static/figs/gpu-logo.png
    :width: 2ex    


Useful Apps
===================================================

- |:timer:| `Timer <http://zhjun-sci.com/apps/timer.html>`_



Error
===================================================

The website is unavailable. Please go back to :doc:`index`, or contact us at `jun.chem@hotmail.com   <mailto:jun.chem@hotmail.com>`_.

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    <!-- Download Links -->
    <ul class="simple">
        <li><p>📦 <a class="download-link" data-file="abcluster-source.tar.gz">ABCluster Source Code (~ 19 MB)</a> This is the <strong>lean</strong> source code of ABCluster. To compile it, you may have to compile some libraries and set optimization and linking options yourself. The bonus is that you can optimize ABCluster at a better level on your machine.</p></li>
        <li><p>📦 <a class="download-link" data-file="abcluster-source-env.tar.gz">ABCluster Source Code with Environment (~ 180 MB)</a> This is the ABCluster source code with <strong>compilation environment</strong>. In principle, on most Linux and macOS systems, you can compile it with just one command <code class="docutils literal notranslate"><span class="pre">./build.sh</span></code>. This is recommended if you want to compile it rapidly.</p></li>
    </ul>