XO: An Extended ONIOM Method

        XO通过容斥原理将分子片方法与传统的ONIOM方法结合起来，在体系划分和计算方法组合上获得了最大的自由度，可以并行高效地使用各种等级的计算方法，研究大型的化学和生物学体系及其相关的反应等。目前，这一方法已被用于蛋白质-药物体系、分子晶体、表界面体系等复杂体系，得到了非常精确的结果。

1. Chen, B.; Xu, X., Discriminating and understanding molecular crystal polymorphism. Journal of Computational Chemistry 2023, 44 (9), 969-979.

2. Bozhu Chen, Xin Xu*, ‘XO-PBC: An Accurate and Efficient Method for Molecular Crystals’, J. Chem. Theory Comput., 2020, 16(7), 4271-4285. DOI: 10.1021/acs.jctc.0c00232.

3. Li Rao, Bo Chi, Yanliang Ren, Yongjian Li, Xin Xu*, Jian Wan*, ‘DOX: A New Computational Protocol for Accurate Prediction of the Protein-Ligand Binding Structures’, J. Comput. Chem., 2016, 37, 336-344. DOI: 10.1002/jcc.24217.

4. Wenping Guo, Anan Wu, Igor Ying Zhang, Xin Xu*, ‘XO: An Extended ONIOM Method for Accurate and Efficient Modeling of Large Systems’, J. Comput. Chem. 2012, 33(27), 2142-2160. DOI: 10.1002/jcc.23051. (cover)

5. Wenping Guo, Anan Wu, Xin Xu*, ‘XO: An Extended ONIOM Method for Accurate and Efficient Geometry Optimization of Large Molecules’, Chem. Phys. Lett., 2010, 498(1-3), 203-208. DOI: 10.1016/j.cplett.2010.08.033.

Some of the applications:

1. Ke, Z.; Weng, J.; Xu, X., Calculating ¹³C NMR chemical shifts of large molecules using the eXtended ONIOM method at high accuracy with a low cost. Journal of Computational Chemistry 2023, 44 (30), 2347-2357.

2. Wei Lin, Chen Yaru, Rao Li*, Liu Jiaqi, Ren Yanliang, Xu Xin*, Wan Jian*, ‘Cov_DOX: A method for structure prediction of covalent protein-ligand bindings’, J. Med. Chem., 2022, 65(7) 5528-5538. DOI:10.1021/acs.jmedchem.1c02007.

3. Liu, J.; Wan, J.; Ren, Y.; Shao, X.; Xu, X.; Rao, L., DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein-Ligand Binding Affinity Prediction. Journal of Chemical Information and Modeling 2023, 63 (15), 4850-4863.

4. Wenjie Yan and Xin Xu*, ‘Accurate Prediction of Nuclear Magnetic Resonance Parameters via the XYG3 Type of Doubly Hybrid Density Functionals’, J. Chem. Theory Comput., 2022, 18(5) 2931-2946. DOI:10.1021/acs.jctc.2c00055.

5. Wenping Guo, Carine Michel, Renate Schwiedernoch, Raphael Wischert, Xin Xu*, Philippe Sautet*, ‘Formation of Acrylates from Ethylene and CO₂ on Ni Complexes: A Mechanistic Viewpoint from a Hybrid DFT Approach’, Organometallics, 2014, 33(22), 6369-6380. DOI: 10.1021/om5006808.

6. Li Rao, Igor Ying Zhang, Wenping Guo, Eric Meggers, Xin Xu*, ‘Nonfitting Protein-Ligand Interaction Scoring Function Based on First-Principles Theoretical Chemistry Methods: Development and Application on Kinase Inhibitors’, J. Comput. Chem., 2013, 34(19), 1636-1646. DOI: 10.1002/jcc.23303.

7. Zhenkun Chu, Gang Fu, Wenping Guo, Xin Xu*, ‘Effect of High-Level Layer Selection in ONIOM on Na⁺ Adsorption in ZSM-5 Zeolite’, J. Theor. Comput. Chem., 2010, 9(S1), 39-47. DOI: 10.1142/S021963361000558X.