GEBF Database (Version 2020)

References

More references of GEBF and PBC-GEBF approaches and theirs applications

Reviews

  1. Fang, T.; Li, Y.; Li, S. Generalized Energy-Based Fragmentation Approach for Modeling Condensed Phase Systems. WIREs Comput. Mol. Sci. 2017, 7 (2), e1297. https://doi.org/10.1002/wcms.1297.
  2. Liao, K.; Cheng, Z.; Li, Y.; Zhao, D.; Li, W.; Li, S. Fast Quantum Chemistry Calculations for Large Molecules and Condensed-Phase Systems: The Developments and Applications of Generalized Energy-Based Fragmentation Approach. Chin. Sci. Bull. 2018, 63 (33), 3427–3441. https://doi.org/10.1360/N972018-00907. (In Chinese)
  3. Li, S.; Li, W.; Ma, J. Generalized Energy-Based Fragmentation Approach and Its Applications to Macromolecules and Molecular Aggregates. Acc. Chem. Res. 2014, 47 (9), 2712–2720. https://doi.org/10.1021/ar500038z.

Softwares & Database

  1. Li, W.; Chen, C.; Zhao, D.; Li, S. LSQC: Low Scaling Quantum Chemistry Program. Int. J. Quantum Chem. 2015, 115 (10), 641–646. https://doi.org/10.1002/qua.24831.
  2. Li, S.; Li, W.; Jiang, Y.; Ma, J.; Fang, T.; Hua, W.; Hua, S.; Dong, H.; Zhao, D.; Liao, K.; Zou, W.; Ni, Z.; Wang, Y.; Shen, X.; Hong, B.: LSQC Program, Version 2.4. Nanjing University, Nanjing, 2019. see https://itcc.nju.edu.cn/lsqc.
  3. Li, S.; Li, W.; Ma, J.; Dong, H.; Li, Y.; Yuan, D.; Hong, B.; Du, J. GEBF Database. 2020. see https://box.nju.edu.cn/published/gebfdatabase.

Book Chapters

  1. Li, W.; Hua, W.; Fang, T.; Li, S. The Energy-Based Fragmentation Approach for Ab Initio Calculations of Large Systems. In Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology; Reimers, J. R., Ed.; Wiley Blackwell, 2011; pp 227–258. https://doi.org/10.1002/9780470930779.ch7.
  2. Li, W.; Dong, H.; Li, S. Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach. In Frontiers in Quantum Systems in Chemistry and Physics; Wilson, S., Grout, P. J., Maruani, J., DelgadoBarrio, G., Piecuch, P., Eds.; Progress in Theoretical Chemistry and Physics; 2008; Vol. 18, pp 289–299. https://doi.org/10.1007/978-1-4020-8707-3_12.
  3. Li, S.; Li, W. Fragment Energy Approach to Hartree–Fock Calculations of Macromolecules. Ann. Rep. Sect. C 2008, 104, 256. https://doi.org/10.1039/b703896h.

Journal Articles

2020

  1. Zhao, D.; Shen, X.; Cheng, Z.; Li, W.; Dong, H.; Li, S. Accurate and Efficient Prediction of NMR Parameters of Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J. Chem. Theory Comput. 2020, 16 (5), 2995–3005. https://doi.org/10.1021/acs.jctc.9b01298.
  2. Cheng, Z.; Zhao, D.; Ma, J.; Li, W.; Li, S. An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems. J. Phys. Chem. A 2020, 124 (24), 5007–5014. https://doi.org/10.1021/acs.jpca.0c04526.

2019

  1. Li, W.; Duan, M.; Liao, K.; Hong, B.; Ni, Z.; Ma, J.; Li, S. Improved Generalized Energy-Based Fragmentation Approach and Its Applications to the Binding Energies of Supramolecular Complexes. Electron. Struct. 2019, 1 (4), 044003. https://doi.org/10.1088/2516-1075/ab5049.
  2. Fu, F.; Liao, K.; Ma, J.; Cheng, Z.; Zheng, D.; Gao, L.; Liu, C.; Li, S.; Li, W. How Intermolecular Interactions Influence Electronic Absorption Spectra: Insights from the Molecular Packing of Uracil in Condensed Phases. Phys. Chem. Chem. Phys. 2019, 21 (7), 4072–4081. https://doi.org/10.1039/C8CP06152A.

2018

  1. Li, Y.; Yuan, D.; Wang, Q.; Li, W.; Li, S. Accurate Prediction of the Structure and Vibrational Spectra of Ionic Liquid Clusters with the Generalized Energy-Based Fragmentation Approach: Critical Role of Ion-Pair-Based Fragmentation. Phys. Chem. Chem. Phys. 2018, 20 (19), 13547–13557. https://doi.org/10.1039/C8CP00513C.
  2. Yuan, D.; Li, Y.; Li, W.; Li, S. Structures and Properties of Large Supramolecular Coordination Complexes Predicted with the Generalized Energy-Based Fragmentation Method. Phys. Chem. Chem. Phys. 2018, 20 (45), 28894–28902. https://doi.org/10.1039/C8CP05548C.

2017

  1. Zhao, D.; Song, R.; Li, W.; Ma, J.; Dong, H.; Li, S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J. Chem. Theory Comput. 2017, 13 (11), 5231–5239. https://doi.org/10.1021/acs.jctc.7b00380.
  2. Yuan, D.; Li, Y.; Ni, Z.; Pulay, P.; Li, W.; Li, S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method. J. Chem. Theory Comput. 2017, 13 (6), 2696–2704. https://doi.org/10.1021/acs.jctc.7b00284.
  3. Li, Y.; Wang, G.; Li, W.; Wang, Y.; Li, S. Understanding the Polymorphism-Dependent Emission Properties of Molecular Crystals Using a Refined QM/MM Approach. Phys. Chem. Chem. Phys. 2017, 19 (27), 17516–17520. https://doi.org/10.1039/C7CP03584E.
  4. Zhang, L.; Li, W.; Fang, T.; Li, S. Accurate Relative Energies and Binding Energies of Large Ice-Liquid Water Clusters and Periodic Structures. J. Phys. Chem. A 2017, 121 (20), 4030–4038. https://doi.org/10.1021/acs.jpca.7b03376.
  5. Zhao, D.; Yang, L.; Yuan, Y.; Wang, H.; Dong, H.; Li, S. Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers. J. Phys. Chem. B 2017, 121 (43), 10064–10072. https://doi.org/10.1021/acs.jpcb.7b09067.
  6. Tao, Y.; Zou, W.; Jia, J.; Li, W.; Cremer, D. Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water? J. Chem. Theory Comput. 2017, 13 (1), 55–76. https://doi.org/10.1021/acs.jctc.6b00735.
  7. Chi, Y.; You, X.; Zhang, L.; Li, W. Utilization of Generalized Energy-Based Fragmentation Method on the Study of Hydrogen Abstraction Reactions of Large Methyl Esters. Combust. Flame 2018, 190, 467–476. https://doi.org/10.1016/j.combustflame.2017.12.021.

2016

  1. Fang, T.; Jia, J.; Li, S. Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach. J. Phys. Chem. A 2016, 120 (17), 2700–2711. https://doi.org/10.1021/acs.jpca.5b10927.
  2. Li, W.; Li, Y.; Lin, R.; Li, S. Generalized Energy-Based Fragmentation Approach for Localized Excited States of Large Systems. J. Phys. Chem. A 2016, 120 (48), 9667–9677. https://doi.org/10.1021/acs.jpca.6b11193.
  3. Yuan, D.; Shen, X.; Li, W.; Li, S. Are Fragment-Based Quantum Chemistry Methods Applicable to Medium-Sized Water Clusters? Phys. Chem. Chem. Phys. 2016, 18 (24), 16491–16500. https://doi.org/10.1039/C6CP01931E.
  4. Liu, P.; Li, W.; Kan, Z.; Sun, H.; Ma, J. Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations. J. Phys. Chem. A 2016, 120 (4), 490–502. https://doi.org/10.1021/acs.jpca.5b10085.
  5. Wen, J.; Li, W.; Chen, S.; Ma, J. Simulations of Molecular Self-Assembled Monolayers on Surfaces: Packing Structures, Formation Processes and Functions Tuned by Intermolecular and Interfacial Interactions. Phys. Chem. Chem. Phys. 2016, 18 (33), 22757–22771. https://doi.org/10.1039/C6CP01049K.

2015

  1. Fang, T.; Li, W.; Gu, F.; Li, S. Accurate Prediction of Lattice Energies and Structures of Molecular Crystals with Molecular Quantum Chemistry Methods. J. Chem. Theory Comput. 2015, 11 (1), 91–98. https://doi.org/10.1021/ct500833k.
  2. Zhang, L.; Li, W.; Fang, T.; Li, S. Ab Initio Molecular Dynamics with Intramolecular Noncovalent Interactions for Unsolvated Polypeptides. Theor. Chem. Acc. 2016, 135 (2), 34. https://doi.org/10.1007/s00214-015-1799-z.
  3. Dong, H.; Li, W.; Sun, J.; Li, S.; Klein, M. L. Understanding the Boron-Nitrogen Interaction and Its Possible Implications in Drug Design. J. Phys. Chem. B 2015, 119 (45), 14393–14401. https://doi.org/10.1021/acs.jpcb.5b07783.
  4. Hua, S. G.; Jin, H.; Ouyang, Y. Z. Contribution of Non-Covalent Interactions to the Gas-Phase Stability of the Double-Helix of b-DNA: A Density Functional Theory Study with GEBF Approach. Wuli Huaxue Xuebao/ Acta Phys. - Chim. Sin. 2015, 31 (7), 1309–1314. https://doi.org/10.3866/PKU.WHXB201505111.

2014

  1. Wang, K.; Li, W.; Li, S. Generalized Energy-Based Fragmentation CCSD(T)-F12a Method and Application to the Relative Energies of Water Clusters (H2O)20. J. Chem. Theory Comput. 2014, 10 (4), 1546–1553. https://doi.org/10.1021/ct401060m.
  2. Guo, Y.; Li, W.; Yuan, D.; Li, S. The Relative Energies of Polypeptide Conformers Predicted by Linear Scaling Second-Order Møller-Plesset Perturbation Theory. Sci. China Chem. 2014, 57 (10), 1393–1398. https://doi.org/10.1007/s11426-014-5181-0.

2013

  1. Hua, S.; Li, W.; Li, S. The Generalized Energy-Based Fragmentation Approach with an Improved Fragmentation Scheme: Benchmark Results and Illustrative Applications. ChemPhysChem 2013, 14 (1), 108–115. https://doi.org/10.1002/cphc.201200867.
  2. Li, W. Linear Scaling Explicitly Correlated MP2-F12 and ONIOM Methods for the Long-Range Interactions of the Nanoscale Clusters in Methanol Aqueous Solutions. J. Chem. Phys. 2013, 138 (1), 014106. https://doi.org/10.1063/1.4773011.

2011

  1. Hua, S.; Xu, L.; Li, W.; Li, S. Cooperativity in Long α- And 310-Helical Polyalanines: Both Electrostatic and van Der Waals Interactions Are Essential. J. Phys. Chem. B 2011, 115 (39), 11462–11469. https://doi.org/10.1021/jp203423w.

2010

  1. Hua, S.; Hua, W.; Li, S. An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules. J. Phys. Chem. A 2010, 114 (31), 8126–8134. https://doi.org/10.1021/jp103074f.
  2. Yang, Z.; Hua, S.; Hua, W.; Li, S. Low-Lying Structures and Stabilities of Large Water Clusters: Investigation Based on the Combination of the AMOEBA Potential and Generalized Energy-Based Fragmentation Approach. J. Phys. Chem. A 2010, 114 (34), 9253–9261. https://doi.org/10.1021/jp1038267.

2009

  1. Dong, H.; Hua, S.; Li, S. Understanding the Role of Intra- and Intermolecular Interactions in the Formation of Single- and Double-Helical Structures of Aromatic Oligoamides: A Computational Study. J. Phys. Chem. A 2009, 113 (7), 1335–1342. https://doi.org/10.1021/jp8071525.
  2. Yan, X.; Jiang, N.; Ma, J. Theoretical Study of Interactions between Human Adult Hemoglobin and Acetate Ion by Polarizable Force Field and Fragmentation Quantum Chemistry Methods. Sci. China Ser. B Chem. 2009, 52 (11), 1925–1931. https://doi.org/10.1007/s11426-009-0273-y.

2008

  1. Hua, W.; Fang, T.; Li, W.; Yu, J. G.; Li, S. Geometry Optimizations and Vibrational Spectra of Large Molecules from a Generalized Energy-Based Fragmentation Approach. J. Phys. Chem. A 2008, 112 (43), 10864–10872. https://doi.org/10.1021/jp8026385.
  2. Li, H.; Li, W.; Li, S.; Ma, J. Fragmentation-Based QM/MM Simulations: Length Dependence of Chain Dynamics and Hydrogen Bonding of Polyethylene Oxide and Polyethylene in Aqueous Solutions. J. Phys. Chem. B 2008, 112 (23), 7061–7070. https://doi.org/10.1021/jp800777e.

2007

  1. Li, W.; Li, S.; Jiang, Y. Generalized Energy-Based Fragmentation Approach for Computing the Ground-State Energies and Properties of Large Molecules. J. Phys. Chem. A 2007, 111 (11), 2193–2199. https://doi.org/10.1021/jp067721q.

最近修改 1103004, 2020-12-02

References
Reviews
Softwares & Database
Book Chapters
Journal Articles