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AuthorTitleYearJournal/ProceedingsReftypeDOI/URL
Cheng, Z., Zhao, D., Ma, J., Li, W. and Li, S. An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems 2020 J. Phys. Chem. A
Vol. 124(24), pp. 5007-5014 
article DOI URL 
Abstract: An on-the-fly fragment-based machine learning (ML) approach was developed to construct the machine learning force field for large complex systems. In this approach, the energy, forces, and molecular properties of the target system are obtained by combining machine learning force fields of various subsystems with the generalized energy-based fragmentation (GEBF) approach. Using nonparametric Gaussian process (GP) model, all the force fields of subsystems are automatically generated online without data selection and parameter optimization. With the GEBF-ML force field constructed for a normal alkane, C60H122, long-time molecular dynamics (MD) simulations are performed on different sizes of alkanes, and the predicted en-ergy, forces, and molecular properties (dipole moment) are favorably comparable with full quantum mechanics (QM) calcu-lations. The predicted IR spectra also show excellent agreement with the direct ab initio MD results. Our results demonstrate that the GEBF-ML method provides an automatic and efficient way to build force fields for a broad range of complex sys-tems such as biomolecules and supramolecular systems.
BibTeX:
@article{Cheng2020-5007,
  author = {Cheng, Zheng and Zhao, Dongbo and Ma, Jing and Li, Wei and Li, Shuhua},
  title = {An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems},
  journal = {J. Phys. Chem. A},
  publisher = {American Chemical Society},
  year = {2020},
  volume = {124},
  number = {24},
  pages = {5007--5014},
  url = {https://doi.org/10.1021/acs.jpca.0c04526 https://pubs.acs.org/doi/10.1021/acs.jpca.0c04526},
  doi = {https://doi.org/10.1021/acs.jpca.0c04526}
}
Barca, G.M.J., Bertoni, C., Carrington, L., Datta, D., De Silva, N., Deustua, J.E., Fedorov, D.G., Gour, J.R., Gunina, A.O., Guidez, E., Harville, T., Irle, S., Ivanic, J., Kowalski, K., Leang, S.S., Li, H., Li, W., Lutz, J.J., Magoulas, I., Mato, J., Mironov, V., Nakata, H., Pham, B.Q., Piecuch, P., Poole, D., Pruitt, S.R., Rendell, A.P., Roskop, L.B., Ruedenberg, K., Sattasathuchana, T., Schmidt, M.W., Shen, J., Slipchenko, L., Sosonkina, M., Sundriyal, V., Tiwari, A., Galvez Vallejo, J.L., Westheimer, B., Włoch, M., Xu, P., Zahariev, F. and Gordon, M.S. Recent developments in the general atomic and molecular electronic structure system 2020 J. Chem. Phys.
Vol. 152(15), pp. 154102 
article DOI URL 
Abstract: A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree–Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
BibTeX:
@article{Barca2020-154102,
  author = {Barca, Giuseppe M J and Bertoni, Colleen and Carrington, Laura and Datta, Dipayan and De Silva, Nuwan and Deustua, J Emiliano and Fedorov, Dmitri G and Gour, Jeffrey R and Gunina, Anastasia O and Guidez, Emilie and Harville, Taylor and Irle, Stephan and Ivanic, Joe and Kowalski, Karol and Leang, Sarom S and Li, Hui and Li, Wei and Lutz, Jesse J and Magoulas, Ilias and Mato, Joani and Mironov, Vladimir and Nakata, Hiroya and Pham, Buu Q and Piecuch, Piotr and Poole, David and Pruitt, Spencer R and Rendell, Alistair P and Roskop, Luke B and Ruedenberg, Klaus and Sattasathuchana, Tosaporn and Schmidt, Michael W and Shen, Jun and Slipchenko, Lyudmila and Sosonkina, Masha and Sundriyal, Vaibhav and Tiwari, Ananta and Galvez Vallejo, Jorge L and Westheimer, Bryce and Włoch, Marta and Xu, Peng and Zahariev, Federico and Gordon, Mark S},
  title = {Recent developments in the general atomic and molecular electronic structure system},
  journal = {J. Chem. Phys.},
  year = {2020},
  volume = {152},
  number = {15},
  pages = {154102},
  url = {https://doi.org/10.1063/5.0005188},
  doi = {https://doi.org/10.1063/5.0005188}
}
Fu, F., Liao, K., Li, W., Ma, J. and Li, S. FAAR Program, Version 1.0 2020   misc  
BibTeX:
@misc{faar2020,
  author = {Fu, Fangjia and Liao, Kang and Li, Wei and Ma, Jing and Li, Shuhua},
  title = {FAAR Program, Version 1.0},
  year = {2020}
}
Wang, X., Fu, F., Peng, K., Huang, Q., Li, W., Chen, X. and Yang, Z. Understanding of Competitive Hydrogen Bond Behavior of Imidazolium-Based Ionic Liquid Mixture around Single-Walled Carbon Nanotubes 2020 J. Phys. Chem. C
Vol. 124(12), pp. 6634-6645 
article DOI URL 
Abstract: Here we have performed molecular dynamics simulations to investigate the structures, dynamics, and hydrogen bonds (HBs) of the imidazolium-based ionic liquid (IL) mixture containing equimolar 1-ethyl-3-methylimidazolium tetrafluoroborate ([Emim][BF4]) and 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6]) around the single-walled carbon nanotubes (CNTs) with three different diameters of 5.42, 10.85, and 21.70 Å. Our simulation results reveal for the first time that the [BF4]− and [PF6]− anions have an obvious competitive HB behavior for the IL mixture around the CNTs, and such HB competition can be further enhanced as the CNT diameter increases. The HBs between the [PF6]− anions and cations are always more and stronger than those between the [BF4]− anions and cations regardless of the CNT diameter, although the enhanced HBs are found for both kinds of anions in the first solvation shell around larger CNTs. Nevertheless, the interfacial [PF6]− anions show a larger HB enhancement than the corresponding [BF4]− anions as the CNT diameter increases. Besides the competitive interactions between the different anions and the CNT, such competitive HB behavior in the IL mixture leads to more [PF6]− anions but less [BF4]− anions aggregating around the larger CNTs, which is significantly different from the previous aggregation behavior of pure ILs around the CNTs. Furthermore, there exist the opposite diameter-dependent changes of average HB number per cation with the [BF4]− and [PF6]− anions. In addition, the enhanced HBs between cations and anions around the larger CNTs result in slower rotations of both the [BF4]− and [PF6]− anions and more pronounced orientational distribution of both the imidazolium cations in the first solvation shell around the CNTs.
BibTeX:
@article{Wang2020-6634,
  author = {Wang, Xueping and Fu, Fangjia and Peng, Kuilin and Huang, Qin and Li, Wei and Chen, Xiangshu and Yang, Zhen},
  title = {Understanding of Competitive Hydrogen Bond Behavior of Imidazolium-Based Ionic Liquid Mixture around Single-Walled Carbon Nanotubes},
  journal = {J. Phys. Chem. C},
  publisher = {American Chemical Society},
  year = {2020},
  volume = {124},
  number = {12},
  pages = {6634--6645},
  url = {https://doi.org/10.1021/acs.jpcc.9b11576},
  doi = {https://doi.org/10.1021/acs.jpcc.9b11576}
}
Zhang, L., Hu, S., Yang, L., Li, W., Li, S., Wang, W. and Zeng, G. H2 Activation by Heterobimetallic Gold(I)/Platinum(0) Complex: Theoretical Understanding of Electronic Processes and Prediction on More Active Species 2020 J. Phys. Chem. C
Vol. 124(8), pp. 4525-4533 
article DOI URL 
Abstract: Mechanistic studies on H2 activation by the Au(I)/Pt(0) bimetallic complex as well as the electronic processes were investigated with the density functional theory method. In the reaction, the H–H bond is heterolytically cleaved through the cooperative functions of the Lewis acid Au(I) center and the Lewis base Pt(0) center, where the Gibbs energy barrier (ΔG°‡) and Gibbs reaction energy (ΔG°) are 22.6 and 8.9 kcal/mol, respectively. In the transition state, the charge transfer (CT1, 0.364 e) occurs from the σ bonding orbital of H2 to the antibonding d orbitals of the Au–Pt moiety. The reverse CT2 (0.205 e) mainly occurs from the occupied d orbitals (dxz and dz2) of the Pt(0) moiety to the σ* antibonding orbital of H2. By substituting the noble metal Pt in the Au(I)/Pt(0) complex for the cheaper metal Ni, the activity of the bimetallic complex is largely improved, where the ΔG°‡ and ΔG° values considerably decrease to 16.7 and −13.7 kcal/mol, respectively. The improvement of activity comes from the facile CTs in the H2 activation by the Au(I)/Ni(0) system.
BibTeX:
@article{Zhang2020-4525,
  author = {Zhang, Lei and Hu, Shiyu and Yang, Linlin and Li, Wei and Li, Shuhua and Wang, Wei and Zeng, Guixiang},
  title = {H2 Activation by Heterobimetallic Gold(I)/Platinum(0) Complex: Theoretical Understanding of Electronic Processes and Prediction on More Active Species},
  journal = {J. Phys. Chem. C},
  publisher = {American Chemical Society},
  year = {2020},
  volume = {124},
  number = {8},
  pages = {4525--4533},
  url = {https://doi.org/10.1021/acs.jpcc.9b09452},
  doi = {https://doi.org/10.1021/acs.jpcc.9b09452}
}
Fu, F., Liao, K., Ma, J., Cheng, Z., Zheng, D., Gao, L., Liu, C., Li, S. and Li, W. How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases 2019 Phys. Chem. Chem. Phys.
Vol. 21(7), pp. 4072-4081 
article DOI URL 
Abstract: The photoexcitation mechanism in photochemistry and photophysics is a key to understanding the photostability and photoreaction of nucleobases. Using a combination of the generalized energy-based fragmentation (GEBF) and quantum mechanical and molecular mechanical (GEBF-QM/MM) approach and the QM/MM approach, we have investigated the electronic absorption spectra for the pi–pi* transition of uracil in aqueous solution, amorphous solid, and crystal. Our results indicate that the intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments. There is a large red-shift (relative to uracil in the gas-phase) for uracil in the amorphous phase, which arises from hydrogen-bonding (HB) and close pi–pi stacking interactions. In contrast, the relatively smaller red-shift of uracil in aqueous solution can be attributed to the cooperative HB and long-range electrostatic and polarization interactions. Due to the HB and weak pi–pi interactions, the red-shift of the crystal is smaller than that of amorphous uracil. Furthermore, the results suggest that a large system is required to obtain the accurate absorption spectra of solutions, whereas small electrostatically embedded cluster models could be used to obtain the corresponding results for amorphous solids and molecular crystals.
BibTeX:
@article{Fu2019-4072,
  author = {Fu, Fangjia and Liao, Kang and Ma, Jing and Cheng, Zheng and Zheng, Dong and Gao, Liuzhou and Liu, Chungen and Li, Shuhua and Li, Wei},
  title = {How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases},
  journal = {Phys. Chem. Chem. Phys.},
  publisher = {The Royal Society of Chemistry},
  year = {2019},
  volume = {21},
  number = {7},
  pages = {4072--4081},
  url = {http://dx.doi.org/10.1039/c8cp06152a http://pubs.rsc.org/en/Content/ArticleLanding/2019/CP/C8CP06152A http://xlink.rsc.org/?DOI=C8CP06152A},
  doi = {https://doi.org/10.1039/C8CP06152A}
}
Li, W. Fragmentation Approach in Quantum Chemistry 2019 Reference Module in Chemistry, Molecular Sciences and Chemical Engineering  incollection DOI URL 
Abstract: An overview of fragmentation approach for the linear or low-scaling quantum chemistry calculations of large systems is presented. The brief history and classification of the fragmentation approach are given first. Then, the basis theories of two types of fragmentation approaches, including density-matrix-based methods and energy-based fragmentation (EBF) methods, are described. In the density-matrix-based methods, the density matrix (or density) of a target system could be obtained from the density matrices (or densities) of various subsystems. Then, the total energy and properties could be computed from the total density matrix (or density). In the EBF methods, the total energy (or energy derivatives) can be directly represented as the combination of the corresponding quantities of subsystems.
BibTeX:
@incollection{Li2019,
  author = {Li, W},
  title = {Fragmentation Approach in Quantum Chemistry},
  booktitle = {Reference Module in Chemistry, Molecular Sciences and Chemical Engineering},
  publisher = {Elsevier},
  year = {2019},
  url = {http://www.sciencedirect.com/science/article/pii/B978012409547211488X},
  doi = {https://doi.org/10.1016/B978-0-12-409547-2.11488-X}
}
Li, W., Duan, M., Liao, K., Hong, B., Ni, Z., Ma, J. and Li, S. Improved generalized energy-based fragmentation approach and its applications to the binding energies of supramolecular complexes 2019 Electronic Structure
Vol. 1(4), pp. 044003 
article DOI URL 
Abstract: Accurate prediction for the binding energies of host-guest complexes is important in the field of supramolecular chemistry. In this article, we have implemented an improved generalized energy-based fragmentation (GEBF) approach for computing the binding energies of supramolecular complexes. In this approach, an new scheme is proposed to generate primitive GEBF subsystems with reasonable size. With this scheme, those subsystems in the complex and the corresponding host molecule are very similar (the guest does not exist in any subsystem of host). Our results for ten supramolecular complexes show that the improved GEBF approach could accurately reproduce the conventional density functional theory (DFT) binding energies in those complexes. The GEBF binding energy errors relative to the corresponding conventional values are usually less than 1 kcal/mol. Furthermore, for each pair of complexes with the same or similar hosts, the GEBF relative binding energy difference between the two complexes with different guests is even below 1 kJ/mol. In addition, the GEBF approach could predict the second-order Møller-Plesset perturbational theory (MP2) energy of a complex with 3382 basis functions within only 3.3 hours by massive parallelization using 312 processors on 13 computer nodes. Therefore, the improved GEBF approach could be a practical tool for predicting the binding energies or relative binding energies of supramolecular complexes.
BibTeX:
@article{Li2019-044003,
  author = {Li, Wei and Duan, Mingzhou and Liao, Kang and Hong, Benkun and Ni, Zhigang and Ma, Jing and Li, Shuhua},
  title = {Improved generalized energy-based fragmentation approach and its applications to the binding energies of supramolecular complexes},
  journal = {Electronic Structure},
  year = {2019},
  volume = {1},
  number = {4},
  pages = {044003},
  url = {http://iopscience.iop.org/article/10.1088/2516-1075/ab5049 https://iopscience.iop.org/article/10.1088/2516-1075/ab5049},
  doi = {https://doi.org/10.1088/2516-1075/ab5049}
}
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. and Hong, B. LSQC Program, Version 2.4 2019   misc URL 
Abstract: Low Scaling Quantum Chemistry (LSQC) program is a quantum chemistry package for linear or low scaling electronic structure calculations of large systems, which is developed by the research group of Professor Shuhua Li and Professor Wei Li in Nanjing University. The original version is LSQC-1.0 published on April 20, 2006, and the current version is LSQC-2.4 published on October 1, 2019. Current LSQC program supports two methods developed by Li group. The first one is the generalized energy-based fragmentation (GEBF) method and the other one is the cluster-in-molecule (CIM) local correlation method. Both methods can achieve linear scaling for electronic structure calculations of large systems and have high parallel efficiency.
BibTeX:
@misc{lsqc2019,
  author = {Li, Shuhua. and Li, Wei and Jiang, Yuansheng and Ma, Jing and Fang, Tao and Hua, Weijie and Hua, Shugui and Dong, Hao and Zhao, Dongbo and Liao, Kang and Zou, Wentian and Ni, Zhigang and Wang, Yuqi and Shen, Xiaoling and Hong, Benkun},
  title = {LSQC Program, Version 2.4},
  year = {2019},
  url = {https://itcc.nju.edu.cn/lsqc/}
}
Ni, Z., Li, W. and Li, S. Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems 2019 J. Comput. Chem.
Vol. 40(10), pp. 1130-1140 
article DOI URL 
Abstract: A fully optimized implementation of the cluster-in-molecule (CIM) local correlation method for faster and more accurate electron correlation calculations of large systems is reported. The speedup comes from the new procedure of constructing virtual localized molecular orbitals of clusters. In the new procedure, Boughton–Pulay projection method is employed instead of a much more expensive Boys localization procedure. In addition, basis set superposition error correction for binding energy calculations and parallelized electron correlation calculations of clusters are now implemented. Benchmark calculations and illustrative applications at the Møller–Plesset perturbation theory, coupled cluster singles and doubles (CCSD), and CCSD with perturbative triples correction levels show that this newly optimized CIM approach is a reliable theoretical tool for electron correlation calculations of various large chemical systems. textcopyright 2018 Wiley Periodicals, Inc.
BibTeX:
@article{Ni2019-1130,
  author = {Ni, Zhigang and Li, Wei and Li, Shuhua},
  title = {Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems},
  journal = {J. Comput. Chem.},
  year = {2019},
  volume = {40},
  number = {10},
  pages = {1130--1140},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.25730 http://doi.wiley.com/10.1002/jcc.25730},
  doi = {https://doi.org/10.1002/jcc.25730}
}
Ni, Z., Wang, Y., Li, W., Pulay, P. and Li, S. Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and Its Application to Geometry Optimizations of Large Systems 2019 J. Chem. Theory Comput.
Vol. 15(6), pp. 3623-3634 
article DOI URL 
Abstract: An efficient analytical energy gradient algorithm for the cluster-in-molecule (CIM) second order Møller–Plesset perturbation theory (MP2) method is presented. In our algorithm, the gradient contributions from the nonseparable term of the two-body density matrix on a given atom is extracted from calculations on a cluster constructed for this atom. The other terms in the CIM-MP2 energy gradient expression are evaluated by constructing the density matrices of the whole system with the contributions from all clusters constructed. For basis sets with diffuse functions, tight CIM parameters are necessary to obtain accurate gradients. Benchmark calculations show that the CIM-MP2 method can accurately reproduce the conventional MP2 gradients and geometries for larger systems. The optimized structure of a 174-atom oligopeptide using the CIM-MP2 method with the cc-pVDZ basis set is in good agreement with the corresponding crystal structure. The present CIM-MP2 gradient program can be used for optimizing the geometries of large systems with hundreds of atoms on ordinary workstations.
BibTeX:
@article{Ni2019-3623,
  author = {Ni, Zhigang and Wang, Yuqi and Li, Wei and Pulay, Peter and Li, Shuhua},
  title = {Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and Its Application to Geometry Optimizations of Large Systems},
  journal = {J. Chem. Theory Comput.},
  publisher = {American Chemical Society},
  year = {2019},
  volume = {15},
  number = {6},
  pages = {3623--3634},
  url = {https://doi.org/10.1021/acs.jctc.9b00259},
  doi = {https://doi.org/10.1021/acs.jctc.9b00259}
}
Wang, X., Fu, F., Peng, K., Yang, Z., Hu, N., Chen, X. and Li, W. Understanding of structures, dynamics, and hydrogen bonds of imidazolium-based ionic liquid mixture from molecular dynamics simulation 2019 Chemical Physics
Vol. 525, pp. 110391 
article DOI URL 
Abstract: Here we employ molecular dynamics simulation to study structures, dynamics, and hydrogen bonds of the imidazolium-based ionic liquid mixture, which consists of equimolar [Emim][BF4] and [Bmim][BF4]. Our simulation results demonstrate that the imidazolium rings of both different cations almost show identical structures with [BF4]− anions regardless of the alkyl chain length. Meanwhile, both kinds of cations almost display the same association/dissociation dynamics with anions. By comparison, the order of diffusion speed is [Emim]+ textgreater [Bmim]+ textgreater [BF4]− while that of rotation speed is [BF4]− textgreater [Emim]+ textgreater [Bmim]+ in the ionic liquid mixture. By analyzing the average numbers of hydrogen bonds (HBs) and the relevant HB dynamics between cations and anions, we find that [Bmim]+ cations have more and stronger HBs with anions than [Emim]+ cations, which should be partly responsible for slower diffusion and rotation of [Bmim]+ cations than those of [Emim]+ cations. Therefore, this simulation study provides a molecular-level understanding of the role of alkyl chain and HB on the relevant structure and dynamics properties in the imidazolium-based ionic liquid mixture.
BibTeX:
@article{Wang2019-110391,
  author = {Wang, Xueping and Fu, Fangjia and Peng, Kuilin and Yang, Zhen and Hu, Na and Chen, Xiangshu and Li, Wei},
  title = {Understanding of structures, dynamics, and hydrogen bonds of imidazolium-based ionic liquid mixture from molecular dynamics simulation},
  journal = {Chemical Physics},
  year = {2019},
  volume = {525},
  pages = {110391},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0301010419302897},
  doi = {https://doi.org/10.1016/j.chemphys.2019.110391}
}
Wang, Y., Ni, Z., Li, W. and Li, S. Cluster-in-Molecule Local Correlation Approach for Periodic Systems 2019 J. Chem. Theory Comput.
Vol. 15(5), pp. 2933-2943 
article DOI URL 
Abstract: In this article, the cluster-in-molecule (CIM) local correlation approach for periodic systems with periodic boundary condition has been developed, which allows electron-correlation calculations of various crystals computationally tractable. In this approach, the correlation energy per unit cell of a periodic system can be evaluated as the summation of the correlation contributions from electron-correlation calculations on a series of finite-sized clusters. Each cluster is defined to contain a subset of localized Wannier functions (WFs) (for the occupied space) and projected atomic orbitals (for the virtual space), which can be derived from a periodic Hartree–Fock calculation. Electron-correlation calculations on clusters at second-order Møller–Plesset perturbation theory (MP2) or coupled cluster singles and doubles (CCSD) can be performed with well-established molecular quantum chemistry packages. We perform illustrative calculations at the MP2 and CCSD levels on several types of crystals (neon lattice, carbon monoxide and ammonia crystals, two ionic liquid crystals, and diamond). The results show that CIM is a powerful framework for accurate electron-correlation calculations of crystals.
BibTeX:
@article{Wang2019-2933,
  author = {Wang, Yuqi and Ni, Zhigang and Li, Wei and Li, Shuhua},
  title = {Cluster-in-Molecule Local Correlation Approach for Periodic Systems},
  journal = {J. Chem. Theory Comput.},
  year = {2019},
  volume = {15},
  number = {5},
  pages = {2933--2943},
  url = {https://doi.org/10.1021/acs.jctc.8b01200 http://pubs.acs.org/doi/10.1021/acs.jctc.8b01200},
  doi = {https://doi.org/10.1021/acs.jctc.8b01200}
}
Yang, H., Fu, F., Li, W., Wei, W., Zhang, Y. and Liu, S. Telomerase and poly(ADP-ribose) polymerase-1 activity sensing based on the high fluorescence selectivity and sensitivity of TOTO-1 towards G bases in single-stranded DNA and poly(ADP-ribose) 2019 Chemical Science
Vol. 10(13), pp. 3706-3714 
article DOI URL 
Abstract: Telomerase and poly(ADP-ribose) polymerase-1 (PARP-1) are two potential cancer biomarkers and are closely related to tumor initiation and malignant progression.
BibTeX:
@article{Yang2019-3706,
  author = {Yang, Haitang and Fu, Fangjia and Li, Wei and Wei, Wei and Zhang, Yuanjian and Liu, Songqin},
  title = {Telomerase and poly(ADP-ribose) polymerase-1 activity sensing based on the high fluorescence selectivity and sensitivity of TOTO-1 towards G bases in single-stranded DNA and poly(ADP-ribose)},
  journal = {Chemical Science},
  publisher = {The Royal Society of Chemistry},
  year = {2019},
  volume = {10},
  number = {13},
  pages = {3706--3714},
  url = {http://dx.doi.org/10.1039/C8SC05770B http://pubs.rsc.org/en/Content/ArticleLanding/2019/SC/C8SC05770B http://xlink.rsc.org/?DOI=C8SC05770B},
  doi = {https://doi.org/10.1039/C8SC05770B}
}
Chi, Y., You, X., Zhang, L. and Li, W. Utilization of generalized energy-based fragmentation method on the study of hydrogen abstraction reactions of large methyl esters 2018 Combust. Flame
Vol. 190, pp. 467-476 
article DOI URL 
Abstract: Abstract Accurate reaction energies and barrier heights are essential for the construction of reliable combustion kinetics models of various fuels. Nevertheless, the computational cost for electronic energy calculations using high-level ab initio methods increases dramatically with the size of molecules. A solution to this problem is to utilize a generalized energy-based fragmentation (GEBF) approach, as it has been found to be effective in reducing the scaling of the computational cost in calculation of energetics and other molecular properties for many large molecules, clusters, and crystals with various quantum chemistry methods. This work attempts to apply this GEBF approach in the study of one important type of reactions of large methyl esters, i.e., the hydrogen abstraction reactions by hydrogen atoms. The energies of stationary points on the potential energy surfaces were examined using both conventional quantum chemistry methods and the GEBF method at the QCISD(T)/CBS// M06-2X/6-311 + + g(d,p) level for CnH2n+1COOCH3 (n = 4, 5) + H reactions. The results show that the unsigned energy deviation of the GEBF method from the conventional method is less than 0.1 kcal/mol, while the computational time is greatly reduced, e.g. up to 90% at the QCISD(T)/cc-pVTZ level. Based on the quantum chemistry calculations, rate constants of the hydrogen abstraction reactions of CnH2n+1COOCH3 (n = 4, 5, 8) by H atoms were computed.
BibTeX:
@article{Chi2018-467,
  author = {Chi, Yawei and You, Xiaoqing and Zhang, Lidong and Li, Wei},
  title = {Utilization of generalized energy-based fragmentation method on the study of hydrogen abstraction reactions of large methyl esters},
  journal = {Combust. Flame},
  year = {2018},
  volume = {190},
  pages = {467--476},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0010218017304947},
  doi = {https://doi.org/10.1016/j.combustflame.2017.12.021}
}
Li, Y., Yuan, D., Wang, Q., Li, W. and 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 2018 Phys. Chem. Chem. Phys.
Vol. 20(19), pp. 13547-13557 
article DOI URL 
Abstract: A generalized energy-based fragmentation (GEBF) approach has been developed to facilitate ab initio calculations of the ground-state energies, structures and vibrational spectra of general ionic liquid (IL) clusters. For the selected IL clusters, the accuracy of the GEBF approach with two different fragmentation schemes (ion-pair-based fragmentation and ion-based fragmentation) is evaluated with the conventional quantum chemistry calculations. Our results demonstrate that for the selected IL clusters, the GEBF approach with the ion-pair-based fragmentation scheme can provide much more accurate descriptions than that with the ion-based fragmentation scheme. The main reason for these results is that the non-integer charge behavior of each ion (cation or anion) in IL systems may induce significant errors for the GEBF approach with the ion-based fragmentation scheme, in which every ion is assumed to have an integer charge. However, this problem can be avoided by the ion-pair-based fragmentation scheme, in which each ion pair is assumed to be electrically neutral. Our illustrative results show that the GEBF approach with a dynamic ion-pair-based fragmentation scheme, in which ion pair fragments are updated for every structure, can provide satisfactory descriptions on the ground-state energies, optimized structures, and vibrational spectra of general IL clusters. The performance of the GEBF approach is found to be almost independent of the basis sets or theoretical methods, and the computational cost of the GEBF approach scales linearly with the system size at density functional theory (DFT) and second-order Møller–Plesset perturbation theory (MP2) levels. Due to its excellent parallel efficiency, the GEBF approach is expected to be a cost-effective tool for investigating the structure, vibrational spectra, as well as other properties of large IL clusters.
BibTeX:
@article{Li2018-13547,
  author = {Li, Yunzhi and Yuan, Dandan and Wang, Qingchun and Li, Wei and Li, Shuhua},
  title = {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},
  journal = {Phys. Chem. Chem. Phys.},
  publisher = {The Royal Society of Chemistry},
  year = {2018},
  volume = {20},
  number = {19},
  pages = {13547--13557},
  url = {http://dx.doi.org/10.1039/C8CP00513C http://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C8CP00513C http://xlink.rsc.org/?DOI=C8CP00513C},
  doi = {https://doi.org/10.1039/C8CP00513C}
}
Liao, K., Cheng, Z., Li, Y., Zhao, D., Li, W. and Li, S. Fast quantum chemistry calculations for large molecules and condensed-phase systems: The developments and applications of generalized energy-based fragmentation approach 2018 Chin. Sci. Bull.
Vol. 63(33), pp. 3427-3441 
article DOI URL 
Abstract: The GEBF approach could be applied to the ground-state energies (including the relative energies or binding energies) of a broad range of large systems including molecular clusters, supramolecular systems, proteins, nucleic acids, and etc. The computational levels include HF, DFT, second-order Møller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), CCSD with triples correction [CCSD(T)], and explicitly correlated MP2-F12 and CCSD(T)-F12x (x=a,b) methods. With the GEBF energy derivatives (including energy gradients, Hessians, and so on), the approaches could be employed for optimizing the molecular geometries, performing ab initio molecular dynamics, computing the vibrational spectroscopies (including the IR and Raman spectroscopies) and nuclear magnetic resonance (NMR) chemical shifts of large systems at the HF, DFT, and MP2 levels. GEBF approach is also extended to the localized excited states by defining those subsystems including local excitation as the active subsystems, which are treated by the excited-state calculations at the time-dependent DFT or approximate equation-of-motion CCSD (CC2) levels. Then the GEBF-TDDFT or GEBF-CC2 could be used to compute electronic absorption spectra of solutions or large molecules with local excitations. The GEBF approach under the periodic boundary conditions (PBC) is also been implemented by constructing the subsystems in a super cell and employing the Ewald summation and compensation field methods to take the effect of the long-range electrostatic interaction of the crystal environment into account. The PBC-GEBF approach has been used to compute the lattice energies, crystal structures, IR and Raman spectra, and NMR chemical shifts of various condensed-phase systems, including molecular crystals, liquids, ionic liquid crystals, and solutions. Thus, the GEBF and PBC-GEBF approaches are expected to be widely applied to the energies, structures, and molecular properties of a broad range of large systems and condensed-phase systems.
BibTeX:
@article{Liao2018-3427,
  author = {Liao, Kang and Cheng, Zheng and Li, Yunzhi and Zhao, Dongbo and Li, Wei and Li, Shuhua},
  title = {Fast quantum chemistry calculations for large molecules and condensed-phase systems: The developments and applications of generalized energy-based fragmentation approach},
  journal = {Chin. Sci. Bull.},
  year = {2018},
  volume = {63},
  number = {33},
  pages = {3427--3441},
  url = {http://engine.scichina.com/doi/10.1360/N972018-00907},
  doi = {https://doi.org/10.1360/N972018-00907}
}
Yuan, D., Li, Y., Li, W. and Li, S. Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method 2018 Phys. Chem. Chem. Phys.
Vol. 20(45), pp. 28894-28902 
article DOI URL 
Abstract: The generalized energy-based fragmentation (GEBF) method has been extended to facilitate ab initio calculations of large supramolecular coordination complexes. For metal-containing coordination complexes, a special fragmentation scheme is proposed for GEBF calculations, in which coordinate bonds between metal ions and ligands are kept intact, and only single covalent bonds in organic ligands are cut into fragments. A simple strategy is exploited for the determination of the ground-state spin multiplicity of each metal ion so that the total spin of all metal-containing subsystems is assigned automatically. With this fragmentation scheme, the GEBF method is demonstrated to provide reliable energies, optimized geometry, nuclear magnetic resonance (NMR) properties and the infrared spectrum for a medium-sized supramolecular coordination complex, which are very consistent with those from the full-system quantum chemistry calculations. The GEBF method is then applied to two large supramolecular coordination complexes to illustrate its capability. For the trimetallic coordination complex Fe2Zn2(RuL2)2 (with 618 atoms), the calculated 1H chemical shifts from GEBF calculations with the B97-2 functional can account well for the experimental NMR spectrum. For the cage-guest complex Pd4L8(BF4−)3, the computed infrared spectrum obtained with the GEBF-M06-2X method can help assign the experimental peaks to the corresponding vibrational motions. The GEBF method combining with advanced electronic structure methods is expected to be a useful tool to understand and interpret structural and spectroscopic information of various supramolecular coordination complexes.
BibTeX:
@article{Yuan2018-28894,
  author = {Yuan, Dandan and Li, Yunzhi and Li, Wei and Li, Shuhua},
  title = {Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method},
  journal = {Phys. Chem. Chem. Phys.},
  publisher = {The Royal Society of Chemistry},
  year = {2018},
  volume = {20},
  number = {45},
  pages = {28894--28902},
  url = {http://dx.doi.org/10.1039/C8CP05548C},
  doi = {https://doi.org/10.1039/C8CP05548C}
}
Li, Y., Wang, G., Li, W., Wang, Y. and Li, S. Understanding the polymorphism-dependent emission properties of molecular crystals using a refined QM/MM approach 2017 Phys. Chem. Chem. Phys.
Vol. 19(27), pp. 17516-17520 
article DOI URL 
Abstract: A refined QM/MM approach demonstrated that a monomer model is suitable for describing the emission spectra of crystals without the pi⋯pi stacking interaction. Whereas for the crystals with notable intermolecular pi⋯pi stacking interaction, the most stable trimer model (or at least a dimer model) should be used for accurately describing the corresponding emission spectra. This approach is applied to understand the emission properties of two kinds of organic polymorphs.
BibTeX:
@article{Li2017-17516,
  author = {Li, Yunzhi and Wang, Guoqiang and Li, Wei and Wang, Yue and Li, Shuhua},
  title = {Understanding the polymorphism-dependent emission properties of molecular crystals using a refined QM/MM approach},
  journal = {Phys. Chem. Chem. Phys.},
  publisher = {The Royal Society of Chemistry},
  year = {2017},
  volume = {19},
  number = {27},
  pages = {17516--17520},
  url = {http://xlink.rsc.org/?DOI=C7CP03584E http://dx.doi.org/10.1039/C7CP03584E},
  doi = {https://doi.org/10.1039/C7CP03584E}
}
Tao, Y., Zou, W., Jia, J., Li, W. and Cremer, D. Different ways of hydrogen bonding in water - Why does warm water freeze faster than cold water? 2017 J. Chem. Theory Comput.
Vol. 13(1), pp. 55-76 
article DOI URL 
Abstract: The properties of liquid water are intimately related to the H-bond network among the individual water molecules. Utilizing vibrational spectroscopy and modeling water with DFT-optimized water clusters (6-mers and 50-mers), 16 out of a possible 36 different types of H-bonds are identified and ordered according to their intrinsic strength. The strongest H-bonds are obtained as a result of a concerted push-pull effect of four peripheral water molecules, which polarize the electron density in a way that supports charge transfer and partial covalent character of the targeted H-bond. For water molecules with tetra- and penta-coordinated O atoms, H-bonding is often associated with a geometrically unfavorable positioning of the acceptor lone pair and donor $$⋆(OH) orbitals so that electrostatic rather than covalent interactions increasingly dominate H-bonding. There is a striking linear depen- dence between the intrinsic strength of H-bonding as measured by the local H-bond stretch- ing force constant and the del...
BibTeX:
@article{Tao2017-55,
  author = {Tao, Yunwen and Zou, Wenli and Jia, Junteng and Li, Wei and Cremer, Dieter},
  title = {Different ways of hydrogen bonding in water - Why does warm water freeze faster than cold water?},
  journal = {J. Chem. Theory Comput.},
  year = {2017},
  volume = {13},
  number = {1},
  pages = {55--76},
  url = {http://dx.doi.org/10.1021/acs.jctc.6b00735},
  doi = {https://doi.org/10.1021/acs.jctc.6b00735}
}
Wei, Y.-Z., Cheng, Z., Li, W. and Zhu, H.-B. Syntheses, Crystal Structures and Photophysical Properties of D10 Transition-Metal (Ag+, Cu+, Cd2+ and Zn2+) Coordination Complexes Based on A Thiophene-Containing Heterocyclic Thioamide 2017 J. Coord. Chem.
Vol. 70(16), pp. 2900-2915 
article DOI URL 
Abstract: AbstractFour d10 transition-metal coordination complexes 1–4 (1: [Ag2(TPT)2(TPTH)2]; 2: [Cu6(TPT)6]textperiodcentered2DMF; 3: [Cd(TPT)2(TPTH)]textperiodcenteredCH3CH2OH, 4: [Zn(TPT)2]n) have been constructed from a newly designed heterocyclic thioamide ligand, TPTH (TPTH = 4-(thiophen-2-yl)-pyrimidine-2-thiol). All complexes have been structurally elucidated by single crystal X-ray diffraction analyses. Except for 4, which shows a one-dimensional (1-D) chain structure, 1–3 are all discrete coordination complexes featuring dinuclear, hexanuclear and mononuclear entities, respectively. Their photophysical properties have been evaluated in the solid state at room temperature by UV–vis diffuse reflectance and luminescence spectra. Among them, 2 exhibits a strong red luminescence ($$em = 699 nm) with a remarkable red-shift of the maximum emission compared to that of the TPTH ligand ($$em = 536 nm). The red emission observed with 2 is ascribed to a LMCT (ligand-to-metal charge transfer) transition which agrees with the DFT calculations.
BibTeX:
@article{Wei2017-2900,
  author = {Wei, Yu-Zhen and Cheng, Zheng and Li, Wei and Zhu, Hai-Bin},
  title = {Syntheses, Crystal Structures and Photophysical Properties of D10 Transition-Metal (Ag+, Cu+, Cd2+ and Zn2+) Coordination Complexes Based on A Thiophene-Containing Heterocyclic Thioamide},
  journal = {J. Coord. Chem.},
  year = {2017},
  volume = {70},
  number = {16},
  pages = {2900--2915},
  url = {https://www.tandfonline.com/doi/full/10.1080/00958972.2017.1364374},
  doi = {https://doi.org/10.1080/00958972.2017.1364374}
}
Yuan, D., Li, Y., Ni, Z., Pulay, P., Li, W. and Li, S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method 2017 J. Chem. Theory Comput.
Vol. 13(6), pp. 2696-2704 
article DOI URL 
Abstract: The generalized energy-based fragmentation (GEBF) method has been applied to investigate relative energies of large water clusters (H2O)n (n = 32, 64) with the coupled-cluster singles and doubles with noniterative triple excitations (CCSD(T)) and second-order Møller–Plesset perturbation theory (MP2) at the complete basis set (CBS) limit. Here large water clusters are chosen to be representative structures sampled from molecular dynamics (MD) simulations of liquid water. Our calculations show that the GEBF method is capable of providing highly accurate relative energies for these water clusters in a cost-effective way. We demonstrate that the relative energies from GEBF-MP2/CBS are in excellent agreement with those from GEBF-CCSD(T)/CBS for these water clusters. With the GEBF-CCSD(T)/CBS relative energies as the benchmark results, we have assessed the performance of several theoretical methods widely used for ab initio MD simulations of liquids and aqueous solutions. These methods include density functiona...
BibTeX:
@article{Yuan2017-2696,
  author = {Yuan, Dandan and Li, Yunzhi and Ni, Zhigang and Pulay, Peter and Li, Wei and Li, Shuhua},
  title = {Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method},
  journal = {J. Chem. Theory Comput.},
  year = {2017},
  volume = {13},
  number = {6},
  pages = {2696--2704},
  url = {http://dx.doi.org/10.1021/acs.jctc.7b00284},
  doi = {https://doi.org/10.1021/acs.jctc.7b00284}
}
Zhang, L., Li, W., Fang, T. and Li, S. Accurate Relative Energies and Binding Energies of Large Ice-Liquid Water Clusters and Periodic Structures 2017 J. Phys. Chem. A
Vol. 121(20), pp. 4030-4038 
article DOI URL 
Abstract: Relative energies and binding energies are crucial quantities,
which determine various molecular properties of ice and water. We developed a
new effective method to compute those energies of bulk ice-liquid water
systems. In this work, ten ice-liquid 144-mers and ten periodic ice-liquid
(H2O)64 systems are taken out from the molecular dynamics simulations in the
melting process of ice-Ih crystals. They are investigated at the levels of
density functional theory (DFT), explicitly correlated second-order
Møller-Plesset perturbation theory (MP2-F12) and coupled-cluster singles and
doubles with noniterative triples corrections [CCSD(T)-F12b] in the framework
of generalized energy-based fragmentation approach. Our results show that the
changing of noncovalent interactions significantly influences the performances
of DFT and electron correlation methods for those systems in the melting
process of ice. Various DFT methods predict quite different results for ice and
mixed ice-liquid structures, whereas give similar results for pure liquid ones.
It also explains that why many DFT-based simulations lead to inaccurate
densities of ice and liquid water. The CCSD(T)-F12b results suggest that the
MP2-F12 method provide satisfactory results and is expected to be employed to
simulate the phase transitions of ice crystal.
BibTeX:
@article{Zhang2017-4030,
  author = {Zhang, Lei and Li, Wei and Fang, Tao and Li, Shuhua},
  title = {Accurate Relative Energies and Binding Energies of Large Ice-Liquid Water Clusters and Periodic Structures},
  journal = {J. Phys. Chem. A},
  year = {2017},
  volume = {121},
  number = {20},
  pages = {4030--4038},
  url = {http://dx.doi.org/10.1021/acs.jpca.7b03376},
  doi = {https://doi.org/10.1021/acs.jpca.7b03376}
}
Zhao, D., Song, R., Li, W., Ma, J., Dong, H. and Li, S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method 2017 J. Chem. Theory Comput.
Vol. 13(11), pp. 5231-5239 
article DOI URL 
Abstract: The generalized energy-based fragmentation (GEBF) method is extended to allow calculations of nuclear magnetic resonance (NMR) chemical shifts of macromolecular and condensed-phase systems feasible at a low computational cost. In this approach, NMR shielding constants in a large system are evaluated as a linear combination of the corresponding quantities from a series of small “electrostatically embedded” subsystems. Comparison of NMR shielding constants from the GEBF-X method [where X is an electronic structure method, such as Hartree–Fock (HF), density functional theory (DFT), ...] with those from the conventional quantum chemistry method for two representative systems verifies that the GEBF approach can reproduce the results of the conventional quantum chemistry method very well. This procedure has further been applied to compute NMR shielding constants of a large foldamer and a supramolecular aggregate, and the 15N shielding constant for CH3CN in the CHCl3 solvent. For the former two systems, the pred...
BibTeX:
@article{Zhao2017-5231,
  author = {Zhao, Dongbo and Song, Ruiheng and Li, Wei and Ma, Jing and Dong, Hao and Li, Shuhua},
  title = {Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method},
  journal = {J. Chem. Theory Comput.},
  year = {2017},
  volume = {13},
  number = {11},
  pages = {5231--5239},
  url = {http://dx.doi.org/10.1021/acs.jctc.7b00380},
  doi = {https://doi.org/10.1021/acs.jctc.7b00380}
}
Huang, Y., Zhou, G., Li, Y., Yang, Z., Shi, M., Wang, X., Chen, X., Zhang, F. and Li, W. Molecular dynamics simulations of temperature-dependent structures and dynamics of ethylammonium nitrate protic ionic liquid: The role of hydrogen bond 2016 Chem. Phys.
Vol. 472, pp. 105-111 
article DOI URL 
Abstract: Molecular dynamics simulations have been employed to systematically investigate the structure and dynamics properties, hydrogen bond (HB) dynamics of protic ionic liquid (IL) ethylammonium nitrate (EAN) in the temperature range between 300 K and 400 K. The simulation results demonstrate clearly that the temperature almost has little influence on the structures of EAN IL, whereas the translational and the rotational motions of both cations and anions become much faster at higher temperatures. Furthermore, both anions and cations are found to display an obvious sub-diffusive behavior. These changes can be attributed to the temperature-dependent HB strength between the cations and the anions, where the strength of HBs decreases significantly with increasing temperature. Accordingly, the ion-pair association/dissociation dynamics decreases considerably with increasing temperature. Therefore, our simulations reveal at a molecular level that the HBs interactions play an essential role in determining the dynamics properties of protic ILs.
BibTeX:
@article{Huang2016-105,
  author = {Huang, Yiping and Zhou, Guobing and Li, Yunzhi and Yang, Zhen and Shi, Man and Wang, Xueping and Chen, Xiangshu and Zhang, Fei and Li, Wei},
  title = {Molecular dynamics simulations of temperature-dependent structures and dynamics of ethylammonium nitrate protic ionic liquid: The role of hydrogen bond},
  journal = {Chem. Phys.},
  year = {2016},
  volume = {472},
  pages = {105--111},
  url = {http://www.sciencedirect.com/science/article/pii/S0301010416300738},
  doi = {https://doi.org/10.1016/j.chemphys.2016.03.020}
}
Li, W., Ni, Z. and Li, S. Cluster-in-molecule local correlation method for post-Hartree–Fock calculations of large systems 2016 Mol. Phy.
Vol. 114(9), pp. 1447-1460 
article DOI URL 
Abstract: ABSTRACTOur recent developments on cluster-in-molecule (CIM) local correlation method are reviewed in this paper. In the CIM method, the correlation energy of a large system can be approximately obtained from electron correlation calculations on a series of clusters, each of which contains a subset of occupied and virtual localised molecular orbitals in a certain region. The CIM method is a linear scaling method and its inherent parallelisation allows electron correlation calculations of very large systems to be feasible at ordinary workstations. In the illustrative applications, this approach is applied to investigate the conformational energy differences, reaction barriers, and binding energies of large systems at the levels of Møller–Plesset perturbation theory and coupled-cluster theory.
BibTeX:
@article{Li2016-1447,
  author = {Li, Wei and Ni, Zhigang and Li, Shuhua},
  title = {Cluster-in-molecule local correlation method for post-Hartree–Fock calculations of large systems},
  journal = {Mol. Phy.},
  year = {2016},
  volume = {114},
  number = {9},
  pages = {1447--1460},
  url = {http://www.tandfonline.com/doi/full/10.1080/00268976.2016.1139755},
  doi = {https://doi.org/10.1080/00268976.2016.1139755}
}
Li, W., Li, Y., Lin, R. and Li, S. Generalized Energy-Based Fragmentation Approach for Localized Excited States of Large Systems 2016 J. Phys. Chem. A
Vol. 120(48), pp. 9667-9677 
article DOI URL 
Abstract: We have extended the generalized energy-based fragmentation (GEBF) approach to localized excited states of large systems. In this approach, the excited-state energy of a large system could be expressed as the combination of the excited-state energies of “active subsystems”, which contains the chromophore center, and the ground-state energies of “inactive subsystems”. The GEBF approach has been implemented at the levels of time-dependent density functional theory (TDDFT) and approximate coupled cluster singles and doubles (CC2) method. Our results show that GEBF-TDDFT can reproduce the TDDFT excitation energies and solvatochromic shifts for large systems and that GEBF-CC2 could be used to validate GEBF-TDDFT result (with different functionals). The GEBF-TDDFT method is found to be able to provide satisfactory or reasonable descriptions on the experimental solvatochromic shifts for the n → pi* transitions of acetone in various solutions, and the lowest pi → pi* transitions of pyridine and uracil in aqueous solutions.
BibTeX:
@article{Li2016-9667,
  author = {Li, Wei and Li, Yunzhi and Lin, Ruochen and Li, Shuhua},
  title = {Generalized Energy-Based Fragmentation Approach for Localized Excited States of Large Systems},
  journal = {J. Phys. Chem. A},
  year = {2016},
  volume = {120},
  number = {48},
  pages = {9667--9677},
  url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpca.6b11193},
  doi = {https://doi.org/10.1021/acs.jpca.6b11193}
}
Liu, P., Li, W., Kan, Z., Sun, H. and Ma, J. Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations 2016 J. Phys. Chem. A
Vol. 120(4), pp. 490-502 
article DOI  
Abstract: The interlocked textlessrod | ringtextgreaterstructures of pseudorotaxanes and [2]rotaxanes are usually maintained by the complex hydrogen-bonding (H-bonding) network between the rod and ring. Ab initio molecular dynamics (AIMD) using generalized energy-based fragmentation (GEBF) approach and polarizable force field (polar FF)-based molecular dynamics (MD) simulations have been performed to investigate the conformational changes of mechanically interlocked systems and to obtain the ensemble-averaged NMR shifts. Factor analysis (FA) demonstrates that the ring H-donor (2,6 pyridinedicarboxamide group) plays an important role in the ring-rod recognition. In comparison to the conventional fixed-charge force field, the polarization effect is crucial to account for the H-bonding interactions in supramolecular systems. In the hybrid scheme, the polar FF-based MD simulations are used to generate different initial states for the AIMD simulations, which are able to give better prediction of ensemble-averaged NMR signals for chemically equivalent amide protons. The magnitude of the deshielding shift of NMR signal is correlated with the length of hydrogen bond (HB). The polarizable FF model with variable charges shows that the dipole-dipole interactions between the flexible diethylene glycol chain of ring and polar solvents induce the upfield shifts of NMR signals of rod H-donors and the directional distribution of the neighboring CH3CN solvents.
BibTeX:
@article{Liu2016-490,
  author = {Liu, Pingying and Li, Wei and Kan, Zigui and Sun, Hui and Ma, Jing},
  title = {Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations},
  journal = {J. Phys. Chem. A},
  year = {2016},
  volume = {120},
  number = {4},
  pages = {490--502},
  doi = {https://doi.org/10.1021/acs.jpca.5b10085}
}
Wang, G., Zhang, H., Zhao, J., Li, W., Cao, J., Zhu, C. and Li, S. Homolytic Cleavage of a B-B Bond by the Cooperative Catalysis of Two Lewis Bases: Computational Design and Experimental Verification 2016 Angew. Chem. Int. Ed.
Vol. 55(20), pp. 5985-5989 
article DOI  
Abstract: Density functional theory (DFT) investigations revealed that 4-cyanopyridine was capable of homolytically cleaving the B-B σ bond of diborane via the cooperative coordination to the two boron atoms of the diborane to generate pyridine boryl radicals. Our experimental verification provides supportive evidence for this new B-B activation mode. With this novel activation strategy, we have experimentally realized the catalytic reduction of azo-compounds to hydrazine derivatives, deoxygenation of sulfoxides to sulfides, and reduction of quinones with B2 (pin)2 at mild conditions.
BibTeX:
@article{Wang2016-5985,
  author = {Wang, Guoqiang and Zhang, Honglin and Zhao, Jiyang and Li, Wei and Cao, Jia and Zhu, Chengjian and Li, Shuhua},
  title = {Homolytic Cleavage of a B-B Bond by the Cooperative Catalysis of Two Lewis Bases: Computational Design and Experimental Verification},
  journal = {Angew. Chem. Int. Ed.},
  year = {2016},
  volume = {55},
  number = {20},
  pages = {5985--5989},
  doi = {https://doi.org/10.1002/anie.201511917}
}
Wen, J., Li, W., Chen, S. and Ma, J. Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions 2016 Phys. Chem. Chem. Phys.
Vol. 18(33), pp. 22757-22771 
article DOI URL 
Abstract: Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.
BibTeX:
@article{Wen2016-22757,
  author = {Wen, Jin and Li, Wei and Chen, Shuang and Ma, Jing},
  title = {Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2016},
  volume = {18},
  number = {33},
  pages = {22757--22771},
  url = {http://xlink.rsc.org/?DOI=C6CP01049K},
  doi = {https://doi.org/10.1039/C6CP01049K}
}
Yuan, D., Shen, X., Li, W. and Li, S. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters? 2016 Phys. Chem. Chem. Phys.
Vol. 18(24), pp. 16491-16500 
article DOI URL 
Abstract: Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion–exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set.
BibTeX:
@article{Yuan2016-16491,
  author = {Yuan, Dandan and Shen, Xiaoling and Li, Wei and Li, Shuhua},
  title = {Are fragment-based quantum chemistry methods applicable to medium-sized water clusters?},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2016},
  volume = {18},
  number = {24},
  pages = {16491--16500},
  url = {http://xlink.rsc.org/?DOI=C6CP01931E},
  doi = {https://doi.org/10.1039/C6CP01931E}
}
Zhang, L., Li, W., Fang, T. and Li, S. Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides 2016 Theor. Chem. Acc.
Vol. 135(2), pp. 34 
article DOI URL 
Abstract: Ab inito molecular dynamics (AIMD) based on the generalized energy-based fragmentation (GEBF) approach is employed for the ultrafast conformational dynamics of two unsolvated polypeptides, 310-helical acetyl(ala) 18backslashhbox NH2 and a subunit of DNA polymerase backslashbeta. In the GEBF approach, the energies and energy gradients of subsystems are obtained with M06-2X functionals, which can describe intramolecular noncovalent interaction. The results are compared with those obtained from the simulations based on AMBER99 and CHARMM22 force fields, and semiempirical density-functional tight-binding (DFTB) and DFTB with empirical dispersion correction (DFTB-D) methods. Our results show that the GEBF-M06-2X simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions. The AMBER99, CHARMM22, DFTB, and DFTB-D simulations give quite different results. The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.
BibTeX:
@article{Zhang2016-34,
  author = {Zhang, Lei and Li, Wei and Fang, Tao and Li, Shuhua},
  title = {Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides},
  journal = {Theor. Chem. Acc.},
  year = {2016},
  volume = {135},
  number = {2},
  pages = {34},
  url = {http://dx.doi.org/10.1007/s00214-015-1799-z},
  doi = {https://doi.org/10.1007/s00214-015-1799-z}
}
Dong, H., Li, W., Sun, J., Li, S. and Klein, M.L. Understanding the Boron-Nitrogen Interaction and Its Possible Implications in Drug Design 2015 J. Phys. Chem. B
Vol. 119(45), pp. 14393-14401 
article DOI  
Abstract: 2-Aminoethoxydiphenylborate (2-APB) is a broad-spectrum modulator of various membrane proteins. Specifically, it exhibits concentration dependent modulation of calcium signaling through store-operated calcium (SOC) channels: low micromolar concentration of 2-APB stimulates SOC entry while a higher concentration induces complete inhibition. Ab initio quantum chemical calculations show that the relative stability of the two major isomers of 2-APB (cyclic and extended) is about 8 kcal/mol. The dual functionality of 2-APB for SOC channels is thus likely associated with its ability to switch among isomeric forms, suited to different binding sites in the SOC channels with distinct binding affinities. Importantly, the moderate relative stability of different isomers results from a delicate balance between the intramolecular boron–nitrogen coordinate bond with strength about −45 kcal/mol and ring strain engendered by cyclic oligomerization. The synergistic effect of these two factors likely makes 2-APB an ideal d...
BibTeX:
@article{Dong2015-14393,
  author = {Dong, Hao and Li, Wei and Sun, Jianwei and Li, Shuhua and Klein, Michael L},
  title = {Understanding the Boron-Nitrogen Interaction and Its Possible Implications in Drug Design},
  journal = {J. Phys. Chem. B},
  year = {2015},
  volume = {119},
  number = {45},
  pages = {14393--14401},
  doi = {https://doi.org/10.1021/acs.jpcb.5b07783}
}
Fang, T., Li, W., Gu, F. and Li, S. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods 2015 J. Chem. Theory Comput.
Vol. 11(1), pp. 91-98 
article DOI  
Abstract: We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals.$$nWe extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals.
BibTeX:
@article{Fang2015-91,
  author = {Fang, Tao and Li, Wei and Gu, Fangwei and Li, Shuhua},
  title = {Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods},
  journal = {J. Chem. Theory Comput.},
  year = {2015},
  volume = {11},
  number = {1},
  pages = {91--98},
  doi = {https://doi.org/10.1021/ct500833k}
}
Li, W., Chen, C., Zhao, D. and Li, S. LSQC: Low scaling quantum chemistry program 2015 Int. J. Quantum Chem.
Vol. 115(10), pp. 641-646 
article DOI URL 
Abstract: A low scaling quantum chemistry program, called LSQC, is described in this article. This version includes two linear scaling methods, generalized energy‐based fragmentation (GEBF) approach and cluster‐in‐molecule (CIM) approach. In the GEBF approach, a variety of electron structure methods (including ab initio and density functional theory) are available for the calculations of ground‐state energies, geometry optimizations, vibrational spectra, and other molecular properties for large systems. In the CIM approach, the electron correlation energies of large systems can be approximately obtained at the second‐order Møller−Plesset perturbation theory and couple cluster levels. In this article, the details and the capabilities of the LSQC program are presented. textcopyright 2014 Wiley Periodicals, Inc.
BibTeX:
@article{Li2015-641,
  author = {Li, Wei and Chen, Chihong and Zhao, Dongbo and Li, Shuhua},
  title = {LSQC: Low scaling quantum chemistry program},
  journal = {Int. J. Quantum Chem.},
  year = {2015},
  volume = {115},
  number = {10},
  pages = {641--646},
  url = {http://dx.doi.org/10.1002/qua.24831},
  doi = {https://doi.org/10.1002/qua.24831}
}
Piecuch, P., Włoch, M., Gour, J.R., Li, W. and Lutz, J.J. Dealing with chemical reaction pathways and electronic excitations in molecular systems via renormalized and active-space coupled-cluster methods 2015 AIP Conf. Proc.
Vol. 1642(1), pp. 172-175 
article DOI URL 
Abstract: Coupled-cluster (CC) theory has become the de facto standard for high-accuracy molecular calculations, but the widely used CC and equation-of-motion (EOM) CC approaches, such as CCSD(T) and EOMCCSD, have difficulties with capturing stronger electron correlations that characterize multi-reference molecular problems. This presentation demonstrates that many of these difficulties can be addressed by exploiting the completely renormalized (CR) CC and EOMCC approaches, such as CR-CC(2,3), CR-EOMCCSD(T), and CR-EOMCC(2,3), and their local correlation counterparts applicable to systems with hundreds of atoms, and the active-space CC/EOMCC approaches, such as CCSDt and EOMCCSDt, and their extensions to valence systems via the electron-attached and ionized formalisms.
BibTeX:
@article{Piecuch2015-172,
  author = {Piecuch, Piotr and Włoch, Marta and Gour, Jeffrey R. and Li, Wei and Lutz, Jesse J.},
  title = {Dealing with chemical reaction pathways and electronic excitations in molecular systems via renormalized and active-space coupled-cluster methods},
  journal = {AIP Conf. Proc.},
  year = {2015},
  volume = {1642},
  number = {1},
  pages = {172--175},
  url = {http://aip.scitation.org/doi/abs/10.1063/1.4906643},
  doi = {https://doi.org/10.1063/1.4906643}
}
Guo, Y., Li, W., Yuan, D. and Li, S. The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory 2014 Sci. China Chem.
Vol. 57(10), pp. 1393-1398 
article DOI URL 
Abstract: We describe an implementation of the cluster-in-molecule (CIM) resolution of the identity (RI) approximation second-order Møller-Plesset perturbation theory (CIM-RI-MP2), with the purpose of extending RI-MP2 calculations to very large systems. For typical conformers of several large polypeptides, we calculated their conformational energy differences with the CIM-RI-MP2 and the generalized energy-based fragmentation MP2 (GEBF-MP2) methods, and compared these results with the density functional theory (DFT) results obtained with several popular functionals. Our calculations show that the conformational energy differences obtained with CIM-RI-MP2 and GEBF-MP2 are very close to each other. In comparison with the GEBF-MP2 and CIM-RI-MP2 relative energies, we found that the DFT functionals (CAM-B3LYP-D3, LC-ωPBE-D3, M05-2X, M06-2X and ωB97XD) can give quite accurate conformational energy differences for structurally similar conformers, but provide less-accurate results for structurally very different conformers.
BibTeX:
@article{Guo2014-1393,
  author = {Guo, Yang and Li, Wei and Yuan, Dandan and Li, Shuhua},
  title = {The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory},
  journal = {Sci. China Chem.},
  year = {2014},
  volume = {57},
  number = {10},
  pages = {1393--1398},
  url = {http://dx.doi.org/10.1007/s11426-014-5181-0},
  doi = {https://doi.org/10.1007/s11426-014-5181-0}
}
Guo, Y., Li, W. and Li, S. Improved cluster-in-molecule local correlation approach for electron correlation calculation of large systems 2014 J. Phys. Chem. A
Vol. 118(39), pp. 8996-9004 
article DOI  
Abstract: An improved cluster-in-molecule (CIM) local correlation approach is developed to allow electron correlation calculations of large systems more accurate and faster. We have proposed a refined strategy of constructing virtual LMOs of various clusters, which is suitable for basis sets of various types. To recover medium-range electron correlation, which is important for quantitative descriptions of large systems, we find that a larger distance threshold ($$) is necessary for highly accurate results. Our illustrative calculations show that the present CIM-MP2 (second-order Møller-Plesser perturbation theory, MP2) or CIM-CCSD (coupled cluster singles and doubles, CCSD) scheme with a suitable $$ value is capable of recovering more than 99.8% correlation energies for a wide range of systems at different basis sets. Furthermore, the present CIM-MP2 scheme can provide reliable relative energy differences as the conventional MP2 method for secondary structures of polypeptides.
BibTeX:
@article{Guo2014-8996,
  author = {Guo, Yang and Li, Wei and Li, Shuhua},
  title = {Improved cluster-in-molecule local correlation approach for electron correlation calculation of large systems},
  journal = {J. Phys. Chem. A},
  year = {2014},
  volume = {118},
  number = {39},
  pages = {8996--9004},
  doi = {https://doi.org/10.1021/jp501976x}
}
Li, S., Li, W. and Ma, J. Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates 2014 Accounts of Chemical Research
Vol. 47(9), pp. 2712-2720 
article DOI  
Abstract: Conspectus The generalized energy-based fragmentation (GEBF) approach provides a very simple way of approximately evaluating the ground-state energy or properties of a large system in terms of ground-state energies of various small "electrostatically embedded" subsystems, which can be calculated with any traditional ab initio quantum chemistry (X) method (X = Hartree-Fock, density functional theory, and so on). Due to its excellent parallel efficiency, the GEBF approach at the X theory level (GEBF-X) allows full quantum mechanical (QM) calculations to be accessible for systems with hundreds and even thousands of atoms on ordinary workstations. The implementation of the GEBF approach at various theoretical levels can be easily done with existing quantum chemistry programs. This Account reviews the methodology, implementation, and applications of the GEBF-X approach. This method has been successfully applied to optimize the structures of various large systems including molecular clusters, polypeptides, proteins, and foldamers. Such investigations could allow us to elucidate the origin and nature of the cooperative interaction in secondary structures of long peptides or the driving force of the self-assembly processes of aromatic oligoamides. These GEBF-based QM calculations reveal that the structures and stability of various complex systems result from a subtle balance of many types of noncovalent interactions such as hydrogen bonding and van der Waals interactions. The GEBF-based ab initio molecular dynamics (AIMD) method also allows the investigation of dynamic behaviors of large systems on the order of tens of picoseconds. It was demonstrated that the conformational dynamics of two model peptides predicted by GEBF-based AIMD are noticeably different from those predicted by the classical force field MD method. With the target of extending QM calculations to molecular aggregates in the condensed phase, we have implemented the GEBF-based multilayer hybrid models, which could provide satisfactory descriptions of the binding energies between a solute molecule and its surrounding waters and the chain-length dependence of the conformational changes of oligomers in aqueous solutions. A coarse-grained polarizable molecular mechanics model, furnished with GEBF-X dipole moments of subsystems, exhibits some advantages of treating the electrostatic polarization with reduced computational costs. We anticipate that the GEBF approach will continue to develop with the ultimate goal of studying complicated phenomena at mesoscopic scales and serve as a practical tool to elucidate the structure and dynamics of chemical and biological systems.
BibTeX:
@article{Li2014-2712,
  author = {Li, Shuhua and Li, Wei and Ma, Jing},
  title = {Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates},
  journal = {Accounts of Chemical Research},
  year = {2014},
  volume = {47},
  number = {9},
  pages = {2712--2720},
  doi = {https://doi.org/10.1021/ar500038z}
}
Li, W. and Li, S. Cluster-in-molecule local correlation method for large systems 2014 Sci. China Chem.
Vol. 57(1), pp. 78-86 
article DOI URL 
Abstract: A linear scaling local correlation method, cluster-in-molecule (CIM) method, was developed in the last decade for large systems. The basic idea of the CIM method is that the electron correlation energy of a large system, within the Moller-Plesset perturbation theory (MP) or coupled cluster (CC) theory, can be approximately obtained from solving the corresponding MP or CC equations of various clusters. Each of such clusters consists of a subset of localized molecular orbitals (LMOs) of the target system, and can be treated independently at various theory levels. In the present article, the main idea of the CIM method is reviewed, followed by brief descriptions of some recent developments, including its multilevel extension and different ways of constructing clusters. Then, some applications for large systems are illustrated. The CIM method is shown to be an efficient and reliable method for electron correlation calculations of large systems, including biomolecules and supramolecular complexes.
BibTeX:
@article{Li2014-78,
  author = {Li, Wei and Li, Shuhua},
  title = {Cluster-in-molecule local correlation method for large systems},
  journal = {Sci. China Chem.},
  year = {2014},
  volume = {57},
  number = {1},
  pages = {78--86},
  url = {http://link.springer.com/10.1007/s11426-013-5022-6},
  doi = {https://doi.org/10.1007/s11426-013-5022-6}
}
Liu, P., Li, W., Liu, L., Wang, L. and Ma, J. Theoretical study on conformation dynamics of three-station molecular shuttle in different environments and its influence on NMR chemical shifts and binding interactions 2014 J. Phys. Chem. A
Vol. 118(39), pp. 9032-9044 
article DOI  
Abstract: Microscopic information on conformational flexibility and macrocycle-thread binding interactions is helpful in rational design of novel multistation mol. shuttles with interesting topol. and functions. Mol. dynamics (MD) was applied to simulate conformational changes of thread and macrocycle of a three-station mol. shuttle in different chem. environments (vacuum, CD3CN-CDCl3 soln., and crystal). In contrast with the highly distorted thread conformation in the gas phase and nonpolar CDCl3 soln., the solvated thread in CD3CN-CDCl3 (1:1) mix solvents exhibited a relatively rigid structure. Exptl. observations of preferential binding at the protonated dibenzylammonium group (station I) were rationalized by quantum chem. calcns. of macrocycle-thread binding energies at three different stations. The orthogonality of site-specific binding interactions at three different stations was also revealed by the nearly const. binding energy obtained at each specific recognition center with the replacement of different neighboring groups and terminal stoppers on the thread. Conformational flexibility has little effect on NMR signals of binding sites, but for some protons that are close to the solvent mols. in the first solvent shell, their chem. shifts are sensitive to the local electrostatic environment caused by nearby solvents. In crystal, $$ stacking induced evident upfield shifts of NMR signals in comparison with the isolated monomer. [on SciFinder(R)]
BibTeX:
@article{Liu2014-9032,
  author = {Liu, Pingying and Li, Wei and Liu, Li and Wang, Leyong and Ma, Jing},
  title = {Theoretical study on conformation dynamics of three-station molecular shuttle in different environments and its influence on NMR chemical shifts and binding interactions},
  journal = {J. Phys. Chem. A},
  year = {2014},
  volume = {118},
  number = {39},
  pages = {9032--9044},
  doi = {https://doi.org/10.1021/jp5020516}
}
Wang, K., Li, W. and Li, S. Generalized energy-based fragmentation CCSD(T)-F12a method and application to the relative energies of water clusters (H2O)20 2014 J. Chem. Theory Comput.
Vol. 10(4), pp. 1546-1553 
article DOI  
Abstract: The generalized energy-based fragmentation (GEBF) approach has been implemented for the explicitly correlated F12a of coupled-cluster with the noniterative triples corrections [CCSD(T)-F12a] method for medium- and large-sized systems. By combining the canonical Hartree?Fock (HF) total energies and the GEBF-X correlation energies, the GEBF-X/HF method is illustrated to be more accurate than the origin GEBF-X method, where X could be any electron correlation method, such as second-order M?ller?Plesset perturbation theory (MP2), MP2-F12, CCSD(T), and CCSD(T)-F12a. By combining the GEBF-X/HF results at the MP2-F12 and CCSD(T)-F12a levels, we can approximately achieve the CCSD(T) complete basis set (CBS) limit. Our test calculations for 10 low-energy isomers of water 20-mers show that for the relative energies of large water clusters, both the basis set and high-level electron correlation effects should be taken into account, in which the former is even more important. In addition, the GEBF-CCSD(T)/HF method at the CBS limit is used to evaluate 32 levels of density functional theory (DFT) methods. The results show that the DFT methods are difficult to predict the relative energies between the isomers of water 20-mers. The GEBF-CCSD(T)/HF method at the CBS limit is expected to be a benchmark for DFT and other electron correlation methods for medium- and large-sized systems with complex structures, in which both the basis set and electron correlation effects are important.$$nThe generalized energy-based fragmentation (GEBF) approach has been implemented for the explicitly correlated F12a of coupled-cluster with the noniterative triples corrections [CCSD(T)-F12a] method for medium- and large-sized systems. By combining the canonical Hartree?Fock (HF) total energies and the GEBF-X correlation energies, the GEBF-X/HF method is illustrated to be more accurate than the origin GEBF-X method, where X could be any electron correlation method, such as second-order M?ller?Plesset perturbation theory (MP2), MP2-F12, CCSD(T), and CCSD(T)-F12a. By combining the GEBF-X/HF results at the MP2-F12 and CCSD(T)-F12a levels, we can approximately achieve the CCSD(T) complete basis set (CBS) limit. Our test calculations for 10 low-energy isomers of water 20-mers show that for the relative energies of large water clusters, both the basis set and high-level electron correlation effects should be taken into account, in which the former is even more important. In addition, the GEBF-CCSD(T)/HF method at the CBS limit is used to evaluate 32 levels of density functional theory (DFT) methods. The results show that the DFT methods are difficult to predict the relative energies between the isomers of water 20-mers. The GEBF-CCSD(T)/HF method at the CBS limit is expected to be a benchmark for DFT and other electron correlation methods for medium- and large-sized systems with complex structures, in which both the basis set and electron correlation effects are important.
BibTeX:
@article{Wang2014-1546,
  author = {Wang, Kedong and Li, Wei and Li, Shuhua},
  title = {Generalized energy-based fragmentation CCSD(T)-F12a method and application to the relative energies of water clusters (H2O)20},
  journal = {J. Chem. Theory Comput.},
  year = {2014},
  volume = {10},
  number = {4},
  pages = {1546--1553},
  doi = {https://doi.org/10.1021/ct401060m}
}
Hua, S., Li, W. and Li, S. The generalized energy-based fragmentation approach with an improved fragmentation scheme: Benchmark results and illustrative applications 2013 ChemPhysChem
Vol. 14(1), pp. 108-115 
article DOI  
Abstract: We propose an improved fragmentation scheme for the generalized$$nenergy-based fragmentation (GEBF) approach, which improves the accuracy of the$$nGEBF approach in total energy calculations and intermolecular interactions. The$$nmain modification is to introduce some two-fragment-centered primitive$$nsubsystems, which are neglected in the previous GEBF implementation. Numerical$$ncalculations demonstrate that the present GEBF approach can provide more$$naccurate ground-state energies and intermolecular interactions. The present$$nGEBF approach with the M06-2X functional and the cc-pVTZ basis set are employed$$nto investigate the structures and binding energies in two dimeric species,$$nwhich are related to pseudopolymorphism of a phenyleneethynylene-based$$np-conjugated molecule. A comparison of the binding free energies in a dimeric$$nspecies and its corresponding model without C-H center dot center dot center$$ndot F contacts reveal that the substitution of fluorine atoms weakens the$$nbinding of monomers in the dimeric species formed by intermolecular O-H center$$ndot center dot center dot O hydrogen bonds, but strengthens the binding in the$$ndimer formed by the pp stacking interaction. Therefore, the C-H center dot$$ncenter dot center dot F contacts in these two dimeric species are demonstrated$$nto play a less significant role.
BibTeX:
@article{Hua2013-108,
  author = {Hua, Shugui and Li, Wei and Li, Shuhua},
  title = {The generalized energy-based fragmentation approach with an improved fragmentation scheme: Benchmark results and illustrative applications},
  journal = {ChemPhysChem},
  year = {2013},
  volume = {14},
  number = {1},
  pages = {108--115},
  doi = {https://doi.org/10.1002/cphc.201200867}
}
Li, W. Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions 2013 J. Chem. Phys.
Vol. 138(1), pp. 014106 
article DOI  
Abstract: A linear scaling quantum chemistry method, generalized energy-based fragmentation (GEBF) approach has been extended to the explicitly correlated second-order Møller-Plesset perturbation theory F12 (MP2-F12) method and own N-layer integrated molecular orbital molecular mechanics (ONIOM) method, in which GEBF-MP2-F12, GEBF-MP2, and conventional density functional tight-binding methods could be used for different layers. Then the long-range interactions in dilute methanol aqueous solutions are studied by computing the binding energies between methanol molecule and water molecules in gas-phase and condensed phase methanol-water clusters with various sizes, which were taken from classic molecular dynamics (MD) snapshots. By comparing with the results of force field methods, including SPC, TIP3P, PCFF, and AMOEBA09, the GEBF-MP2-F12 and GEBF-ONIOM methods are shown to be powerful and efficient for studying the long-range interactions at a high level. With the GEBF-ONIOM(MP2-F12:MP2) and GEBF-ONIOM(MP2-F12:MP2:cDFTB) methods, the diameters of the largest nanoscale clusters under studies are about 2.4 nm (747 atoms and 10 209 basis functions with aug-cc-pVDZ basis set) and 4 nm (3351 atoms), respectively, which are almost impossible to be treated by conventional MP2 or MP2-F12 method. Thus, the GEBF-F12 and GEBF-ONIOM methods are expected to be a practical tool for studying the nanoscale clusters in condensed phase, providing an alternative benchmark for ab initio and density functional theory studies, and developing new force fields by combining with classic MD simulations.
BibTeX:
@article{Li2013-014106,
  author = {Li, Wei},
  title = {Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions},
  journal = {J. Chem. Phys.},
  year = {2013},
  volume = {138},
  number = {1},
  pages = {014106},
  doi = {https://doi.org/10.1063/1.4773011}
}
Meng, S., Li, W., Yin, X. and Xie, J. A comprehensive theoretical study of the hydrogen bonding interactions and microscopic solvation structures of a pyridyl-urea-based hydrogelator in aqueous solution 2013 Comput. Theor. Chem.
Vol. 1006, pp. 76-84 
article DOI URL 
Abstract: The solvent effects, intermolecular hydrogen-bonding interactions, and supramolecular structures of N,N'-bis(4-pyridyl) urea, a hydrogelator, in aqueous solution were studied through density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT calculations show that N,N'-bis(4-pyridyl) urea is polarized from gas phase to highly polar aqueous solution. Correspondingly, the magnitude of the dipole moments of N,N'-bis(4-pyridyl) urea is enhanced as the polarity of the medium increases, which suggests that significant intermolecular interactions may exist in its aqueous solution. Both DFT calculations and MD simulations demonstrate that explicit O...HO, N...HO, and NH...O hydrogen-bonding interactions coexist in aqueous solution and are evenly distributed around N,N'-bis(4-pyridyl) urea, which explains why N,N'-bis(4-pyridyl) urea is a hydrogelator. The hydrogen-bond strength trend is NH...OtextgreaterN...HOtextgreaterO...HO for N,N'-bis(4-pyridyl) urea...H2O dimers. The natural bond orbital analysis shows that the intermolecular nY→$$XH* orbital interaction dominates the XH...Y hydrogen-bonding interactions in N,N'-bis(4-pyridyl) urea...H2O dimers. In addition, the hydrogen-bonded supramolecular clusters (solute+solvent molecules) are also obtained from MD simulations and DFT optimizations. The hydrogen-bond lengths and angles from DFT optimizations are in good agreement with the values from the experimentally obtained crystal structures of N,N'-bis(4-pyridyl) urea with ethylene glycol and water molecules, whereas MD simulations displayed the wider structural variety characteristic of more realistic solutions. textcopyright2012 Elsevier B.V.
BibTeX:
@article{Meng2013-76,
  author = {Meng, Suci and Li, Wei and Yin, Xiulian and Xie, Jimin},
  title = {A comprehensive theoretical study of the hydrogen bonding interactions and microscopic solvation structures of a pyridyl-urea-based hydrogelator in aqueous solution},
  journal = {Comput. Theor. Chem.},
  year = {2013},
  volume = {1006},
  pages = {76--84},
  url = {http://www.sciencedirect.com/science/article/pii/S2210271X12005816},
  doi = {https://doi.org/10.1016/j.comptc.2012.11.011}
}
Guo, Y., Li, W. and Li, S. An improved localized molecular-orbital assembler approach for Hartree-Fock calculations of general large molecules 2012 Chem. Phys. Lett.
Vol. 539-540, pp. 186-190 
article DOI  
Abstract: An improved localized molecular-orbital assembler (LMOA) approach is developed for ground-state Hartree-Fock (HF) calculations of general large systems. Different from the original LMOA approach (W. Li and S. Li, J. Chem. Phys. 122 (2005) 194109), each subsystem is placed into background point charges, which are used to model the electrostatic and polarization interactions between a given subsystem and all other atoms (beyond this subsystem). For a wide range of neutral and charged systems, the present LMOA-HF approach is demonstrated to offer a significant improvement on the original LMOA-HF approach, providing satisfactory descriptions on their total HF energies and energy gradients. textcopyright2012 Elsevier B.V. All rights reserved.
BibTeX:
@article{Guo2012-186,
  author = {Guo, Yang and Li, Wei and Li, Shuhua},
  title = {An improved localized molecular-orbital assembler approach for Hartree-Fock calculations of general large molecules},
  journal = {Chem. Phys. Lett.},
  year = {2012},
  volume = {539-540},
  pages = {186--190},
  doi = {https://doi.org/10.1016/j.cplett.2012.05.004}
}
Kozlowski, P.M., Kumar, M., Piecuch, P., Li, W., Bauman, N.P., Hansen, J.A., Lodowski, P. and Jaworska, M. The cobalt-methyl bond dissociation in methylcobalamin: New benchmark analysis based on density functional theory and completely renormalized coupled-cluster calculations 2012 J. Chem. Theory Comput.
Vol. 8(6), pp. 1870-1894 
article DOI URL 
Abstract: The Co-C-Me bond dissociation in methylcobalamin (MeCbl), modeled by the Im-[Co(III)corrin]-Me+ system consisting of 58 atoms, is examined using the coupled-cluster (CC), density-functional theory (DFT), complete-active-space self-consistent-field (CASSCF), and CASSCF-based second-order perturbation theory (CASPT2) approaches. The multilevel variant of the local cluster-in-molecule framework, employing the completely renormalized (CR) CC method with singles, doubles, and noniterative triples, termed CR-CC(2,3), to describe higher-order electron correlation effects in the region where the Co-C-Me bond breaking takes place, and the canonical CC approach with singles and doubles (CCSD) to capture the remaining correlation effects, abbreviated as CR-CC(2,3)/CCSD, is used to obtain the benchmark potential energy curve characterizing the Co-C-Me dissociation in the MeCbl cofactor. The Co-C-Me, bond dissociation energy (BDE) resulting from the CR-CC(2,3) /CCSD calculations for the Im-[Co(III)corrin]-Me+ system using the 6-31G* basis set, corrected for the zero-point energies (ZPEs) and the effect of replacing the 6-31G* basis by 6-311++G**, is about 38 kcal/mol, in excellent agreement with the experimental values characterizing MeCbl of 37 +/- 3 and 36 +/- 4 kcal/mol. Of all DFT functionals examined, the best dissociation energies and the most accurate description of the Co-C-Me bond breaking in the Im-[Co(III)corrin]-Me+ system are provided by B97-D and BP86 corrected for dispersion using the D3 correction of Grimme et al., which give 35 and 40 kcal/mol, respectively, when the 6-311++G** basis set is employed and when the results are corrected for ZPEs and basis set superposition error. None of the other DFT approaches examined provide results that fall into the experimental range of the Co-C-Me dissociation energies in MeCbl of 32-40 kcal/mol. The hybrid DFT functionals with a substantial amount of the Hartree-Fock (HF) exchange, such as B3LYP, considerably underestimate the calculated dissociation energies, with the magnitude of the error being proportional to the percentage of the HF exchange in the functional. It is argued that the overstabilization of diradical structures that emerge as the Co-C-Me bond is broken and, to some extent, the neglect of dispersion interactions at shorter Co-C-Me distances, postulated in previous studies, are the main factors that explain the substantial underestimation of the Co-C-Me BDE by B3LYP and other hybrid functionals. Our calculations suggest that CASSCF and CASPT2 may have difficulties with providing a reliable description of the Co-C-Me bond breaking in MeCbl, since using adequate active spaces is prohibitively expensive.
BibTeX:
@article{Kozlowski2012-1870,
  author = {Kozlowski, Pawel M and Kumar, Manoj and Piecuch, Piotr and Li, Wei and Bauman, Nicholas P and Hansen, Jared A and Lodowski, Piotr and Jaworska, Maria},
  title = {The cobalt-methyl bond dissociation in methylcobalamin: New benchmark analysis based on density functional theory and completely renormalized coupled-cluster calculations},
  journal = {J. Chem. Theory Comput.},
  year = {2012},
  volume = {8},
  number = {6},
  pages = {1870--1894},
  url = {http://dx.doi.org/10.1021/ct300170y},
  doi = {https://doi.org/10.1021/ct300170y}
}
Li, W., Guo, Y. and Li, S. A refined cluster-in-molecule local correlation approach for predicting the relative energies of large systems 2012 Phys. Chem. Chem. Phys.
Vol. 14(21), pp. 7854-7862 
article DOI URL 
Abstract: A refined cluster-in-molecule (CIM) method for local correlation calculations of large molecules is presented. In the present work, two new strategies are introduced to further improve the CIM approach: (1) Some medium-range electron correlation energies, which are neglected in the previous CIM approach, are taken into account. (2) A much simpler procedure using only a distance threshold is used to construct various clusters. To cover the medium-range correlation effect as much as possible, some two-atom-centered clusters are built, in addition to one-atom-centered clusters. Our test calculations at the second order perturbation theory (MP2) level show that the refined CIM method can recover about 99.9% of the conventional MP2 correlation energy using an appropriate distance threshold. The accuracy of the present CIM method is capable of providing reliable relative energies of medium-sized systems such as polyalanines with 10 residues, and water molecules with 50 water molecules. For polyalanines with up to 30 residues, we have demonstrated that the computational cost of the CIM-MP2 calculation increases linearly with the molecular size, but the required memory and disc-space do not need to increase for large systems. The improved CIM method has been used to compute the relative energy of ice-like (H(2)O)(96) clusters (with 2400 basis functions) and to predict the dimerization energy of a double-helical foldamer (with 2330 basis functions). The present CIM method is expected to be a practical local correlation method for describing the relative energies of large systems.
BibTeX:
@article{Li2012-7854,
  author = {Li, Wei and Guo, Yang and Li, Shuhua},
  title = {A refined cluster-in-molecule local correlation approach for predicting the relative energies of large systems},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2012},
  volume = {14},
  number = {21},
  pages = {7854--7862},
  url = {http://xlink.rsc.org/?DOI=c2cp23916g},
  doi = {https://doi.org/10.1039/c2cp23916g}
}
Hua, S., Xu, L., Li, W. and Li, S. Cooperativity in long α- And 310-helical polyalanines: Both electrostatic and van der waals interactions are essential 2011 J. Phys. Chem. B
Vol. 115(39), pp. 11462-11469 
article DOI  
Abstract: We have employed the generalized energy-based fragmentation (GEBF) approach to investigate the structures, energies, and enthalpies of alpha-helices, 3(10)-helices, and beta-strands for capped polyalanines, acetyl(ala)(N)NH(2), with N values from 8 to 40 at several theoretical levels. The M06-2X functional is demonstrated to be much more accurate than the B3LYP functional for peptides under study. On the basis of the GEBF-M06-2X results, we find that alpha-helices are more stable than the corresponding 3(10)-helices for all peptides with N textgreater= 10. The cooperative interaction in both helices have not reached their asymptotic limits even for N = 40. By comparing the performance of the M06-2X, B3LYP, and the van der Waals corrected B3LYP, we show that both electrostatic and van der Waals interactions are essential for describing the cooperative interaction in long helices. In addition, the greater cooperativity of alpha-helices over 3(10)-helices in long helices is found to originate mainly from the much stronger van der Waals interaction in alpha-helices.
BibTeX:
@article{Hua2011-11462,
  author = {Hua, Shugui and Xu, Lina and Li, Wei and Li, Shuhua},
  title = {Cooperativity in long α- And 310-helical polyalanines: Both electrostatic and van der waals interactions are essential},
  journal = {J. Phys. Chem. B},
  year = {2011},
  volume = {115},
  number = {39},
  pages = {11462--11469},
  doi = {https://doi.org/10.1021/jp203423w}
}
Li, W., Hua, W., Fang, T. and Li, S. The Energy-Based Fragmentation Approach for Ab Initio Calculations of Large Systems 2011 Comput. Methods Large Syst. Electron. Struct. Approaches Biotechnol. Nanotechnol., pp. 227-258  inproceedings  
BibTeX:
@inproceedings{Li2011-227,
  author = {Li, Wei and Hua, Weijie and Fang, Tao and Li, Shuhua},
  title = {The Energy-Based Fragmentation Approach for Ab Initio Calculations of Large Systems},
  booktitle = {Comput. Methods Large Syst. Electron. Struct. Approaches Biotechnol. Nanotechnol.},
  publisher = {Wiley Blackwell},
  year = {2011},
  pages = {227--258}
}
Arora, P., Li, W., Piecuch, P., Evans, J.W., Albao, M. and Gordon, M.S. Diffusion of atomic oxygen on the Si(100) surface 2010 J. Phys. Chem. C
Vol. 114(29), pp. 12649-12658 
article DOI  
Abstract: The processes of etching and diffusion of atomic oxygen on the reconstructed Si(100)-2 ? 1 surface are investigated using an embedded cluster QM/MM (Quantum Mechanics/Molecular Mechanics) method, called SIMOMM (Surface Integrated Molecular Orbital Molecular Mechanics). Hopping of an oxygen atom along the silicon dimer rows on a Si15H16 cluster embedded in an Si136H92 MM cluster model is studied using the SIMOMM/UB3LYP (unrestricted density functional theory (UDFT) with the Becke three-parameter Lee?Yang?Parr (B3LYP) hybrid functional) approach, the Hay?Wadt effective core potential, and its associated double-? plus polarization basis set. The relative energies at stationary points on the diffusion potential energy surface were also obtained with three coupled-cluster (CC) methods, including the canonical CC approach with singles, doubles, and noniterative quasi-perturbative triples (CCSD(T)), the canonical left-eigenstate completely renormalized (CR) analogue of CCSD(T), termed CR-CC(2,3), and the linear scaling variant of CR-CC(2,3) employing the cluster-in-molecule (CIM) local correlation ansatz, abbreviated as CIM-CR-CC(2,3). The pathway and energetics for the diffusion of oxygen from one dimer to another are presented, with the activation energy estimated to be 71.9 and 74.4 kcal/mol at the canonical CR-CC(2,3)/6-31G(d) and extrapolated, CIM-based, canonical CR-CC(2,3)/6-311G(d) levels of theory, respectively. The canonical and CIM CR-CC(2,3)/6-31G(d) barrier heights (excluding zero point vibrational energy contributions) for the etching process are both 87.3 kcal/mol. The processes of etching and diffusion of atomic oxygen on the reconstructed Si(100)-2 ? 1 surface are investigated using an embedded cluster QM/MM (Quantum Mechanics/Molecular Mechanics) method, called SIMOMM (Surface Integrated Molecular Orbital Molecular Mechanics). Hopping of an oxygen atom along the silicon dimer rows on a Si15H16 cluster embedded in an Si136H92 MM cluster model is studied using the SIMOMM/UB3LYP (unrestricted density functional theory (UDFT) with the Becke three-parameter Lee?Yang?Parr (B3LYP) hybrid functional) approach, the Hay?Wadt effective core potential, and its associated double-? plus polarization basis set. The relative energies at stationary points on the diffusion potential energy surface were also obtained with three coupled-cluster (CC) methods, including the canonical CC approach with singles, doubles, and noniterative quasi-perturbative triples (CCSD(T)), the canonical left-eigenstate completely renormalized (CR) analogue of CCSD(T), termed CR-CC(2,3), and the linear scaling variant of CR-CC(2,3) employing the cluster-in-molecule (CIM) local correlation ansatz, abbreviated as CIM-CR-CC(2,3). The pathway and energetics for the diffusion of oxygen from one dimer to another are presented, with the activation energy estimated to be 71.9 and 74.4 kcal/mol at the canonical CR-CC(2,3)/6-31G(d) and extrapolated, CIM-based, canonical CR-CC(2,3)/6-311G(d) levels of theory, respectively. The canonical and CIM CR-CC(2,3)/6-31G(d) barrier heights (excluding zero point vibrational energy contributions) for the etching process are both 87.3 kcal/mol.
BibTeX:
@article{Arora2010-12649,
  author = {Arora, Pooja and Li, Wei and Piecuch, Piotr and Evans, James W and Albao, Marvin and Gordon, Mark S},
  title = {Diffusion of atomic oxygen on the Si(100) surface},
  journal = {J. Phys. Chem. C},
  year = {2010},
  volume = {114},
  number = {29},
  pages = {12649--12658},
  doi = {https://doi.org/10.1021/jp102998y}
}
Li, W. and Piecuch, P. Multilevel extension of the cluster-in-molecule local correlation methodology: Merging coupled-cluster and møller-plesset perturbation theories 2010 J. Phys. Chem. A
Vol. 114(24), pp. 6721-6727 
article DOI  
Abstract: A multilevel extension of the local correlation “cluster-in-molecule” (CIM) framework, which enables one to combine different quantum chemistry methods to treat different regions in a large molecular system without splitting it into ad hoc fragments and saturating dangling bonds, is proposed. The resulting schemes combine higher-level methods, such as the completely renormalized coupled-cluster (CC) approach with singles, doubles, and noniterative triples, termed CR-CC(2,3), to treat the reactive part of a large molecular system, and lower- order methods, such as the second-order Møller-Plesset perturbation theory (MP2), to handle the chemically inactive regions. The multilevel CIM-CC/MP2 approaches preserve the key features of all CIM methods, such as the use of orthonormal localized orbitals and coarse-grain parallelism, while substantially reducing the already relatively low costs of the single-level CIM-CC calculations. Illustrative calculations include bond breaking in dodecane and the reactions of the bis(2,4,4-trimethylpentyl)dithiophosphinic acid with one and two water molecules. 1.
BibTeX:
@article{Li2010-6721,
  author = {Li, Wei and Piecuch, Piotr},
  title = {Multilevel extension of the cluster-in-molecule local correlation methodology: Merging coupled-cluster and møller-plesset perturbation theories},
  journal = {J. Phys. Chem. A},
  year = {2010},
  volume = {114},
  number = {24},
  pages = {6721--6727},
  doi = {https://doi.org/10.1021/jp1038738}
}
Li, W. and Piecuch, P. Improved design of orbital domains within the cluster-in-molecule local correlation framework: Single-environment cluster-in-molecule ansatz and its application to local coupled-cluster approach with singles and doubles 2010 J. Phys. Chem. A
Vol. 114(33), pp. 8644-8657 
article DOI  
Abstract: The improved variant of the local correlation coupled-cluster (CC) framework termed "cluster-in-molecule" (CIM), defining the single-environment (SE) CIM-CC approach, is presented and tested at the CC singles and doubles (CCSD) level. In the proposed SECIM-CC method, the previous design of the CIM orbital subsystems [Li, W.; Gour, J. R.; Piecuch, P.; Li, S. J. Chem. Phys. 2009, 131, 114109], referred to as the dual-environment (DE) CIM-CC approach, which is based on the ideas of central orbitals and the associated primary and secondary environments, is replaced by the simplified design in which the central localized molecular orbitals (LMOs) and the corresponding environment LMOs are first assigned to each nonhydrogen atom and the hydrogen atoms that are bound to it. The SECIM-CC approach offers improvements in the DECIM-CC results, particularly for weakly bound molecular clusters using diffuse basis functions. Through the use of a single parameter to define the environment LMOs and through the assignment of subsystem LMOs to atoms, the SECIM-CC calculations are easy to control and the CIM subsystems do not unnecessarily vary with the nuclear geometry, creating smoother potential energy surfaces. The performance of SECIM-CCSD is illustrated by the calculations for normal alkanes and water clusters described by the 6-31G(d), 6-31++G(d,p), and 6-311++G(d,p) basis sets.
BibTeX:
@article{Li2010-8644,
  author = {Li, Wei and Piecuch, Piotr},
  title = {Improved design of orbital domains within the cluster-in-molecule local correlation framework: Single-environment cluster-in-molecule ansatz and its application to local coupled-cluster approach with singles and doubles},
  journal = {J. Phys. Chem. A},
  year = {2010},
  volume = {114},
  number = {33},
  pages = {8644--8657},
  doi = {https://doi.org/10.1021/jp100782u}
}
Li, W., Piecuch, P., Gour, J.R. and Li, S. Local correlation calculations using standard and renormalized coupled-cluster approaches 2009 J. Chem. Phys.
Vol. 131(11), pp. 114109 
article DOI  
Abstract: The linear scaling local correlation approach, termed "cluster-in-molecule" (CIM), is extended to the coupled-cluster (CC) theory with singles and doubles (CCSD) and CC methods with singles, doubles, and noniterative triples, including CCSD(T) and the completely renormalized CR-CC(2,3) approach. The resulting CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) methods are characterized by (i) the linear scaling of the CPU time with the system size, (ii) the use of orthonormal orbitals in the CC subsystem calculations, (iii) the natural parallelism, (iv) the high computational efficiency, enabling calculations for much larger systems and at higher levels of CC theory than previously possible, and (v) the purely noniterative character of local triples corrections. By comparing the results of the canonical and CIM-CC calculations for normal alkanes and water clusters, it is shown that the CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) approaches accurately reproduce the corresponding canonical CC correlation and relative energies, while offering savings in the computer effort by orders of magnitude.
BibTeX:
@article{Li2009-114109,
  author = {Li, Wei and Piecuch, Piotr and Gour, Jeffrey R. and Li, Shuhua},
  title = {Local correlation calculations using standard and renormalized coupled-cluster approaches},
  journal = {J. Chem. Phys.},
  year = {2009},
  volume = {131},
  number = {11},
  pages = {114109},
  doi = {https://doi.org/10.1063/1.3218842}
}
Li, W., Piecuch, P. and Gour, J.R. Linear Scaling Local Correlation Extensions of the Standard and Renormalized Coupled-Cluster Methods 2009
Vol. 19Adv. Theory At. Mol. Syst. Concept. Comput. Adv. Quantum Chem., pp. 131-195 
incollection DOI URL 
BibTeX:
@incollection{Li2009-131,
  author = {Li, Wei and Piecuch, Piotr and Gour, Jeffrey R},
  title = {Linear Scaling Local Correlation Extensions of the Standard and Renormalized Coupled-Cluster Methods},
  booktitle = {Adv. Theory At. Mol. Syst. Concept. Comput. Adv. Quantum Chem.},
  publisher = {SPRINGER},
  year = {2009},
  volume = {19},
  pages = {131--195},
  url = {http://link.springer.com/10.1007/978-90-481-2596-88},
  doi = {https://doi.org/10.1007/978-90-481-2596-8_8}
}
Zhao, Y., Tishchenko, O., Gour, J.R., Li, W., Lutz, J.J., Piecuch, P. and Truhlar, D.G. Thermochemical kinetics for multireference systems: Addition reactions of ozone 2009 J. Phys. Chem. A
Vol. 113(19), pp. 5786-5799 
article DOI URL 
Abstract: The 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals gives accurate forward barrier heights; however, it significantly underestimates reaction energies.
BibTeX:
@article{Zhao2009-5786,
  author = {Zhao, Yan and Tishchenko, Oksana and Gour, Jeffrey R and Li, Wei and Lutz, Jesse J and Piecuch, Piotr and Truhlar, Donald G},
  title = {Thermochemical kinetics for multireference systems: Addition reactions of ozone},
  journal = {J. Phys. Chem. A},
  year = {2009},
  volume = {113},
  number = {19},
  pages = {5786--5799},
  url = {http://dx.doi.org/10.1021/jp811054n},
  doi = {https://doi.org/10.1021/jp811054n}
}
Hua, W., Fang, T., Li, W., Yu, J.G. and Li, S. Geometry optimizations and vibrational spectra of large molecules from a generalized energy-based fragmentation approach 2008 J. Phys. Chem. A
Vol. 112(43), pp. 10864-10872 
article DOI  
Abstract: The generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J. Phys. Chem. A 2007, 111, 2193) is extended for geometry optimizations and vibrational spectra calculations of general large molecules or clusters. In this approach, the total energy and its derivatives, and some molecular properties, of a target system are obtained from conventional calculations on a series of subsystems derived from the target system. Each subsystem is electronically embedded in the background point charges generated by all other atoms outside the subsystem so that the long-range interactions and polarization effects between remote fragments are approximately taken into account. The approach computationally scales linearly with the system size and can be easily implemented for large-scale parallelization. By comparing the results from the conventional and GEBF calculations for several test molecules including a polypeptide and a water cluster, we demonstrate that the GEBF approach is able to provide quite reliable predictions for molecular geometries, vibrational frequencies, and thermochemistry data and satisfactory descriptions for vibrational intensities, for general molecules with polar or charged groups.
BibTeX:
@article{Hua2008-10864,
  author = {Hua, Weijie and Fang, Tao and Li, Wei and Yu, Jian Guo and Li, Shuhua},
  title = {Geometry optimizations and vibrational spectra of large molecules from a generalized energy-based fragmentation approach},
  journal = {J. Phys. Chem. A},
  year = {2008},
  volume = {112},
  number = {43},
  pages = {10864--10872},
  doi = {https://doi.org/10.1021/jp8026385}
}
Li, S. and Li, W. Fragment energy approach to Hartree–Fock calculations of macromolecules 2008 Ann. Rep. Sect. C
Vol. 104, pp. 256 
article DOI URL 
Abstract: This review provides a brief introduction to energy-based fragmentation (EBF) approaches for fast and reliable quantum chemical calculations of macromolecules. The main idea of various EBF approaches is to evaluate the total energy of the target system from energies of a series of small subsystems. The theoretical foundation of these EBF approaches is attributed to the transferability of the intra- and inter-fragment energy components. Two different fragment energy approaches are introduced, but more emphasis is put on the simple EBF approach, which is applicable at both Hartree-Fock (HF) and post-HF levels. The generalized EBF approach (GEBF) is then introduced to treat charged or highly polar macromolecules. Illustrative calculations show that the GEBF approach is capable of giving reasonably reliable predictions for the total energies, optimized structures, and dipole moments or static polarizabilities, for general macromolecules.
BibTeX:
@article{Li2008-256,
  author = {Li, Shuhua and Li, Wei},
  title = {Fragment energy approach to Hartree–Fock calculations of macromolecules},
  journal = {Ann. Rep. Sect. C},
  publisher = {The Royal Society of Chemistry},
  year = {2008},
  volume = {104},
  pages = {256},
  url = {http://xlink.rsc.org/?DOI=b703896h},
  doi = {https://doi.org/10.1039/b703896h}
}
Li, W., Dong, H. and Li, S. Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach 2008
Vol. 18Front. Quantum Syst. Chem. Phys., pp. 289-299 
inproceedings DOI  
Abstract: A generalized energy-based fragmentation (GEBF) approach we developed recently [57] is applied to investigate the relative energies of many conformers of two proteins (PDB id: 2ET1 and 1CMR) and one water cluster (H(2)O)(20). The GEBF results are compared with those from conventional quantum chemistry methods, empirical molecular mechanics (MM), and semi-empirical quantum mechanical methods (AM1, PM3). Our computational results show that for all three systems, not only the total energies but also the relative stabilities of their different conformers predicted by the GEBF approach are fairly consistent with those from the corresponding conventional quantum chemistry method, while the widely used MM and semi-empirical QM methods give poor descriptions for the relative energies of different conformers,
BibTeX:
@inproceedings{Li2008-289,
  author = {Li, Wei and Dong, Hao and Li, Shuhua},
  title = {Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach},
  booktitle = {Front. Quantum Syst. Chem. Phys.},
  year = {2008},
  volume = {18},
  pages = {289--299},
  doi = {https://doi.org/10.1007/978-1-4020-8707-3_12}
}
Li, H., Li, W., Li, S. and Ma, J. Fragmentation-based QM/MM simulations: Length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions 2008 J. Phys. Chem. B
Vol. 112(23), pp. 7061-7070 
article DOI  
Abstract: Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.
BibTeX:
@article{Li2008-7061,
  author = {Li, Hui and Li, Wei and Li, Shuhua and Ma, Jing},
  title = {Fragmentation-based QM/MM simulations: Length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions},
  journal = {J. Phys. Chem. B},
  year = {2008},
  volume = {112},
  number = {23},
  pages = {7061--7070},
  doi = {https://doi.org/10.1021/jp800777e}
}
Li, W., Li, S. and Jiang, Y. Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules 2007 J. Phys. Chem. A
Vol. 111(11), pp. 2193-2199 
article DOI  
Abstract: We present a generalized energy-based fragmentation (GEBF) approach for approximately predicting the ground-state energies and molecular properties of large molecules, especially those charged and polar molecules. In this approach, the total energy (or properties) of a large molecule can be approximately obtained from energy (or properties) calculations on various small subsystems, each of which is constructed to contain a certain fragment and its local surroundings within a given distance. In the quantum chemistry calculation of a given subsystem, those distant atoms (outside this subsystem) are modeled as background point charges at the corresponding nuclear centers. This treatment allows long-range electrostatic interaction and polarization effects between distant fragments to be taken into account approximately, which are very important for polar and charged molecules. We also propose a new fragmentation scheme for constructing subsystems. Our test calculations at the Hartree-Fock and second-order Møller-Plesser perturbation theory levels demonstrate that the approach could yield satisfactory ground-state energies, the dipole moments, and static polarizabilities for polar and charged molecules such as water clusters and proteins.
BibTeX:
@article{Li2007-2193,
  author = {Li, Wei and Li, Shuhua and Jiang, Yuansheng},
  title = {Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules},
  journal = {J. Phys. Chem. A},
  year = {2007},
  volume = {111},
  number = {11},
  pages = {2193--2199},
  doi = {https://doi.org/10.1021/jp067721q}
}
Li, S., Shen, J., Li, W. and Jiang, Y. An efficient implementation of the "cluster-in-molecule" approach for local electron correlation calculations 2006 J. Chem. Phys.
Vol. 125(7), pp. 74109 
article DOI  
Abstract: An efficient implementation of the “cluster-in-molecule” (CIM) approach is presented for performing local electron correlation calculations in a basis of orthogonal occupied and virtual localized molecular orbitals (LMOs). The main idea of this approach is that significant excitation amplitudes can be approximately obtained by solving the coupled cluster (or Møller-Plesset perturbation theory)equations of a series of “clusters,” each of which contains a subset of occupied and virtual LMOs. In the present implementation, we have proposed a simple approach for constructing virtual LMOs of clusters, and new ways of constructing clusters and extracting the correlation contributions from calculations on clusters, which are more efficient than those suggested in the original work. More importantly, linear scaling of computational time of the CIM approach is achieved by evaluating the transformed two-electron integrals over LMOs using simple truncation techniques in limited operations (independent of the molecular size). With typical thresholds, for a variety of molecules our test calculations demonstrate that more than 99% of the conventional MP2 or coupled cluster with doubles correlation energies can be recovered in the present CIM approach.
BibTeX:
@article{Li2006-074109,
  author = {Li, Shuhua and Shen, Jun and Li, Wei and Jiang, Yuansheng},
  title = {An efficient implementation of the "cluster-in-molecule" approach for local electron correlation calculations},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {125},
  number = {7},
  pages = {74109},
  doi = {https://doi.org/10.1063/1.2244566}
}
Li, W., Fang, T. and Li, S. A fragment energy assembler method for Hartree-Fock calculations of large molecules 2006 J. Chem. Phys.
Vol. 124(15), pp. 154102 
article DOI  
Abstract: We present a fragment energy assembler approach for approximate Hartree-Fock (HF) calculations of macromolecules. In this method, a macromolecule is divided into small fragments with appropriate size, and then each fragment is capped by its neighboring fragments to form a subsystem. The total energy of the target system is evaluated as the sum of the fragment energies of all fragments, which are available from conventional HF calculations on all subsystems. By applying the method to a broad range of molecules, we demonstrate that the present approach could yield satisfactory HF energies for all studied systems.
BibTeX:
@article{Li2006-154102,
  author = {Li, Wei and Fang, Tao and Li, Shuhua},
  title = {A fragment energy assembler method for Hartree-Fock calculations of large molecules},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {124},
  number = {15},
  pages = {154102},
  doi = {https://doi.org/10.1063/1.2186997}
}
Ma, J., Li, S. and Li, W. A multireference configuration interaction method based on the separated electron pair wave functions 2006 J. Comput. Chem.
Vol. 27(1), pp. 39-47 
article DOI  
Abstract: A multireference configurational interaction method based on the separated electron pair (SEP) wave functions, SEP-CI approach, has been developed as an approximation to the traditional CASSCF method. It differs from the CASSCF method in that active orbitals are obtained from the SEP wave function without further optimization in the subsequent CI calculations, and the active space is automatically constructed according to the occupation coefficients of SEP natural orbitals. These features make the present SEP-CI method computationally much less demanding than the CASSCF method. The applicability of the SEP-CI method is illustrated with sample calculations on the insertion reaction of BeH2 and dissociation energies of LiH, BH, FH, H2O, and N-2.
BibTeX:
@article{Ma2006-39,
  author = {Ma, Jing and Li, Shuhua and Li, Wei},
  title = {A multireference configuration interaction method based on the separated electron pair wave functions},
  journal = {J. Comput. Chem.},
  year = {2006},
  volume = {27},
  number = {1},
  pages = {39--47},
  doi = {https://doi.org/10.1002/jcc.20319}
}
Li, W. and Li, S. A localized molecular-orbital assembler approach for Hartree–Fock calculations of large molecules 2005 J. Chem. Phys.
Vol. 122(19), pp. 194109 
article DOI URL 
Abstract: An improved localized molecular-orbital assembler (LMOA) approach is developed for ground-state Hartree-Fock (HF) calculations of general large systems. Different from the original LMOA approach (W. Li and S. Li, J. Chem. Phys. 122 (2005) 194109), each subsystem is placed into background point charges, which are used to model the electrostatic and polarization interactions between a given subsystem and all other atoms (beyond this subsystem). For a wide range of neutral and charged systems, the present LMOA-HF approach is demonstrated to offer a significant improvement on the original LMOA-HF approach, providing satisfactory descriptions on their total HF energies and energy gradients. textcopyright2012 Elsevier B.V. All rights reserved.
BibTeX:
@article{Li2005-194109,
  author = {Li, Wei and Li, Shuhua},
  title = {A localized molecular-orbital assembler approach for Hartree–Fock calculations of large molecules},
  journal = {J. Chem. Phys.},
  year = {2005},
  volume = {122},
  number = {19},
  pages = {194109},
  url = {http://aip.scitation.org/doi/10.1063/1.1898212},
  doi = {https://doi.org/10.1063/1.1898212}
}
Li, S., Li, W. and Fang, T. An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules 2005 J. Am. Chem. Soc.
Vol. 127(19), pp. 7215-7226 
article DOI  
Abstract: An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules at the Hartree?Fock (HF) and post-HF levels is described. The physical foundation of this approach is attributed to the ?quantum locality? of the electron correlation energy and the HF total energy, which is revealed by a new energy decomposition analysis of the HF total energy proposed in this work. This approach is based on the molecular fractionation with conjugated caps (MFCC) scheme (Zhang, D. W.; Zhang, J. Z. H. J. Chem. Phys. 2003, 119, 3599), by which a macromolecule is partitioned into various capped fragments and conjugated caps formed by two adjacent caps. We find that the MFCC scheme, if corrected by the interaction between non-neighboring fragments, can be used to predict the total energy of large molecules only from energy calculations on a series of small subsystems. The approach, named as energy-corrected MFCC (EC-MFCC), computationally achieves linear scaling with the molecular size. Our test calculations on a broad range of medium- and large molecules demonstrate that this approach is able to reproduce the conventional HF and second-order M?ller?Plesset perturbation theory (MP2) energies within a few millihartree in most cases. With the EC-MFCC optimization algorithm described in this work, we have obtained the optimized structures of long oligomers of trans-polyacetylene and BN nanotubes with up to about 400 atoms, which are beyond the reach of traditional computational methods. In addition, the EC-MFCC approach is also applied to estimate the heats of formation for a series of organic compounds. This approach provides an appealing approach alternative to the traditional additivity rules based on either bond or group contributions for the estimation of thermochemical properties.
BibTeX:
@article{Li2005-7215,
  author = {Li, Shuhua and Li, Wei and Fang, Tao},
  title = {An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules},
  journal = {J. Am. Chem. Soc.},
  year = {2005},
  volume = {127},
  number = {19},
  pages = {7215--7226},
  doi = {https://doi.org/10.1021/ja0427247}
}
Li, W. and Li, S. Divide-and-conquer local correlation approach to the correlation energy of large molecules 2004 J. Chem. Phys.
Vol. 121(14), pp. 6649-6657 
article DOI  
Abstract: A divide-and-conquer local correlation approach for correlation energy calculations on large molecules is proposed for any post-Hartree-Fock correlation method. The main idea of this approach is to decompose a large system into various fragments capped by their local environments. The total correlation energy of the whole system can be approximately obtained as the summation of correlation energies from all capped fragments, from which correlation energies from all adjacent caps are removed. This approach computationally achieves linear scaling even for medium-sized systems. Our test calculations for a wide range of molecules using the 6-31G or 6-31G( * *) basis set demonstrate that this simple approach recovers more than 99.0% of the conventional second-order Moller-Plesset perturbation theory and coupled cluster with single and double excitations correlation energies.
BibTeX:
@article{Li2004-6649,
  author = {Li, Wei and Li, Shuhua},
  title = {Divide-and-conquer local correlation approach to the correlation energy of large molecules},
  journal = {J. Chem. Phys.},
  year = {2004},
  volume = {121},
  number = {14},
  pages = {6649--6657},
  doi = {https://doi.org/10.1063/1.1792051}
}
Li, S.-H., Li, W. and Ma, J. A Quick Estimate of the Correlation Energy for Alkanes 2003 Chin. J. Chem.
Vol. 21(11), pp. 1422-1429 
article DOI URL 
Abstract: Within the localized molecular orbital description, the intra‐and interorbital pair correlation energies calculated with the coupled cluster doubles (CCD) theory have been obtained for methane, ethane, propane, butane, isobutane, pentane, isopentane and neopentane using the 6–31G* basis set. The results showed the quantitative transferability of pair correlation energies and gross orbital correlation energies within this series of molecules. Based on the gross orbital correlation energies of five sample alkanes (butane, isobutane, pentane, isopentane and neopentane), we have derived a simple linear relationship to estimate the CCD correlation energy for an arbitrary large alkane. The correlation energy predicted by this simple relationship remarkably recovers more than 98.9% of the exact CCD correlation energy for a number of alkanes containing six to eight carbon atoms. The relative stability of less branched isomers can be correctly predicted.
BibTeX:
@article{Li2003-1422,
  author = {Li, Shu-Hua and Li, Wei and Ma, Jing},
  title = {A Quick Estimate of the Correlation Energy for Alkanes},
  journal = {Chin. J. Chem.},
  year = {2003},
  volume = {21},
  number = {11},
  pages = {1422--1429},
  url = {http://doi.wiley.com/10.1002/cjoc.20030211106},
  doi = {https://doi.org/10.1002/cjoc.20030211106}
}