References
K. Babu and Shridhar R. Gadre. Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach. Journal of Computational Chemistry, 24(4):484–495, 2003.
K. Babu, V. Ganesh, Shridhar R. Gadre, and Nour E. Ghermani. Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals. Theoretical Chemistry Accounts, 111(2-6):255–263, 2004.
S.F. Boys and F. Bernardi. The calculation of small molecular interactions by the differences of separate total energies. some procedures with reduced errors. Molecular Physics, 19(4):553–566, 1970.
X. H. Chen, D. W. Zhang, and J. Z. H. Zhang. Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules. The Journal of Chemical Physics, 120(2):839–844, 2004.
Zheng Cheng, Dongbo Zhao, Jing Ma, Wei Li, and Shuhua Li. An on-the-fly approach to construct generalized energy-based fragmentation machine learning force fields of complex systems. The Journal of Physical Chemistry A, 124(24):5007–5014, May 2020. doi:10.1021/acs.jpca.0c04526.
Michael A. Collins and Vitali A. Deev. Accuracy and efficiency of electronic energies from systematic molecular fragmentation. The Journal of Chemical Physics, 125(10):104104, 2006. doi:10.1063/1.2347710.
Erin E. Dahlke, Hannah R. Leverentz, and Donald G. Truhlar. Evaluation of the electrostatically embedded many-body expansion and the electrostatically embedded many-body expansion of the correlation energy by application to low-lying water hexamers. Journal of Chemical Theory and Computation, 4(1):33–41, 2008.
Erin E. Dahlke and Donald G. Truhlar. Electrostatically embedded many-body correlation energy, with applications to the calculation of accurate second-order møller-plesset perturbation theory energies for large water clusters. Journal of Chemical Theory and Computation, 3(4):1342–1348, 2007.
Erin E. Dahlke and Donald G. Truhlar. Electrostatically embedded many-body expansion for large systems, with applications to water clusters. Journal of Chemical Theory and Computation, 3(1):46–53, 2007.
Erin E. Dahlke and Donald G. Truhlar. Electrostatically embedded many-body expansion for simulations. Journal of Chemical Theory and Computation, 4(1):1–6, 2008.
Vitali Deev and Michael A. Collins. Approximateab initioenergies by systematic molecular fragmentation. The Journal of Chemical Physics, 122(15):154102, 2005. doi:10.1063/1.1879792.
Hao Dong, Shugui Hua, and Shuhua Li. Understanding the role of intra- and intermolecular interactions in the formation of single- and double-helical structures of aromatic oligoamides: a computational study. The Journal of Physical Chemistry A, 113(7):1335–1342, January 2009. doi:10.1021/jp8071525.
M. Elango, V. Subramanian, Anuja P. Rahalkar, Shridhar R. Gadre, and N. Sathyamurthy. Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach. The Journal of Physical Chemistry A, 112(33):7699–7704, 2008.
Tao Fang, Junteng Jia, and Shuhua Li. Vibrational spectra of molecular crystals with the generalized energy-based fragmentation approach. The Journal of Physical Chemistry A, 120(17):2700–2711, April 2016. doi:10.1021/acs.jpca.5b10927.
Tao Fang, Wei Li, Fangwei Gu, and Shuhua Li. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods. Journal of Chemical Theory and Computation, 11(1):91–98, December 2014. doi:10.1021/ct500833k.
Tao Fang, Yunzhi Li, and Shuhua Li. Generalized energy-based fragmentation approach for modeling condensed phase systems. WIREs Computational Molecular Science, January 2017. doi:10.1002/wcms.1297.
Dmitri G. Fedorov and Kazuo Kitaura. The importance of three-body terms in the fragment molecular orbital method. The Journal of Chemical Physics, 120(15):6832–6840, 2004.
Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, and Shiro Koseki. A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO). Journal of Computational Chemistry, 25(6):872–880, 2004.
Joachim Friedrich, Haoyu Yu, Hannah R. Leverentz, Peng Bai, J. Ilja Siepmann, and Donald G. Truhlar. Water 26-mers drawn from bulk simulations: benchmark binding energies for unprecedentedly large water clusters and assessment of the electrostatically embedded three-body and pairwise additive approximations. The Journal of Physical Chemistry Letters, 5(4):666–670, 2014. doi:10.1021/jz500079e.
Fangjia Fu, Kang Liao, Jing Ma, Zheng Cheng, Dong Zheng, Liuzhou Gao, Chungen Liu, Shuhua Li, and Wei Li. How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases. Physical Chemistry Chemical Physics, 21(7):4072–4081, 2019. doi:10.1039/C8CP06152A.
Jonathan P. Furtado, Anuja P. Rahalkar, Sudhanshu Shanker, Pradipta Bandyopadhyay, and Shridhar R. Gadre. Facilitating minima search for large water clusters at the MP2 level via molecular tailoring. The Journal of Physical Chemistry Letters, 3(16):2253–2258, 2012.
Shridhar R. Gadre and V. Ganesh. Molecular tailoring approach: towards PC-based ab initio treatment of large molecules. Journal of Theoretical and Computational Chemistry, 05(04):835–855, 2006.
Shridhar R. Gadre, K. V. Jovan Jose, and Anuja P. Rahalkar. Molecular tailoring approach for exploring structures, energetics and properties of clusters. Journal of Chemical Sciences, 122(1):47–56, 2010.
Shridhar R. Gadre, Anuja Rahalkar, and Shri V. Ganesh. Ab initio treatment of large molecules: cut-and-stitch the tailor's way. IANCAS Bulletin, 4:267–276, 2006.
Shridhar R. Gadre, Rajendra N. Shirsat, and Ajay C. Limaye. Molecular tailoring approach for simulation of electrostatic properties. The Journal of Physical Chemistry, 98(37):9165–9169, 1994.
Shridhar R. Gadre, Sachin D. Yeole, and Nityananda Sahu. Quantum chemical investigations on molecular clusters. Chemical Reviews, 114(24):12132–12173, 2014.
V. Ganesh, Rameshwar K. Dongare, P. Balanarayan, and Shridhar R. Gadre. Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies. The Journal of Chemical Physics, 125(10):104109, 2006.
Benkun Hong, Tao Fang, Wei Li, and Shuhua Li. Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach. The Journal of Chemical Physics, January 2023. doi:10.1063/5.0137072.
Duy Hua, Hannah R. Leverentz, Elizabeth A. Amin, and Donald G. Truhlar. Assessment and validation of the electrostatically embedded many-body expansion for metal-ligand bonding. Journal of Chemical Theory and Computation, 7(2):251–255, 2011.
Shugui Hua, Weijie Hua, and Shuhua Li. An efficient implementation of the generalized energy-based fragmentation approach for general large molecules. The Journal of Physical Chemistry A, 114(31):8126–8134, July 2010. doi:10.1021/jp103074f.
Shugui Hua, Wei Li, and Shuhua Li. The generalized energy-based fragmentation approach with an improved fragmentation scheme: benchmark results and illustrative applications. ChemPhysChem, 14(1):108–115, December 2012. doi:10.1002/cphc.201200867.
Shugui Hua, Lina Xu, Wei Li, and Shuhua Li. Cooperativity in long $\upalpha $- and 3$\less $sub$\greater $10$\less $/sub$\greater $-helical polyalanines: both electrostatic and van der waals interactions are essential. The Journal of Physical Chemistry B, 115(39):11462–11469, September 2011. doi:10.1021/jp203423w.
Weijie Hua, Tao Fang, Wei Li, Jian-Guo Yu, and Shuhua Li. Geometry optimizations and vibrational spectra of large molecules from a generalized energy-based fragmentation approach. The Journal of Physical Chemistry A, 112(43):10864–10872, 2008.
Lulu Huang, Lou Massa, and Jerome Karle. Kernel energy method illustrated with peptides. International Journal of Quantum Chemistry, 103(6):808–817, 2005.
Yuichi Inadomi, Tatsuya Nakano, Kazuo Kitaura, and Umpei Nagashima. Definition of molecular orbitals in fragment molecular orbital method. Chemical Physics Letters, 364(1-2):139–143, 2002.
Miho Isegawa, Bo Wang, and Donald G. Truhlar. Electrostatically embedded molecular tailoring approach and validation for peptides. Journal of Chemical Theory and Computation, 9(3):1381–1393, 2013. doi:10.1021/ct300845q.
Nan Jiang, Jing Ma, and Yuansheng Jiang. Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules. The Journal of Chemical Physics, 124(11):114112, 2006.
Nan Jiang, Ren Xiang Tan, and Jing Ma. Simulations of solid-state vibrational circular dichroism spectroscopy of (s)-alternarlactam by using fragmentation quantum chemical calculations. The Journal of Physical Chemistry B, 115(12):2801–2813, March 2011. doi:10.1021/jp110152q.
K. V. Jovan Jose and Shridhar R. Gadre. Electrostatic guidelines and molecular tailoring for density functional investigation of structures and energetics of (li)n clusters. The Journal of Chemical Physics, 129(16):164314, 2008.
K. V. Jovan Jose and Shridhar R. Gadre. Ab initio study on (CO2 ) n clusters via electrostatics- and molecular tailoring-based algorithm. International Journal of Quantum Chemistry, 109(10):2238–2247, 2009.
Kazuo Kitaura, Eiji Ikeo, Toshio Asada, Tatsuya Nakano, and Masami Uebayasi. Fragment molecular orbital method: an approximate computational method for large molecules. Chemical Physics Letters, 313(3-4):701–706, 1999.
Kazuo Kitaura, Takuya Sawai, Toshio Asada, Tatsuya Nakano, and Masami Uebayasi. Pair interaction molecular orbital method: an approximate computational method for molecular interactions. Chemical Physics Letters, 312(2-4):319–324, 1999.
Kazuo Kitaura, Sin-Ichirou Sugiki, Tatsuya Nakano, Yuto Komeiji, and Masami Uebayasi. Fragment molecular orbital method: analytical energy gradients. Chemical Physics Letters, 336(1-2):163–170, 2001.
Yuto Komeiji, Tatsuya Nakano, Kaori Fukuzawa, Yutaka Ueno, Yuichi Inadomi, Tadashi Nemoto, Masami Uebayasi, Dmitri G. Fedorov, and Kazuo Kitaura. Fragment molecular orbital method: application to molecular dynamics simulation, `ab initio FMO-MD'. Chemical Physics Letters, 372(3-4):342–347, 2003.
Elbek K. Kurbanov, Hannah R. Leverentz, Donald G. Truhlar, and Elizabeth A. Amin. Electrostatically embedded many-body expansion for neutral and charged metalloenzyme model systems. Journal of Chemical Theory and Computation, 8(1):1–5, 2012.
Elbek K. Kurbanov, Hannah R. Leverentz, Donald G. Truhlar, and Elizabeth A. Amin. Analysis of the errors in the electrostatically embedded many-body expansion of the energy and the correlation energy for zn and cd coordination complexes with five and six ligands and use of the analysis to develop a generally successful fragmentation strategy. Journal of Chemical Theory and Computation, 9(6):2617–2628, 2013.
Hannah R. Leverentz, Katie A. Maerzke, Samuel J. Keasler, J. Ilja Siepmann, and Donald G. Truhlar. Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer. Physical Chemistry Chemical Physics, 14(21):7669, 2012.
Hannah R. Leverentz and Donald G. Truhlar. Electrostatically embedded many-body approximation for systems of water, ammonia, and sulfuric acid and the dependence of its performance on embedding charges. Journal of Chemical Theory and Computation, 5(6):1573–1584, 2009.
Hui Li, Wei Li, Shuhua Li, and Jing Ma. Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions. The Journal of Physical Chemistry B, 112(23):7061–7070, 2008.
Shuhua Li and Wei Li. Fragment energy approach to hartree–fock calculations of macromolecules. Annual Reports Section "C" (Physical Chemistry), 104:256, 2008.
Shuhua Li, Wei Li, and Tao Fang. An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. Journal of the American Chemical Society, 127(19):7215–7226, 2005.
Shuhua Li, Wei Li, and Jing Ma. Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. Accounts of Chemical Research, 47(9):2712–2720, May 2014. doi:10.1021/ar500038z.
Wei Li. Linear scaling explicitly correlated MP2-f12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions. The Journal of Chemical Physics, 138(1):014106, January 2013. doi:10.1063/1.4773011.
Wei Li, Chihong Chen, Dongbo Zhao, and Shuhua Li. LSQC: low scaling quantum chemistry program. International Journal of Quantum Chemistry, 115(10):641–646, November 2014. doi:10.1002/qua.24831.
Wei Li, Hao Dong, Jing Ma, and Shuhua Li. Structures and spectroscopic properties of large molecules and condensed-phase systems predicted by generalized energy-based fragmentation approach. Accounts of Chemical Research, 54(1):169–181, December 2020. doi:10.1021/acs.accounts.0c00580.
Wei Li, Mingzhou Duan, Kang Liao, Benkun Hong, Zhigang Ni, Jing Ma, and Shuhua Li. Improved generalized energy-based fragmentation approach and its applications to the binding energies of supramolecular complexes. Electronic Structure, 1(4):044003, November 2019. doi:10.1088/2516-1075/ab5049.
Wei Li and Shuhua Li. Divide-and-conquer local correlation approach to the correlation energy of large molecules. The Journal of Chemical Physics, 121(14):6649–6657, 2004.
Wei Li and Shuhua Li. A localized molecular-orbital assembler approach for hartree–fock calculations of large molecules. The Journal of Chemical Physics, 122(19):194109, 2005.
Wei Li, Shuhua Li, and Yuansheng Jiang. Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules. The Journal of Physical Chemistry A, 111(11):2193–2199, 2007.
Wei Li, Yunzhi Li, Ruochen Lin, and Shuhua Li. Generalized energy-based fragmentation approach for localized excited states of large systems. The Journal of Physical Chemistry A, 120(48):9667–9677, November 2016. doi:10.1021/acs.jpca.6b11193.
Yunzhi Li, Dong Wang, Fangjia Fu, Qiying Xia, Wei Li, and Shuhua Li. Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy-based fragmentation method. Journal of Computational Chemistry, 43(10):704–716, February 2022. doi:10.1002/jcc.26828.
Yunzhi Li, Guoqiang Wang, Wei Li, Yue Wang, and Shuhua Li. Understanding the polymorphism-dependent emission properties of molecular crystals using a refined qm/mm approach. Physical Chemistry Chemical Physics, 19(27):17516–17520, 2017. doi:10.1039/C7CP03584E.
Yunzhi Li, Dandan Yuan, Qingchun Wang, Wei Li, and Shuhua Li. 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. Physical Chemistry Chemical Physics, 20(19):13547–13557, 2018. doi:10.1039/C8CP00513C.
Meiyi Liu, Yingjie Wang, Yakun Chen, Martin J. Field, and Jiali Gao. QM/MM through the 1990s: the first twenty years of method development and applications. Israel Journal of Chemistry, 54(8-9):1250–1263, 2014. doi:10.1002/ijch.201400036.
Pingying Liu, Wei Li, Zigui Kan, Hui Sun, and Jing Ma. Factor analysis of conformations and nmr signals of rotaxanes: aimd and polarizable md simulations. The Journal of Physical Chemistry A, 120(4):490–502, January 2016. doi:10.1021/acs.jpca.5b10085.
Pingying Liu, Wei Li, Li Liu, Leyong Wang, and Jing Ma. Theoretical study on conformation dynamics of three-station molecular shuttle in different environments and its influence on nmr chemical shifts and binding interactions. The Journal of Physical Chemistry A, 118(39):9032–9044, July 2014. doi:10.1021/jp5020516.
A. Subha Mahadevi, Anuja P. Rahalkar, Shridhar R. Gadre, and G. Narahari Sastry. Ab initio investigation of benzene clusters: molecular tailoring approach. The Journal of Chemical Physics, 133(16):164308, 2010.
Yuji Mochizuki, Shigeru Koikegami, Tatsuya Nakano, Shinji Amari, and Kazuo Kitaura. Large scale MP2 calculations with fragment molecular orbital scheme. Chemical Physics Letters, 396(4-6):473–479, 2004.
Tatsuya Nakano, Tsuguchika Kaminuma, Toshiyuki Sato, Yutaka Akiyama, Masami Uebayasi, and Kazuo Kitaura. Fragment molecular orbital method: application to polypeptides. Chemical Physics Letters, 318(6):614–618, 2000.
Tatsuya Nakano, Tsuguchika Kaminuma, Toshiyuki Sato, Kaori Fukuzawa, Yutaka Akiyama, Masami Uebayasi, and Kazuo Kitaura. Fragment molecular orbital method: use of approximate electrostatic potential. Chemical Physics Letters, 351(5-6):475–480, 2002.
Benjamin W. Noffke, Daniel Beckett, Liang-shi Li, and Krishnan Raghavachari. Aromatic fragmentation based on a ring overlap scheme: an algorithm for large polycyclic aromatic hydrocarbons using the molecules-in-molecules fragmentation-based method. Journal of Chemical Theory and Computation, 16(4):2160–2171, 2020.
Helena W. Qi, Hannah R. Leverentz, and Donald G. Truhlar. Water 16-mers and hexamers: assessment of the three-body and electrostatically embedded many-body approximations of the correlation energy or the nonlocal energy as ways to include cooperative effects. The Journal of Physical Chemistry A, 117(21):4486–4499, 2013.
Anuja P. Rahalkar and Shridhar R. Gadre. Tailoring approach for obtaining molecular orbitals of large systems. Journal of Chemical Sciences, 124(1):149–158, 2012.
Anuja P. Rahalkar, V. Ganesh, and Shridhar R. Gadre. Enabling ab initio hessian and frequency calculations of large molecules. The Journal of Chemical Physics, 129(23):234101, 2008.
Anuja P. Rahalkar, Michio Katouda, Shridhar R. Gadre, and Shigeru Nagase. Molecular tailoring approach in conjunction with MP2 and ri-MP2 codes: a comparison with fragment molecular orbital method. Journal of Computational Chemistry, 31:2405–2418, 2010.
Anuja P. Rahalkar, Sachin D. Yeole, and Shridhar R. Gadre. Acetylene aggregates via cluster-building algorithm and molecular tailoring approach. Theoretical Chemistry Accounts, 2012.
Anuja P. Rahalkar, V. Yeole, Sachin D.vand Ganesh, and Shridhar R. Gadre. Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters. Springer Netherlands, Dordrecht, 2011.
Shoba Ranganathan and Jill E. Gready. Hybrid quantum and molecular mechanical (QM/MM) studies on the pyruvate to $\less $scp$\greater $l$\less $/scp$\greater $-lactate interconversion in $\less $scp$\greater $l$\less $/scp$\greater $-lactate dehydrogenase. The Journal of Physical Chemistry B, 101(28):5614–5618, 1997. doi:10.1021/jp971051u.
Nityananda Sahu and Shridhar R. Gadre. Molecular tailoring approach: a route for ab initio treatment of large clusters. Accounts of Chemical Research, 47(9):2739–2747, 2014.
Nityananda Sahu, Sachin D. Yeole, and Shridhar R. Gadre. Appraisal of molecular tailoring approach for large clusters. The Journal of Chemical Physics, 138(10):104101, 2013.
Hideo Sekino, Yasuo Sengoku, Shinichiro Sugiki, and Noriyuki Kurita. Molecular orbital analysis based on fragment molecular orbital scheme. Chemical Physics Letters, 378(5-6):589–597, 2003.
Anastassia Sorkin, Erin E. Dahlke, and Donald G. Truhlar. Application of the electrostatically embedded many-body expansion to microsolvation of ammonia in water clusters. Journal of Chemical Theory and Computation, 4(5):683–688, 2008.
Sin-ichirou Sugiki, Noriyuki Kurita, Yasuo Sengoku, and Hideo Sekino. Fragment molecular orbital method with density functional theory and DIIS convergence acceleration. Chemical Physics Letters, 382(5-6):611–617, 2003.
Yunwen Tao, Wenli Zou, Junteng Jia, Wei Li, and Dieter Cremer. Different ways of hydrogen bonding in water - why does warm water freeze faster than cold water? Journal of Chemical Theory and Computation, 13(1):55–76, December 2016. doi:10.1021/acs.jctc.6b00735.
Jeremy O. B. Tempkin, Hannah R. Leverentz, Bo Wang, and Donald G. Truhlar. Screened electrostatically embedded many-body method. The Journal of Physical Chemistry Letters, 2(17):2141–2144, 2011.
Bo Wang and Donald G. Truhlar. Including charge penetration effects in molecular modeling. Journal of Chemical Theory and Computation, 6(11):3330–3342, 2010.
Bo Wang, Ke R. Yang, Xuefei Xu, Miho Isegawa, Hannah R. Leverentz, and Donald G. Truhlar. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates. Accounts of Chemical Research, 47(9):2731–2738, 2014. doi:10.1021/ar500068a.
Fang Wang, Dongbo Zhao, Hao Dong, Ling Jiang, Yunfei Liu, and Shuhua Li. Terahertz spectra of DNA nucleobase crystals: a joint experimental and computational study. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 179:255–260, May 2017. doi:10.1016/j.saa.2017.02.037.
Kedong Wang, Wei Li, and Shuhua Li. Generalized energy-based fragmentation CCSD(t)-f12a method and application to the relative energies of water clusters (h2o)20. Journal of Chemical Theory and Computation, 10(4):1546–1553, March 2014. doi:10.1021/ct401060m.
Zhen Yang, Shugui Hua, Weijie Hua, and Shuhua Li. Low-lying structures and stabilities of large water clusters: investigation based on the combination of the AMOEBA potential and generalized energy-based fragmentation approach. The Journal of Physical Chemistry A, 114(34):9253–9261, July 2010. doi:10.1021/jp1038267.
Zhen Yang, Shugui Hua, Weijie Hua, and Shuhua Li. Structures of neutral and protonated water clusters confined in predesigned hosts: a quantum mechanical/molecular mechanical study. The Journal of Physical Chemistry B, 115(25):8249–8256, June 2011. doi:10.1021/jp2030736.
Sachin D. Yeole and Shridhar R. Gadre. On the applicability of fragmentation methods to conjugated $\uppi $ systems within density functional framework. The Journal of Chemical Physics, 132(9):094102, 2010.
Sachin D. Yeole, Nityananda Sahu, and Shridhar R. Gadre. Structures, energetics and vibrational spectra of CO2 clusters through molecular tailoring and cluster building algorithm. Physical Chemistry Chemical Physics, 14(21):7718, 2012.
Dandan Yuan, Yunzhi Li, Wei Li, and Shuhua Li. Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method. Physical Chemistry Chemical Physics, 20(45):28894–28902, 2018. doi:10.1039/C8CP05548C.
Dandan Yuan, Yunzhi Li, Zhigang Ni, Peter Pulay, Wei Li, and Shuhua Li. Benchmark relative energies for large water clusters with the generalized energy-based fragmentation method. Journal of Chemical Theory and Computation, 13(6):2696–2704, May 2017. doi:10.1021/acs.jctc.7b00284.
Dandan Yuan, Xiaoling Shen, Wei Li, and Shuhua Li. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters? Physical Chemistry Chemical Physics, 18(24):16491–16500, 2016. doi:10.1039/C6CP01931E.
D. W. Zhang, X. H. Chen, and J. Z. H. Zhang. Molecular caps for full quantum mechanical computation of peptide-water interaction energy. Journal of Computational Chemistry, 24(15):1846–1852, 2003.
Da W. Zhang, Yun Xiang, and John Z. H. Zhang. New advance in computational chemistry:\hspace 0.167em full quantum mechanical ab initio computation of streptavidin-biotin interaction energy. The Journal of Physical Chemistry B, 107(44):12039–12041, 2003.
Da W. Zhang and J. Z. H. Zhang. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy. The Journal of Chemical Physics, 119(7):3599–3605, 2003. doi:10.1063/1.1591727.
Lei Zhang, Wei Li, Tao Fang, and Shuhua Li. Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides. Theoretical Chemistry Accounts, January 2016. doi:10.1007/s00214-015-1799-z.
Lei Zhang, Wei Li, Tao Fang, and Shuhua Li. Accurate relative energies and binding energies of large ice–liquid water clusters and periodic structures. The Journal of Physical Chemistry A, 121(20):4030–4038, May 2017. doi:10.1021/acs.jpca.7b03376.
Dongbo Zhao, Xiaoling Shen, Zheng Cheng, Wei Li, Hao Dong, and Shuhua Li. Accurate and efficient prediction of NMR parameters of condensed-phase systems with the generalized energy-based fragmentation method. Journal of Chemical Theory and Computation, 16(5):2995–3005, April 2020. doi:10.1021/acs.jctc.9b01298.
Dongbo Zhao, Ruiheng Song, Wei Li, Jing Ma, Hao Dong, and Shuhua Li. Accurate prediction of NMR chemical shifts in macromolecular and condensed-phase systems with the generalized energy-based fragmentation method. Journal of Chemical Theory and Computation, 13(11):5231–5239, October 2017. doi:10.1021/acs.jctc.7b00380.