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Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

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Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K.
* To whom correspondence should be addressed. E-mail: [email protected]
Cite this: J. Chem. Inf. Model. 2009, 49, 4, 944–955
Publication Date (Web):March 23, 2009
https://doi.org/10.1021/ci900009f
Copyright © 2009 American Chemical Society

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    Abstract

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    We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol−1 for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol−1. For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

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    Energies of complexation, monomer and dimer energies for each complex. This information is available free of charge via the Internet at http://pubs.acs.org.

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    76. Yueping Wang, Jiangyuan Wang, Peng Zhong, Yiming Li, Christopher Cong Lai, Yanping He. Molecular insight into the interaction mechanisms of an annulated pyrazole (DB08446) with HIV-1 RT: a QM and QM/QM′ study. Monatshefte für Chemie - Chemical Monthly 2018, 149 (10) , 1919-1929. https://doi.org/10.1007/s00706-018-2239-2
    77. Jolene P. Reid, Matthew S. Sigman. Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts. Nature Reviews Chemistry 2018, 2 (10) , 290-305. https://doi.org/10.1038/s41570-018-0040-8
    78. E.S. Kartashynska, Yu.B. Vysotsky, V.B. Fainerman, D. Vollhardt, R. Miller. Quantum-chemical analysis of condensed monolayer phases of N-alkanoyl-substituted alanine at the air/water interface. Colloids and Surfaces A: Physicochemical and Engineering Aspects 2018, 546 , 346-359. https://doi.org/10.1016/j.colsurfa.2018.03.027
    79. Imre Bakó, Anikó Lábas, Kersti Hermansson, Ákos Bencsura, Julianna Oláh. How can we detect hydrogen bond local cooperativity in liquid water: A simulation study. Journal of Molecular Liquids 2017, 245 , 140-146. https://doi.org/10.1016/j.molliq.2017.08.023
    80. Damien E. Coupry, Matthew A. Addicoat, Thomas Heine. Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes. The Journal of Chemical Physics 2017, 147 (16) https://doi.org/10.1063/1.4985196
    81. Wiktoria Jedwabny, Joanna Panecka-Hofman, Edyta Dyguda-Kazimierowicz, Rebecca C. Wade, W. Andrzej Sokalski. Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition. Journal of Computer-Aided Molecular Design 2017, 31 (8) , 715-728. https://doi.org/10.1007/s10822-017-0035-4
    82. Karim Elhadj Merabti, Sihem Azizi, Jacqueline Ridard, Bernard Lévy, Isabelle Demachy. π -Stacking interactions in YFP, quantum mechanics and force field evaluations in the S 0 and S 1 states. Chemical Physics 2017, 493 , 157-165. https://doi.org/10.1016/j.chemphys.2017.07.002
    83. Megan L. Peach, Raul E. Cachau, Marc C. Nicklaus. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. Journal of Molecular Recognition 2017, 30 (8) https://doi.org/10.1002/jmr.2618
    84. Shenghui Chen, Shuangqing Sun, Chunling Li, Charles U. Pittman, Thomas E. Lacy, Songqing Hu, Steven R. Gwaltney. Molecular dynamics simulations of the graphene sheet aggregation in dodecane. Journal of Nanoparticle Research 2017, 19 (6) https://doi.org/10.1007/s11051-017-3893-8
    85. Michael Feig. Computational protein structure refinement: almost there, yet still so far to go. WIREs Computational Molecular Science 2017, 7 (3) https://doi.org/10.1002/wcms.1307
    86. Zhuang-lin Shen, Yi-qi Xia, Qiu-song Yang, Wen-de Tian, Kang Chen, Yu-qiang Ma. Polymer–Nucleic Acid Interactions. Topics in Current Chemistry 2017, 375 (2) https://doi.org/10.1007/s41061-017-0131-x
    87. Konrad Patkowski. Benchmark Databases of Intermolecular Interaction Energies: Design, Construction, and Significance. 2017, 3-91. https://doi.org/10.1016/bs.arcc.2017.06.004
    88. Fujie Tang, Tatsuhiko Ohto, Taisuke Hasegawa, Mischa Bonn, Yuki Nagata. π + –π + stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces. Physical Chemistry Chemical Physics 2017, 19 (4) , 2850-2856. https://doi.org/10.1039/C6CP07034E
    89. Wiktoria Jedwabny, Szymon Kłossowski, Trupta Purohit, Tomasz Cierpicki, Jolanta Grembecka, Edyta Dyguda-Kazimierowicz. Theoretical models of inhibitory activity for inhibitors of protein–protein interactions: targeting menin–mixed lineage leukemia with small molecules. MedChemComm 2017, 8 (12) , 2216-2227. https://doi.org/10.1039/C7MD00170C
    90. James Luccarelli, Ian M. Jones, Sam Thompson, Andrew D. Hamilton. Unpicking the determinants of amide NH⋯OC hydrogen bond strength with diphenylacetylene molecular balances. Organic & Biomolecular Chemistry 2017, 15 (43) , 9156-9163. https://doi.org/10.1039/C7OB02026K
    91. A. D. Glova, S. V. Larin, S. G. Falkovich, V. M. Nazarychev, D. A. Tolmachev, N. V. Lukasheva, S. V. Lyulin. Molecular dynamics simulations of oligoester brushes: the origin of unusual conformations. Soft Matter 2017, 13 (37) , 6627-6638. https://doi.org/10.1039/C7SM01419H
    92. Lin Zhang, Zhitong Bai, Ling Liu. Exceptional Thermal Conductance across Hydrogen‐Bonded Graphene/Polymer Interfaces. Advanced Materials Interfaces 2016, 3 (13) https://doi.org/10.1002/admi.201600211
    93. Nicolas Foloppe, I-Jen Chen. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding. Bioorganic & Medicinal Chemistry 2016, 24 (10) , 2159-2189. https://doi.org/10.1016/j.bmc.2016.03.022
    94. Nusret Yilmazer, Martin Korth. Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods. International Journal of Molecular Sciences 2016, 17 (5) , 742. https://doi.org/10.3390/ijms17050742
    95. David Zanuy, Jordi Poater, Miquel Solà, Ian W. Hamley, Carlos Alemán. Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly. Physical Chemistry Chemical Physics 2016, 18 (2) , 1265-1278. https://doi.org/10.1039/C5CP04269K
    96. Muhammad Yousuf, Il Seung Youn, Jeonghun Yun, Lubna Rasheed, Rosendo Valero, Genggongwo Shi, Kwang S. Kim. Violation of DNA neighbor exclusion principle in RNA recognition. Chemical Science 2016, 7 (6) , 3581-3588. https://doi.org/10.1039/C5SC03740A
    97. Qian Peng, Fernanda Duarte, Robert S. Paton. Computing organic stereoselectivity – from concepts to quantitative calculations and predictions. Chemical Society Reviews 2016, 45 (22) , 6093-6107. https://doi.org/10.1039/C6CS00573J
    98. Luis Simón, Robert S. Paton. QM/MM study on the enantioselectivity of spiroacetalization catalysed by an imidodiphosphoric acid catalyst: how confinement works. Organic & Biomolecular Chemistry 2016, 14 (11) , 3031-3039. https://doi.org/10.1039/C6OB00045B
    99. Wilian A. Cortopassi, Kiran Kumar, Robert S. Paton. Cation–π interactions in CREBBP bromodomain inhibition: an electrostatic model for small-molecule binding affinity and selectivity. Organic & Biomolecular Chemistry 2016, 14 (46) , 10926-10938. https://doi.org/10.1039/C6OB02234K
    100. Maximilian F. Koch, Sabrina Harteis, Iris D. Blank, Galina Pestel, Lutz F. Tietze, Christian Ochsenfeld, Sabine Schneider, Stephan A. Sieber. Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues. Angewandte Chemie International Edition 2015, 54 (46) , 13550-13554. https://doi.org/10.1002/anie.201505749
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