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1

Chelli, Riccardo, Roberto Righini, Salvatore Califano, and Piero Procacci. "Towards a polarizable force field for molecular liquids." Journal of Molecular Liquids 96-97 (April 2002): 87–100. http://dx.doi.org/10.1016/s0167-7322(01)00329-4.

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2

Starovoytov, Oleg N., Pengzhi Zhang, Piotr Cieplak, and Margaret S. Cheung. "Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state." Physical Chemistry Chemical Physics 19, no. 34 (2017): 22969–80. http://dx.doi.org/10.1039/c7cp03177g.

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Free energy surface of the light-harvesting triad employing a non-polarizable force field (NFF) and a polarizable force field (PFF) shows that induced polarization limits the motion of rotation about chemical bonds as well as bending at the porphyrin, which are prominent using the NFF, thus limiting the conformational space of the triad.
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3

Chaban, Vitaly V. "Force field development and simulations of senior dialkyl sulfoxides." Physical Chemistry Chemical Physics 18, no. 15 (2016): 10507–15. http://dx.doi.org/10.1039/c5cp08006a.

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Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.
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4

Hånde, Ragnhild, Vivien Ramothe, Stéphane Tesson, et al. "Classical Polarizable Force Field to Study Hydrated Hectorite: Optimization on DFT Calculations and Validation against XRD Data." Minerals 8, no. 5 (2018): 205. http://dx.doi.org/10.3390/min8050205.

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Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimenta
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5

Duvail, Magali, Thomas Dumas, Amaury Paquet, Amaury Coste, Laurence Berthon, and Philippe Guilbaud. "UO22+ structure in solvent extraction phases resolved at molecular and supramolecular scales: a combined molecular dynamics, EXAFS and SWAXS approach." Physical Chemistry Chemical Physics 21, no. 15 (2019): 7894–906. http://dx.doi.org/10.1039/c8cp07230b.

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6

Riahi, Saleh, Benoît Roux, and Christopher N. Rowley. "QM/MM molecular dynamics simulations of the hydration of Mg(II) and Zn(II) ions." Canadian Journal of Chemistry 91, no. 7 (2013): 552–58. http://dx.doi.org/10.1139/cjc-2012-0515.

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The hydration of Mg2+ and Zn2+ is examined using molecular dynamics simulations using 3 computational approaches of increasing complexity: the CHARMM nonpolarizable force field based on the TIP3P water model, the Drude polarizable force field based on the SWM4-NDP water model, and a combined QM/MM approach in which the inner coordination sphere is represented using a high-quality density functional theory (DFT) model (PBE/def2-TZVPP), and the remainder of the bulk water solvent is represented using the polarizable SWM4-NDP water model. The characteristic structural distribution functions (radi
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7

Thaunay, Florian, Jean-Pierre Dognon, Gilles Ohanessian, and Carine Clavaguéra. "Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field." Physical Chemistry Chemical Physics 17, no. 39 (2015): 25968–77. http://dx.doi.org/10.1039/c5cp02270c.

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The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.
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8

Knappeova, Barbora, Vojtech Mlynsky, Martin Pykal, et al. "Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes." Journal of Chemical Theory and Computations 20, no. 15 (2024): 6917–29. https://doi.org/10.5281/zenodo.14183169.

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Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrid duplexes have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of polypurine tract (PPT) and Dickerson–Drew dodecamer hybrid
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9

Dong, Dengpan, Xiaoyu Wei, Justin B. Hooper, Hongchao Pan, and Dmitry Bedrov. "Role of cationic groups on structural and dynamical correlations in hydrated quaternary ammonium-functionalized poly(p-phenylene oxide)-based anion exchange membranes." Physical Chemistry Chemical Physics 20, no. 29 (2018): 19350–62. http://dx.doi.org/10.1039/c8cp02211a.

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10

Nottoli, Michele, Benedetta Mennucci, and Filippo Lipparini. "Excited state Born–Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA." Physical Chemistry Chemical Physics 22, no. 35 (2020): 19532–41. http://dx.doi.org/10.1039/d0cp03688a.

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We present the implementation of excited state Born–Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field.
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11

Zhang, Jing, Li-Dong Gong, and Zhong-Zhi Yang. "Recent Development and Applications of the ABEEM/MM Polarizable Force Field." Journal of Computational Biophysics and Chemistry 21, no. 04 (2022): 485–98. http://dx.doi.org/10.1142/s2737416521420084.

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In this paper, we review both development and applications of the atom-bond electronegativity equalization method fused into molecular mechanics, i.e., ABEEM/MM polarizable force field (FF). We will focus on the applications of the ABEEM/MM in pure water systems, chemical and biomolecular ion-containing systems, small molecules and biomolecules, etc. The results show that the performance of ABEEM/MM is generally better than that of the commonly used nonpolarizable force fields.
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12

Borodin, Oleg. "Polarizable Force Field Development and Molecular Dynamics Simulations of Ionic Liquids." Journal of Physical Chemistry B 113, no. 33 (2009): 11463–78. http://dx.doi.org/10.1021/jp905220k.

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13

Meher, B. R., M. V. Satish Kumar, and Pradipta Bandyopadhyay. "Molecular dynamics simulation of HIV-protease with polarizable and non-polarizable force fields." Indian Journal of Physics 83, no. 1 (2009): 81–90. http://dx.doi.org/10.1007/s12648-009-0005-3.

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14

Cheng, YingXing, and Toon Verstraelen. "A new framework for frequency-dependent polarizable force fields." Journal of Chemical Physics 157, no. 12 (2022): 124106. http://dx.doi.org/10.1063/5.0115151.

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A frequency-dependent extension of the polarizable force field “Atom-Condensed Kohn–Sham density functional theory approximated to the second-order” (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2 ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequency-dependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation
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15

Jeong, Kyeong-jun, Jesse G. McDaniel, and Arun Yethiraj. "Deep Eutectic Solvents: Molecular Simulations with a First-Principles Polarizable Force Field." Journal of Physical Chemistry B 125, no. 26 (2021): 7177–86. http://dx.doi.org/10.1021/acs.jpcb.1c01692.

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16

Nakayama, N., S. Obata, K. Ohta, and H. Goto. "Development of polarizable force field for the prediction of molecular crystal structures." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (2008): C207. http://dx.doi.org/10.1107/s0108767308093355.

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17

Lin, Fang-Yu, Pedro E. M. Lopes, Edward Harder, Benoît Roux, and Alexander D. MacKerell. "Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator." Journal of Chemical Information and Modeling 58, no. 5 (2018): 993–1004. http://dx.doi.org/10.1021/acs.jcim.8b00132.

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18

Ainsworth, Richard I., Devis Di Tommaso, Jamieson K. Christie, and Nora H. de Leeuw. "Polarizable force field development and molecular dynamics study of phosphate-based glasses." Journal of Chemical Physics 137, no. 23 (2012): 234502. http://dx.doi.org/10.1063/1.4770295.

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19

Kolafa, Jiř[idot], and Mark Ratner. "Oligomers of Poly(Ethylene Oxide): Molecular Dynamics with a Polarizable Force Field." Molecular Simulation 21, no. 1 (1998): 1–26. http://dx.doi.org/10.1080/08927029808022047.

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20

Szklarczyk, Oliwia M., Stephan J. Bachmann, and Wilfred F. van Gunsteren. "A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons." Journal of Computational Chemistry 35, no. 10 (2014): 789–801. http://dx.doi.org/10.1002/jcc.23551.

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21

Bernardino, Kalil, and Mauro C. C. Ribeiro. "Relating the structure and dynamics of ionic liquids under shear by means of reverse non-equilibrium molecular dynamics simulations." Physical Chemistry Chemical Physics 23, no. 25 (2021): 13984–95. http://dx.doi.org/10.1039/d1cp01205c.

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The effect of shear rate on the viscosity and the structure of 1-ethyl-3-methylimidazolium based ionic liquids with three different anions was studied by means of RNEMD simulations using polarizable force field and correlated with Carreau equation.
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22

Baker, Christopher M. "Polarizable force fields for molecular dynamics simulations of biomolecules." Wiley Interdisciplinary Reviews: Computational Molecular Science 5, no. 2 (2015): 241–54. http://dx.doi.org/10.1002/wcms.1215.

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23

An, Dong, Sara Y. Cheng, Teresa Head-Gordon, Lin Lin, and Jianfeng Lu. "Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation." Journal of Computational Physics 438 (August 2021): 110338. http://dx.doi.org/10.1016/j.jcp.2021.110338.

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24

Harder, Edward, Benoit Roux, and Alex D. MacKerell. "Molecular Dynamics Simulation of Phospholipid Bilayers and Monolayers Using a Polarizable Force Field." Biophysical Journal 98, no. 3 (2010): 10a. http://dx.doi.org/10.1016/j.bpj.2009.12.061.

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25

Belsare, Saurabh, Alexander Esser, Dominik Marx, and Teresa Head-Gordon. "Studying Solvation of Small Biomolecules via Molecular Dynamics using a Polarizable Force Field." Biophysical Journal 112, no. 3 (2017): 497a. http://dx.doi.org/10.1016/j.bpj.2016.11.2688.

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26

Cao, Liaoran, Hong Ren, Jing Miao, Wei Guo, Yan Li, and Guohui Li. "Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions." Frontiers of Chemical Science and Engineering 10, no. 2 (2016): 203–12. http://dx.doi.org/10.1007/s11705-016-1572-4.

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27

Jiang, H., K. D. Jordan, and C. E. Taylor. "Molecular Dynamics Simulations of Methane Hydrate Using Polarizable Force Fields." Journal of Physical Chemistry B 111, no. 23 (2007): 6486–92. http://dx.doi.org/10.1021/jp068505k.

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28

Jaffrelot Inizan, Théo, Frédéric Célerse, Olivier Adjoua, et al. "High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling." Chemical Science 12, no. 13 (2021): 4889–907. http://dx.doi.org/10.1039/d1sc00145k.

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29

Vázquez-Montelongo, Erik Antonio, José Enrique Vázquez-Cervantes, and G. Andrés Cisneros. "Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids." International Journal of Molecular Sciences 21, no. 3 (2020): 697. http://dx.doi.org/10.3390/ijms21030697.

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Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems involving these solvents. Classical molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of IL systems have provided significant insights at the atomic level. Here, we present a review of the development and application of the multipolar and polarizable force field AMOEBA for ionic liquid systems, termed AMOEBA–IL. The parametrization approach for AMOEBA–IL relies on the reproduction of total quantum me
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30

Lemkul, Justin A. "Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes." Nucleic Acids Research 48, no. 2 (2019): 561–75. http://dx.doi.org/10.1093/nar/gkz1154.

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Abstract DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions
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31

Wojtkowiak, Kamil, Aneta Jezierska, and Jarosław J. Panek. "Interactions between Artificial Channel Protein, Water Molecules, and Ions Based on Theoretical Approaches." Symmetry 14, no. 4 (2022): 691. http://dx.doi.org/10.3390/sym14040691.

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Contemporary techniques of molecular modeling allow for rational design of several specific classes of artificial proteins. Transmembrane channels are among these classes. A recent successful synthesis of self-assembling, highly symmetrical 12- or 16-helix channels by David Baker’s group prompted us to study interactions between one of these proteins, TMHC6, and low-molecular-weight components of the environment: water molecules and ions. To examine protein stability in a polar environment, molecular dynamics (MD) with classical force fields of the AMBER family was employed. Further characteri
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32

Chu, Huiying, Xiangda Peng, Yan Li, Yuebin Zhang, and Guohui Li. "A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids." Molecules 23, no. 1 (2017): 77. http://dx.doi.org/10.3390/molecules23010077.

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33

Wu, Johnny C., Jean-Philip Piquemal, Robin Chaudret, Peter Reinhardt, and Pengyu Ren. "Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field." Journal of Chemical Theory and Computation 6, no. 7 (2010): 2059–70. http://dx.doi.org/10.1021/ct100091j.

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34

Lindert, Steffen, Denis Bucher, Peter Eastman, Vijay Pande, and J. Andrew McCammon. "Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units." Journal of Chemical Theory and Computation 9, no. 11 (2013): 4684–91. http://dx.doi.org/10.1021/ct400514p.

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35

Li, Hui, Janamejaya Chowdhary, Lei Huang, Xibing He, Alexander D. MacKerell, and Benoît Roux. "Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids." Journal of Chemical Theory and Computation 13, no. 9 (2017): 4535–52. http://dx.doi.org/10.1021/acs.jctc.7b00262.

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36

Noskov, Sergei Yu, Guillaume Lamoureux, and Benoît Roux. "Molecular Dynamics Study of Hydration in Ethanol−Water Mixtures Using a Polarizable Force Field†." Journal of Physical Chemistry B 109, no. 14 (2005): 6705–13. http://dx.doi.org/10.1021/jp045438q.

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37

Narui, Yoshie, Florencia Velez-Cortes, Zachary Johnson, and Marcos Sotomayor. "Steered Molecular Dynamics Simulations of Inner-Ear Cadherins using the Drude Polarizable Force Field." Biophysical Journal 110, no. 3 (2016): 177a. http://dx.doi.org/10.1016/j.bpj.2015.11.988.

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38

Lagardère, Louis, Luc-Henri Jolly, Filippo Lipparini, et al. "Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields." Chemical Science 9, no. 4 (2018): 956–72. http://dx.doi.org/10.1039/c7sc04531j.

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39

Esser, Alexander, Saurabh Belsare, Dominik Marx, and Teresa Head-Gordon. "Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field." Physical Chemistry Chemical Physics 19, no. 7 (2017): 5579–90. http://dx.doi.org/10.1039/c6cp07388c.

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We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics (AIMD) simulations.
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40

Bernardes, Carlos E. S. "DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields." Journal of Chemical Information and Modeling 62, no. 6 (2022): 1471–78. http://dx.doi.org/10.1021/acs.jcim.1c01431.

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41

Kognole, Abhishek A., Jumin Lee, Sang‐Jun Park, et al. "CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field." Journal of Computational Chemistry 43, no. 5 (2021): 359–75. http://dx.doi.org/10.1002/jcc.26795.

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42

Pacaud, Fabien, Jean-Marc Delaye, Thibault Charpentier, Laurent Cormier, and Mathieu Salanne. "Structural study of Na2O–B2O3–SiO2 glasses from molecular simulations using a polarizable force field." Journal of Chemical Physics 147, no. 16 (2017): 161711. http://dx.doi.org/10.1063/1.4992799.

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43

Asthana, Abhishek, and Dean R. Wheeler. "A polarizable reactive force field for water to enable molecular dynamics simulations of proton transport." Journal of Chemical Physics 138, no. 17 (2013): 174502. http://dx.doi.org/10.1063/1.4798457.

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44

Xu, Tao, and ShiWei Yin. "Effective polarization energy of the naphthalene molecular crystal: a study on the polarizable force field." Science China Chemistry 57, no. 10 (2014): 1375–82. http://dx.doi.org/10.1007/s11426-014-5182-z.

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45

König, Gerhard, Frank Pickard, Jing Huang, et al. "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes." Molecules 23, no. 10 (2018): 2695. http://dx.doi.org/10.3390/molecules23102695.

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Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge a
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46

Zhang, Ling, and J. Ilja Siepmann. "Development of the trappe force field for ammonia." Collection of Czechoslovak Chemical Communications 75, no. 5 (2010): 577–91. http://dx.doi.org/10.1135/cccc2009540.

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The transferable potentials for phase equilibria (TraPPE) force field is extended through the development of a non-polarizable five-site ammonia model. In this model, the electrostatic interactions are represented by three positive partial charges placed at the hydrogen position and a compensating partial charge placed on an M site that is located on the C3 molecular axis and displaced from the nitrogen atom toward the hydrogen atoms. The repulsive and dispersive interactions are represented by placing a single Lennard–Jones site at the position of the nitrogen atom. Starting from the five-sit
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47

Chu, Huiying, Xiangda Peng, Yan Li, Yuebin Zhang, Hanyi Min, and Guohui Li. "Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids." Molecular Physics 116, no. 7-8 (2018): 1037–50. http://dx.doi.org/10.1080/00268976.2018.1436201.

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48

Bedrov, Dmitry, Jean-Philip Piquemal, Oleg Borodin, Alexander D. MacKerell, Benoît Roux, and Christian Schröder. "Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields." Chemical Reviews 119, no. 13 (2019): 7940–95. http://dx.doi.org/10.1021/acs.chemrev.8b00763.

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49

Haskins, Justin B., Alper Kinaci, and Tahir Çağın. "Molecular Dynamics Simulations of Piezoelectric Materials for Energy Harvesting Applications." Materials Science Forum 792 (August 2014): 54–64. http://dx.doi.org/10.4028/www.scientific.net/msf.792.54.

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The previously proposed polarizable charge equilibrium (PQEq) force field model is parameterized for studying lead titanate (PT), lead zirconate (PZ), and their alloys: lead zirconate titanate (PZT). Several molecular dynamics (MD) simulations are performed to assess the degree of accuracy of the model. The phase transition temperatures, which are generally inaccurate in MD, are shown to be similar to experimental measurements. Also, the calculation of the ferroelectric hysteretic behavior, including the spontaneous polarization, saturated polarization and coercive fields, with extended MD is
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50

Kaminski, George A., Harry A. Stern, B. J. Berne, and Richard A. Friesner. "Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry." Journal of Physical Chemistry A 108, no. 4 (2004): 621–27. http://dx.doi.org/10.1021/jp0301103.

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