ACS Publications. Most Trusted. Most Cited. Most Read
Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Theory Comput. 2013, 9, 6, 2733-2748
    Article

    Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent
    Click to copy article linkArticle link copied!

    View Author Information
    University of Florida, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435, United States
    *Phone: 352-392-6973. Fax: 352-392-8722. E-mail: [email protected]
    Other Access OptionsSupporting Information (3)

    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2013, 9, 6, 2733–2748
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ct400146w
    Published May 8, 2013
    Copyright © 2013 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12–6 Lennard-Jones (LJ) term plus an electrostatic potential, is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models, and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work, we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz–Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for a systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion–oxygen distance in the first solvation shell (IOD), and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P, and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the interaction between the metal ions and water molecules at short-range. Moreover, the extent of underestimation increases successively for the TIP3P, SPC/E, TIP4PEW, and TIP4P water models. Nonetheless, we fitted a curve to describe the relationship between ε (the well depth) and radius (Rmin/2) from experimental data on noble gases to facilitate the generation of the best possible compromise models. Hence, by targeting different experimental values, we developed three sets of parameters for M(II) cations for three different water models (TIP3P, SPC/E, and TIP4PEW). These parameters we feel represent the best possible compromise that can be achieved using the nonbonded model for the ions in combination with simple water models. From a computational uncertainty analysis we estimate that the uncertainty in our computed HFEs is on the order of ±1 kcal/mol. Further improvements will require more advanced nonbonded models likely with inclusion of polarization.

    Copyright © 2013 American Chemical Society

    Subjects

    what are subjects

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    Details of the parameter fitting scheme, results from TI simulations, figures, and data sets for parametrized HFE, IOD, and CN values for various ion in different water models. This material is available free of charge via the Internet at http://pubs.acs.org.

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 549 publications.

    1. Valentina Migliorati, Eleonora De Santis, Paola D’Angelo. Does Pb2+ Form Holodirected or Hemidirected Solvation Geometries in Water?. The Journal of Physical Chemistry B 2024, 128 (47) , 11748-11758. https://doi.org/10.1021/acs.jpcb.4c05646
    2. Matthew Saunders, Abibat Adekoya-Olowofela, Sabrina Downing, Sagar A. Pandit. Adsorption Modes of Na+, Li+, and Mg2+ to a Model Zwitterionic Lipid Bilayer. Langmuir 2024, Article ASAP.
    3. Sk Habibullah, Lipika Baidya, Sunil Kumar, Govardhan Reddy. Metal Ion Sensing by Tetraloop-like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion–RNA Inner-Shell Contacts. The Journal of Physical Chemistry B 2024, 128 (46) , 11389-11401. https://doi.org/10.1021/acs.jpcb.4c06122
    4. Bailey Hanson, Madelyn Smith, Pengfei Li. Accuracy of Discrete-Continuum Solvation Model for Cations: A Benchmark Study. The Journal of Physical Chemistry B 2024, Article ASAP.
    5. Fangchen Hu, Yuwei Zhang, Pengfei Li, Ruibo Wu, Fei Xia. Development of Accurate Force Fields for Mg2+ and Triphosphate Interactions in ATP·Mg2+ and GTP·Mg2+ Complexes. Journal of Chemical Theory and Computation 2024, Article ASAP.
    6. Leonardo Coello Escalante, David T. Limmer. Microscopic Origin of Twist-Dependent Electron Transfer Rate in Bilayer Graphene. Nano Letters 2024, 24 (46) , 14868-14874. https://doi.org/10.1021/acs.nanolett.4c04690
    7. Theis I. So̷lling, Martin P. Andersson, Safwat Abdel-Azeim, Ahmed M. El Zohry, Jesse Lee Beauchamp. Transition Metal Ions in Solution: Complexed Ion Speciation at the Air–Liquid Interface. Langmuir 2024, Article ASAP.
    8. Manas Mondal, Yi Qin Gao. Atomistic Insights into Sequence-Mediated Spontaneous Association of Short RNA Chains. Biochemistry 2024, 63 (21) , 2916-2936. https://doi.org/10.1021/acs.biochem.4c00293
    9. Anqi Guo, Pengtu Zhang, Shiling Yuan. Effect of Inorganic Additive Strategy on the Stability of VO2+ in Vanadium Redox Flow Battery Electrolyte by Molecular Dynamics. The Journal of Physical Chemistry B 2024, 128 (42) , 10460-10468. https://doi.org/10.1021/acs.jpcb.4c04090
    10. Pasquale Rapacciuolo, Claudia Finamore, Cristina Di Giorgio, Bianca Fiorillo, Carmen Massa, Ginevra Urbani, Silvia Marchianò, Martina Bordoni, Chiara Cassiano, Elva Morretta, Lucio Spinelli, Antonio Lupia, Federica Moraca, Michele Biagioli, Valentina Sepe, Maria Chiara Monti, Bruno Catalanotti, Stefano Fiorucci, Angela Zampella. Design, Synthesis, and Pharmacological Evaluation of Dual FXR-LIFR Modulators for the Treatment of Liver Fibrosis. Journal of Medicinal Chemistry 2024, 67 (20) , 18334-18355. https://doi.org/10.1021/acs.jmedchem.4c01651
    11. Tomasz K. Piskorz, Bernadette Lee, Shaoqi Zhan, Fernanda Duarte. Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures. Journal of Chemical Theory and Computation 2024, 20 (20) , 9060-9071. https://doi.org/10.1021/acs.jctc.4c00850
    12. Guodong Hu, Xue Yu, Zhaojun Li. Unveiling Putative Excited State and Transmission of Binding Information in the Fluoride Riboswitch. Journal of Chemical Information and Modeling 2024, 64 (19) , 7555-7564. https://doi.org/10.1021/acs.jcim.4c00852
    13. Madelyn Smith, Richa Khatiwada, Pengfei Li. Exploring Ion Polarizabilities and Their Correlation with van der Waals Radii: A Theoretical Investigation. Journal of Chemical Theory and Computation 2024, 20 (19) , 8505-8516. https://doi.org/10.1021/acs.jctc.4c00632
    14. Guobin Li, Xin Peng, Lingfeng Yu, Di Wang, He Zhao, Qiang Chen, Jiduo Zhao, Ke Zhou, Yahui Xue. Nanofluidic Thermoelectric Transducer with Ultrahigh and Tunable Sensitivity. The Journal of Physical Chemistry Letters 2024, 15 (39) , 9863-9870. https://doi.org/10.1021/acs.jpclett.4c02370
    15. Stefano Muscat, Gianfranco Martino, Jacopo Manigrasso, Marco Marcia, Marco De Vivo. On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules. Journal of Chemical Theory and Computation 2024, 20 (16) , 6992-7008. https://doi.org/10.1021/acs.jctc.4c00773
    16. Zhen Li, Subhamoy Bhowmik, Luca Sagresti, Giuseppe Brancato, Madelyn Smith, David E. Benson, Pengfei Li, Kenneth M. Merz, Jr.. Simulating Metal-Imidazole Complexes. Journal of Chemical Theory and Computation 2024, 20 (15) , 6706-6716. https://doi.org/10.1021/acs.jctc.4c00581
    17. Sathish K. Mudedla, Hayoung Lee, Jeom Ji Kim, Seong Hun Jang, Munikumar R. Doddareddy, Swetha Y. Sanam, Rochish Gundabathula, Jang-June Park, Sangwook Wu. Molecular Dynamics Simulation on the Suppression Mechanism of Phosphorylation to Ser222 by Allosteric Inhibitors Targeting MEK1/2 Kinase. ACS Omega 2024, 9 (29) , 31946-31956. https://doi.org/10.1021/acsomega.4c03615
    18. Mengyuan Xue, Xiaozhe Ren, Yuyang Zhang, Jing Liu, Tianying Yan. Improving Aqueous Zinc Ion Batteries with Alkali Metal Ions. ACS Applied Materials & Interfaces 2024, 16 (26) , 33559-33570. https://doi.org/10.1021/acsami.4c05372
    19. Sergej Friesen, Sergey E. Kruchinin, Marina V. Fedotova, Richard Buchner. Cation-Binding of Glutamate in Aqueous Solution. The Journal of Physical Chemistry B 2024, 128 (23) , 5746-5755. https://doi.org/10.1021/acs.jpcb.4c02373
    20. Basak Koca Fındık, Majid Jafari, Lin Frank Song, Zhen Li, Viktorya Aviyente, Kenneth M. Merz, Jr.. Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution. Journal of Chemical Theory and Computation 2024, 20 (10) , 4298-4307. https://doi.org/10.1021/acs.jctc.4c00218
    21. Shuxin Zhao, Jin Liu, Zhicheng Zuo. Secondary Conformational Checkpoint in CRISPR-Cas9. Journal of Chemical Theory and Computation 2024, 20 (9) , 3440-3448. https://doi.org/10.1021/acs.jctc.4c00120
    22. Amrita Goswami, Alejandro Peña-Torres, Elvar Ö. Jónsson, Sergei A. Egorov, Hannes Jónsson. Evidence of Sharp Transitions between Octahedral and Capped Trigonal Prism States of the Solvation Shell of the Aqueous Fe3+ Ion. The Journal of Physical Chemistry Letters 2024, 15 (17) , 4523-4530. https://doi.org/10.1021/acs.jpclett.4c00756
    23. Kayla A. Croney, James McCarty. Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. The Journal of Physical Chemistry B 2024, 128 (13) , 3102-3112. https://doi.org/10.1021/acs.jpcb.3c07972
    24. Timothy J. Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M. York. Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of Chemical Theory and Computation 2024, 20 (5) , 2058-2073. https://doi.org/10.1021/acs.jctc.3c01401
    25. Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino. Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. Journal of Chemical Information and Modeling 2024, 64 (5) , 1593-1604. https://doi.org/10.1021/acs.jcim.3c01919
    26. Arka Bera, Tanmay Sarkar Akash, Raashiq Ishraaq, Turash Haque Pial, Siddhartha Das. Hydrogen Bonding Inside Anionic Polymeric Brush Layer: Machine Learning-Driven Exploration of the Relative Roles of the Polymer Steric Effect, Charging, and Type of Screening Counterions. Macromolecules 2024, 57 (4) , 1581-1592. https://doi.org/10.1021/acs.macromol.3c02127
    27. Fangchen Hu, Yiqiu Wang, Juan Zeng, Xianming Deng, Fei Xia, Xin Xu. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations. The Journal of Physical Chemistry B 2024, 128 (6) , 1418-1427. https://doi.org/10.1021/acs.jpcb.3c07666
    28. Magali Duvail, Diego Moreno Martinez, Lara Žiberna, Erwann Guillam, Jean-François Dufrêche, Philippe Guilbaud. Modeling Lanthanide Ions in Solution: A Versatile Force Field in Aqueous and Organic Solvents. Journal of Chemical Theory and Computation 2024, 20 (3) , 1282-1292. https://doi.org/10.1021/acs.jctc.3c01162
    29. Luke Landry, Pengfei Li. Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of Chemical Information and Modeling 2024, 64 (3) , 812-824. https://doi.org/10.1021/acs.jcim.3c01815
    30. Ming Cai, Jicai Feng, Jian Wang, Peng Chen, Zhiwei Ge, Wei Liu, Peilong Sun, Liehong Wu, Jianyong Wu. Characterization of Various Noncovalent Polyphenol–Starch Complexes and Their Prebiotic Activities during In Vitro Digestion and Fermentation. Journal of Agricultural and Food Chemistry 2024, 72 (4) , 2250-2262. https://doi.org/10.1021/acs.jafc.3c09327
    31. Julian M. Delgado, Péter R. Nagy, Sameer Varma. Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes. Journal of Chemical Information and Modeling 2024, 64 (2) , 378-392. https://doi.org/10.1021/acs.jcim.3c01513
    32. Monsurat M. Lawal, Priti Roy, Martin McCullagh. Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. The Journal of Physical Chemistry B 2024, 128 (2) , 492-503. https://doi.org/10.1021/acs.jpcb.3c06714
    33. Kushal Singh, Govardhan Reddy. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. Journal of Chemical Theory and Computation 2024, 20 (1) , 421-435. https://doi.org/10.1021/acs.jctc.3c00999
    34. Qi Li, Ke Zhou, Bin Zhu, Xueli Liu, Junchao Lao, Jun Gao, Lei Jiang. Artificial Sodium Channels for Enhanced Osmotic Energy Harvesting. Journal of the American Chemical Society 2023, 145 (51) , 28038-28048. https://doi.org/10.1021/jacs.3c08902
    35. Nadja K. Singer, Leticia González, Antonio Monari. Molecular Photoswitches Regulating the Activity of the Human Serotonin Transporter. The Journal of Physical Chemistry Letters 2023, 14 (46) , 10333-10339. https://doi.org/10.1021/acs.jpclett.3c02655
    36. Grant W. Larson, Peter K. Windsor, Elizabeth Smithwick, Ke Shi, Hideki Aihara, Anoop Rama Damodaran, Ambika Bhagi-Damodaran. Understanding ATP Binding to DosS Catalytic Domain with a Short ATP-Lid. Biochemistry 2023, 62 (22) , 3283-3292. https://doi.org/10.1021/acs.biochem.3c00306
    37. Changhao Zhu, Xuye He, Yun Shi, Zhenkang Wang, Baojiu Hao, Wanhao Chen, Hao Yang, Lifang Zhang, Haoqing Ji, Jie Liu, Chenglin Yan, Jinqiu Zhou, Tao Qian. Strong Replaces Weak: Design of H-Bond Interactions Enables Cryogenic Aqueous Zn Metal Batteries. ACS Nano 2023, 17 (21) , 21614-21625. https://doi.org/10.1021/acsnano.3c06687
    38. Yazdan Maghsoud, Vindi M. Jayasinghe-Arachchige, Pratibha Kumari, G. Andrés Cisneros, Jin Liu. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. Journal of Chemical Information and Modeling 2023, 63 (21) , 6834-6850. https://doi.org/10.1021/acs.jcim.3c01284
    39. Sunil Kumar, Govardhan Reddy. Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch. The Journal of Physical Chemistry B 2023, 127 (43) , 9267-9281. https://doi.org/10.1021/acs.jpcb.3c03941
    40. João T. S. Coimbra, Pedro A. Fernandes, Maria J. Ramos. Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 2023, 63 (20) , 6354-6365. https://doi.org/10.1021/acs.jcim.3c00962
    41. Süleyman Selim Çınaroğlu, Philip C. Biggin. Computed Protein–Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. Journal of Chemical Information and Modeling 2023, 63 (19) , 6095-6108. https://doi.org/10.1021/acs.jcim.3c01041
    42. R. A. Talmazan, M. Podewitz. PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent. Journal of Chemical Information and Modeling 2023, 63 (17) , 5400-5407. https://doi.org/10.1021/acs.jcim.3c00798
    43. Leah Fuhrman Javitt, Surajit Kalita, Kshatresh Dutta Dubey, David Ehre, Sason Shaik, Meir Lahav, Igor Lubomirsky. Electro-Freezing of Supercooled Water Is Induced by Hydrated Al3+ and Mg2+ Ions: Experimental and Theoretical Studies. Journal of the American Chemical Society 2023, 145 (34) , 18904-18911. https://doi.org/10.1021/jacs.3c05004
    44. Jokent T. Gaza, Ricky B. Nellas. Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study. Journal of Chemical Information and Modeling 2023, 63 (15) , 4654-4663. https://doi.org/10.1021/acs.jcim.3c00559
    45. Terence Zhi Xiang Hong, Hieu Trung Kieu, Liming You, Adrian Wing-Keung Law, Kun Zhou. A Molecular Dynamics Study Employing Bimetallic Co–CuHAB Nanosheets for Seawater Desalination. ACS ES&T Water 2023, 3 (8) , 2296-2306. https://doi.org/10.1021/acsestwater.3c00072
    46. Jun Ohnuki, Yasuhiro Arimura, Tomonori Kono, Kuniki Kino, Hitoshi Kurumizaka, Mitsunori Takano. Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK. Journal of the American Chemical Society 2023, 145 (29) , 15963-15970. https://doi.org/10.1021/jacs.3c03926
    47. Riccardo Rozza, Pavel Janoš, Alessandra Magistrato. Monovalent Ionic Atmosphere Modulates the Selection of Suboptimal RNA Sequences by Splicing Factors’ RNA Recognition Motifs. Journal of Chemical Information and Modeling 2023, 63 (10) , 3086-3093. https://doi.org/10.1021/acs.jcim.3c00110
    48. Koteswara Rao Gorantla, Bhabani S. Mallik. Copper Complex Catalyzed Two-Electron and Proton Shuttle Mechanism of O–O Bond Formation from DFT-Based Metadynamics Simulations. The Journal of Physical Chemistry A 2023, 127 (17) , 3788-3795. https://doi.org/10.1021/acs.jpca.3c00088
    49. Pan Sun, Erik A. Binter, Trung Vo, Ilan Benjamin, Mrinal K. Bera, Binhua Lin, Wei Bu, Mark L. Schlossman. Relevance of Surface Adsorption and Aqueous Complexation for the Separation of Co(II), Ni(II), and Fe(III). The Journal of Physical Chemistry B 2023, 127 (15) , 3505-3515. https://doi.org/10.1021/acs.jpcb.2c08412
    50. Fikret Aydin, Marcos F. Calegari Andrade, Robert S. Stinson, Alexandra Zagalskaya, Daniel Schwalbe-Koda, Zejie Chen, Shubham Sharma, Amitesh Maiti, Daniel V. Esposito, Shane Ardo, Tuan Anh Pham, Tadashi Ogitsu. Mechanistic Insights on Permeation of Water over Iron Cations in Nanoporous Silicon Oxide Films for Selective H2 and O2 Evolution. ACS Applied Materials & Interfaces 2023, 15 (14) , 17814-17824. https://doi.org/10.1021/acsami.2c22865
    51. Madelyn Smith, Zhen Li, Luke Landry, Kenneth M. Merz, Jr., Pengfei Li. Consequences of Overfitting the van der Waals Radii of Ions. Journal of Chemical Theory and Computation 2023, 19 (7) , 2064-2074. https://doi.org/10.1021/acs.jctc.2c01255
    52. Souvik Sinha, Chinmai Pindi, Mohd Ahsan, Pablo R. Arantes, Giulia Palermo. Machines on Genes through the Computational Microscope. Journal of Chemical Theory and Computation 2023, 19 (7) , 1945-1964. https://doi.org/10.1021/acs.jctc.2c01313
    53. Brendan E. Hawkins, Theresa Schoetz, Leo W. Gordon, Surabh KT, Jonah Wang, Robert J. Messinger. Reversible Zinc Electrodeposition at −60 °C Using a Deep Eutectic Electrolyte for Low-Temperature Zinc Metal Batteries. The Journal of Physical Chemistry Letters 2023, 14 (9) , 2378-2386. https://doi.org/10.1021/acs.jpclett.3c00150
    54. Jinzhe Zeng, Yujun Tao, Timothy J. Giese, Darrin M. York. QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of Chemical Theory and Computation 2023, 19 (4) , 1261-1275. https://doi.org/10.1021/acs.jctc.2c01172
    55. Saikat Pal, Amit Kumar, Harish Vashisth. Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. Journal of Chemical Information and Modeling 2023, 63 (3) , 1002-1011. https://doi.org/10.1021/acs.jcim.2c01487
    56. Zhen Li, Lin Frank Song, Gaurav Sharma, Basak Koca Fındık, Kenneth M. Merz, Jr.. Accurate Metal–Imidazole Interactions. Journal of Chemical Theory and Computation 2023, 19 (2) , 619-625. https://doi.org/10.1021/acs.jctc.2c01081
    57. Madelyn Smith, Pengfei Li. Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of Chemical Information and Modeling 2023, 63 (1) , 354-361. https://doi.org/10.1021/acs.jcim.2c01411
    58. Gaurav Sharma, Lin Frank Song, Kenneth M. Merz. Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. Journal of Chemical Information and Modeling 2022, 62 (24) , 6574-6585. https://doi.org/10.1021/acs.jcim.1c01283
    59. Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. Journal of Chemical Information and Modeling 2022, 62 (24) , 6762-6774. https://doi.org/10.1021/acs.jcim.2c00537
    60. Ke Zhou, Chen Qian, Yilun Liu. Quantifying the Structure of Water and Hydrated Monovalent Ions by Density Functional Theory-Based Molecular Dynamics. The Journal of Physical Chemistry B 2022, 126 (49) , 10471-10480. https://doi.org/10.1021/acs.jpcb.2c05330
    61. Turash Haque Pial, Siddhartha Das. Specific Ion and Electric Field Controlled Diverse Ion Distribution and Electroosmotic Transport in a Polyelectrolyte Brush Grafted Nanochannel. The Journal of Physical Chemistry B 2022, 126 (49) , 10543-10553. https://doi.org/10.1021/acs.jpcb.2c05524
    62. Tianyi Yang, Li Han, Shuanghong Huo. Dynamics and Allosteric Information Pathways of Unphosphorylated c-Cbl. Journal of Chemical Information and Modeling 2022, 62 (23) , 6148-6159. https://doi.org/10.1021/acs.jcim.2c01022
    63. Wenlang Liu, Zhenhao Liu, Hao Liu, Lance M. Westerhoff, Zheng Zheng. Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein–Ligand Sampling. Journal of Chemical Information and Modeling 2022, 62 (22) , 5645-5665. https://doi.org/10.1021/acs.jcim.2c00278
    64. Piya Patra, Yi Qin Gao. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation. The Journal of Physical Chemistry B 2022, 126 (45) , 9187-9206. https://doi.org/10.1021/acs.jpcb.2c05749
    65. Adrian Gołębiowski, Paweł Pomastowski, Katarzyna Rafińska, Petar Zuvela, Ming Wah Wong, Oleksandra Pryshchepa, Piotr Madajski, Bogusław Buszewski. Functionalization of Alpha-Lactalbumin by Zinc Ions. ACS Omega 2022, 7 (43) , 38459-38474. https://doi.org/10.1021/acsomega.2c03674
    66. Angela Parise, Giada Ciardullo, Mario Prejanò, Aurélien de la Lande, Tiziana Marino. On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. Journal of Chemical Information and Modeling 2022, 62 (20) , 4916-4927. https://doi.org/10.1021/acs.jcim.2c01002
    67. Kosma Szutkowski, Dominika Tubacka, Patryk Florczak, Danuta Kruk. Long-Range Li-Ion 3D Diffusion in the High-Temperature Hexagonal Phase of LiBH4 Studied by 7Li Pulsed Field Gradient NMR and MD Simulations. The Journal of Physical Chemistry C 2022, 126 (37) , 15936-15943. https://doi.org/10.1021/acs.jpcc.2c03658
    68. Sathish Kumar Mudedla, Boyli Ghosh, Gaurao V. Dhoke, SeKyu Oh, Sangwook Wu. QM/MM Simulations for the Broken-Symmetry Catalytic Reaction Mechanism of Human Arginase I. ACS Omega 2022, 7 (36) , 32536-32548. https://doi.org/10.1021/acsomega.2c04116
    69. Bin Sun, Peter M. Kekenes-Huskey. Calmodulin’s Interdomain Linker Is Optimized for Dynamics Signal Transmission and Calcium Binding. Journal of Chemical Information and Modeling 2022, 62 (17) , 4210-4221. https://doi.org/10.1021/acs.jcim.2c00587
    70. Alexandre C. Oliveira, Hugo A. L. Filipe, João P. Prates Ramalho, Armindo Salvador, Carlos F. G. C. Geraldes, Maria João Moreno, Luís M. S. Loura. Modeling Gd3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents. Inorganic Chemistry 2022, 61 (30) , 11837-11858. https://doi.org/10.1021/acs.inorgchem.2c01597
    71. Saikat Pal, Rituparna Roy, Sandip Paul. Deciphering the Role of ATP on PHF6 Aggregation. The Journal of Physical Chemistry B 2022, 126 (26) , 4761-4775. https://doi.org/10.1021/acs.jpcb.2c01768
    72. Minjie Kang, Zhicheng Zuo, Zhixiang Yin, Jianrong Gu. Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition. Journal of Chemical Information and Modeling 2022, 62 (12) , 3057-3066. https://doi.org/10.1021/acs.jcim.1c01562
    73. Maxwell R. Tucker, Stefano Piana, Dazhi Tan, Michael V. LeVine, David E. Shaw. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes. The Journal of Physical Chemistry B 2022, 126 (24) , 4442-4457. https://doi.org/10.1021/acs.jpcb.1c10971
    74. Ali Rahnamoun, Kurt A. O’Hearn, Mehmet Cagri Kaymak, Zhen Li, Kenneth M. Merz, Jr., Hasan Metin Aktulga. A Polarizable Cationic Dummy Metal Ion Model. The Journal of Physical Chemistry Letters 2022, 13 (23) , 5334-5340. https://doi.org/10.1021/acs.jpclett.2c01279
    75. Tingting Xu, Bin Wu, Linxiao Hou, Yanran Zhu, Fangmeng Sheng, Zhang Zhao, Yun Dong, Jiandang Liu, Bangjiao Ye, Xingya Li, Liang Ge, Huanting Wang, Tongwen Xu. Highly Ion-Permselective Porous Organic Cage Membranes with Hierarchical Channels. Journal of the American Chemical Society 2022, 144 (23) , 10220-10229. https://doi.org/10.1021/jacs.2c00318
    76. Matteo Busato, Alessandro Tofoni, Giorgia Mannucci, Francesco Tavani, Alessandra Del Giudice, Andrea Colella, Mauro Giustini, Paola D’Angelo. On the Role of Water in the Formation of a Deep Eutectic Solvent Based on NiCl2·6H2O and Urea. Inorganic Chemistry 2022, 61 (23) , 8843-8853. https://doi.org/10.1021/acs.inorgchem.2c00864
    77. Abdul Basit, Ajeet Kumar Yadav, Pradipta Bandyopadhyay. Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. Journal of Chemical Information and Modeling 2022, 62 (11) , 2821-2834. https://doi.org/10.1021/acs.jcim.2c00428
    78. Julie Puyo-Fourtine, Marie Juillé, Jérôme Hénin, Carine Clavaguéra, Elise Duboué-Dijon. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. The Journal of Physical Chemistry B 2022, 126 (22) , 4022-4034. https://doi.org/10.1021/acs.jpcb.2c01158
    79. Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud. Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model. Journal of Chemical Information and Modeling 2022, 62 (10) , 2432-2445. https://doi.org/10.1021/acs.jcim.2c00153
    80. Tomasz K. Piskorz, Vicente Martí-Centelles, Tom A. Young, Paul J. Lusby, Fernanda Duarte. Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities. ACS Catalysis 2022, 12 (10) , 5806-5826. https://doi.org/10.1021/acscatal.2c00837
    81. Zhen Li, Kenneth M. Merz, Jr. Systematic Evaluation of Ion Diffusion and Water Exchange. Journal of Chemical Theory and Computation 2022, 18 (5) , 3017-3026. https://doi.org/10.1021/acs.jctc.1c01189
    82. Marvin P. Bernhardt, Yuki Nagata, Nico F. A. van der Vegt. Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion–Water Pair Potentials Based on Ab Initio Molecular Dynamics Data. The Journal of Physical Chemistry Letters 2022, 13 (16) , 3712-3717. https://doi.org/10.1021/acs.jpclett.2c00121
    83. Paulius Kantakevičius, Calvin Mathiah, Linus O. Johannissen, Sam Hay. Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion–Protein Interactions. Journal of Chemical Theory and Computation 2022, 18 (4) , 2367-2374. https://doi.org/10.1021/acs.jctc.1c00898
    84. Gaurav Sharma, Kenneth M. Merz. Mechanism of Zinc Transport through the Zinc Transporter YiiP. Journal of Chemical Theory and Computation 2022, 18 (4) , 2556-2568. https://doi.org/10.1021/acs.jctc.1c00927
    85. David J. Huggins. Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation 2022, 18 (4) , 2616-2630. https://doi.org/10.1021/acs.jctc.1c01208
    86. Toru Saito, Yu Takano. QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease. The Journal of Physical Chemistry B 2022, 126 (10) , 2087-2097. https://doi.org/10.1021/acs.jpcb.1c10200
    87. Kara K. Grotz, Nadine Schwierz. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. Journal of Chemical Theory and Computation 2022, 18 (1) , 526-537. https://doi.org/10.1021/acs.jctc.1c00791
    88. Bianca Fiorillo, Silvia Marchianò, Federica Moraca, Valentina Sepe, Adriana Carino, Pasquale Rapacciuolo, Michele Biagioli, Vittorio Limongelli, Angela Zampella, Bruno Catalanotti, Stefano Fiorucci. Discovery of Bile Acid Derivatives as Potent ACE2 Activators by Virtual Screening and Essential Dynamics. Journal of Chemical Information and Modeling 2022, 62 (1) , 196-209. https://doi.org/10.1021/acs.jcim.1c01126
    89. Yejie Qiu, Yang Jiang, Yongguang Zhang, Haiyang Zhang. Rational Design of Nonbonded Point Charge Models for Monovalent Ions with Lennard-Jones 12–6 Potential. The Journal of Physical Chemistry B 2021, 125 (49) , 13502-13518. https://doi.org/10.1021/acs.jpcb.1c09103
    90. Zongfan Yang, Rebecca M. Twidale, Silvia Gervasoni, Reynier Suardíaz, Charlotte K. Colenso, Eric J. M. Lang, James Spencer, Adrian J. Mulholland. Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. Journal of Chemical Information and Modeling 2021, 61 (11) , 5658-5672. https://doi.org/10.1021/acs.jcim.1c01109
    91. Elisa Donati, Pietro Vidossich, Marco De Vivo. Molecular Mechanism of Phosphate Steering for DNA Binding, Cleavage Localization, and Substrate Release in Nucleases. ACS Catalysis 2021, 11 (21) , 13244-13254. https://doi.org/10.1021/acscatal.1c03346
    92. Manuel David Peris-Díaz, Roman Guran, Carmen Domene, Vivian de los Rios, Ondrej Zitka, Vojtech Adam, Artur Krężel. An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species. Journal of the American Chemical Society 2021, 143 (40) , 16486-16501. https://doi.org/10.1021/jacs.1c05495
    93. Iurii Chubak, Laura Scalfi, Antoine Carof, Benjamin Rotenberg. NMR Relaxation Rates of Quadrupolar Aqueous Ions from Classical Molecular Dynamics Using Force-Field Specific Sternheimer Factors. Journal of Chemical Theory and Computation 2021, 17 (10) , 6006-6017. https://doi.org/10.1021/acs.jctc.1c00690
    94. Gouri S. Jas, Ed W. Childs, C. Russell Middaugh, Krzysztof Kuczera. Probing the Internal Dynamics and Shape of Simple Peptides in Urea, Guanidinium Hydrochloride, and Proline Solutions with Time-Resolved Fluorescence Anisotropy and Atomistic Cosolvent Simulations. The Journal of Physical Chemistry B 2021, 125 (39) , 10972-10984. https://doi.org/10.1021/acs.jpcb.1c06838
    95. Yongguang Zhang, Yang Jiang, Yejie Qiu, Haiyang Zhang. Rational Design of Nonbonded Point Charge Models for Highly Charged Metal Cations with Lennard-Jones 12-6 Potential. Journal of Chemical Information and Modeling 2021, 61 (9) , 4613-4629. https://doi.org/10.1021/acs.jcim.1c00723
    96. Arathi Anil Sushma, Bingqing Zhao, Irina B. Tsvetkova, Carolina Pérez-Segura, Jodi A. Hadden-Perilla, James P. Reilly, Bogdan Dragnea. Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles. The Journal of Physical Chemistry B 2021, 125 (37) , 10494-10505. https://doi.org/10.1021/acs.jpcb.1c06395
    97. Gaurav Sharma, Kenneth M. Merz. Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter. Biochemistry 2021, 60 (36) , 2727-2738. https://doi.org/10.1021/acs.biochem.1c00415
    98. Yongguang Zhang, Yang Jiang, Jiarong Peng, Haiyang Zhang. Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential. Journal of Chemical Information and Modeling 2021, 61 (8) , 4031-4044. https://doi.org/10.1021/acs.jcim.1c00580
    99. Randall T. Cygan, Jeffery A. Greathouse, Andrey G. Kalinichev. Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces. The Journal of Physical Chemistry C 2021, 125 (32) , 17573-17589. https://doi.org/10.1021/acs.jpcc.1c04600
    100. Andriy Stelmakh, Marcel Aebli, Andrij Baumketner, Maksym V. Kovalenko. On the Mechanism of Alkylammonium Ligands Binding to the Surface of CsPbBr3 Nanocrystals. Chemistry of Materials 2021, 33 (15) , 5962-5973. https://doi.org/10.1021/acs.chemmater.1c01081
    Load more citations
    Download PDF
    Go to Journal of Chemical Theory and Computation
    Get e-Alerts
    Get e-Alerts

    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2013, 9, 6, 2733–2748
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ct400146w
    Published May 8, 2013
    Copyright © 2013 American Chemical Society
    Request reuse permissions

    Article Views

    10k

    Altmetric

    -

    Citations

    549
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.