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Florez E, Zapata-Escobar AD, Ferraro F, Ibargüen Becerra C, Chamorro Y, Maldonado AF. Coordination of Mercury(II) in Water Promoted over Hydrolysis in Solvated Clusters [Hg(H 2O) 1-6] (aq)2+: Insights from Relativistic Effects and Free Energy Analysis. J Phys Chem A 2023; 127:8032-8049. [PMID: 37672217 DOI: 10.1021/acs.jpca.3c02927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Understanding the nature of the interaction between mercury(II) ions, Hg2+, and water molecules is crucial to describe the stability and chemical behavior of structures formed during solvation, as well as the conditions that favor the Hg2+ coordination or inducing water hydrolysis. In our study, we explored exhaustively the potential energy surface of Hg2+ with up to six water molecules. We analyzed electronic and Gibbs free energies, binding, and nuclear magnetic resonance parameters. We used the zeroth-order regular approximation Hamiltonian, including scalar and spin-orbit relativistic corrections for free energy calculations and geometry optimizations to explore the interplay between electron correlation and relativistic effects. We analyzed intermolecular interactions with energy decomposition analysis, quantum theory of atoms in molecules, and natural bond orbital. Additionally, we used the four-component Dirac Hamiltonian to compute solvent effect on the magnetic shielding and J-coupling constants. Our results revealed that the water hydrolysis by Hg2+ requires a minimum of three water molecules. We found that the interaction between Hg2+ and water molecules is an orbital interaction due to relativistic effects and the most stable structures are opened-shape clusters, reducing the number of oxygen-mercury contacts and maximizing the formation of hydrogen bonds among water molecules. In these types of clusters, Hg2+ promotes the water hydrolysis over coordination with oxygen atoms. However, when we considered the change associated with the transfer of a cluster from the ideal gas to a solvated system, our solvation free energy analysis revealed that closed-shape clusters are more favorable, maximizing the number of oxygen-mercury contacts and reducing the formation of hydrogen bonds among water molecules. This finding suggests that, under room conditions, the coordination of Hg2+ is more favorable than hydrolysis. Our results have significant implications for understanding Hg2+ behavior in water, helping to develop targeted strategies for mercury remediation and management, and contributing to advancements in the broader field of environmental chemistry.
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Affiliation(s)
- Edison Florez
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University, 0632 Auckland, New Zealand
| | - Andy D Zapata-Escobar
- Institute for Modeling and Innovative Technology (IMIT), CONICET-UNNE, W3404AAS Corrientes, Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University, W3404AAS Corrientes, Argentina
| | - Franklin Ferraro
- Departamento de Ciencias Básicas, Universidad Católica Luis Amigó, 050034 Medellín, Colombia
| | - César Ibargüen Becerra
- Institute of Chemistry, University of Antioquia, 050010 Medellín, Colombia
- Facultad de Arquitectura e Ingeniería, Institución Universitaria Colegio Mayor de Antioquia (IUCMA), 050034 Medellín, Colombia
| | - Yuly Chamorro
- Van Swinderen Institute for Particle Physics and Gravity, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Alejandro F Maldonado
- Institute for Modeling and Innovative Technology (IMIT), CONICET-UNNE, W3404AAS Corrientes, Argentina
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Wang R, Wang J, Zhu Y, Yu F, Yang Y, Wang Z. A Covalent‐Like Feature of Intermolecular Hydrogen Bonding in Energetic Molecules 3,6‐Dihydrazino‐s‐tetrazine (DHT). ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rui Wang
- Institute of Atomic and Molecular Physics Jilin University Changchun 130012 P.R. China
| | - Jia Wang
- College of Information Technology Jilin Normal University Siping 136000 P.R. China
| | - Yu Zhu
- Institute of Atomic and Molecular Physics Jilin University Changchun 130012 P.R. China
| | - Famin Yu
- Institute of Atomic and Molecular Physics Jilin University Changchun 130012 P.R. China
| | - Yanqiang Yang
- Institute of Fluid Physics China Academy of Engineering Physics Mianyang 621900 P.R. China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics Institute of Theoretical Chemistry Jilin University Changchun 130012 P.R. China
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Alford RF, Leaver-Fay A, Jeliazkov JR, O’Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput 2017; 13:3031-3048. [PMID: 28430426 PMCID: PMC5717763 DOI: 10.1021/acs.jctc.7b00125] [Citation(s) in RCA: 813] [Impact Index Per Article: 116.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.
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Affiliation(s)
- Rebecca F. Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Jeliazko R. Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Matthew J. O’Meara
- Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Frank P. DiMaio
- Department of Biochemistry, University of Washington, J-Wing Health Sciences Building, Box 357350, Seattle, Washington 98195, United States
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Maxim V. Shapovalov
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, New York 10003
- Center for Computational Biology, Flatiron Institute, Simons Foundation, 162 5 Avenue, New York, New York 10010, United States
| | - Vikram K. Mulligan
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Kalli Kappel
- Biophysics Program, Stanford University, 450 Serra Mall, Stanford, California 94305, United States
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Michael S. Pacella
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, New York 10003
- Center for Computational Biology, Flatiron Institute, Simons Foundation, 162 5 Avenue, New York, New York 10010, United States
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
| | - Rhiju Das
- Biophysics Program, Stanford University, 450 Serra Mall, Stanford, California 94305, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California 94158, United States
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
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