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Chen X, Cifuentes-Lopez A, Shao X, Lin L, Prokopchuk D, Pavanello M. Unraveling the Hydration Shell Structure and Dynamics of Group 10 Aqua Ions. J Phys Chem Lett 2024; 15:5517-5528. [PMID: 38749061 DOI: 10.1021/acs.jpclett.4c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
We present ab initio simulations based on subsystem DFT of group 10 aqua ions accurately compared against experimental data on hydration structure. Our simulations provide insights into the molecular structures and dynamics of hydration shells, offering recalibrated interpretations of experimental results. We observe a soft, but distinct second hydration shell in Palladium (Pd) due to a balance between thermal fluctuations, metal-water interactions, and hydrogen bonding. Nickel (Ni) and platinum (Pt) exhibit more rigid hydration shells. Notably, our simulations align with experimental findings for Pd, showing axial hydration marked by a broad peak at about 3 Å in the Pd-O radial distribution function, revising the previously sharp "mesoshell" prediction. We introduce the "hydrogen bond dome" concept to describe a resilient network of hydrogen-bonded water molecules around the metal, which plays a critical role in the axial hydration dynamics.
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Affiliation(s)
- Xin Chen
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | | | - Xuecheng Shao
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Lirong Lin
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Demyan Prokopchuk
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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2
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Petrov AI. Quantum chemical modeling of the thermodynamics of the formation of Au(III), Pd(II), and Pt(II) chloride complexes. J Mol Model 2022; 28:391. [DOI: 10.1007/s00894-022-05381-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
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3
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Pappalardo RR, Caralampio DZ, Martínez JM, Sánchez Marcos E. Hydration of Heavy Alkaline-Earth Cations Studied by Molecular Dynamics Simulations and X-ray Absorption Spectroscopy. Inorg Chem 2021; 60:13578-13587. [PMID: 34387993 PMCID: PMC8512670 DOI: 10.1021/acs.inorgchem.1c01888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physicochemical properties of the three heaviest alkaline-earth cations, Sr2+, Ba2+, and Ra2+ in water have been studied by means of classical molecular dynamics (MD) simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The polarizable and flexible model of water MCDHO2 was adopted. The theoretical-experimental comparison of structural, dynamical, energetic, and spectroscopical properties of Sr2+ and Ba2+ aqueous solutions is satisfactory, which supports the methodology developed. This good behavior allows a reasonable reliability for the predicted Ra2+ physicochemical data not experimentally determined yet. Simulated extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge spectroscopy spectra have been computed from the snapshots of the MD simulations and compared with the experimental information available for Sr2+ and Ba2+. For the Ra2+ case, the Ra L3-edge EXAFS spectrum is proposed. Structural and dynamical properties of the aqua ions for the three cations have been obtained and analyzed. Along the [M(H2O)n]m+ series, the M-O distance for the first-hydration shell is 2.57, 2.81, and 2.93 Å for Sr2+, Ba2+, and Ra2+, respectively. The hydration number also increases when one is going down along the group: 8.1, 9.4, and 9.8 for Sr2+, Ba2+, and Ra2+, respectively. Whereas [Sr(H2O)8]2+ is a typical aqua ion with a well-defined structure, the Ba2+ and Ra2+ hydration provides a picture exhibiting an average between the ennea- and the deca-hydration. These results show a similar chemical behavior of Ba2+ and Ra2+ aqueous solutions and support experimental studies on the removal of Ra-226 of aquifers by different techniques, where Ra2+ is replaced by Ba2+. A comparison of the heavy alkaline ions, Rb+ and Cs+, with the heavy alkaline-earth ions is made.
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Affiliation(s)
- Rafael R Pappalardo
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - Daniel Z Caralampio
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - José M Martínez
- Department of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
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4
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Saleh M, Zam ZZ, Hofer TS. Solvent influence on the presence of axial ligand coordination: A QMCF-MD study of the structural and dynamical properties of Pd(II) and Pd(II) tetra-ammine in aqueous solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Palladium Oxide Nanoparticles: Preparation, Characterization and Catalytic Activity Evaluation. COATINGS 2020. [DOI: 10.3390/coatings10030207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stable palladium oxide nanoparticles were prepared in aqueous suspension with a very simple procedure, by dissolving palladium nitrate in water at a concentration around 10−4 M. UV-visible absorption spectroscopy was adopted to follow the formation of these nanoparticles, which were characterized by TEM microscopy, along with XRD, XPS and Raman measurements. DFT calculations allowed to interpret the Raman data and to clarify the species present at the surface of the nanoparticles. The catalytic activity of the latter was evaluated by monitoring the reduction of p-nitrophenol to p-aminophenol. This investigation paves the way to the use of these colloidal nanoparticles in processes of heterogeneous catalysis, in particular those concerning the catalytic degradation of aromatic derivatives that represent a serious danger for the environment as pollutants, as in the case of p-nitrophenol.
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Pérez-Conesa S, Torrico F, Martínez JM, Pappalardo RR, Marcos ES. A general study of actinyl hydration by molecular dynamics simulations usingab initioforce fields. J Chem Phys 2019; 150:104504. [DOI: 10.1063/1.5083216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergio Pérez-Conesa
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Francisco Torrico
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
| | - José M. Martínez
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
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7
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Minervini T, Cardey B, Foley S, Ramseyer C, Enescu M. Fate of cisplatin and its main hydrolysed forms in the presence of thiolates: a comprehensive computational and experimental study. Metallomics 2019; 11:833-844. [DOI: 10.1039/c8mt00371h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiolations and bidentations drive the chemical fate of cisplatin compounds in intracellular medium.
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Affiliation(s)
- Thibault Minervini
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Bruno Cardey
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Sarah Foley
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Christophe Ramseyer
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Mironel Enescu
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
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8
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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9
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Development of a polarizable and flexible model of the hydrated ion potential to study the intriguing case of Sc(III) hydration. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2075-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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11
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Caralampio DZ, Martínez JM, Pappalardo RR, Marcos ES. The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity. Phys Chem Chem Phys 2017; 19:28993-29004. [DOI: 10.1039/c7cp05346k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydration shells around Rb+ and Cs+ are not symmetric; the cation and the 1st-shell water mass center are separated by ∼0.4 Å, and this is supported by agreement between the theoretical and experimental EXAFS spectrum.
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Affiliation(s)
| | - José M. Martínez
- Departmento de Quimica Fisica
- Universidad de Sevilla
- 41012-Seville
- Spain
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12
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Pérez-Conesa S, Torrico F, Martínez JM, Pappalardo RR, Sánchez Marcos E. A hydrated ion model of [UO2]2+ in water: Structure, dynamics, and spectroscopy from classical molecular dynamics. J Chem Phys 2016; 145:224502. [DOI: 10.1063/1.4971432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergio Pérez-Conesa
- Departamento de Química Física, Universidad de Seville, 41012 Seville, Spain
| | - Francisco Torrico
- Departamento de Química Física, Universidad de Seville, 41012 Seville, Spain
| | - José M. Martínez
- Departamento de Química Física, Universidad de Seville, 41012 Seville, Spain
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13
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Šebesta F, Sláma V, Melcr J, Futera Z, Burda JV. Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields. J Chem Theory Comput 2016; 12:3681-8. [DOI: 10.1021/acs.jctc.6b00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Vladislav Sláma
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Josef Melcr
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Zdeněk Futera
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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14
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Melchior A, Tolazzi M, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Two Cisplatin Aqua-Derivatives Studied by Quantum Mechanics and Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:1735-44. [DOI: 10.1021/ct500975a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andrea Melchior
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - Marilena Tolazzi
- Department
of Environmental and Physical Chemistry, University of Udine, 33100 Udine, Udine, Italy
| | - José Manuel Martínez
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
| | - Rafael R. Pappalardo
- Department
of Physical Chemistry, University of Seville, 41012 Seville, Seville, Spain
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15
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Galbis E, Hernández-Cobos J, Pappalardo RR, Marcos ES. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf3+. J Chem Phys 2014; 140:214104. [DOI: 10.1063/1.4879549] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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16
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Melchior A, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Cisplatin Studied by an Effective Ab Initio Pair Potential Including Solute–Solvent Polarization. J Chem Theory Comput 2013; 9:4562-73. [DOI: 10.1021/ct400433c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Melchior
- University of Udine, Department of Environmental and
Physical Chemistry, 33100 Udine, Italy
- University of Seville, Department of Physical Chemistry, 41012 Seville, Spain
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17
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Torapava N, Elding LI, Mändar H, Roosalu K, Persson I. Structures of polynuclear complexes of palladium(ii) and platinum(ii) formed by slow hydrolysis in acidic aqueous solution. Dalton Trans 2013; 42:7755-60. [DOI: 10.1039/c3dt32859g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Mori H, Hirayama N, Komeiji Y, Mochizuki Y. Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD). COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Bowron DT, Beret EC, Martin-Zamora E, Soper AK, Sánchez Marcos E. Axial Structure of the Pd(II) Aqua Ion in Solution. J Am Chem Soc 2011; 134:962-7. [DOI: 10.1021/ja206422w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel T. Bowron
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | | | | | - Alan K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
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20
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Martín EI, Martínez JM, Sánchez Marcos E. Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine. J Chem Phys 2011; 134:024503. [PMID: 21241116 DOI: 10.1063/1.3528934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.
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Affiliation(s)
- Elisa I Martín
- Departamento de Química Física, Universidad de Sevilla, E-41012 Sevilla, Spain
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21
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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22
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Fu CF, Tian SX. Molecular dynamics study of solvation differences between cis- and transplatin molecules in water. J Chem Phys 2010; 132:174507. [DOI: 10.1063/1.3426029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Truflandier LA, Autschbach J. Probing the Solvent Shell with 195Pt Chemical Shifts: Density Functional Theory Molecular Dynamics Study of PtII and PtIV Anionic Complexes in Aqueous Solution. J Am Chem Soc 2010; 132:3472-83. [DOI: 10.1021/ja9096863] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
| | - Jochen Autschbach
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
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24
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Hofer TS, Rode BM, Pribil AB, Randolf BR. Simulations of Liquids and Solutions Based on Quantum Mechanical Forces. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62004-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Beret EC, Pappalardo RR, Marx D, Sánchez Marcos E. Characterizing Pt-derived anticancer drugs from first principles: the case of oxaliplatin in aqueous solution. Chemphyschem 2009; 10:1044-52. [PMID: 19253929 DOI: 10.1002/cphc.200900027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular compound ethyldiamine-oxalatoplatinum(II), EDO-Pt, is used as a model to study the oxaliplatin anticancer drug in aqueous solution by means of ab initio computer simulation. Gas-phase structure optimizations have been performed for both oxaliplatin and its EDO-Pt mimic along with Car-Parrinello molecular dynamics simulations of EDO-Pt in gas phase and in aqueous solution. The coordination of Pt(II) is square-planar on average, with Pt-N and Pt-O(I) distances of 2.04 A in solution. The diamine ligand has a bent structure, while the oxalate ligand is planar on average. The complex features a very rigid structure during the simulation and the charge distribution describes a dipole with its negative pole on the oxalate ligand and the positive pole on the Pt-diamine side. The solvation pattern of EDO-Pt is most well-defined around the amine and oxalate groups and is quantified by means of radial and spatial distribution functions of water molecules around the complex. Decomposition of radial distribution functions into their contributions from different regions (axial and equatorial) reveals an "anionic hydration" pattern of the metal cation by the solvent, which is analogous in nature to the bare Pt(II) aqua ion. A qualitative prediction on the kinetics of ligand exchange in oxaliplatin is derived based on its axial hydration pattern.
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Affiliation(s)
- Elizabeth C Beret
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
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26
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Hofer TS, Randolf BR, Rode BM, Persson I. The hydrated platinum(ii) ion in aqueous solution—a combined theoretical and EXAFS spectroscopic study. Dalton Trans 2009:1512-5. [DOI: 10.1039/b819248k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Beret EC, Martínez JM, Pappalardo RR, Marcos ES, Doltsinis NL, Marx D. Explaining Asymmetric Solvation of Pt(II) versus Pd(II) in Aqueous Solution Revealed by Ab Initio Molecular Dynamics Simulations. J Chem Theory Comput 2008; 4:2108-21. [DOI: 10.1021/ct800010q] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Elizabeth C. Beret
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
| | - José M. Martínez
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
| | - Rafael R. Pappalardo
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
| | - Enrique Sánchez Marcos
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
| | - Nikos L. Doltsinis
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Departamento de Quimica Fisica, Universidad de Sevilla, 41012 Sevilla, Spain, and Lehrstuhl für Theoretische Chemie, Ruhr—Universität Bochum, 44780 Bochum, Germany
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28
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Lopes JF, Rocha WR, Dos Santos HF, De Almeida WB. Theoretical study of the potential energy surface for the interaction of cisplatin and their aquated species with water. J Chem Phys 2008; 128:165103. [DOI: 10.1063/1.2909979] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Tarazona-Vasquez F, Balbuena PB. Pt(II) Uptake by Dendrimer Outer Pockets: 1. Solventless Ligand Exchange Reaction. J Phys Chem B 2008; 112:4172-81. [DOI: 10.1021/jp0761517] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Perla B. Balbuena
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843
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Beret EC, Pappalardo RR, Doltsinis NL, Marx D, Sánchez Marcos E. Aqueous PdII and PtII: Anionic Hydration Revealed by Car–Parrinello Simulations. Chemphyschem 2008; 9:237-40. [DOI: 10.1002/cphc.200700435] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Yazyev OV, Helm L. Nuclear Spin Relaxation Parameters of MRI Contrast Agents – Insight from Quantum Mechanical Calculations. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200701013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Oleg V. Yazyev
- Institut de Théorie des Phénomènes Physiques, Ecole Polytechnique Fédérale de Lausanne, and Institut Romand de Recherche Numérique en Physique des Matériaux (IRRMA), EPFL‐PPH, 1015 Lausanne, Switzerland, Fax: +41‐21‐693‐9875
| | - Lothar Helm
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, EPFL‐BCH, 1015 Lausanne, Switzerland, Fax: +41‐21‐693‐9875
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32
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Tarazona-Vasquez F, Balbuena PB. Dendrimer−Tetrachloroplatinate Precursor Interactions. 1. Hydration of Pt(II) Species and PAMAM Outer Pockets. J Phys Chem A 2007; 111:932-44. [PMID: 17266235 DOI: 10.1021/jp065014r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory is used to investigate the structure and energetics of the tetrachloroplatinate anion and its hydrolysis products at several degrees of hydration, as well as those of outer dendrimer pockets hosting such species. The number of water molecules able to saturate an unprotonated outer dendrimer pocket is found to be two, as inferred from calculated thermodynamic data. However, such a number could not be established for a protonated pocket where the dendrimer adopts a more open configuration. An analysis of possible pocket configurations is done on the basis of the orientations of the amide O atoms in the outer pockets. The effect of explicit water on the infrared spectra of the dendrimer pockets is reported and compared to experimental values.
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Lopes JF, de A Menezes VS, Duarte HA, Rocha WR, De Almeida WB, Dos Santos HF. Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution. J Phys Chem B 2006; 110:12047-54. [PMID: 16800515 DOI: 10.1021/jp057448c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Lennard-Jones (12-6) parameters were obtained for all atoms of cisplatin molecule using the ab initio quantum mechanical potential energy surface for the water-cisplatin interaction as reference data. The parameters found were (epsilon/kcal.mol(-1) and sigma/angstroms) 1.0550, 3.6590 (Pt); 0.0381, 4.6272 (Cl); 0.0455, 3.3783 (N); and 0.0185, 0.0936 (H) and provided very good results for the description of the aqueous solution of cisplatin through Monte Carlo simulation. From statistical analysis of solute-solvent interactions, we observed that the NH3 groups are involved in 53% of the calculated hydrogen bonds with a significant contribution from chlorides (41%) and only 6% involving the Pt center. This is in agreement with the expected behavior for such molecules. Two hydration shells with 22 and 81 water molecules, respectively, centered around 4.6 and 7.3 angstroms were found from the center of mass pair correlation function analysis. The cisplatin atomic Lennard-Jones parameters are reported for the first time, and they might be useful for studying the structure, properties, and processes of cisplatin-like molecules in aqueous solution, including explicitly the solvent effect.
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Affiliation(s)
- Juliana Fedoce Lopes
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Martelos, CEP 36036-900, Juiz de Fora, MG, Brazil
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