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Rose T, Bursch M, Mewes JM, Grimme S. Fast and Robust Modeling of Lanthanide and Actinide Complexes, Biomolecules, and Molecular Crystals with the Extended GFN-FF Model. Inorg Chem 2024; 63:19364-19374. [PMID: 39334529 DOI: 10.1021/acs.inorgchem.4c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2024]
Abstract
Lanthanides (Ln) and actinides (An) have recently become important tools in biomedical and materials science. However, the development of computational methods able to describe such elements in various environments has not kept up with the pace of the field. Addressing this challenge, this work introduces and showcases an extension of the GFN-FF to An alongside a reparameterization for Ln. This development fills a gap for fast computational methods that are out-of-the-box applicable to large f-element-containing systems with thousands of atoms. We discuss the reparameterization of the charge model and the covalent topology setup and showcase the model through various applications: Molecular dynamics simulations, optimization of Ln-containing biomolecules, and optimizations of several periodic structures. With the presented improvements, GFN-FF is a powerful method that routinely delivers robust and accurate geometries for large Ln/An systems with thousands of atoms.
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Affiliation(s)
- Thomas Rose
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, Bonn 53115, Germany
| | | | | | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, Bonn 53115, Germany
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2
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Raposo-Hernández G, Pappalardo RR, Réal F, Vallet V, Sánchez Marcos E. Toward a realistic theoretical electronic spectra of metal aqua ions in solution: The case of Ce(H2O)n3+ using statistical methods and quantum chemistry calculations. J Chem Phys 2024; 161:144109. [PMID: 39387406 DOI: 10.1063/5.0228155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024] Open
Abstract
Accurately predicting spectra for heavy elements, often open-shell systems, is a significant challenge typically addressed using a single cluster approach with a fixed coordination number. Developing a realistic model that accounts for temperature effects, variable coordination numbers, and interprets experimental data is even more demanding due to the strong solute-solvent interactions present in solutions of heavy metal cations. This study addresses these challenges by combining multiple methodologies to accurately predict realistic spectra for highly charged metal cations in aqueous media, with a focus on the electronic absorption spectrum of Ce3+ in water. Utilizing highly correlated relativistic quantum mechanical (QM) wavefunctions and structures from molecular dynamics (MD) simulations, we show that the convolution of individual vertical transitions yields excellent agreement with experimental results without the introduction of empirical broadening. Good results are obtained for both the normalized spectrum and that of absolute intensity. The study incorporates a statistical machine learning algorithm, Gaussian Mixture Models-Nuclear Ensemble Approach (GMM-NEA), to convolute individual spectra. The microscopic distribution provided by MD simulations allows us to examine the contributions of the octa- and ennea-hydrate of Ce3+ in water to the final spectrum. In addition, the temperature dependence of the spectrum is theoretically captured by observing the changing population of these hydrate forms with temperature. We also explore an alternative method for obtaining statistically representative structures in a less demanding manner than MD simulations, derived from QM Wigner distributions. The combination of Wigner-sampling and GMM-NEA broadening shows promise for wide application in spectroscopic analysis and predictions, offering a computationally efficient alternative to traditional methods.
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Affiliation(s)
| | - Rafael R Pappalardo
- Department of Physical Chemistry, University of Seville, 41012 Seville, Spain
| | - Florent Réal
- Université de Lille, CNRS, UMR 8523-PhLAM, Physique des Lasers, Atomes et Molecules, F-59000 Lille, France
| | - Valérie Vallet
- Université de Lille, CNRS, UMR 8523-PhLAM, Physique des Lasers, Atomes et Molecules, F-59000 Lille, France
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3
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Lu JB, Zhang YY, Jiang XL, Ye LW, Li J. Improved Gaussian basis sets for norm-conserving 4f-in-core pseudopotentials of trivalent lanthanides (Ln = Ce-Lu). J Chem Phys 2024; 161:134115. [PMID: 39373205 DOI: 10.1063/5.0228388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 09/11/2024] [Indexed: 10/08/2024] Open
Abstract
The first-principles quantum chemical computations often scale as Nk (N = basis sets; k = 1-4 for linear scaling, Hartree-Fock or density functional theory methods), which makes the development of accurate pseudopotentials and efficient basis sets necessary ingredients in modeling of heavy elements such as lanthanides and actinides. Recently, we have developed 4f-in-core norm-conserving pseudopotentials and associated basis sets for the trivalent lanthanides [Lu et al., J. Chem. Theory Comput. 19, 82-96 (2023)]. In the present paper, we present a unified approach to optimize high-quality Gaussian basis sets for modeling and simulations of condensed-phase systems. The newly generated basis sets not only capture the low total energy and fairly reasonable condition number of overlap matrix of lanthanide-containing systems, but also exhibit good transferability and reproducibility. These advantages ensure the accuracy of the basis sets while avoiding linear dependency concern of atom-centered basis sets. The performance of the basis sets is further illustrated in lanthanide molecular and condensed-phase systems by using Gaussian-plane wave density functional approach of CP2K. These new basis sets can be of particular interest to model structurally complicated lanthanide molecules, clusters, solutions, and solid systems.
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Affiliation(s)
- Jun-Bo Lu
- Fundamental Science Center of Rare Earths, Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou 341000, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yang-Yang Zhang
- Fundamental Science Center of Rare Earths, Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou 341000, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xue-Lian Jiang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lian-Wei Ye
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Jun Li
- Fundamental Science Center of Rare Earths, Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou 341000, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China
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Duvail M, Moreno Martinez D, Žiberna L, Guillam E, Dufrêche JF, Guilbaud P. Modeling Lanthanide Ions in Solution: A Versatile Force Field in Aqueous and Organic Solvents. J Chem Theory Comput 2024. [PMID: 38221754 DOI: 10.1021/acs.jctc.3c01162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
In this paper, we propose a new nonpolarizable force field for describing the Ln3+ (Ln = lanthanide) series based on a 12-6-4 Lennard-Jones potential. The development of the force field was performed in pure water by adjusting both the ion-oxygen distance and the hydration free energy. This force field accurately reproduces the Ln3+ hydration properties through the series, especially the coordination number that is hardly accessible using a nonpolarizable force field. Then, the validity and the transferability of the current force field were evaluated for two different systems containing Ln3+ in various solvents, namely, 0.1 mol L-1 La(NO3)3 salts in methanol and Eu(NO3)3 salts in solvent organic phases composed of DMDOHEMA molecules in n-heptane. The good agreement between our simulations and the data available in the literature confirms the accuracy of the force field for describing the lanthanide cations in both aqueous and nonaqueous media.
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Affiliation(s)
- Magali Duvail
- ICSM, University of Montpellier, CEA, CNRS, ENSCM, 30207 Bagnols-sur-Cèze, France
| | - Diego Moreno Martinez
- CEA, DES, ISEC, DMRC, LILA, University of Montpellier, Marcoule, 30207 Bagnols-sur-Cèze, France
| | - Lara Žiberna
- ICSM, University of Montpellier, CEA, CNRS, ENSCM, 30207 Bagnols-sur-Cèze, France
| | - Erwann Guillam
- ICSM, University of Montpellier, CEA, CNRS, ENSCM, 30207 Bagnols-sur-Cèze, France
| | | | - Philippe Guilbaud
- CEA, DES, ISEC, DMRC, University of Montpellier, Marcoule, 30207 Bagnols-sur-Cèze, France
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5
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Zhang W, Zhou L, Yan T, Chen M. Speciation of La 3+-Cl - Complexes in Hydrothermal Fluids from Deep Potential Molecular Dynamics. J Phys Chem B 2023; 127:8926-8937. [PMID: 37812657 DOI: 10.1021/acs.jpcb.3c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The stability of rare earth element (REE) complexes plays a crucial role in quantitatively assessing their hydrothermal migration and transformation. However, reliable data are lacking under high-temperature hydrothermal conditions, which hampers our understanding of the association behavior of REE. Here a deep learning potential model for the LaCl3-H2O system in hydrothermal fluids is developed based on the first-principles density functional theory calculations. The model accurately predicts the radial distribution functions compared to ab initio molecular dynamics (AIMD) simulations. Furthermore, species of La-Cl complexes, the dissociation pathway of the La-Cl complexes dissociation process, and the potential of mean forces and corresponding association constants (logK) for LaCln3-n (n = 1-4) are extensively investigated under a wide range of temperatures and pressures. Empirical density models for logK calculation are fitted with these data and can accurately predict logK data from both experimental results and AIMD simulations. The distribution of La-Cl species is also evaluated across a wide range of temperatures, pressures, and initial chloride concentration conditions. The results show that La-Cl complexes are prone to forming in a low-density solution, and the number of bonded Cl- ions increases with rising temperature. In contrast, in a high-density solution, La3+ dominates and becomes the more prevalent species.
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Affiliation(s)
- Wei Zhang
- School of Geography and Environmental Science (School of Karst Science), Guizhou Normal University, Guiyang 550025, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550025, China
- Research Center of Karst Ecological Civilization, Guizhou Normal University, Guiyang 550025, China
| | - Li Zhou
- School of Geography and Environmental Science (School of Karst Science), Guizhou Normal University, Guiyang 550025, China
| | - Tinggui Yan
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
| | - Mohan Chen
- HEDPS, CAPT, College of Engineering and School of Physics, Peking University, Beijing 100871, China
- AI for Science Institute, Beijing 100080, China
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6
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McElhany SJ, Summers TJ, Shiery RC, Cantu DC. Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions. J Chem Inf Model 2023; 63:2699-2706. [PMID: 37083437 DOI: 10.1021/acs.jcim.3c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Rapid and accurate approaches to characterizing the coordination structure of an ion are important for designing ligands and quantifying structure-property trends. Here, we introduce AFICS (Analysis of the First Ion Coordination Sphere), a tool written in Python 3 for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. The principal feature of AFICS is its ability to quantify the distortion a coordination geometry undergoes compared to uniform polyhedra. This work applies the toolkit to analyze molecular dynamics simulations of the well-defined coordination structure of aqueous Cr3+ along with the more ambiguous structure of aqueous Eu3+ chelated to ethylenediaminetetraacetic acid. The tool is targeted for analyzing ions with fluxional or irregular coordination structures (e.g., solution structures of f-block elements) but is generalized such that it may be applied to other systems.
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Affiliation(s)
- Stuart J McElhany
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Thomas J Summers
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Richard C Shiery
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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7
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Lu JB, Jiang XL, Hu HS, Li J. Norm-Conserving 4f-in-Core Pseudopotentials and Basis Sets Optimized for Trivalent Lanthanides (Ln = Ce-Lu). J Chem Theory Comput 2023; 19:82-96. [PMID: 36512750 DOI: 10.1021/acs.jctc.2c00922] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present here a set of scalar-relativistic norm-conserving 4f-in-core pseudopotentials, together with complementary valence-shell Gaussian basis sets, for the lanthanide (Ln) series (Ce-Lu). The Goedecker, Teter, and Hutter (GTH) formalism is adopted with the generalized gradient approximation (GGA) for the exchange-correlation Perdew-Burke-Ernzerhof (PBE) functional. The 4f-in-core pseudopotentials are built through attributing 4f-subconfiguration 4fn (n = 1-14) for Ln (Ln = Ce-Lu) into the atomic core region, making it possible to circumvent the difficulty of the description of the open 4fn valence shell. A wide variety of computational benchmarks and tests have been carried out on lanthanide systems including Ln3+-containing molecular complexes, aqueous solutions, and bulk solids to validate the accuracy, reliability, and efficiency of the optimized 4f-in-core GTH pseudopotentials and basis sets. The 4f-in-core GTH pseudopotentials successfully replicate the main features of lanthanide structural chemistry and reaction energetics, particularly for nonredox reactions. The chemical bonding features and solvation shells, hydrolysis energetics, acidity constants, and solid-state properties of selected lanthanide systems are also discussed in detail by utilizing these new 4f-in-core GTH pseudopotentials. This work bridges the idea of keeping highly localized 4f electrons in the atomic core and efficient pseudopotential formalism of GTH, thus providing a highly efficient approach for studying lanthanide chemistry in multi-scale modeling of constituent-wise and structurally complicated systems, including electronic structures of the condensed phase and first-principles molecular dynamics simulations.
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Affiliation(s)
- Jun-Bo Lu
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xue-Lian Jiang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Han-Shi Hu
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Jun Li
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China
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8
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D'Angelo P, Migliorati V, Gibiino A, Busato M. Direct Observation of Contact Ion-Pair Formation in La 3+ Methanol Solution. Inorg Chem 2022; 61:17313-17321. [PMID: 36255362 PMCID: PMC9627567 DOI: 10.1021/acs.inorgchem.2c02932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
An approach combining molecular dynamics (MD) simulations
and X-ray
absorption spectroscopy (XAS) has been used to carry out a comparative
study about the solvation properties of dilute La(NO3)3 solutions in water and methanol, with the aim of elucidating
the still elusive coordination of the La3+ ion in the latter
medium. The comparison between these two systems enlightened a different
behavior of the nitrate counterions in the two environments: while
in water the La(NO3)3 salt is fully dissociated
and the La3+ ion is coordinated by water molecules only,
the nitrate anions are able to enter the metal first solvation shell
to form inner-sphere complexes in methanol solution. The speciation
of the formed complexes showed that the 10-fold coordination is preferential
in methanol solution, where the nitrate anions coordinate the La3+ cations in a monodentate fashion and the methanol molecules
complete the solvation shell to form an overall bicapped square antiprism
geometry. This is at variance with the aqueous solution where a more
balanced situation is observed between the 9- and 10-fold coordination.
An experimental confirmation of the MD results was obtained by La
K-edge XAS measurements carried out on 0.1 M La(NO3)3 solutions in the two solvents, showing the distinct presence
of the nitrate counterions in the La3+ ion first solvation
sphere of the methanol solution. The analysis of the extended X-ray
absorption fine structure (EXAFS) part of the absorption spectrum
collected on the methanol solution was carried out starting from the
MD results and confirmed the structural arrangement observed by the
simulations. The formation of contact ion pairs between
the La3+ ions and the nitrate anions has been demonstrated
in diluted methanol
solution using a combined approach using Molecular Dynamics simulations
and X-ray absorption spectroscpy.
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Affiliation(s)
- Paola D'Angelo
- Department of Chemistry, University of Rome "La Sapienza", P.le Aldo Moro 5, 00185 Rome, Italy
| | - Valentina Migliorati
- Department of Chemistry, University of Rome "La Sapienza", P.le Aldo Moro 5, 00185 Rome, Italy
| | - Alice Gibiino
- Department of Chemistry, University of Rome "La Sapienza", P.le Aldo Moro 5, 00185 Rome, Italy
| | - Matteo Busato
- Department of Chemistry, University of Rome "La Sapienza", P.le Aldo Moro 5, 00185 Rome, Italy
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9
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Zhang W, Yan T. A molecular dynamics investigation of La3+ and Lu3+-ligand speciation in aqueous solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Stemplinger S, Duvail M, Dufrêche JF. Molecular dynamics simulations of Eu(NO3)3 salt with DMDOHEMA in n-alkanes: Unravelling curvature properties in liquid-liquid extraction. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Driscoll DM, Shiery RC, Balasubramanian M, Fulton JL, Cantu DC. Ionic Contraction across the Lanthanide Series Decreases the Temperature-Induced Disorder of the Water Coordination Sphere. Inorg Chem 2021; 61:287-294. [PMID: 34919399 DOI: 10.1021/acs.inorgchem.1c02837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In liquid, temperature affects the structures of lanthanide complexes in multiple ways that depend upon complex interactions between ligands, anions, and solvent molecules. The relative simplicity of lanthanide aqua ions (Ln3+) make them well suited to determine how temperature induces structural changes in lanthanide complexes. We performed a combination of ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) measurements, both at 25 and 90 °C, to determine how temperature affects the first- and second-coordination spheres of three Ln3+ (Ce3+, Sm3+, and Lu3+) aqua ions. AIMD simulations show first lanthanide coordination spheres that are similar at 25 and 90 °C, more so for the Lu3+ ion that remains as eight-coordinate than for the Ce3+ and Sm3+ ions that change their preferred coordination number from nine (at 25 °C) to eight (at 90 °C). The measured EXAFS spectra are very similar at 25 and 90 °C, for the Ce3+, Sm3+, and Lu3+ ions, suggesting that the dynamical disorder of the Ln3+ ions in liquid water is sufficient such that temperature-induced changes do not clearly manifest changes in the structure of the three ions. Both AIMD simulations and EXAFS measurements show very similar structures of the first coordination sphere of the Lu3+ ion at 25 and 90 °C.
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Affiliation(s)
- Darren M Driscoll
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Richard C Shiery
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | | | - John L Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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12
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Nakayama N, Hijikata M, Ohmagari H, Tanaka H, Inazuka Y, Saito D, Obata S, Ohta K, Kato M, Goto H, Hasegawa M. Computational studies for crystal structures of helicate lanthanide complexes based on X-ray analyses. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Naofumi Nakayama
- CONFLEX Co., Shinagawa Center Bldg., 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Masahiro Hijikata
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Hitomi Ohmagari
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
- Mirai Molecular Materials Design Institute, Aoyama Gakuin University, Sagamihara, Kanagawa 252-5258, Japan
| | - Hideyuki Tanaka
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yudai Inazuka
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Daisuke Saito
- Department of Chemistry, Faculty of Science, Hokkaido University, North-10 West-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Shigeaki Obata
- CONFLEX Co., Shinagawa Center Bldg., 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Kazuo Ohta
- CONFLEX Co., Shinagawa Center Bldg., 3-23-17 Takanawa, Minato-ku, Tokyo 108-0074, Japan
| | - Masako Kato
- Department of Chemistry, Faculty of Science, Hokkaido University, North-10 West-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Applied Chemistry for Environment, School of Biological and Environmental Sciences, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Hitoshi Goto
- Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Miki Hasegawa
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
- Mirai Molecular Materials Design Institute, Aoyama Gakuin University, Sagamihara, Kanagawa 252-5258, Japan
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13
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Smirnov PR, Grechin OV. Structure of the Nearest Environment of Ions in Aqueous Solutions of Praseodymium Chloride in a Wide Range of Concentrations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s003602442110023x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Ta AT, Golzwarden JVA, Jensen MP, Vyas S. Behaviors of ALSEP Organic Extractants: an Atomic Perspective Derived from Molecular Dynamics Simulation. SOLVENT EXTRACTION AND ION EXCHANGE 2021. [DOI: 10.1080/07366299.2021.1956104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- An T. Ta
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States
| | | | - Mark P. Jensen
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States
- Nuclear Science and Engineering Program, Colorado School of Mines, Golden, Colorado, United States
| | - Shubham Vyas
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States
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15
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Cantu DC. Predicting lanthanide coordination structures in solution with molecular simulation. Methods Enzymol 2021; 651:193-233. [PMID: 33888204 DOI: 10.1016/bs.mie.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The chemical and physical properties of lanthanide coordination complexes can significantly change with small variations in their molecular structure. Further, in solution, coordination structures (e.g., lanthanide-ligand complexes) are dynamic. Resolving solution structures, computationally or experimentally, is challenging because structures in solution have limited spatial restrictions and are responsive to chemical or physical changes in their surroundings. To determine structures of lanthanide-ligand complexes in solution, a molecular simulation approach is presented in this chapter, which concurrently considers chemical reactions and molecular dynamics. Lanthanide ion, ligand, solvent, and anion molecules are explicitly included to identify, in atomic resolution, lanthanide coordination structures in solution. The computational protocol described is applicable to determining the molecular structure of lanthanide-ligand complexes, particularly with ligands known to bind lanthanides but whose structures have not been resolved, as well as with ligands not previously known to bind lanthanide ions. The approach in this chapter is also relevant to elucidating lanthanide coordination in more intricate structures, such as in the active site of enzymes.
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Affiliation(s)
- David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, NV, United States.
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16
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Shiery RC, Fulton JL, Balasubramanian M, Nguyen MT, Lu JB, Li J, Rousseau R, Glezakou VA, Cantu DC. Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy. Inorg Chem 2021; 60:3117-3130. [PMID: 33544594 DOI: 10.1021/acs.inorgchem.0c03438] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To resolve the fleeting structures of lanthanide Ln3+ aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln3+ aqua ions in explicit water solvent using pseudopotentials and basis sets recently optimized for lanthanides and (ii) measured the symmetry of the hydrating waters about Ln3+ ions (Nd3+, Dy3+, Er3+, Lu3+) for the first time with extended X-ray absorption fine structure (EXAFS). EXAFS spectra were measured experimentally and generated from AIMD trajectories to directly compare simulation, which concurrently considers the electronic structure and the atomic dynamics in solution, with experiment. We performed a comprehensive evaluation of EXAFS multiple-scattering analysis (up to 6.5 Å) to measure Ln-O distances and angular correlations (i.e., symmetry) and elucidate the molecular geometry of the first hydration shell. This evaluation, in combination with symmetry-dependent L3- and L1-edge spectral analysis, shows that the AIMD simulations remarkably reproduces the experimental EXAFS data. The error in the predicted Ln-O distances is less than 0.07 Å for the later lanthanides, while we observed excellent agreement with predicted distances within experimental uncertainty for the early lanthanides. Our analysis revealed a dynamic, symmetrically disordered first coordination shell, which does not conform to a single molecular geometry for most lanthanides. This work sheds critical light on the highly elusive coordination geometry of the Ln3+ aqua ions.
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Affiliation(s)
- Richard C Shiery
- Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - John L Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - Manh-Thuong Nguyen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jun-Bo Lu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Roger Rousseau
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | - David C Cantu
- Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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17
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Gao Y, Grover P, Schreckenbach G. Stabilization of hydrated Ac III cation: the role of superatom states in actinium-water bonding. Chem Sci 2021; 12:2655-2666. [PMID: 34164034 PMCID: PMC8179294 DOI: 10.1039/d0sc02342f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 01/03/2021] [Indexed: 12/02/2022] Open
Abstract
225Ac-based radiopharmaceuticals have the potential to become invaluable in designated cancer therapy. However, the limited understanding of the solution chemistry and bonding properties of actinium has hindered the development of existing and emerging targeted radiotherapeutics, which also poses a significant challenge in the discovery of new agents. Herein, we report the geometric and electronic structural properties of hydrated AcIII cations in the [AcIII(H2O) n ]3+ (n = 4-11) complexes in aqueous solution and gas-phase using density functional theory. We found that nine water molecules coordinated to the AcIII cation is the most stable complex due to an enhanced hydration Gibbs free energy. This complex adopts a closed-shell 18-electron configuration (1S 21P 61D 10) of a superatom state, which indicates a non-negligible covalent character and involves H2O → AcIII σ donation interaction between s-/p-/d-type atomic orbitals of the Ac atom and 2p atomic orbitals of the O atoms. Furthermore, potentially existing 10-coordinated complexes need to overcome an energy barrier (>0.10 eV) caused by hydrogen bonding to convert to 9-coordination. These results imply the importance of superatom states in actinide chemistry generally, and specifically in AcIII solution chemistry, and highlight the conversion mechanism between different coordination numbers.
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Affiliation(s)
- Yang Gao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China Chengdu Sichuan 610054 China
- Department of Chemistry, University of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Payal Grover
- Department of Chemistry, University of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba Winnipeg Manitoba R3T 2N2 Canada
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18
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Janicki R, Starynowicz P. Analysis of charge density in nonaaquagadolinium(III) trifluoromethanesulfonate - insight into Gd III-OH 2 bonding. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:572-580. [PMID: 32831276 DOI: 10.1107/s2052520620006903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The experimental charge-density distribution in [Gd(H2O)9](CF3SO3)3 has been analysed and compared with the theoretical density functional theory calculations. Although the Gd-OH2 bonds are mainly ionic, a covalent contribution is detectable when inspecting both the topological parameters of these bonds and the natural bond orbital results. This contribution originates from small electron transfer from the lone pairs of oxygen atoms to empty 5d and 6s spin orbitals of Gd3+.
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Affiliation(s)
- Rafał Janicki
- Wydział Chemii, Uniwersytet Wrocławski, ul. F. Joliot-Curie 14, Wrocław, 50-383, Poland
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19
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Finney AR, Lectez S, Freeman CL, Harding JH, Stackhouse S. Ion Association in Lanthanide Chloride Solutions. Chemistry 2019; 25:8725-8740. [PMID: 31017723 PMCID: PMC6619345 DOI: 10.1002/chem.201900945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 12/24/2022]
Abstract
A better understanding of the solution chemistry of the lanthanide (Ln) salts in water would have wide ranging implications in materials processing, waste management, element tracing, medicine and many more fields. This is particularly true for minerals processing, given governmental concerns about lanthanide security of supply and the drive to identify environmentally sustainable processing routes. Despite much effort, even in simple systems, the mechanisms and thermodynamics of LnIII association with small anions remain unclear. In the present study, molecular dynamics (MD), using a newly developed force field, provide new insights into LnCl3 (aq) solutions. The force field accurately reproduces the structure and dynamics of Nd3+ , Gd3+ and Er3+ in water when compared to calculations using density functional theory (DFT). Adaptive-bias MD simulations show that the mechanisms for ion pairing change from dissociative to associative exchange depending upon cation size. Thermodynamics of association reveal that whereas ion pairing is favourable, the equilibrium distribution of species at low concentration is dominated by weakly bound solvent-shared and solvent-separated ion pairs, rather than contact ion pairs, reconciling a number of contrasting observations of LnIII -Cl association in the literature. In addition, we show that the thermodynamic stabilities of a range of inner sphere and outer sphere LnCl x ( 3 - x ) + coordination complexes are comparable and that the kinetics of anion binding to cations may control solution speciation distributions beyond ion pairs. The techniques adopted in this work provide a framework with which to investigate more complex solution chemistries of cations in water.
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Affiliation(s)
- Aaron R. Finney
- Department of Materials Science and Engineering, Sir Robert, Hadfield BuildingUniversity of SheffieldSheffieldS1 3JDUK
| | - Sébastien Lectez
- School of Earth and EnvironmentUniversity of LeedsLeedsLS2 9JTUK
| | - Colin L. Freeman
- Department of Materials Science and Engineering, Sir Robert, Hadfield BuildingUniversity of SheffieldSheffieldS1 3JDUK
| | - John H. Harding
- Department of Materials Science and Engineering, Sir Robert, Hadfield BuildingUniversity of SheffieldSheffieldS1 3JDUK
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20
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Spezia R, Migliorati V, D’Angelo P. Response to “Comment on ‘On the development of polarizable and Lennard-Jones force fields to study hydration structure and dynamics of actinide(III) ions based on effective ionic radii’” [J. Chem. Phys. 150, 097101 (2019)]. J Chem Phys 2019; 150:097102. [DOI: 10.1063/1.5087193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Riccardo Spezia
- LAMBE, Université d’Evry Val d’Essonne, CEA, CNRS, Université Paris Saclay, F-91025 Evry, France
| | | | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Roma, Italy
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21
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Migliorati V, Filipponi A, Sessa F, Lapi A, Serva A, D'Angelo P. Solvation structure of lanthanide(iii) bistriflimide salts in acetonitrile solution: a molecular dynamics simulation and EXAFS investigation. Phys Chem Chem Phys 2019; 21:13058-13069. [DOI: 10.1039/c9cp01417a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Lanthanide3+ ions in acetonitrile solutions of bistriflimide salts form 10-fold coordination complexes composed of both solvent molecules and counterions
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Affiliation(s)
| | - Adriano Filipponi
- Dipartimento di Scienze Fisiche e Chimiche
- Università degli Studi dell’Aquila, Via Vetoio
- 67100 L’Aquila
- Italy
| | - Francesco Sessa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Andrea Lapi
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
- Istituto CNR di Metodologie Chimiche-IMC
| | - Alessandra Serva
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Paola D'Angelo
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
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22
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Liu Z, Chai Z, Wang D. The folding equilibria of enterobactin enantiomers and their interaction with actinides. Phys Chem Chem Phys 2019; 21:16017-16031. [DOI: 10.1039/c9cp01656b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The helicity preference of Ent enantiomers was enhanced when binding with Fe3+ while disrupted when binding with actinides.
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Affiliation(s)
- Ziyi Liu
- Multidisciplinary Initiative Center
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing
- China
| | - Zhifang Chai
- Multidisciplinary Initiative Center
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing
- China
| | - Dongqi Wang
- Multidisciplinary Initiative Center
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing
- China
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23
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Bley M, Duvail M, Guilbaud P, Dufrêche JF. Activity Coefficients of Aqueous Sodium, Calcium, and Europium Nitrate Solutions from Osmotic Equilibrium MD Simulations. J Phys Chem B 2018; 122:7726-7736. [DOI: 10.1021/acs.jpcb.8b04950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Bley
- ICSM, CEA, CNRS, ENSCM, Univ Montpellier, BP
17171, F-30207 Bagnols-sur-Cèze, France
| | - Magali Duvail
- ICSM, CEA, CNRS, ENSCM, Univ Montpellier, BP
17171, F-30207 Bagnols-sur-Cèze, France
| | - Philippe Guilbaud
- Nuclear Energy Division, Research Department on Mining and Fuel Recycling Processes (SPDS/LILA), CEA, BP 17171, F-30207 Bagnols sur Cèze, France
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24
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Klinkhammer C, Böhm F, Sharma V, Schwaab G, Seitz M, Havenith M. Anion dependent ion pairing in concentrated ytterbium halide solutions. J Chem Phys 2018; 148:222802. [PMID: 29907060 DOI: 10.1063/1.5016549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have studied ion pairing of ytterbium halide solutions. THz spectra (30-400 cm-1) of aqueous YbCl3 and YbBr3 solutions reveal fundamental differences in the hydration structures of YbCl3 and YbBr3 at high salt concentrations: While for YbBr3 no indications for a changing local hydration environment of the ions were experimentally observed within the measured concentration range, the spectra of YbCl3 pointed towards formation of weak contact ion pairs. The proposed anion specificity for ion pairing was confirmed by supplementary Raman measurements.
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Affiliation(s)
| | - Fabian Böhm
- Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Vinay Sharma
- Applied Physics and Laser Technology, NIIT University, Neemrana, India
| | - Gerhard Schwaab
- Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Michael Seitz
- Institute of Inorganic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Martina Havenith
- Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
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25
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Structural parameters of the nearest environment of ions in aqueous solutions of ytterbium chloride. Russ Chem Bull 2018. [DOI: 10.1007/s11172-018-2031-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Migliorati V, Serva A, Sessa F, Lapi A, D’Angelo P. Influence of Counterions on the Hydration Structure of Lanthanide Ions in Dilute Aqueous Solutions. J Phys Chem B 2018; 122:2779-2791. [DOI: 10.1021/acs.jpcb.7b12571] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Valentina Migliorati
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Serva
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sessa
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Lapi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
- Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione c/o Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola D’Angelo
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
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27
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Rudolph WW, Irmer G. Raman spectroscopic characterization of light rare earth ions: La 3+, Ce 3+, Pr 3+, Nd 3+ and Sm 3+ - hydration and ion pair formation. Dalton Trans 2018; 46:4235-4244. [PMID: 28280811 DOI: 10.1039/c7dt00008a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Raman spectra of aqueous La3+, Ce3+, Pr3+, Nd3+ and Sm3+ - perchlorate solutions were measured and weak strongly polarized Raman bands were detected at 343 cm-1, 344 cm-1, 347 cm-1, 352 cm-1 and 363 cm-1, respectively. The full width at half height for these bands is quite broad (∼50 cm-1) in the isotropic spectrum and the band width increases with increasing solute concentration. The polarized Raman bands were assigned to the breathing modes of the nona-aqua ions of the mentioned rare earth ions. Published structural results confirmed that these ions exist as nona-hydrates in aqueous solutions [Ln(H2O)9]3+. The Ln-O bond distances of these rare earth ions correlate well with the band positions of the nona-aqua ions [Ln(OH2)9]+3 (Ln = La3+, Ce3+, Pr3+, Nd3+ and Sm3+) and the force constants were calculated for these breathing modes. The strength of the force constants increase with decreasing the Ln-O bond distances (La-O > Ce-O > Pr-O > Nd-O > Sm-O). While the fully hydrated ions are stable in dilute perchlorate solutions (∼0.2 mol L-1), in concentrated perchlorate solutions outer-sphere ion pairs and contact ion pairs are formed (C > 1.5 mol L-1). In a hydrate melt at 161 °C of Ce(ClO4)3 plus 6H2O, the contact ion pairs are the dominate species. The Raman bands of the ligated perchlorate and the Ce-O breathing mode of the partially hydrated ion pair at 326 cm-1 were measured and characterized. In cerium chloride solutions chloro-complex formation was detected over the measured concentration range from 0.270-2.167 mol L-1. The chloro-complexes in CeCl3(aq) are weak and diminish rapidly with dilution and disappear at a concentration <0.1 mol L-1. In a CeCl3 solution, with additional HCl, a series of chloro-complex species of the type [Ce(OH2)9-nCln]+3-n (n = 1, 2) were detected.
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Affiliation(s)
- Wolfram W Rudolph
- Medizinische Fakultät der TU Dresden, Institut für Virologie im MTZ, Fiedlerstr. 42, 01307 Dresden, Germany.
| | - Gert Irmer
- Technische Universität Bergakademie Freiberg, Institut für Theoretische Physik, Leipziger Str. 23, 09596 Freiberg, Germany
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28
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Qiao B, Skanthakumar S, Soderholm L. Comparative CHARMM and AMOEBA Simulations of Lanthanide Hydration Energetics and Experimental Aqueous-Solution Structures. J Chem Theory Comput 2018; 14:1781-1790. [DOI: 10.1021/acs.jctc.7b01018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Baofu Qiao
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - S. Skanthakumar
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - L. Soderholm
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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29
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Macchiagodena M, Mancini G, Pagliai M, Barone V. Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies. Phys Chem Chem Phys 2018; 18:25342-25354. [PMID: 27711662 DOI: 10.1039/c6cp04666e] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this contribution we show that it is possible to build accurate force fields for small organic molecules allowing the reliable reproduction of a large panel of bulk properties, which are seldom addressed in the same context. Starting from the results obtained in recent studies, we developed a protocol for charge estimation and virtual site generation for the amide class of molecules. The parametrization of electrostatic properties is based on population analysis and orbital localization of quantum mechanical computations rooted in density functional theory and the polarizable continuum model, without any additional external information. The new protocol, coupled to other recent studies in our group targeted at an accurate fitting of internal degrees of freedom, makes available a method for building force fields from scratch (excluding for the moment intermolecular van der Waals interactions) with focus on reproducing the structure and dynamics of hydrogen bonded liquids, yielding results that are in line or better than those delivered by current general force fields. The approach is tested on the demanding series formed by formamide and its two N-methyl derivatives, N-methylformamide and N,N-dimethylformamide. We show that the atomistic structure of the liquids arising from classical molecular dynamics (MD) simulations employing the new force field is in full agreement with X-ray and neutron diffraction experiments and the corresponding spatial distribution functions are in remarkable agreement with the results of ab initio MD simulations. It is noteworthy that the latter result has never been obtained before without using ad hoc (and system dependent) scale factors and that, in addition, our parameter-free procedure is able to reproduce static dielectric constants over a wide range of values without sacrificing the force field accuracy with respect to other observables. Finally, we are able to explain the trend of static dielectric constants followed by the three amides in terms of properties obtained from the simulations, namely hydrogen bond patterns and reorientational lifetimes.
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Affiliation(s)
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy. and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Marco Pagliai
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy. and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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30
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Sessa F, D’Angelo P, Migliorati V. Combined distribution functions: A powerful tool to identify cation coordination geometries in liquid systems. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.11.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Friesen S, Krickl S, Luger M, Nazet A, Hefter G, Buchner R. Hydration and ion association of La3+ and Eu3+ salts in aqueous solution. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00248g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lanthanide ions affect water out to the third shell and form double solvent-separated and solvent-shared ion pairs.
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Affiliation(s)
- Sergej Friesen
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Sebastian Krickl
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Magdalena Luger
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Andreas Nazet
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Glenn Hefter
- Chemistry Department
- Murdoch University
- Murdoch
- Australia
| | - Richard Buchner
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
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32
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Spezia R, Migliorati V, D’Angelo P. On the development of polarizable and Lennard-Jones force fields to study hydration structure and dynamics of actinide(III) ions based on effective ionic radii. J Chem Phys 2017; 147:161707. [DOI: 10.1063/1.4989969] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Bley M, Duvail M, Guilbaud P, Dufrêche JF. Simulating Osmotic Equilibria: A New Tool for Calculating Activity Coefficients in Concentrated Aqueous Salt Solutions. J Phys Chem B 2017; 121:9647-9658. [DOI: 10.1021/acs.jpcb.7b04011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Bley
- Institut
de Chimie Séparative de Marcoule (ICSM), UMR 5257, CEA, Université Montpellier, CNRS, ENSCM, BP 17171, 30207 Bagnols-sur-Cèze, France
| | - Magali Duvail
- Institut
de Chimie Séparative de Marcoule (ICSM), UMR 5257, CEA, Université Montpellier, CNRS, ENSCM, BP 17171, 30207 Bagnols-sur-Cèze, France
| | - Philippe Guilbaud
- Nuclear
Energy Division, Research Department on Mining and Fuel Recycling
Processes (SPDS/LILA), CEA, BP 17171, F-30207 Bagnols sur Cèze, France
| | - Jean-François Dufrêche
- Institut
de Chimie Séparative de Marcoule (ICSM), UMR 5257, CEA, Université Montpellier, CNRS, ENSCM, BP 17171, 30207 Bagnols-sur-Cèze, France
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34
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Montagna M, Spezia R, Bodo E. Solvation Properties of the Actinide Ion Th(IV) in DMSO and DMSO:Water Mixtures through Polarizable Molecular Dynamics. Inorg Chem 2017; 56:11929-11937. [DOI: 10.1021/acs.inorgchem.7b01900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Montagna
- Chemistry Department, University of Rome “La Sapienza”, P. A. Moro 5, 00185, Rome, Italy
| | - Riccardo Spezia
- LAMBE, Université d’Evry Val d’Essonne, CEA, CNRS, Université Paris Saclay, F-91025 Evry, France
| | - Enrico Bodo
- Chemistry Department, University of Rome “La Sapienza”, P. A. Moro 5, 00185, Rome, Italy
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35
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Migliorati V, Serva A, Terenzio FM, D’Angelo P. Development of Lennard-Jones and Buckingham Potentials for Lanthanoid Ions in Water. Inorg Chem 2017; 56:6214-6224. [DOI: 10.1021/acs.inorgchem.7b00207] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessandra Serva
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Filippo Maria Terenzio
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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36
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Serva A, Migliorati V, Spezia R, D'Angelo P. How Does CeIII
Nitrate Dissolve in a Protic Ionic Liquid? A Combined Molecular Dynamics and EXAFS Study. Chemistry 2017; 23:8424-8433. [DOI: 10.1002/chem.201604889] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Alessandra Serva
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Valentina Migliorati
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Riccardo Spezia
- LAMBE CEA, CNRS; Université Paris Saclay; 91025 Evry Cedex France
- LAMBE Université d'Evry; 91025 Evry Cedex France
| | - Paola D'Angelo
- Dipartimento di Chimica; Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
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37
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Sessa F, Spezia R, D'Angelo P. Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex. J Chem Phys 2017; 144:204505. [PMID: 27250314 DOI: 10.1063/1.4951714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.
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Affiliation(s)
- Francesco Sessa
- Dipartimento di Chimica, Università di Roma "La Sapienza," P. le A. Moro 5, 00185 Roma, Italy
| | - Riccardo Spezia
- CNRS, UMR 8587, Laboratoire Analyse et Modelisation Pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Blvd. F. Mitterrand, 91025 Evry Cedex, France
| | - Paola D'Angelo
- Dipartimento di Chimica, Università di Roma "La Sapienza," P. le A. Moro 5, 00185 Roma, Italy
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38
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Qiao B, Ferru G, Ellis RJ. Complexation Enhancement Drives Water-to-Oil Ion Transport: A Simulation Study. Chemistry 2016; 23:427-436. [DOI: 10.1002/chem.201604470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Baofu Qiao
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
| | - Geoffroy Ferru
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
| | - Ross J. Ellis
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831 USA
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39
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Morales N, Galbis E, Martínez JM, Pappalardo RR, Sánchez Marcos E. Identifying Coordination Geometries of Metal Aquaions in Water: Application to the Case of Lanthanoid and Actinoid Hydrates. J Phys Chem Lett 2016; 7:4275-4280. [PMID: 27732784 DOI: 10.1021/acs.jpclett.6b02067] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The angular distribution function (ADF) associated with the oxygen-metal ion-oxygen angle (OMO) of several trivalent lanthanoid and actinoid aquaions has been used to identify the most probable coordination geometry of these aquaions in aqueous solutions. The ADFs extracted from the molecular dynamics trajectories have been compared with continuous distribution functions corresponding to the geometry of a reference polyhedron pattern. The procedure incorporates specific quantum-mechanical information on the aquaion under study. The new method is applied to the analysis of four M(H2O)n3+ aquaions in water, M = Lu and Cf for n = 8, and M = La and Ac for n = 9. For those that are 8-coordinated, the square antiprism (SA) coordination geometry is preferred. For the 9-fold coordination, the simulation ADFs are more similar to the continuous ADF derived from a Gyro-elongated-SA rather than to the usually proposed trigonal tricapped prism. Advantages of these continuous distributions with respect to the usually employed discrete distributions are emphasized as well as further applications are suggested.
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Affiliation(s)
- Noelia Morales
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - Elsa Galbis
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - José M Martínez
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
| | - Rafael R Pappalardo
- Department of Physical Chemistry, University of Seville , 41012 Seville, Spain
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40
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Migliorati V, D’Angelo P. Unraveling the Sc3+ Hydration Geometry: The Strange Case of the Far-Coordinated Water Molecule. Inorg Chem 2016; 55:6703-11. [DOI: 10.1021/acs.inorgchem.6b00962] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento
di Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento
di Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
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41
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Bodo E, Macaluso V, Spezia R. Solvent Structure around Lanthanoid(III) Ions in Liquid DMSO As Revealed by Polarizable Molecular Dynamics Simulations. J Phys Chem B 2015; 119:13347-57. [DOI: 10.1021/acs.jpcb.5b06317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Enrico Bodo
- Department
of Chemistry, University of Rome “La Sapienza”, Rome, Italy
| | - Veronica Macaluso
- Department
of Chemistry, University of Rome “La Sapienza”, Rome, Italy
| | - Riccardo Spezia
- LAMBE
CNRS UMR8587, Universite dEvry val dEssonne, Blvd F. Mitterrand, Bat̂ Maupertuis, 91025 Evry, France
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42
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Duvail M, Villard A, Nguyen TN, Dufrêche JF. Thermodynamics of Associated Electrolytes in Water: Molecular Dynamics Simulations of Sulfate Solutions. J Phys Chem B 2015; 119:11184-95. [DOI: 10.1021/acs.jpcb.5b03088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Magali Duvail
- Institut de Chimie Séparative
de Marcoule (ICSM), UMR 5257, CEA-CNRS-Université Montpellier-ENSCM, Site
de Marcoule, Bâtiment 426, BP 17171, F-30207 Bagnols-sur-Cèze Cedex, France
| | - Arnaud Villard
- Institut de Chimie Séparative
de Marcoule (ICSM), UMR 5257, CEA-CNRS-Université Montpellier-ENSCM, Site
de Marcoule, Bâtiment 426, BP 17171, F-30207 Bagnols-sur-Cèze Cedex, France
| | - Thanh-Nghi Nguyen
- Institut de Chimie Séparative
de Marcoule (ICSM), UMR 5257, CEA-CNRS-Université Montpellier-ENSCM, Site
de Marcoule, Bâtiment 426, BP 17171, F-30207 Bagnols-sur-Cèze Cedex, France
| | - Jean-François Dufrêche
- Institut de Chimie Séparative
de Marcoule (ICSM), UMR 5257, CEA-CNRS-Université Montpellier-ENSCM, Site
de Marcoule, Bâtiment 426, BP 17171, F-30207 Bagnols-sur-Cèze Cedex, France
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43
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Rudolph WW, Irmer G. Hydration and ion pair formation in common aqueous La(III) salt solutions--a Raman scattering and DFT study. Dalton Trans 2015; 44:295-305. [PMID: 25379866 DOI: 10.1039/c4dt03003f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Raman spectra of aqueous lanthanum perchlorate, triflate (trifluorosulfonate), chloride and nitrate solutions were measured over a broad concentration (0.121-3.050 mol L(-1)) range at room temperature (23 °C). A very weak mode at 343 cm(-1) with a full width at half height at 49 cm(-1) in the isotropic spectrum suggests that the nona-aqua La(III) ion is thermodynamically stable in dilute perchlorate solutions (∼0.2 mol L(-1)) while in concentrated perchlorate solutions outer-sphere ion pairs and contact ion pairs are formed. The La(3+) nona-hydrate was also detected in a 1.2 mol L(-1) La(CF3SO3)3(aq). In lanthanum chloride solutions chloro-complex formation was detected over the measured concentration range from 0.5-3.050 mol L(-1). The chloro-complexes in LaCl3(aq) are fairly weak and disappear with dilution. At a concentration <0.1 mol L(-1) almost all complexes disappeared. In LaCl3 solutions, with additional HCl, a series of chloro-complexes of the type [La(OH2)(9-n)Cln](+3-n) (n = 1-3) were formed. The La(NO3)3(aq) spectra were compared with a spectrum of a 0.409 mol L(-1) NaNO3(aq) and it was concluded that in La(NO3)3(aq) over the concentration range from 0.121-1.844 mol L(-1), nitrato-complexes, [La(OH2)(9-n)(NO3)n](+3-n) (n = 1, 2) were formed. These nitrato-complexes are quite weak and disappear with dilution <0.01 mol L(-1). DFT geometry optimizations and frequency calculations are reported for a lanthanum-nona-hydrate with a polarizable dielectric continuum in order to take the solvent into account. The bond distances and angles for the cluster geometry of [La(OH2)9](3+) with the polarizable dielectric continuum are in good agreement with data from recent structural experimental measurements and high quality simulations. The DFT frequency of the La-O stretching mode at 328.2 cm(-1), is only slightly smaller than the experimental one.
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Affiliation(s)
- Wolfram W Rudolph
- Medizinische Fakultät der TU Dresden, Institut für Virologie im MTZ, Fiedlerstr. 42, 01307 Dresden, Germany.
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44
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Bodo E, Chiricotto M, Spezia R. Structural, energetic, and electronic properties of La(III)-dimethyl sulfoxide clusters. J Phys Chem A 2014; 118:11602-11. [PMID: 25405769 DOI: 10.1021/jp507312y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By using accurate density functional theory calculations, we have studied the cluster complexes of a La(3+) ion interacting with a small number of dimethyl sulfoxide (DMSO) molecules of growing size (from 1 to 12). Extended structural, energetic, and electronic structure analyses have been performed to provide a complete picture of the physical properties that are the basis of the interaction of La(III) with DMSO. Recent experimental data in the solid and liquid phase have suggested a coordination number of 8 DMSO molecules with a square antiprism geometry arranged similarly in the liquid and crystalline phases. By using a cluster approach on the La(3+)(DMSO)n gas phase isolated structures, we have found that the 8-fold geometry, albeit less regular than in the crystal, is probably the most stable cluster. Furthermore, we provide new evidence of a 9-fold complexation geometric arrangement that is competitive (at least energetically) with the 8-fold one and that might suggest the existence of transient structures with higher coordination numbers in the liquid phase.
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Affiliation(s)
- Enrico Bodo
- Department of Chemistry, University of Rome "La Sapienza" , 00185 Rome, Italy
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45
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Spezia R, Jeanvoine Y, Vuilleumier R. Developing polarizable potential for molecular dynamics of Cm(III)-carbonate complexes in liquid water. J Mol Model 2014; 20:2398. [DOI: 10.1007/s00894-014-2398-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022]
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46
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Zhang J, Heinz N, Dolg M. Understanding Lanthanoid(III) Hydration Structure and Kinetics by Insights from Energies and Wave functions. Inorg Chem 2014; 53:7700-8. [DOI: 10.1021/ic500991x] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jun Zhang
- Institute for Theoretical
Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
| | - Norah Heinz
- Institute for Theoretical
Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
| | - Michael Dolg
- Institute for Theoretical
Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
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47
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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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48
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Mancini G, Brancato G, Barone V. Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies. J Chem Theory Comput 2014; 10:1150-1163. [PMID: 26543440 DOI: 10.1021/ct400988e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present the current status of development of our code for performing Molecular Dynamics (MD) simulations exploiting a polarizable force field based on the Fluctuating Charge (FQ) method and non-Periodic Boundary Conditions (NPBC). Continuing on the path set in a previous work, we increased the capabilities of the code by implementing a number of new features, including: a non-iterative algorithm for rigid trigonal molecule simulations; two additional temperature coupling schemes; a meta-dynamics based approach for effective free energy evaluations. Although these are well known algorithms, each present in one or more widely used MD packages, they have now been tested, for the first time, in the context of the FQ model coupled with NPBC. As case studies, we considered three aqueous ions of increasing charge, namely Na+, Ca2+ and La3+, at infinite dilution. In particular, by exploiting a computational approach recently proposed by our group and based on the metadynamics technique, we focused on the important role played by solvent polarization on ionic hydration structures, also investigating the free energy landscapes of ion coordination and the water exchange rates. Such an approach, previously tested with standard non-polarizable models, was applied here to evaluate the effects of explicit polarization on water exchange barriers between different solvent coordination structures. Moreover, we have analyzed and discussed in some detail non-linear electrostatic effects arising from solvent polarization while going from a mono- to a di- and trivalent ion.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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49
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Grechin OV, Smirnov PR. Coordination of ions in aqueous solutions of dysprosium chloride according to the X-ray diffraction data. RUSS J COORD CHEM+ 2014. [DOI: 10.1134/s1070328414020043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Smirnov PR, Grechin OV, Trostin VN. Concentration dependence of the structure of aqueous solutions of lutetium nitrate according to X-ray diffraction. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414020253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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