1
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Summers TJ, Diaz Sanchez J, Cantu DC. Effect of ion to ligand ratio on the aqueous to organic relative solubility of a lanthanide-ligand complex. Phys Chem Chem Phys 2024. [PMID: 39086219 DOI: 10.1039/d4cp02586e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
In the solvent extraction of rare earth elements, mechanistic aspects remain unclear regarding where and how extractant molecules coordinate metal ions and transport them from the aqueous phase into the organic phase. Molecular dynamics simulations were used to examine how unprotonated di(2-ethylhexyl)phosphoric acid (DEHP-) ligands that coordinate the Gd3+ ion can transfer the ion across the water-organic interface. Using the umbrella sampling technique, potential of mean force profiles were constructed to quantify the relative solubility of the Gd3+ ion coordinated to 0-3 DEHP- ligands in either water, 1-octanol, or hexane solvents and at the water-organic interfaces. The simulations show the Gd-DEHP- complexes, at varying Ln-ligand ratios, preferentially solvate on water-organic interfaces. While the Gd(DEHP-)3 complex will diffuse past the aqueous-organic interface into the octanol solvent, it is thermodynamically preferred for the Gd(DEHP-)3 complex to remain in the water-hexane interface when there is no amphiphilic layer of excess ligand.
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Affiliation(s)
- Thomas J Summers
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, NV, USA.
| | - Jesus Diaz Sanchez
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, NV, USA.
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, NV, USA.
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2
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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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3
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Summers TJ, Sobrinho JA, de Bettencourt-Dias A, Kelly SD, Fulton JL, Cantu DC. Solution Structures of Europium Terpyridyl Complexes with Nitrate and Triflate Counterions in Acetonitrile. Inorg Chem 2023; 62:5207-5218. [PMID: 36940386 DOI: 10.1021/acs.inorgchem.3c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Lanthanide-ligand complexes are key components of technological applications, and their properties depend on their structures in the solution phase, which are challenging to resolve experimentally or computationally. The coordination structure of the Eu3+ ion in different coordination environments in acetonitrile is examined using ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. AIMD simulations are conducted for the solvated Eu3+ ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions. EXAFS spectra are calculated directly from AIMD simulations and then compared to experimentally measured EXAFS spectra. In acetonitrile solution, both nitrate and triflate anions are shown to coordinate directly to the Eu3+ ion forming either ten- or eight-coordinate solvent complexes where the counterions are binding as bidentate or monodentate structures, respectively. Coordination of a terpyridyl ligand to the Eu3+ ion limits the available binding sites for the solvent and anions. In certain cases, the terpyridyl ligand excludes any solvent binding and limits the number of coordinated anions. The solution structure of the Eu-terpyridyl complex with nitrate counterions is shown to have a similar arrangement of Eu3+ coordinating molecules as the crystal structure. This study illustrates how a combination of AIMD and EXAFS can be used to determine how ligands, solvent, and counterions coordinate with the lanthanide ions in solution.
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Affiliation(s)
- Thomas J Summers
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557-0388, United States
| | - Josiane A Sobrinho
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557-0705, United States
| | | | - Shelly D Kelly
- X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439-4801, 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 89557-0388, United States
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4
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Devi M, Paul S. The chaotropic effect of ions on the self-aggregating propensity of Whitlock's molecular tweezers. Phys Chem Chem Phys 2022; 24:14452-14471. [PMID: 35661176 DOI: 10.1039/d2cp00033d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular tweezers feature the first class of artificial receptors to pique the interest of researchers and emerge as an effective therapeutic candidate. The exceptional structure and exquisite binding specificity of tweezers establish this overall class of receptors as a promising tool, with abundant applications. However, their inclination to self-aggregate by mutual π-π stacking interactions of their aromatic arms diminishes their efficacy as a therapeutic candidate. Therefore, following up on sporadic studies, since the discovery of the Hofmeister series, on the ability of ions to either solvate (salting-in) or induce aggregation (salting-out) of hydrophobic solutes, the notions of ion-specificity effects are utilized on tweezer moieties. The impacts of three different aluminum salts bearing anions Cl-, ClO4- and SCN- on the self-association propensity of Whitlock's caffeine-pincered molecular tweezers are investigated, with a specific emphasis placed on elucidating the varied behavior of the ions on the hydration ability of tweezers. The comparative investigation is conducted employing a series of all-atom molecular dynamics simulations of five tweezer molecules in pure water and three salt solutions, at two different concentrations each, maintaining a temperature of 300 K and a pressure of 1 atm, respectively. Radial distribution functions, coordination numbers, and SASA calculations display a steady reduction in the aggregation proclivity of the receptor molecules with an increase in salt concentration, as progressed along the Hofmeister series. Orientational preferences between the tweezer arms reveal a disruptive effect in the regular π-π stacking interactions, in the presence of high concentrations of ClO4- and SCN- ions, while preferential interactions and tetrahedral order parameters unveil the underlying mechanism, by which the anions alter the solubility of the hydrophobic molecules. Overall, it is observed that SCN- exhibits the highest salting-in effect, followed by ClO4-, with both anions inhibiting tweezer aggregation through different mechanisms. ClO4- ions impart an effect by moderately interacting with the solute molecules as well as modifying the water structure of the bulk solution promoting solvation, whereas, SCN- ions engage entirely in interaction with specific tweezer sites. Cl- being the most charge-dense of the three anionic species experiences stronger hydration and therefore, imparts a very negligible salting-in effect.
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Affiliation(s)
- Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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5
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Migliorati V, D’Angelo P. Deep eutectic solvents: A structural point of view on the role of the anion. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Kozari E, Sigalov M, Pines D, Fingerhut BP, Pines E. Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H 7 + O 3 Complex in Solution. Chemphyschem 2021; 22:716-725. [PMID: 33599024 PMCID: PMC8252526 DOI: 10.1002/cphc.202001046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/13/2021] [Indexed: 12/17/2022]
Abstract
Infrared (IR) absorption in the 1000–3700 cm−1 range and 1H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7+O3, in acetonitrile. The core H7+O3 motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H7+O3 structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H7+O3 in the OH stretch region, which reaffirms the assignment of the H7+O3 spectra to a hybrid‐complex structure: a protonated water dimer strongly hydrogen‐bonded to a third water molecule with the proton exchanging between the two possible shared‐proton Zundel‐like centers. The H7+O3 structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H7+O3 structures may support proton transport within larger water solvates.
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Affiliation(s)
- Eve Kozari
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Mark Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, 12489, Germany
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
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7
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Migliorati V, Lapi A, D'Angelo P. Unraveling the solvation geometries of the lanthanum(iii) bistriflimide salt in ionic liquid/acetonitrile mixtures. Phys Chem Chem Phys 2020; 22:20434-20443. [PMID: 32915187 DOI: 10.1039/d0cp03977b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
La(Tf2N)3 in C8(mim)2(Tf2N)2/acetonitrile mixtures forms 10-fold coordination complexes composed of both acetonitrile molecules and Tf2N− anions.
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Affiliation(s)
| | - Andrea Lapi
- 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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8
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Luminescent Lanthanide Metal Organic Frameworks as Chemosensing Platforms towards Agrochemicals and Cations. SENSORS 2019; 19:s19051260. [PMID: 30871122 PMCID: PMC6427543 DOI: 10.3390/s19051260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/03/2019] [Accepted: 03/07/2019] [Indexed: 02/03/2023]
Abstract
Since the first studies of luminescent sensors based on metal organic frameworks (MOFs) about ten years ago, there has been an increased interest in the development of specific sensors towards cations, anions, explosives, small molecules, solvents, etc. However, the detection of toxic compounds related to agro-industry and nuclear activity is noticeably scarce or even non-existent. In this work, we report the synthesis and characterization of luminescent lanthanide-based MOFs (Ln-MOFs) with diverse crystalline architectures obtained by solvothermal methods. The luminescent properties of the lanthanides, and the hypersensitive transitions of Eu3+ (5D0→7F2) and Tb3+ (5D4→7F5) intrinsically found in the obtained MOFs in particular, were evaluated and employed as chemical sensors for agrochemical and cationic species. The limit of detection (LOD) of Tb-PSA MOFs (PSA = 2-phenylsuccinate) was 2.9 ppm for [UO22+] and 5.6 ppm for [Cu2+]. The variations of the 4f–4f spectral lines and the quenching/enhancement effects of the Ln-MOFs in the presence of the analytes were fully analyzed and discussed in terms of a combinatorial “host–guest” vibrational and “in-silico” interaction studies.
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9
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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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10
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Tsushima S. Lanthanide-induced conformational change of methanol dehydrogenase involving coordination change of cofactor pyrroloquinoline quinone. Phys Chem Chem Phys 2019; 21:21979-21983. [DOI: 10.1039/c9cp03953h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Classical molecular dynamics simulations combined with fragment molecular orbital calculations were employed to rationalize the enzymatic activities of MDH carrying different lanthanides.
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Affiliation(s)
- Satoru Tsushima
- Institute of Resource Ecology
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
- Dresden
- Germany
- Tokyo Tech World Research Hub Initiative (WRHI)
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11
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12
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Schurhammer R, Wipff G. Formation of Aqueous Biphasic Systems with an Ionic Liquid Induced by Metallic Salts: Nanoscopic Views from Molecular Dynamics Simulations. J Phys Chem B 2018; 122:10143-10157. [PMID: 30351128 DOI: 10.1021/acs.jpcb.8b06193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of aqueous biphasic systems (ABSs) based on aqueous ionic liquid (IL)/salt mixtures has been investigated via molecular dynamics simulations (with IL butyl-methyl-imidazolium triflate; salts NaCl, CsCl, SrCl2, and EuCl3). The analysis of ion distributions, solvation, and mutual interactions during the dynamics reveals the heterogeneity of all solutions due to ion segregation into mutually exclusive IL and salt domains, even in monophasic solutions ("ionic sociology"). Ion segregation and ABS formation are found to increase with (i) the salt content and (ii) the IL content, (iii) in the order Na+ < Sr2+ < Eu3+, and (iv) when the IL ion "polarity" is diminished, following experimental trends. The structuration of the solution is rationalized as a synergistic water transfer from the best donating ion pair (first hydration shell of hydrophobic moieties of IL ions) to the best accepting pair (M n+ and Cl- ions, beyond their first shell). In ABSs, the IL- and salt-containing phases are linked by a well-defined "interface" that decreases in width when MCl n becomes more hydrophilic and/or more concentrated. In the IL-rich phase of ABSs, the hydration of IL ions and their mutual interactions are shown to be similar to those displayed at aqueous interfaces.
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Affiliation(s)
- Rachel Schurhammer
- Chimie de la Matière Complexe, UMR CNRS 7140 , 1, rue B. Pascal , 67000 Strasbourg , France
| | - Georges Wipff
- Chimie de la Matière Complexe, UMR CNRS 7140 , 1, rue B. Pascal , 67000 Strasbourg , France
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13
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Sun P, Huang K, Liu H. Specific Salt Effect on the Interaction between Rare Earth Ions and Trioctylphosphine Oxide Molecules at the Organic-Aqueous Two-Phase Interface: Experiments and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11374-11383. [PMID: 30180592 DOI: 10.1021/acs.langmuir.8b02301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the essence of the specific salt effect on the enhancement of the transport of metal ions across the liquid/liquid interface during the process of solvent extraction is of crucial importance for the development of a new approach to extract and selectively separate various valuable metals from complex aqueous solutions. However, some abnormal experimental phenomena involved in the salt effect on the liquid/liquid solvent extraction could not be understood only from the conventional interpretation based on the salting-out ability of salt ions. The knowledge into the microscopic mechanism behind the specific salt effect was urgent. Herein, as an example, the effect of adding various salts on the extraction performance of rare earth ion Pr3+ using trioctylphosphine oxide (TOPO) as the organic extractant was investigated. It was revealed that the difference in the interface propensity of different salt anions enriched at the organic-aqueous two-phase interface played a crucial role in promoting the interaction of TOPO molecules with Pr3+ ions, despite the occurrence of the salting-out effect of those salt anions with the increase of their concentrations in aqueous solutions. The interfacial interaction mechanism obtained by molecular dynamics simulations revealed that both the interface propensity and the salting-out ability of the coexisting salt anions contributed to the enhancement in the extraction of Pr3+ into the TOPO organic phase. However, when the concentrations of coexisting salts in aqueous solutions were low enough, the extraction of Pr3+ was mainly dominated by the interface propensity of those added salt anions but not their salting-out ability. With the increase in the concentration of salts, the salting-out effect gradually became significant and, therefore, began to join with the interface propensity of salt anions to co-dominate the transport of Pr3+ ions across the liquid/liquid interface. The present study highlights the microscopic nature of the salt effect on promoting the extraction of rare earth ions and suggests that the interaction of organic extractant molecules with rare earth ions at liquid/liquid interface was dependent not only upon the salting-out ability of the coexisting salt ions but also their interface propensity.
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Affiliation(s)
- Pan Sun
- Chinese Academy of Sciences (CAS) Key Laboratory of Green Process and Engineering, Institute of Process Engineering , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Kun Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Green Process and Engineering, Institute of Process Engineering , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
- School of Metallurgical and Ecological Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Haidian, Beijing 100083 , People's Republic of China
| | - Huizhou Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Green Process and Engineering, Institute of Process Engineering , Chinese Academy of Sciences , Beijing 100190 , People's Republic of China
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14
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Zhang X, Zhang L, Jin T, Pan ZJ, Chen ZN, Zhang Q, Zhuang W. Salting-in/Salting-out Mechanism of Carbon Dioxide in Aqueous Electrolyte Solutions. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1711230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xia Zhang
- Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhi-jun Pan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhe-ning Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Qiang Zhang
- Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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15
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Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein. J Mol Model 2017; 23:298. [PMID: 28956172 DOI: 10.1007/s00894-017-3471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
Abstract
Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO4 and NaF salts to the solution. The process is separated into two parts. In the first, 'promotion' phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, 'rearrangement' phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins's rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.
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16
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Dahms F, Fingerhut BP, Nibbering ETJ, Pines E, Elsaesser T. Large-amplitude transfer motion of hydrated excess protons mapped by ultrafast 2D IR spectroscopy. Science 2017; 357:491-495. [DOI: 10.1126/science.aan5144] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/27/2017] [Indexed: 11/02/2022]
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17
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Guillaumont D, Guilbaud P, Sorel C, Gutierrez F, Chalmet S, Defranceschi M. Modeling Selectivity in Liquid/Liquid Extraction. NUCL SCI ENG 2017. [DOI: 10.13182/nse06-a2607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- D. Guillaumont
- CEA-VRH, DEN/DRCP/SCPS/LCAM, BP17171, F-30207 Bagnols-sur-Cèze, France
| | - Ph. Guilbaud
- CEA-VRH, DEN/DRCP/SCPS/LCAM, BP17171, F-30207 Bagnols-sur-Cèze, France
| | - C. Sorel
- CEA-VRH, DEN/DRCP/SCPS/LCAM, BP17171, F-30207 Bagnols-sur-Cèze, France
| | - F. Gutierrez
- CEA-VRH, DEN/DRCP/SCPS/LCAM, BP17171, F-30207 Bagnols-sur-Cèze, France
| | - S. Chalmet
- CEA-VRH, DEN/DRCP/SCPS/LCAM, BP17171, F-30207 Bagnols-sur-Cèze, France
| | - M. Defranceschi
- CEA-Saclay, Bât. 121, DEN/DSOE/RB, F-91191 Gif-sur-Yvette Cedex, France
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18
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Choi JH, Cho M. Ion aggregation in high salt solutions. VI. Spectral graph analysis of chaotropic ion aggregates. J Chem Phys 2016; 145:174501. [DOI: 10.1063/1.4966246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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19
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Santos DP, Longo RL. Molecular Dynamics Simulations of Specific Anion Adsorption on Sulfobetaine (SB3-14) Micelles. J Phys Chem B 2016; 120:2771-80. [DOI: 10.1021/acs.jpcb.5b12475] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diego P. Santos
- Departamento
de Química
Fundamental, Universidade Federal de Pernambuco, 50.740-560 Recife, PE, Brazil
| | - Ricardo L. Longo
- Departamento
de Química
Fundamental, Universidade Federal de Pernambuco, 50.740-560 Recife, PE, Brazil
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20
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Nieszporek K, Podkościelny P, Nieszporek J. Transitional hydrogen bonds in aqueous perchlorate solution. Phys Chem Chem Phys 2016; 18:5957-63. [PMID: 26838544 DOI: 10.1039/c5cp07831h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The water–perchlorate classical hydrogen bond can turn into a bifurcated or trifurcated one.
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Affiliation(s)
- Krzysztof Nieszporek
- Department of Theoretical Chemistry
- Maria Curie-Sklodowska University
- 20-031 Lublin
- Poland
| | | | - Jolanta Nieszporek
- Department of Analytical Chemistry and Instrumental Analysis
- Maria Curie-Sklodowska University
- 20-031 Lublin
- Poland
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21
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Chopra M, Choudhury N. Molecular dynamics simulation study of distribution and dynamics of aqueous solutions of uranyl ions: the effect of varying temperature and concentration. Phys Chem Chem Phys 2015; 17:27840-50. [PMID: 26439497 DOI: 10.1039/c5cp03769g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigating the characteristics of actinyl ions has been of great interest due to their direct relevance in the nuclear fuel cycle. All-atom molecular dynamics simulations have been employed to study the orientational structure and dynamics of aqueous solutions of uranyl ions of various concentrations. The orientational structure of water around a uranyl ion has been thoroughly investigated by calculating different orientational probability distributions corresponding to different molecular axes of water. The orientational distribution of water molecules in the first coordination shell of a uranyl ion is found to be markedly different from that in bulk water. Analysis of counterion distribution around the uranyl ion reveals the presence of nitrate ions along with water molecules in the first solvation shell. From the comparison of the number of coordinated water and nitrate ions at various uranyl nitrate concentrations, it is evident that these two species compete for occupying the first solvation shell of the uranyl ion. Orientational dynamics of water molecules about different molecular axes of water in the vicinity of uranyl ions have also been investigated and decreasing orientational mobility of water with increasing uranyl concentration has been found. However, it is observed that the orientational dynamics remains more or less the same whether we consider all the water molecules in the aqueous solution or only the solvation shell water molecules. The effect of temperature on the translational and orientational characteristics of the aqueous uranyl solutions has also been studied in detail.
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Affiliation(s)
- Manish Chopra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai - 400 085, India
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22
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Janowski PA, Liu C, Deckman J, Case DA. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Protein Sci 2015; 25:87-102. [PMID: 26013419 DOI: 10.1002/pro.2713] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 11/12/2022]
Abstract
Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics.
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Affiliation(s)
- Pawel A Janowski
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
| | - Chunmei Liu
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854.,The College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province, 450001, People's Republic of China
| | - Jason Deckman
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey, 08854
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23
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Piccinelli F, Bettinelli M, Melchior A, Grazioli C, Tolazzi M. Structural, optical and sensing properties of novel Eu(iii) complexes with furan- and pyridine-based ligands. Dalton Trans 2015; 44:182-92. [DOI: 10.1039/c4dt02326a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Effect of the ligand's donor ability on the luminescence sensing of nitrate anions.
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Affiliation(s)
- Fabio Piccinelli
- Laboratorio Materiali Luminescenti
- DB
- Università di Verona
- and INSTM
- UdR Verona
| | - Marco Bettinelli
- Laboratorio Materiali Luminescenti
- DB
- Università di Verona
- and INSTM
- UdR Verona
| | - Andrea Melchior
- Dipartimento di Chimica
- Fisica e Ambiente
- Università di Udine
- 33100 Udine
- Italy
| | - Cristian Grazioli
- Dipartimento di Chimica
- Fisica e Ambiente
- Università di Udine
- 33100 Udine
- Italy
| | - Marilena Tolazzi
- Dipartimento di Chimica
- Fisica e Ambiente
- Università di Udine
- 33100 Udine
- Italy
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24
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Chopra M, Choudhury N. Effect of Uranyl Ion Concentration on Structure and Dynamics of Aqueous Uranyl Solution: A Molecular Dynamics Simulation Study. J Phys Chem B 2014; 118:14373-81. [DOI: 10.1021/jp506477s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Manish Chopra
- Radiation
Safety Systems Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Niharendu Choudhury
- Radiation
Safety Systems Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400 085, India
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25
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Kim S, Kim H, Choi JH, Cho M. Ion aggregation in high salt solutions: Ion network versus ion cluster. J Chem Phys 2014; 141:124510. [DOI: 10.1063/1.4896227] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Jun-Ho Choi
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
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26
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Bogár F, Bartha F, Násztor Z, Fábián L, Leitgeb B, Dér A. On the Hofmeister Effect: Fluctuations at the Protein–Water Interface and the Surface Tension. J Phys Chem B 2014; 118:8496-504. [DOI: 10.1021/jp502505c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ferenc Bogár
- MTA-SZTE
Supramolecular and Nanostructured Materials Research Group of Hungarian
Academy of Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Ferenc Bartha
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Zoltán Násztor
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - László Fábián
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Balázs Leitgeb
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
- Department
of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - András Dér
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
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27
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Ioannou F, Leontidis E, Archontis G. Helix Formation by Alanine-Based Peptides in Pure Water and Electrolyte Solutions: Insights from Molecular Dynamics Simulations. J Phys Chem B 2013; 117:9866-76. [DOI: 10.1021/jp406231g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Filippos Ioannou
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Epameinondas Leontidis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
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28
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Wu H, Cummings OT, Wick CD. Computational Investigation on the Effect of Alumina Hydration on Lithium Ion Mobility in Poly(ethylene oxide) LiClO4 Electrolytes. J Phys Chem B 2012; 116:14922-32. [DOI: 10.1021/jp307794r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Wu
- Louisiana Tech University, Ruston, Louisiana 71270,
United States
| | | | - Collin D. Wick
- Louisiana Tech University, Ruston, Louisiana 71270,
United States
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29
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Bühl M, Sieffert N, Partouche A, Chaumont A, Wipff G. Speciation of La(III) Chloride Complexes in Water and Acetonitrile: A Density Functional Study. Inorg Chem 2012. [DOI: 10.1021/ic302255a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Bühl
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews,
Fife KY16 9ST, U.K
| | - Nicolas Sieffert
- UMR-5250
CNRS, Département de Chimie Moléculaire, Université Joseph Fourier Grenoble I, BP 53,
38041 Grenoble Cedex 9, France
| | - Aurélie Partouche
- UMR-5250
CNRS, Département de Chimie Moléculaire, Université Joseph Fourier Grenoble I, BP 53,
38041 Grenoble Cedex 9, France
| | - Alain Chaumont
- UMR 7177 CNRS, Laboratoire MSM, Institut
de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Georges Wipff
- UMR 7177 CNRS, Laboratoire MSM, Institut
de Chimie, 1 rue Blaise Pascal, 67000 Strasbourg, France
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30
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Chaumont A, Wipff G. Bromide complexation by the Eu(III) lanthanide cation in dry and humid ionic liquids: a molecular dynamics PMF study. Chemphyschem 2012; 13:1677-86. [PMID: 22556119 DOI: 10.1002/cphc.201200063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Indexed: 11/08/2022]
Abstract
We report a molecular dynamics study on the EuBr(n)(3-n) complexes (n=0 to 6) formed upon complexation of Br(-) by Eu(3+) in the [BMI][PF(6)], [BMI][Tf(2)N] and [MeBu(3)N][Tf(2)N] ionic liquids (ILs), to compare the effect of the IL anion (PF(6)(-) versus Tf(2)N(-)), the IL cation (BMI(+) versus MeBu(3)N(+)) and the "IL humidity" on their solvation and stability. In "dry" solutions all complexes remain stable and the first coordination shell of Eu(3+) is purely anionic (Br(-) and IL anions), surrounded by IL cations (BMI(+) or MeBu(3)N(+) ions). Long range "onion type" solvation features (up to 20 Å from Eu(3+)), with alternating cation-rich and anion-rich solvent shells, are observed around the different complexes. The comparison of gas phase-optimized structures of EuBr(n)(3-n) complexes (that are unstable for n=5 and 6) with those observed in solution points to the importance of solvation forces on the nature of the complex, with a higher stabilization by imidazolium- than by ammonium-based dry ILs. Adding water to the IL has different effects, depending on the IL. In the highly hygroscopic [BMI][PF(6)] IL, Br(-) ligands are displaced by water, to finally form Eu(H(2)O)(9)(3+). In the less "humid" [BMI][Tf(2)N], the EuBr(n)(3-n) complexes do not dissociate and coordinate at most 1-2 H(2)O molecules. We also calculated the free-energy profiles (Potential of Mean Force calculations) for the stepwise complexation of Br(-), and found significant solvent effects. EuBr(6)(3-) is predicted to form in both [BMI][PF(6)] and [BMI][Tf(2)N], but not in [MeBu(3)N][Tf(2)N], mainly due to weaker interactions with the cationic solvation shell. First steps are found to be more exergonic in the PF(6)(-)- than in the Tf(2)N(-)-based IL. Molecular dynamics (MD) comparisons between ILs and classical solvents (acetonitrile and water) are also reported, affording good agreement with the experimental observations of Br(-) complexation by trivalent lanthanides in these classical solvents.
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Affiliation(s)
- Alain Chaumont
- Laboratoire MSM, UMR CNRS 7177, Institut de Chimie, 1 rue B. Pascal, 67 000 Strasbourg, France
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31
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Bodizs G, Helm L. NMR and Electron Paramagnetic Resonance Studies of [Gd(CH3CN)9]3+ and [Eu(CH3CN)9]2+: Solvation and Solvent Exchange Dynamics in Anhydrous Acetonitrile. Inorg Chem 2012; 51:5881-8. [DOI: 10.1021/ic300478c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriella Bodizs
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie
chimiques, EPFL-BCH, CH-1015 Lausanne, Switzerland
| | - Lothar Helm
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie
chimiques, EPFL-BCH, CH-1015 Lausanne, Switzerland
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32
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Trans influence and covalent bonding in a new octahedral lanthanum(III) complex of diphenylmorpholinyl phosphinamide. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Wang D, van Gunsteren WF, Chai Z. Recent advances in computational actinoid chemistry. Chem Soc Rev 2012; 41:5836-65. [DOI: 10.1039/c2cs15354h] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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34
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Di Bernardo P, Melchior A, Tolazzi M, Zanonato PL. Thermodynamics of lanthanide(III) complexation in non-aqueous solvents. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.07.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Reif MM, Hünenberger PH. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions. J Chem Phys 2011; 134:144103. [PMID: 21495738 DOI: 10.1063/1.3567020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions (finite or periodic system, system or box size) and treatment of electrostatic interactions (Coulombic, lattice-sum, or cutoff-based) used during these simulations. However, as shown by Kastenholz and Hünenberger [J. Chem. Phys. 124, 224501 (2006)], correction terms can be derived for the effects of: (A) an incorrect solvent polarization around the ion and an incomplete or/and inexact interaction of the ion with the polarized solvent due to the use of an approximate (not strictly Coulombic) electrostatic scheme; (B) the finite-size or artificial periodicity of the simulated system; (C) an improper summation scheme to evaluate the potential at the ion site, and the possible presence of a polarized air-liquid interface or of a constraint of vanishing average electrostatic potential in the simulated system; and (D) an inaccurate dielectric permittivity of the employed solvent model. Comparison with standard experimental data also requires the inclusion of appropriate cavity-formation and standard-state correction terms. In the present study, this correction scheme is extended by: (i) providing simple approximate analytical expressions (empirically-fitted) for the correction terms that were evaluated numerically in the above scheme (continuum-electrostatics calculations); (ii) providing correction terms for derivative thermodynamic single-ion solvation properties (and corresponding partial molar variables in solution), namely, the enthalpy, entropy, isobaric heat capacity, volume, isothermal compressibility, and isobaric expansivity (including appropriate standard-state correction terms). The ability of the correction scheme to produce methodology-independent single-ion solvation free energies based on atomistic simulations is tested in the case of Na(+) hydration, and the nature and magnitude of the correction terms for derivative thermodynamic properties is assessed numerically.
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Affiliation(s)
- Maria M Reif
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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36
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Would the solvent effect be the main cause of band shift in the theoretical absorption spectrum of large lanthanide complexes? J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Bertran O, Trickey SB, Torras J. Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system. J Comput Chem 2010; 31:2669-76. [PMID: 20740567 DOI: 10.1002/jcc.21553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian03 and Amber packages were added to the PUPIL suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for nondoped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. We discuss briefly some difficult problems of quantum zone SCF convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals.
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Affiliation(s)
- Oscar Bertran
- Departament de Física Aplicada, EUETII, Universitat Politècnica de Catalunya, Pça del Rei 15, Igualada 08700, Spain
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38
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Asciutto EK, General IJ, Xiong K, Xiong K, Asher SA, Madura JD. Sodium perchlorate effects on the helical stability of a mainly alanine peptide. Biophys J 2010; 98:186-96. [PMID: 20338840 DOI: 10.1016/j.bpj.2009.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 09/09/2009] [Accepted: 10/07/2009] [Indexed: 10/19/2022] Open
Abstract
Sodium perchlorate salt (NaClO(4)) is commonly used as an internal intensity standard in ultraviolet resonance Raman (UVRR) spectroscopy experiments. It is well known that NaClO(4) can have profound effects on peptide stability. The impact of NaClO(4) on protein stability in UVRR experiments has not yet been fully investigated. It is well known from experiment that protein stability is strongly affected by the solution composition (water, salts, osmolytes, etc.). Therefore, it is of the utmost importance to understand the physical basis on which the presence of salts and osmolytes in the solution impact protein structure and stability. The aim of this study is to investigate the effects of NaClO(4), on the helical stability of an alanine peptide in water. Based upon replica-exchange molecular dynamics data, it was found that NaClO(4) solution strongly stabilizes the helical state and that the number of pure helical conformations found at room temperature is greater than in pure water. A thorough investigation of the anion effects on the first and second solvation shells of the peptide, along with the Kirkwood-Buff theory for solutions, allows us to explain the physical mechanisms involved in the observed specific ion effects. A direct mechanism was found in which ClO(4)(-) ions are strongly attracted to the folded backbone.
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Affiliation(s)
- Eliana K Asciutto
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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39
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Gaillard C, Chaumont A, Billard I, Hennig C, Ouadi A, Georg S, Wipff G. Competitive Complexation of Nitrates and Chlorides to Uranyl in a Room Temperature Ionic Liquid. Inorg Chem 2010; 49:6484-94. [DOI: 10.1021/ic100170t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Gaillard
- Institut de Physique Nucléaire de Lyon, CNRS-IN2P3, 4 rue Enrico Fermi, 69622 Villeurbanne cedex, France
| | - A. Chaumont
- Laboratoire MSM, UMR 7177, Institut de Chimie, 4 rue B. Pascal, 67000 Strasbourg, France
| | - I. Billard
- Institut Pluridisciplinaire Hubert Curien, DRS, Chimie Nucléaire, 23 rue du Lœss, 67037 Strasbourg cedex 2, France
| | - C. Hennig
- Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, P.O. Box 510119, 01314 Dresden, Germany
| | - A. Ouadi
- Institut Pluridisciplinaire Hubert Curien, DRS, Chimie Nucléaire, 23 rue du Lœss, 67037 Strasbourg cedex 2, France
| | - S. Georg
- Institut Pluridisciplinaire Hubert Curien, DRS, Chimie Nucléaire, 23 rue du Lœss, 67037 Strasbourg cedex 2, France
| | - G. Wipff
- Laboratoire MSM, UMR 7177, Institut de Chimie, 4 rue B. Pascal, 67000 Strasbourg, France
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40
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Antonio MR, Jing J, Burton-Pye BP, Francesconi LC. Series behavior of lanthanoid(iii) complexes with the α-1-Wells-Dawson heteropolyoxoanion in acetonitrile: electrochemistry and Ln coordination. Dalton Trans 2010; 39:7980-92. [PMID: 20672167 DOI: 10.1039/c0dt00394h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mark R Antonio
- Chemical Sciences & Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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41
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General IJ, Asciutto EK, Madura JD. Structure of Aqueous Sodium Perchlorate Solutions. J Phys Chem B 2008; 112:15417-25. [DOI: 10.1021/jp806269w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ignacio J. General
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Eliana K. Asciutto
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Jeffry D. Madura
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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42
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Steele H, Taylor RJ. A theoretical study of the inner-sphere disproportionation reaction mechanism of the pentavalent actinyl ions. Inorg Chem 2007; 46:6311-8. [PMID: 17625833 DOI: 10.1021/ic070235c] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The inner-sphere mechanisms of the disproportionation reactions of U(V), Np(V), and Pu(V) ions have been studied using a quantum mechanical approach. The U(V) disproportionation proceeds via the formation of a dimer (a cation-cation complex) followed by two successive protonations at the axial oxygens of the donor uranyl ion. Bond lengths and spin multiplicities indicate that electron transfer occurs after the first protonation. A solvent water molecule then breaks the complex into solvated U(OH)2(2+) and UO2(2+) ions. Pu(V) behaves similarly, but Np(V) appears not to follow this path. The observations from quantum modeling are consistent with existing experimental data on actinyl(V) disproportionation reactions.
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Gaillard C, Chaumont A, Billard I, Hennig C, Ouadi A, Wipff G. Uranyl Coordination in Ionic Liquids: The Competition between Ionic Liquid Anions, Uranyl Counterions, and Cl-Anions Investigated by Extended X-ray Absorption Fine Structure and UV−Visible Spectroscopies and Molecular Dynamics Simulations. Inorg Chem 2007; 46:4815-26. [PMID: 17503808 DOI: 10.1021/ic061864+] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first coordination sphere of the uranyl cation in room-temperature ionic liquids (ILs) results from the competition between its initially bound counterions, the IL anions, and other anions (e.g., present as impurities or added to the solution). We present a joined spectroscopic (UV-visible and extended X-ray absorption fine structure)-simulation study of the coordination of uranyl initially introduced either as UO2X2 salts (X-=nitrate NO3-, triflate TfO-, perchlorate ClO4-) or as UO2(SO4) in a series of imidazolium-based ILs (C4mimA, A-=PF6-, Tf2N-, BF4- and C4mim=1-methyl-3-butyl-imidazolium) as well as in the Me3NBuTf2N IL. The solubility and dissociation of the uranyl salts are found to depend on the nature of X- and A-. The addition of Cl- anions promotes the solubilization of the nitrate and triflate salts in the C4mimPF6 and the C4mimBF4 ILs via the formation of chloro complexes, also formed with other salts. The first coordination sphere of uranyl is further investigated by molecular dynamics (MD) simulations on associated versus dissociated forms of UO2X2 salts in C4mimA ILs as a function of A- and X- anions. Furthermore, the comparison of UO2Cl(4)2-, 2 X- complexes with dissociated X- anions, to the UO2X2, 4 Cl- complexes with dissociated chlorides, shows that the former is more stable. The case of fluoro complexes is also considered, as a possible result of fluorinated IL anion's degradation, showing that UO2F42- should be most stable in solution. In all cases, uranyl is found to be solvated as formally anionic UO2XnAmClp2-n-m-p complexes, embedded in a cage of stabilizing IL imidazolium or ammonium cations.
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Affiliation(s)
- C Gaillard
- Institut Pluridisciplinaire Hubert Curien, DRS, Chimie Nucléaire, 23 Rue du Loess, 67037 Strasbourg Cedex 2, France.
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Guillaumont D, Bazin H, Benech JM, Boyer M, Mathis G. Luminescent Eu(III) and Gd(III) Trisbipyridine Cryptates: Experimental and Theoretical Study of the Substituent Effects. Chemphyschem 2007; 8:480-8. [PMID: 17226873 DOI: 10.1002/cphc.200600669] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Synthesis, absorption spectra and luminescebce properties of a series of lanthanide trisbipyridine cryptates Ln within R-Bpy x R-Bpy x R-Bpy, where Ln = Eu, Gd and R = H, COOH, COOCH3, CONH(CH2)2NH2 are described. Comparison of the unsubstituted parent compound with the substituted compounds shows that bipyridine substitution doesn't alter significantly the photophysical properties of the lanthanide cryptate. The absorption maximum is slightly red-shifted when three bipyridines are substituted, whereas substituting one bipyridines has a negligible effect on the absorption spectra. The experimental triplet state energy is between 21600 and 22 100 cm(-1) for the series of compounds and the luminescence lifetimes at 77 K are between 0.5 and 0.8 ms in HO2 and equal to 1.7 ms in D2O. The experimental characterizations are completed by DFT and TD-DFT calculations to assess the ability of these approaches to predict absorption maxima, triplet state energies and structural parameters of lanthanide cryptates and to characterize the electronic structure of the excited states. The calculations on the unsubstituted parent and substituted compounds show that absorption maxima and lowest 3pipi* triplet state energies can be accurately determined from density functional theory (DFT) and time-dependent (TD) DFT calculations.
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Affiliation(s)
- Dominique Guillaumont
- Direction de l'Energie Nucléaire, Commissariat a l'Energie Atomique, Valrhô, BP 17171, 30207 Bagnols/Cèze, France.
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45
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Gaillard C, Billard I, Chaumont A, Mekki S, Ouadi A, Denecke MA, Moutiers G, Wipff G. Europium(III) and Its Halides in Anhydrous Room-Temperature Imidazolium-Based Ionic Liquids: A Combined TRES, EXAFS, and Molecular Dynamics Study. Inorg Chem 2005; 44:8355-67. [PMID: 16270974 DOI: 10.1021/ic051055a] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Combining spectroscopic techniques (TRES and EXAFS) and molecular dynamics simulations, we have investigated the state of trivalent europium dissolved in room-temperature ionic liquids (RTILs), as a function of the RTIL anion and in the presence of added chloride anions. The studied RTILs are based on the 1-butyl-3-methyl-imidazolium (Bumim+) cation and differ by their anionic counterparts: BF4-, PF6-, Tf- (triflate, CF3SO3-), and Tf2N- [(CF3SO2)2N-]. The results show the strong influence of the RTIL nature on the first solvation shell of europium and on its complexation with chloride. Depending on the RTIL, europium(III), which was introduced in solution as a triflate salt, is found to be solvated either by RTIL anions only or as neutral undissociated EuTf3 moieties completed by solvent anions. Kinetic effects, related to the viscosity of the RTIL and the nature of the europium salt, also markedly influence the coordination of added Cl- or F- anions to the metal.
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Affiliation(s)
- Clotilde Gaillard
- Institut de Recherches Subatomiques, CNRS-IN2P3, B.P. 28, 67037 Strasbourg Cedex 2, France.
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Cantuel M, Bernardinelli G, Muller G, Riehl JP, Piguet C. The First Enantiomerically Pure Helical Noncovalent Tripod for Assembling Nine-Coordinate Lanthanide(III) Podates. Inorg Chem 2004; 43:1840-9. [PMID: 15018502 DOI: 10.1021/ic035292u] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Decomplexation of the trivalent lanthanide, Ln(III), from the racemic bimetallic triple-stranded helicates [LnCr(L8)(3)](6+) provides the inert chiral tripodal nonadentate receptor [Cr(L8)(3)](3+). Elution of the latter podand with Na(2)Sb(2)[(+)-C(4)O(6)H(2)](2).5H(2)O through a cation exchange column allows its separation into its inert helical enantiomers M-(+)(589)-[Cr(L8)(3)](3+) and P-(-)(589)-[Cr(L8)(3)](3+), whose absolute configurations are assigned by using CD spectroscopy and exciton theory. Recombination with Ln(III) restores the original triple-stranded helicates [LnCr(L8)(3)](6+), and the associated thermodynamic parameters unravel the contribution of electrostatic repulsion and preorganization to the complexation process. Combining M-(+)(589)-[Cr(L8)(3)](3+) with Eu(III) produces the enantiomerically pure d-f helicate MM-(-)(589)-[EuCr(L8)(3)](CF(3)SO(3))(6).4CH(3)CN, whose X-ray crystal structure (EuCrC(113)H(111)N(25)O(21)S(6)F(18), monoclinic, P2(1), Z = 2) unambiguously confirms the absolute left-handed configuration for the final helix. The associated ligand-centered and metal-centered chiro-optical properties recorded for the complexes MM-[LnCr(L8)(3)](6+) and PP-[LnCr(L8)(3)](6+) (Ln = Eu, Gd, Tb) show a strong effect of helicity on specific rotary dispersions, CD and CPL spectra.
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Affiliation(s)
- Martine Cantuel
- Department of Inorganic, Analytical and Applied Chemistry, University of Geneva, 30 Quai E. Ansermet, CH-1211 Geneva 4, Switzerland
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Le Borgne T, Altmann P, André N, Bünzli JCG, Bernardinelli G, Morgantini PY, Weber J, Piguet C. Tuning facial–meridional isomerisation in monometallic nine-co-ordinate lanthanide complexes with unsymmetrical tridentate ligands. Dalton Trans 2004:723-33. [PMID: 15252492 DOI: 10.1039/b316035a] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unsymmetrical tridentate benzimidazole-pyridine-carboxamide units in ligands L1-L4 react with trivalent lanthanides, Ln(III), to give the nine-co-ordinate triple-helical complexes [Ln(Li)3]3+ (i = 1-4) existing as mixtures of C3-symmetrical facial and C1-symmetrical meridional isomers. Although the beta13 formation constants are 3-4 orders of magnitude smaller for these complexes than those found for the D3-symmetrical analogues [Ln(Li)3]3+ (i = 5-6) with symmetrical ligands, their formation at the millimolar scale is quantitative and the emission quantum yield of [Eu(L2)3]3+ is significantly larger. The fac-[Ln(Li)3]3+ <--> mer-[Ln(Li)3]3+ (i = 1-4) isomerisation process in acetonitrile is slow enough for Ln = Lu(III) to be quantified by 1H NMR below room temperature. The separation of enthalpic and entropic contributions shows that the distribution of the facial and meridional isomers can be tuned by the judicious peripheral substitution of the ligands affecting the interstrand interactions. Molecular mechanics (MM) calculations suggest that one supplementary interstrand pi-stacking interaction stabilises the meridional isomers, while the facial isomers benefit from more favourable electrostatic contributions. As a result of the mixture of facial and meridional isomers in solution, we were unable to obtain single crystals of 1:3 complexes, but the X-ray crystal structures of their nine-co-ordinate precursors [Eu(L1)2(CF3SO3)2(H2O)](CF3SO3)(C3H5N)2(H2O) (6, C45H54EuF9N10O13S3, monoclinic, P2(1)/c, Z = 4) and [Eu(L4)2(CF3SO3)2(H2O)](CF3SO3)(C4H4O)(1.5) (7, C51H66EuF9N8O(15.5)S3, triclinic, P1, Z = 2) provide crucial structural information on the binding mode of the unsymmetrical tridentate ligands.
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Affiliation(s)
- Thierry Le Borgne
- Department of Inorganic, Analytical and Applied Chemistry, University of Geneva, Switzerland
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Dobler M, Hirata M. Molecular dynamics simulations of lanthanide(iii) diphenyldimethylpyridinyl–dicarboxyamide complexes in water and in methanol: evidence for both first and second sphere complexes. Phys Chem Chem Phys 2004. [DOI: 10.1039/b314656a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Le Borgne T, Bénech JM, Floquet S, Bernardinelli G, Aliprandini C, Bettens P, Piguet C. Monometallic lanthanide complexes with tridentate 2,6-dicarboxamidopyridine ligands. Influence of peripheral substitutions on steric congestion and antenna effect. Dalton Trans 2003. [DOI: 10.1039/b307413g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Kim HS. Monte Carlo Simulation Study of Solvent Effect on Δlog Ks of Rb+ and K+ Ion to 18-Crown-6. J Phys Chem B 2002. [DOI: 10.1021/jp021190y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hag-Sung Kim
- Department of Environmental Industrial Chemistry, Ulsan College, Ulsan, 680-749, South Korea
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