51
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Bukharov MS, Shtyrlin VG, Gilyazetdinov EM, Serov NY, Madzhidov TI. Hydration of copper(II) amino acids complexes. J Comput Chem 2017; 39:821-826. [DOI: 10.1002/jcc.25154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Mikhail S. Bukharov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Valery G. Shtyrlin
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Edward M. Gilyazetdinov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Nikita Yu. Serov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
| | - Timur I. Madzhidov
- Kazan Federal University, A. M. Butlerov Chemistry Institute, 18 Kremlevskaya St; Kazan 420008 Russian Federation
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52
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Characterization of the F−-water and Cl−-water hydrogen bonds in aqueous solution: From “interior” (I) to “surface” (S) states. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.10.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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53
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Moin ST, Hofer TS. Hydration of iron-porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study. Phys Chem Chem Phys 2017; 19:30822-30833. [PMID: 29135005 DOI: 10.1039/c7cp04436d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe2+-P and Fe3+-P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe2+-P accommodates one water molecule in the first coordination sphere of the Fe2+ ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe3+-P, thus forming a hexa-coordinated species. Comparison of dynamical properties such as the vibrational power spectrum and ligand mean residence times to other metal-free porphyrin systems demonstrate the ions' influence on the hydration structure, enabling a characterisation of the strong interaction of the ions which greatly reduces the hydrogen bonding potential of the complex. The association of water molecules with the metal ions in both solutes was quantified by computing the free energy of binding obtained via the potential of mean force. This further confirmed the strong association of water to the metal ions which was conversely weak as inferred from the energetic data for the Fe2+-P system.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi, Karachi-75270, Pakistan.
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54
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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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55
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Prasetyo N, Utami W, Armunanto R, Hofer TS. Exploring structure and dynamics of solvated Ca(II) in liquid ammonia: A quantum mechanical charge field (QMCF) molecular dynamics simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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56
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Chaiyasit P, Tongraar A, Kerdcharoen T. Characteristics of methylammonium ion (CH 3 NH 3 + ) in aqueous electrolyte solution: An ONIOM-XS MD simulation study. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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57
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Moin ST, Hofer TS. Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration. MOLECULAR BIOSYSTEMS 2017; 12:2288-2295. [PMID: 27194391 DOI: 10.1039/c6mb00133e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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58
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Molecular Dynamics Simulations of Hydroxyapatite Nanopores in Contact with Electrolyte Solutions: The Effect of Nanoconfinement and Solvated Ions on the Surface Reactivity and the Structural, Dynamical, and Vibrational Properties of Water. CRYSTALS 2017. [DOI: 10.3390/cryst7020057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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59
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Biswas S, Mallik BS. Ultrafast Vibrational Spectroscopy of Aqueous Solution of Methylamine from First Principles MD Simulations. ChemistrySelect 2017. [DOI: 10.1002/slct.201601391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sohag Biswas
- Department of Chemistry; Indian Institute of Technology Hyderabad, Kandi, Sangareddy -; 502285 Telangana India
| | - Bhabani S. Mallik
- Department of Chemistry; Indian Institute of Technology Hyderabad, Kandi, Sangareddy -; 502285 Telangana India
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60
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Saleh M, Hofer TS. Palladium(ii) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD). Dalton Trans 2017; 46:9630-9638. [DOI: 10.1039/c7dt01548h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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61
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Gering KL. Prediction of Electrolyte Conductivity: Results from a Generalized Molecular Model Based on Ion Solvation and a Chemical Physics Framework. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2016.12.083] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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62
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Caralampio DZ, Martínez JM, Pappalardo RR, Marcos ES. The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity. Phys Chem Chem Phys 2017; 19:28993-29004. [DOI: 10.1039/c7cp05346k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydration shells around Rb+ and Cs+ are not symmetric; the cation and the 1st-shell water mass center are separated by ∼0.4 Å, and this is supported by agreement between the theoretical and experimental EXAFS spectrum.
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Affiliation(s)
| | - José M. Martínez
- Departmento de Quimica Fisica
- Universidad de Sevilla
- 41012-Seville
- Spain
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63
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Characteristics of K + and Rb + as “structure-breaking” ions in dilute aqueous solution: Insights from ONIOM-XS MD simulations. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.09.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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64
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Prasetyo N, Armunanto R. Revisiting structure and dynamics of Ag+ in 18.6% aqueous ammonia: An ab initio quantum mechanical charge field simulation. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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65
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D’Angelo P, Migliorati V, Sessa F, Mancini G, Persson I. XANES Reveals the Flexible Nature of Hydrated Strontium in Aqueous Solution. J Phys Chem B 2016; 120:4114-24. [DOI: 10.1021/acs.jpcb.6b01054] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paola D’Angelo
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Valentina Migliorati
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sessa
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126 Pisa, Italy
| | - Ingmar Persson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences (SLU), SE-750 07 Uppsala, Sweden
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66
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Wilkins DM, Manolopoulos DE, Dang LX. Nuclear quantum effects in water exchange around lithium and fluoride ions. J Chem Phys 2016; 142:064509. [PMID: 25681925 DOI: 10.1063/1.4907554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell is found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.
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Affiliation(s)
- David M Wilkins
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Liem X Dang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 93352, USA
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67
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Sessa F, D’Angelo P, Guidoni L, Migliorati V. Hidden Hydration Structure of Halide Ions: an Insight into the Importance of Lone Pairs. J Phys Chem B 2015; 119:15729-37. [DOI: 10.1021/acs.jpcb.5b10636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Sessa
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola D’Angelo
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Leonardo Guidoni
- Dipartimento
di Scienze Fisiche e Chimiche, Università degli Studi Dell’Aquila, Via Vetoio, L’Aquila, Italy
| | - Valentina Migliorati
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
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68
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Passler PP, Rode BM. The properties of trivalent praseodymium, neodymium, promethium and samarium ions in water: A quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.065] [Citation(s) in RCA: 2] [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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69
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70
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Passler PP, Rode BM. Thulium(III) and ytterbium(III) in aqueous solution ab initio quantum mechanical charge field molecular dynamics studies. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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71
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Mehandzhiyski AY, Riccardi E, van Erp TS, Trinh TT, Grimes BA. Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water. J Phys Chem B 2015; 119:10710-9. [DOI: 10.1021/acs.jpcb.5b05616] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aleksandar Y. Mehandzhiyski
- Ugelstad
Laboratory, Department of Chemical Engineering, Norwegian University of Science and Technology, SemSælandsvei 4, NO-7491 Trondheim, Norway
| | - Enrico Riccardi
- Department
of Chemistry, Norwegian University of Science and Technology, Høgskoleringen
5 Realfagbygget blokk D, 3.etg., NO-7491 Trondheim, Norway
| | - Titus S. van Erp
- Department
of Chemistry, Norwegian University of Science and Technology, Høgskoleringen
5 Realfagbygget blokk D, 3.etg., NO-7491 Trondheim, Norway
| | - Thuat T. Trinh
- Department
of Chemistry, Norwegian University of Science and Technology, Høgskoleringen
5 Realfagbygget blokk D, 3.etg., NO-7491 Trondheim, Norway
| | - Brian A. Grimes
- Ugelstad
Laboratory, Department of Chemical Engineering, Norwegian University of Science and Technology, SemSælandsvei 4, NO-7491 Trondheim, Norway
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72
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Sripa P, Tongraar A, Kerdcharoen T. Structure and dynamics of the Li+ hydrates: A comparative study of conventional QM/MM and ONIOM-XS MD simulations. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.04.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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73
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Tirler AO, Passler PP, Rode BM. The lanthanoid hydration properties beyond the ‘Gadolinium Break’: Dysprosium (III) and holmium (III), an ab initio quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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74
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Kabbalee P, Sripa P, Tongraar A, Kerdcharoen T. Solvation structure and dynamics of K+ in aqueous ammonia solution: Insights from an ONIOM-XS MD simulation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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75
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Tirler AO, Hofer TS. A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics. J Phys Chem B 2015; 119:8613-22. [PMID: 26090779 DOI: 10.1021/acs.jpcb.5b03938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.
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Affiliation(s)
- Andreas O Tirler
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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76
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Vchirawongkwin S, Kritayakornupong C, Tongraar A, Vchirawongkwin V. Hydration properties determining the reactivity of nitrite in aqueous solution. Dalton Trans 2015; 43:12164-74. [PMID: 24840033 DOI: 10.1039/c4dt00273c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The knowledge of the hydration properties of the nitrite ion is key to understanding its reaction mechanism controlled by solvent effects. Here, ab initio quantum mechanical charge field molecular dynamics was performed to obtain the structural and dynamical properties of the hydration shell in an aqueous solution of nitrite ions, elucidated by data analysis using a molecular approach and an extended quantitative analysis of all superimposed trajectories with three-dimensional alignment (density map). The pattern of the power spectra corresponded to the experimental data, indicating the suitability of the Hartree-Fock method coupled with double-ζ plus polarization and diffuse functional basis sets to study this system. The density maps revealed the structure of the hydration shell, that presented a higher density in the N-O bond direction than in the axis vertical to the molecular plane, whereas the atomic and molecular radial distribution functions provided vague information. The number of actual contacts indicated 4.6 water molecules interacting with a nitrite ion, and 1.5 extra water molecules located in the molecular hydration shell, forming a H-bonding network with the bulk water. The mean residence times for the water ligands designated the strength of the hydration spheres for the oxygen sites, whilst the results for the nitrogen sites over-estimated the number of water molecules from other sites and indicated a weak structure. These results show the influence of the water molecules surrounding the nitrite ion creating an anisotropic hydration shell, suggesting that the reactive sites are situated above and below the molecular plane with a lower water density.
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Affiliation(s)
- Saowapak Vchirawongkwin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Rangsit University, Patumthani 12000, Thailand
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77
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Di Tommaso D, Ruiz-Agudo E, de Leeuw NH, Putnis A, Putnis CV. Modelling the effects of salt solutions on the hydration of calcium ions. Phys Chem Chem Phys 2015; 16:7772-85. [PMID: 24643252 DOI: 10.1039/c3cp54923b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Classical molecular dynamics simulations of several aqueous alkali halide salt solutions have been used to determine the effect of electrolytes on the structure of water and the hydration properties of calcium ions. Compared with the simulations of Ca(2+) ions in pure liquid water, the frequency of water exchange in the first hydration shell of calcium, which is a fundamental process in controlling the reactivity of calcium(ii) aqua-ions, is drastically reduced in the presence of other electrolytes in solution. The strong stabilization of the hydration shell of Ca(2+) occurs not only when the halide anions are directly coordinated to calcium, but also when the alkali and halide ions are placed at or outside the second coordination shell of Ca(2+), suggesting that the reactivity of the first solvation shell of the calcium ion can be influenced by the specific affinity of other ions in solution for the water molecules coordinated to Ca(2+). Analysis of the hydrogen-bonded structure of water in the vicinity of the calcium ion shows that the average number of hydrogen bonds per water molecules, which is 1.8 in pure liquid water, decreases as the concentration of alkali-halide salts in solution increases, and that the temporal fluctuations of hydrogen bonds are significantly larger than those obtained for Ca(2+) in pure liquid water. This effect has been explained in terms of the dynamics of reorganization of the O-H···X(-) (X = F, Cl and Br) hydrogen bond. This work shows the importance of solution composition in determining the hydrogen-bonding network and ligand-exchange dynamics around metal ions, both in solution and at the mineral-water interfaces, which in turn has implications for interactions occurring at the mineral-water interface, ultimately controlling the mobilization of ions in the environment as well as in industrial processes.
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Affiliation(s)
- Devis Di Tommaso
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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78
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Pham TT, Lemaire T, Capiez-Lernout E, Lewerenz M, To QD, Christie JK, Di Tommaso D, de Leeuw NH, Naili S. Properties of water confined in hydroxyapatite nanopores as derived from molecular dynamics simulations. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1653-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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79
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Lv SS, Liu YR, Huang T, Feng YJ, Jiang S, Huang W. Stability of Hydrated Methylamine: Structural Characteristics and H2N···H–O Hydrogen Bonds. J Phys Chem A 2015; 119:3770-9. [DOI: 10.1021/acs.jpca.5b00616] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sha-Sha Lv
- School
of Physics and Materials Science, Anhui University, Hefei, Anhui 230601, China
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ya-Juan Feng
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuai Jiang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei Huang
- School
of Physics and Materials Science, Anhui University, Hefei, Anhui 230601, China
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
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80
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Canaval LR, Passler PP, Rode BM. The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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81
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Eklund L, Hofer TS, Persson I. Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS. Dalton Trans 2015; 44:1816-28. [PMID: 25473816 PMCID: PMC4281468 DOI: 10.1039/c4dt02580f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.
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Affiliation(s)
- Lars Eklund
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
| | - Tomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
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82
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Preferential solvation and dynamics of Li+ in aqueous ammonia solution: An ONIOM-XS MD simulation study. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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83
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Lithium(I) in liquid ammonia: A quantum mechanical charge field (QMCF) molecular dynamics simulation study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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84
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Jiang T, Boereboom JM, Michel C, Fleurat-Lessard P, Bulo RE. Proton Transfer in Aqueous Solution: Exploring the Boundaries of Adaptive QM/MM. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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85
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Messner CB, Bonn GK, Hofer TS. QM/MM MD simulations of La(iii)–phosphopeptide complexes. MOLECULAR BIOSYSTEMS 2015; 11:232-8. [DOI: 10.1039/c4mb00424h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical simulations have been used to study the structural and dynamical properties of a La(iii)–phosphopeptide complex.
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Affiliation(s)
- Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry
- Leopold-Franzens University
- 6020 Innsbruck
- Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Leopold-Franzens University
- 6020 Innsbruck
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86
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Canaval LR, Rode BM. The hydration properties of Eu(II) and Eu(III): An ab initio quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.10.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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87
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Vchirawongkwin V, Tongraar A, Kritayakornupong C. Characterization of structure and dynamics of the solvated indium(III) ion by an extended QM/MM molecular dynamics simulation. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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88
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Moin ST, Hofer TS. Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study. Phys Chem Chem Phys 2014; 16:26075-83. [DOI: 10.1039/c4cp03697b] [Citation(s) in RCA: 3] [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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89
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Messner CB, Lutz OMD, Rainer M, Huck CW, Hofer TS, Rode BM, Bonn GK. Structure and dynamics of chromatographically relevant Fe(III)-chelates. J Phys Chem B 2014; 118:12232-8. [PMID: 25301257 DOI: 10.1021/jp505193y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Immobilized metal ion affinity chromatography (IMAC) is an important chromatographic technique for biomolecules. In order to get a detailed understanding of the hydration of immobilized Fe(III), complexes of Fe(III) with methyl substituted iminodiacetate ([Fe(MSIDA)(H2O)3](+)) as well as with methyl substituted nitrilotriacetate ([Fe(MSNTA)(H2O)2]) were simulated in aqueous solutions with the quantum mechanical charge field molecular dynamics (QMCF MD) approach. The simulations were carried out at the Hartree-Fock (HF) level of theory, since cluster calculations at the HF, MP2, and B3LYP levels of theory showed that this method results in a good compromise between computational effort and accuracy. None of the coordinating water molecules were exchanged during the simulation period of 15 ps. The Fe-OH2O bond distances as well as the Fe-OH2O stretching motions differed among the coordinating water molecules, indicating different bond strengths. For the water molecules in the second hydration layer, mean residence times of 2.7 and 1.9 ps were obtained for [Fe(MSIDA)(H2O)3](+) and [Fe(MSNTA)(H2O)2], respectively. Furthermore, infrared measurements were carried out to characterize the most prominent bond features of aqueous Fe(III)-NTA and to discuss these results in conjunction with the computationally derived frequencies.
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Affiliation(s)
- Christoph B Messner
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
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90
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Migliorati V, Sessa F, Aquilanti G, D’Angelo P. Unraveling halide hydration: A high dilution approach. J Chem Phys 2014; 141:044509. [DOI: 10.1063/1.4890870] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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91
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Lim LHV, Lloren AV, Lamorena RB. The effect of urea in the nucleation process of CO2 clathrate hydrates. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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92
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Kohagen M, Mason PE, Jungwirth P. Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. J Phys Chem B 2014; 118:7902-9. [DOI: 10.1021/jp5005693] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miriam Kohagen
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
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93
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Bhattacharjee A, Weiss AKH, Artero V, Field MJ, Hofer TS. Electronic Structure and Hydration of Tetramine Cobalt Hydride Complexes. J Phys Chem B 2014; 118:5551-61. [DOI: 10.1021/jp502651s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anirban Bhattacharjee
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Alexander K. H. Weiss
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
| | - Vincent Artero
- Laboratoire
de Chimie et Biologie des Métaux (UMR 5249, CNRS,
CEA, Université Grenoble I), DSV/iRTSV,
CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Thomas S. Hofer
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
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94
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Moin ST, Weiss AK, Rode BM. Ionized CO2 and SO2 in aqueous environment: Ab initio QMCF-MD studies. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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95
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Sakwarathorn T, Pongstabodee S, Vchirawongkwin V, Canaval LR, Tirler AO, Hofer TS. Characteristics of selenate in aqueous solution – An ab initio QMCF-MD study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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96
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Wiedemair MJ, Weiss AKH, Rode BM. Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation. Phys Chem Chem Phys 2014; 16:7368-76. [DOI: 10.1039/c3cp54986k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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97
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Moin ST, Hofer TS. Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations. ACTA ACUST UNITED AC 2014; 10:117-27. [DOI: 10.1039/c3mb70300b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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98
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Eklund L, Hofer TS, Weiss AKH, Tirler AO, Persson I. Structure and water exchange of the hydrated thiosulfate ion in aqueous solution using QMCF MD simulation and large angle X-ray scattering. Dalton Trans 2014; 43:12711-20. [DOI: 10.1039/c4dt01010h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Experimental and simulation data of the thiosulfate ion show large similarities in hydration structure and mechanism with the sulfate ion but with weaker hydration of the terminal sulfur atom in thiosulfate.
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Affiliation(s)
- Lars Eklund
- Department of Chemistry and Biotechnology
- Swedish University of Agricultural Sciences
- SE-750 07 Uppsala, Sweden
| | - Tomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Andreas O. Tirler
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology
- Swedish University of Agricultural Sciences
- SE-750 07 Uppsala, Sweden
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99
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Tiwari SP, Rai N, Maginn EJ. Dynamics of actinyl ions in water: a molecular dynamics simulation study. Phys Chem Chem Phys 2014; 16:8060-9. [DOI: 10.1039/c3cp54556c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of actinyl ions (AnO2n+) in aqueous solutions is important not only for the design of advanced separation processes but also for understanding the fate of actinides in the environment.
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Affiliation(s)
- Surya Prakash Tiwari
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame, USA
| | - Neeraj Rai
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame, USA
- Dave C. Swalm School of Chemical Engineering
- Mississippi State University
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame, USA
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100
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Tirler AO, Weiss AKH, Hofer TS. A Comparative Quantum Mechanical Charge Field Study of Uranyl Mono- and Dicarbonate Species in Aqueous Solution. J Phys Chem B 2013; 117:16174-87. [DOI: 10.1021/jp407179s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas O. Tirler
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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