1
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Listyarini R, Kriesche BM, Hofer TS. Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H 2O. J Chem Theory Comput 2024; 20:3028-3045. [PMID: 38595064 PMCID: PMC11044269 DOI: 10.1021/acs.jctc.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Bernhard M. Kriesche
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
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2
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Nochebuena J, Liu S, Cisneros GA. Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations. J Chem Phys 2024; 160:134301. [PMID: 38557841 DOI: 10.1063/5.0203020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, USA
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3
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Moison H, Aufort J, Benoit M, Méheut M. On Local Structure Equilibration of Ca 2+ in Solution by Ab Initio Molecular Dynamics. J Phys Chem B 2024; 128:3167-3181. [PMID: 38525554 DOI: 10.1021/acs.jpcb.3c07308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Analyzing the stable isotopic ratio of Ca offers valuable insights into a wide range of applications from climate reconstruction to bone cancer diagnosis and agricultural nutrient improvement. While the first hydration shell of Ca in solution is expected to play a major role in its fractionation properties, the coordination of Ca in water remains a subject of debate. In this work, Ca2+ in water has been modeled by means of ab initio molecular dynamics simulations using various exchange and correlation functionals and at different temperatures. Results show a significant effect of the functional on the average Ca2+ coordination, depending on its tendency to over- or understructure liquid water. The BLYP functional with Grimme-D2 correction was judged as the most accurate among those tested based on its accuracy to reproduce water structural and diffusion properties. Using this functional, the effect of temperature has been systematically investigated, focusing on means to limit the uncertainty in our assessments of the average coordination of Ca2+ ions by (1) estimating the number of water exchanges in the simulations and (2) implementing a statistical approach based on Markov chains. The findings indicate, especially, that our simulations at 300, 350, and 400 K do not yield converged results due to potential equilibration problems. These observations impose substantial constraints on the trustworthiness of numerous estimates in the existing literature that depend on trajectories with insufficient exchanges. We estimate Ca2+ coordination values of 6.8 ± 0.1, 6.8 ± 0.1, 6.7 ± 0.2, and 6.7 ± 0.2 at 600, 550, 500, and 450 K respectively. At lower temperatures (300, 350, and 400 K), while obtaining definitive values for Ca2+ coordination remains challenging, our research does indicate a potential temperature-related influence on coordination with an average Ca2+ coordination at 300 K as low as 6.2.
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Affiliation(s)
- Hugo Moison
- GET, OMP, Université Paul Sabatier, 14, avenue Édouard Belin, 31400 Toulouse, France
| | - Julie Aufort
- GET, OMP, Université Paul Sabatier, 14, avenue Édouard Belin, 31400 Toulouse, France
- IMPMC, Sorbonne Université, 4, place Jussieu, 75252 Paris Cedex 5, France
| | - Magali Benoit
- CEMES CNRS and Université Toulouse, 39 rue Jeanne Marvig, 31055 Toulouse, France
| | - Merlin Méheut
- GET, OMP, Université Paul Sabatier, 14, avenue Édouard Belin, 31400 Toulouse, France
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4
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Migliorati V, D’Angelo P, Sessa F. Going beyond Radial Hydration Models: The Hidden Structures of Chloride and Iodide Aqua Ions Revealed by the Use of Lone Pairs. J Phys Chem B 2023; 127:10843-10850. [PMID: 38064661 PMCID: PMC10749448 DOI: 10.1021/acs.jpcb.3c06185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
A novel model of hydration for the chloride and iodide ions in water is proposed, which overcomes the limitations of conventional radial models. A new approach, based on a representation of the halide lone pairs, highlighted a subset of first shell water molecules featuring preferential strong interactions with the ion lone pairs, giving rise to tetrahedral hydration structures in both Cl- and I- aqueous solutions. By adopting a novel descriptor correlated to the halide-water interaction energy, we were able to split the conventional first solvation shell into a tight first hydration shell, composed of water molecules strongly interacting with the ions via hydrogen bonds, and a loose first shell containing molecules that are only slightly perturbed by the halide electrostatic charge. The picture emerging from our findings indicates that lone pairs play an important role in the description of systems where hydrogen bonds are the main interactions taking place in the solvation process.
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Affiliation(s)
- Valentina Migliorati
- Dipartimento
di Chimica, “La Sapienza”
Università di Roma, P.le Aldo Moro 5, Rome 00185, Italy
| | - Paola D’Angelo
- Dipartimento
di Chimica, “La Sapienza”
Università di Roma, P.le Aldo Moro 5, Rome 00185, Italy
| | - Francesco Sessa
- Department
of Chemical Sciences, University of Naples
Federico II, Comp. Univ. Monte Sant’Angelo, Naples 80126, Italy
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5
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Nochebuena J, Piquemal JP, Liu S, Cisneros GA. Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields. J Chem Theory Comput 2023; 19:7715-7730. [PMID: 37888874 DOI: 10.1021/acs.jctc.3c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise nonpolarizable force fields, thanks to the incorporation of polarization effects. In this study, we assess the performance of the AMOEBA polarizable force field and the AMBER and OPLS nonpolarizable pairwise force fields in capturing positive and negative cooperativity recently explored in neutral and charged molecular clusters using density functional theory. Our findings show that polarizable and nonpolarizable force fields qualitatively reproduce the relative cooperativity observed in electron structure calculations. However, AMBER and OPLS fail to describe absolute cooperativity. In contrast, AMOEBA accounts for the absolute cooperativity by considering interactions beyond pairwise interactions. According to the energy decomposition analysis, it is observed that the electrostatic interactions calculated with the AMBER and OPLS force fields seem to play an important and counterintuitive role in reproducing the adiabatic interaction energies calculated with density functional theory. However, it is important to note that these force fields, due to their nature, do not explicitly incorporate many-body effects, which limits their ability to accurately describe cooperativity. On the other hand, frustration in polarizable and nonpolarizable force fields is caused by changes in bond stretching and angle bending terms of the building blocks when they are forming a complex.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie théorique, Sorbonne Université, UMR 7616 CNRS, Paris 75005, France
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
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6
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Jamal S, Naz Z, Moin ST, Hofer TS. Deciphering Structural and Dynamical Properties of Hydrated Cobalt Porphyrins via Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation. J Phys Chem B 2023. [PMID: 37220311 DOI: 10.1021/acs.jpcb.3c00837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The present study successfully implemented the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism for the investigation of structural and dynamical properties of hydrated cobalt-porphyrin complexes. Considering the significance of cobalt ions in biological systems (for instance, vitamin B12), which reportedly incorporate cobalt ions in a d6, low spin, +3 state chelated in the corrin ring, an analog of porphyrin, the current study is focused on cobalt in the oxidation states +2 and +3 bound to the parent porphyrin lead structures embedded in an aqueous solution. These cobalt-porphyrin complexes were investigated in terms of their structural and dynamical properties at the quantum chemical level. The structural attributes of these hydrated complexes revealed the contrasting features of the water binding to these solutes, including a detailed evaluation of the associated dynamics. The study also yielded notable findings in regard to the respective electronic configurations vs coordination, which suggested that Co(II)-POR possesses a 5-fold square pyramidal coordination geometry in an aqueous solution containing the metal ion coordinating to four nitrogen atoms of the porphyrin ring and one axial water as the fifth ligand. On the other hand, high-spin Co(III)-POR was hypothesized to be more stable due to the smaller size-to-charge ratio of the cobalt ion, but the high-spin complex demonstrated unstable structural and dynamical behavior. However, the corresponding properties of the hydrated Co(III)LS-POR revealed a stable structure in an aqueous solution, thus suggesting the Co(III) ion to be in a low-spin state when bound to the porphyrin ring. Moreover, the structural and dynamical data were augmented by computing the free energy of water binding to the cobalt ions and the solvent-accessible surface area, which provide further information on thermochemical properties of the metal-water interaction and the hydrogen bonding potential of the porphyrin ring in these hydrated systems.
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Affiliation(s)
- Sehrish Jamal
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Zobia Naz
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S Hofer
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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7
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Reidelbach M, Bai M, Schneeberger M, Zöllner MS, Kubicek K, Kirchberg H, Bressler C, Thorwart M, Herrmann C. Solvent Dynamics of Aqueous Halides before and after Photoionization. J Phys Chem B 2023; 127:1399-1413. [PMID: 36728132 DOI: 10.1021/acs.jpcb.2c07992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Electron transfer reactions can be strongly influenced by solvent dynamics. We study the photoionization of halides in water as a model system for such reactions. There are no internal nuclear degrees of freedom in the solute, allowing the dynamics of the solvent to be uniquely identified. We simulate the equilibrium solvent dynamics for Cl-, Br-, I-, and their respective neutral atoms in water, comparing quantum mechanical/molecular mechanical (QM/MM) and classical molecular dynamics (MD) methods. On the basis of the obtained configurations, we calculate the extended X-ray absorption fine structure (EXAFS) spectra rigorously based on the MD snapshots and compare them in detail with other theoretical and experimental results available in the literature. We find our EXAFS spectra based on QM/MM MD simulations in good agreement with their experimental counterparts for the ions. Classical MD simulations for the ions lead to EXAFS spectra that agree equally well with the experiment when it comes to the oscillatory period of the signal, even though they differ from the QM/MM radial distribution functions extracted from the MD. The amplitude is, however, considerably overestimated. This suggests that to judge the reliability of theoretical simulation methods or to elucidate fine details of the atomistic dynamics of the solvent based on EXAFS spectra, the amplitude as well as the oscillatory period need to be considered. If simulations fail qualitatively, as does the classical MD for the aqueous neutral halogen atoms, the resulting EXAFS will also be strongly affected in both oscillatory period and amplitude. The good reliability of QM/MM-based EXAFS simulations, together with clear qualitative differences in the EXAFS spectra found between halides and their atomic counterparts, suggests that a combined theory and experimental EXAFS approach is suitable for elucidating the nonequilibrium solvent dynamics in the photoionization of halides and possibly also for electron transfer reactions in more complex systems.
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Affiliation(s)
- Marco Reidelbach
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Mei Bai
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Michaela Schneeberger
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Martin Sebastian Zöllner
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
| | - Katharina Kubicek
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,Department of Physics, Universität Hamburg, Notkestr. 85, 22607Hamburg, Germany.,European XFEL, Holzkoppel 4, 22869Schenefeld, Germany
| | - Henning Kirchberg
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Christian Bressler
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,Department of Physics, Universität Hamburg, Notkestr. 85, 22607Hamburg, Germany.,European XFEL, Holzkoppel 4, 22869Schenefeld, Germany
| | - Michael Thorwart
- The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany.,I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607Hamburg, Germany
| | - Carmen Herrmann
- Department of Chemistry, Universität Hamburg, Harbor Bldg. 610, Luruper Chaussee 149, 22761Hamburg, Germany.,The Hamburg Centre of Ultrafast Imaging, Luruper Chaussee 149, 22761Hamburg, Germany
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8
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Mandal S, Kar R, Meyer B, Nair NN. Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe 2+ /Fe 3+ Redox Reaction. Chemphyschem 2023; 24:e202200617. [PMID: 36169153 DOI: 10.1002/cphc.202200617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/27/2022] [Indexed: 02/03/2023]
Abstract
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe2+ /Fe3+ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, standard plane-wave based AIMD at that level of theory is typically 150 times slower than GGA for systems containing ∼100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe2+ /Fe3+ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe2+ /Fe3+ system computed from these simulations are compared with the available experimental data for validation.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
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9
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Listyarini RV, Kriesche BM, Hofer TS. The solvation structure of CO2 in dichloromethane – A comparative correlated, semi-empirical and classical MD simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Irregular structure of the hydrated Ag+ in aqueous solution and its Dynamics: An insight from perturbation theory hybrid forces molecular dynamics simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Yamaguchi A, Nagata K, Kobayashi K, Tanaka K, Kobayashi T, Tanida H, Shimojo K, Sekiguchi T, Kaneta Y, Matsuda S, Yokoyama K, Yaita T, Yoshimura T, Okumura M, Takahashi Y. Extended X-ray absorption fine structure spectroscopy measurements and ab initio molecular dynamics simulations reveal the hydration structure of the radium(II) ion. iScience 2022; 25:104763. [PMID: 35992079 PMCID: PMC9386089 DOI: 10.1016/j.isci.2022.104763] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/27/2022] [Accepted: 07/09/2022] [Indexed: 12/02/2022] Open
Abstract
Radium is refocused from the viewpoint of an environmental pollutant and cancer therapy using alpha particles, where it mainly exists as a hydrated ion. We investigated the radium hydration structure and the dynamics of water molecules by extended X-ray absorption fine structure (EXAFS) spectroscopy and ab initio molecular dynamics (AIMD) simulation. The EXAFS experiment showed that the coordination number and average distance between radium ion and the oxygen atoms in the first hydration shell are 9.2 ± 1.9 and 2.87 ± 0.06 Å, respectively. They are consistent with those obtained from the AIMD simulations, 8.4 and 2.88 Å. The AIMD simulations also revealed that the water molecules in the first hydration shell of radium are less structured and more mobile than those of barium, which is an analogous element of radium. Our results indicate that radium can be more labile than barium in terms of interactions with water.
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Affiliation(s)
- Akiko Yamaguchi
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 148-4 Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
- Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Kojiro Nagata
- Radioisotope Research Center, Institute for Radiation Sciences, Osaka University, 2-4 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keita Kobayashi
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 148-4 Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Kazuya Tanaka
- Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Tohru Kobayashi
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Hajime Tanida
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Kojiro Shimojo
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Tetsuhiro Sekiguchi
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Yui Kaneta
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Shohei Matsuda
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Keiichi Yokoyama
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Tsuyoshi Yaita
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirataka, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Takashi Yoshimura
- Radioisotope Research Center, Institute for Radiation Sciences, Osaka University, 2-4 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiko Okumura
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 148-4 Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Yoshio Takahashi
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
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12
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Prasetyo N, Hidayat Y. Lability of the first solvation shell of silver cations in liquid ammonia: A quantum mechanical charge field molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Saputri WD, Pranowo HD, Hofer TS. Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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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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15
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Prasetyo N. The effect of electron correlation in unraveling the hydration properties of Sc3+ in aqueous solution: A rigid body quantum mechanics/molecular mechanics simulation study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Theoretical insight on the solvation properties of Zn2+ in pure liquid ammonia: A quantum mechanical molecular charges field molecular dynamics (QMCF-MD) study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Saleh M, Zam ZZ, Hofer TS. Solvent influence on the presence of axial ligand coordination: A QMCF-MD study of the structural and dynamical properties of Pd(II) and Pd(II) tetra-ammine in aqueous solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Hidayat Y, Rahmawati F, Nurcahyo IF, Prasetyo N, Pranowo HD. Hybrid Forces Molecular Dynamics on the Lability, Dynamics and “Structure Breaking Effect” of Cs+ in Liquid Ammonia. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuniawan Hidayat
- Department of Chemistry, Faculty of Mathematics and Sciences, Sebelas Maret University, Jl. Ir Sutami 36A Surakarta, 57126, Indonesia
- Austria-Indonesia Centre (AIC) for Computational Chemistry, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Fitria Rahmawati
- Department of Chemistry, Faculty of Mathematics and Sciences, Sebelas Maret University, Jl. Ir Sutami 36A Surakarta, 57126, Indonesia
| | - IF Nurcahyo
- Department of Chemistry, Faculty of Mathematics and Sciences, Sebelas Maret University, Jl. Ir Sutami 36A Surakarta, 57126, Indonesia
| | - Niko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia
- Austria-Indonesia Centre (AIC) for Computational Chemistry, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia
- Austria-Indonesia Centre (AIC) for Computational Chemistry, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia
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Kim S, Wang X, Jang J, Eom K, Clegg SL, Park G, Di Tommaso D. Hydrogen-Bond Structure and Low-Frequency Dynamics of Electrolyte Solutions: Hydration Numbers from ab Initio Water Reorientation Dynamics and Dielectric Relaxation Spectroscopy. Chemphyschem 2020; 21:2334-2346. [PMID: 32866322 PMCID: PMC7702081 DOI: 10.1002/cphc.202000498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Indexed: 11/16/2022]
Abstract
We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl2 ) solutions at different concentrations (0.6-2.8 mol kg-1 ) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction.
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Affiliation(s)
- Seonmyeong Kim
- Center for THz-driven Biomedical SystemDepartment of Physics and AstronomySeoul National UniversityGwanak-gu08826South Korea
- Advanced Institutes of Convergence TechnologySeoul National UniversitySuwon-SiGyeonggi-do16229South Korea
| | - Xiangwen Wang
- School of Biological and Chemical SciencesMaterials Research InstituteThomas Young CentreQueen Mary University of LondonMile End RoadLondonE1 4NSUnited Kingdom
| | - Jeongmin Jang
- Center for THz-driven Biomedical SystemDepartment of Physics and AstronomySeoul National UniversityGwanak-gu08826South Korea
- Advanced Institutes of Convergence TechnologySeoul National UniversitySuwon-SiGyeonggi-do16229South Korea
| | - Kihoon Eom
- Center for THz-driven Biomedical SystemDepartment of Physics and AstronomySeoul National UniversityGwanak-gu08826South Korea
- Advanced Institutes of Convergence TechnologySeoul National UniversitySuwon-SiGyeonggi-do16229South Korea
| | - Simon L. Clegg
- School of Environmental SciencesUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - Gun‐Sik Park
- Center for THz-driven Biomedical SystemDepartment of Physics and AstronomySeoul National UniversityGwanak-gu08826South Korea
- Advanced Institutes of Convergence TechnologySeoul National UniversitySuwon-SiGyeonggi-do16229South Korea
| | - Devis Di Tommaso
- School of Biological and Chemical SciencesMaterials Research InstituteThomas Young CentreQueen Mary University of LondonMile End RoadLondonE1 4NSUnited Kingdom
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20
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First solvation shell structure and dynamics of solvated Ca2+ in dilute aqueous ammonia by first principle approach: a QMCF MD simulation study. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Saputri WD, Pranowo HD, Schuler MJ, Hofer TS. Cu 2+ in liquid ammonia-The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics. J Comput Chem 2020; 41:2168-2176. [PMID: 32735755 DOI: 10.1002/jcc.26379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/13/2020] [Indexed: 11/06/2022]
Abstract
The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Manuel J Schuler
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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22
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Wang X, Toroz D, Kim S, Clegg SL, Park GS, Di Tommaso D. Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions. Phys Chem Chem Phys 2020; 22:16301-16313. [PMID: 32647838 DOI: 10.1039/d0cp01957g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell.
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Affiliation(s)
- Xiangwen Wang
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Dimitrios Toroz
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Seonmyeong Kim
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Simon L Clegg
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gun-Sik Park
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Devis Di Tommaso
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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Saputri WD, Sulaiman SS, Sari FR, Sudiono S, Pranowo HD, Saleh M, Hofer TS. Co3+ and Ir3+ in pure liquid ammonia: Structure and dynamics from ab initio quantum mechanical charge field molecular dynamics. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112205] [Citation(s) in RCA: 1] [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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24
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Prasetyo N, Hofer TS. Carbon dioxide in liquid ammonia: An ab initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) simulation study on structure, dynamics and thermodynamics of solvation. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Bux K, Moin ST. Solvation of cholesterol in different solvents: a molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:1154-1167. [PMID: 31848548 DOI: 10.1039/c9cp05303d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To the best of our knowledge, molecular dynamics simulations of an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, were reported for the first time to gain insights into the structural and dynamical properties. The study was mainly focused on the evaluation of solvation of cholesterol with respect to its hydrophilic and hydrophobic structural components in the form of respective functional groups interacting with the solvents. Structural evaluations suggested that both hydrophilic and hydrophobic groups of cholesterol were interacting with the solvents, in particular methanol and dimethyl sulfoxide, which presented both types of interactions that are polar and non-polar. On the other hand, the highly polar water and non-polar benzene demonstrated extreme solvation behavior, since water was involved only in hydrogen bonding to the solute hydroxyl group and non-polar benzene formed strong van der Waals interactions only. Furthermore, the hydrophobic effect of cholesterol was also analyzed mainly in polar solvents, as the effect was more pronounced in the polar environment thereby preventing the solvent mobility in the solvation layer(s). The dynamical properties in terms of lateral diffusion and hydrogen bond dynamics as well as free energies of solvation also corroborated the findings based on the structural data and the hydrophobic character of cholesterol was later quantified by the computation of the averaged solvent accessible surface area. The polarity effect of the solvents on the aggregation property of cholesterol was further investigated, which is of big concern from the clinical point of view due to its major role in cardiovascular ailments. It was another major finding of the present study that aggregation was shown to be facilitated by highly polar solvents like water.
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Affiliation(s)
- Khair Bux
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi-75270, Pakistan.
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Science, University of Karachi, Karachi-75270, Pakistan.
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids. Int J Mol Sci 2020; 21:ijms21030697. [PMID: 31973103 PMCID: PMC7037047 DOI: 10.3390/ijms21030697] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 01/25/2023] Open
Abstract
Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems involving these solvents. Classical molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of IL systems have provided significant insights at the atomic level. Here, we present a review of the development and application of the multipolar and polarizable force field AMOEBA for ionic liquid systems, termed AMOEBA–IL. The parametrization approach for AMOEBA–IL relies on the reproduction of total quantum mechanical (QM) intermolecular interaction energies and QM energy decomposition analysis. This approach has been used to develop parameters for imidazolium– and pyrrolidinium–based ILs coupled with various inorganic anions. AMOEBA–IL has been used to investigate and predict the properties of a variety of systems including neat ILs and IL mixtures, water exchange reactions on lanthanide ions in IL mixtures, IL–based liquid–liquid extraction, and effects of ILs on an aniline protection reaction.
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Affiliation(s)
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA; (E.A.V.-M.); (J.E.V.-C.)
- Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA
- Correspondence:
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28
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Exploring preferential solvation, structure and dynamical properties or Rb+ in aqueous ammonia solution using ab initio Quantum Mechanical Charge Field (QMCF). J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Naz Z, Moin ST, Hofer TS. Hydration of Closely Related Manganese and Magnesium Porphyrins in Aqueous Solutions: Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:10769-10779. [PMID: 31738566 DOI: 10.1021/acs.jpcb.9b07639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.
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Affiliation(s)
- Zobia Naz
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi 75270 , Pakistan
| | - 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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Koskamp J, Ruiz-Hernandez SE, Di Tommaso D, Elena AM, De Leeuw NH, Wolthers M. Reconsidering Calcium Dehydration as the Rate-Determining Step in Calcium Mineral Growth. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:26895-26903. [PMID: 31737161 PMCID: PMC6849658 DOI: 10.1021/acs.jpcc.9b06403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The dehydration of cations is generally accepted as the rate-limiting step in many processes. Molecular dynamics (MD) can be used to investigate the dynamics of water molecules around cations, and two different methods exist to obtain trajectory-based water dehydration frequencies. Here, these two different post-processing methods (direct method versus survival function) have been implemented to obtain calcium dehydration frequencies from a series of trajectories obtained using a range of accepted force fields. None of the method combinations reproduced the commonly accepted experimental water exchange frequency of 10-8.2 s-1. Instead, our results suggest much faster water dynamics, comparable with more accurate ab initio MD simulations and with experimental values obtained using neutron scattering techniques. We obtained the best agreement using the survival function method to characterize the water dynamics, and we show that different method combinations significantly affect the outcome. Our work strongly suggests that the fast water exchange kinetics around the calcium ions is not rate-limiting for reactions involving dissolved/solvated calcium. Our results further suggest that, for alkali and most of the earth alkali metals, mechanistic rate laws for growth, dissolution, and adsorption, which are based on the principle of rate-limiting cation dehydration, need careful reconsideration.
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Affiliation(s)
- Janou
A. Koskamp
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
| | | | - Devis Di Tommaso
- Materials
Research Institute and School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | | | - Nora H. De Leeuw
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
- School
of Chemistry, Cardiff University, Main Building Park Place, Cardiff CF10 3AT, United Kingdom
| | - Mariette Wolthers
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
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Migliorati V, Caruso A, D’Angelo P. Unraveling the Hydration Properties of the Ba2+ Aqua Ion: the Interplay of Quantum Mechanics, Molecular Dynamics, and EXAFS Spectroscopy. Inorg Chem 2019; 58:14551-14559. [DOI: 10.1021/acs.inorgchem.9b02204] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessandro Caruso
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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32
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Yang X, Cheng K, Jia GZ. Microwave heating and non-thermal effects of sodium chloride aqueous solution. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1662505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xin Yang
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
| | - Ke Cheng
- College of Optoelectronic Technology, Chengdu University of Information technology, Chengdu, People’s Republic of China
| | - Guo-zhu Jia
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
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Saputri WD, Wijaya K, Pranowo HD, Hofer TS. The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-1115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Karna Wijaya
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Thomas S. Hofer
- University of Innsbruck , Theoretical Chemistry Division , Innsbruck , Austria
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Lynes O, Austin J, Kerridge A. Ab initio molecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl. Phys Chem Chem Phys 2019; 21:13809-13820. [PMID: 31210212 DOI: 10.1039/c9cp00142e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of the Mg2+, Ca2+, Sr2+ and UO22+ ions in either a pure aqueous environment or an environment containing two hydroxide ions have been carried out at the density functional level of theory, employing the generalised gradient approximation via the PBE exchange-correlation functional. Calculated mean M-O bond lengths in the first solvation shell of the aquo systems compared very well to existing experimental and computational literature, with bond lengths well within values measured previously and coordination numbers in line with previously calculated values. When applied to systems containing additional hydroxide ions, the methodology revealed increased bond lengths in all systems. Proton transfer events (PTEs) were recorded and were found to be most prevalent in the strontium hydroxide systems, likely due to the low charge density of the ion and the consequent lack of hydroxide coordination. For all alkaline earths, intrashell PTEs which occurred outside of the first solvation shell were most prevalent. Only three PTEs were identified in the entire simulation data of the uranium dihydroxide system, indicating the clear impact of the increased charge density of the hexavalent uranium ion on the strength of metal-oxygen bonds in aqueous solution. Broadly, systems containing more charge dense ions were found to exhibit fewer PTEs than those containing ions of lower charge density.
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Affiliation(s)
- Olivia Lynes
- Department of Chemistry, Faraday Building, Lancaster University, Lancaster, LA1 4YB, UK.
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35
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Investigation of the preferential solvation and dynamical properties of Cu+ in 18.6% aqueous ammonia solution using ab initio quantum mechanical charge field (QMCF) molecular dynamics and NBO analysis. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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36
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Friesen S, Hefter G, Buchner R. Cation Hydration and Ion Pairing in Aqueous Solutions of MgCl2 and CaCl2. J Phys Chem B 2019; 123:891-900. [DOI: 10.1021/acs.jpcb.8b11131] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sergej Friesen
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg 93040, Germany
| | - Glenn Hefter
- Chemistry Department, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg 93040, Germany
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37
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38
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Prasetyo N, Hofer TS. Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study. J Chem Theory Comput 2018; 14:6472-6483. [PMID: 30336013 DOI: 10.1021/acs.jctc.8b00557] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solvation of carbon dioxide in solution represents a key step for the capture and fixation CO2 in nature, which may be further influenced by the formation of (bi)carbonate species and/or the formation of CO2 clusters in solution. The latter processes are strongly dependent on the exact environment of the liquid state (e.g., pH value, solvated ions, etc.) and may interfere with the experimental determination of structural, dynamical, and thermodynamic properties. In this work a hybrid quantum mechanical/molecular mechanical (QM/MM) simulation approach at correlated ab initio level of theory resolution-of-identity second-order Møller-Plesset Perturbation Theory (RI-MP2) has been applied in the framework of thermodynamic integration (TI) to study structure, dynamics, and the hydration free energy of a single carbon dioxide molecule in aqueous solution. A detailed analysis of the individual QM/MM potential energy contributions demonstrate that the overall potential remains highly consistent over the entire sampling phase and that no artificial contributions are influencing the determination of the hydration free energy. The latter value of 0.01 ± 0.92 kcal/mol was found in very good agreement with the values of 0.06 and 0.24 kcal/mol obtained via quasi-chemical theory and experimental measurements, respectively. In order to obtain detailed information about the C- and O C-water interaction, conically restricted regions with respect to the main axis of the CO2 molecule have been employed in structural analysis. The presented data not only provide detailed information about the hydration properties of CO2 but act as a critical validation of the simulation technique, which will be beneficial in the study of nonaqueous solvents such as pure and aqueous NH3 solutions, which have been suggested as potential candidates to capture CO2 from anthropogenic sources.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82A , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara, Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara, Yogyakarta 55281 , Indonesia
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82A , A-6020 Innsbruck , Austria
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39
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Roy S, Bryantsev VS. Finding Order in the Disordered Hydration Shell of Rapidly Exchanging Water Molecules around the Heaviest Alkali Cs+ and Fr+. J Phys Chem B 2018; 122:12067-12076. [DOI: 10.1021/acs.jpcb.8b08414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Santanu Roy
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Vyacheslav S. Bryantsev
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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40
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - 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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41
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Electroinduced drift of solvated ions in salt solution of Ce and Ni. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1502-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Bux K, Ali SA, Moin ST. Hydration facilitates oxygenation of hemocyanin: perspectives from molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:925-938. [PMID: 29974187 DOI: 10.1007/s00249-018-1316-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 05/31/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations were applied to deoxy- and oxy-hemocyanins using newly developed force field parameters for the dicopper site to evaluate their structural and dynamical properties. Data obtained from the simulations provided information of the oxygenation effect on the active site and overall topology of the protein that was analyzed by root-mean-square deviations, b-factors, and dicopper coordination geometries. Domain I of the protein was found to demonstrate higher flexibility with respect to domain II because of the interfacial rotation between domain I and II that was further endorsed by computing correlative domain movements for both forms of the protein. The oxygenation effect on the overall structure of the protein or polypeptide subunit was further explored via gyration radii evaluated for the metal-binding domain and for the whole subunit. The evaluation of hydration dynamics was carried out to understand the water mediated role of amino acid residues of the solvent tunnel facilitating the entry of oxygen molecule to the dicopper site of hemocyanin.
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Affiliation(s)
- Khair Bux
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Syed Abid Ali
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - 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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43
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Marcus Y. A relationship between the effect of uni-univalent electrolytes on the structure of water and on its volatility. J Chem Phys 2018; 148:222807. [PMID: 29907023 DOI: 10.1063/1.5009311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effect of ions on the structure of water in dilute solutions, whether they are structure-makers or structure-breakers, is manifested also in the volatility of the water. For more than 40 uni-univalent electrolytes, there is a linearly increasing relationship between 2φ(m = 0.4) - φ(m = 0.2), where φ is the osmotic coefficient and m is the molality, and the difference between the viscosity B-coefficients of the cation and anion. Exceptions to this relationship are electrolytes with highly structure-making anions and with hydrophobic cations.
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Affiliation(s)
- Yizhak Marcus
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel
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44
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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45
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Tu YJ, Lin Z, Allen MJ, Cisneros GA. Molecular dynamics investigation of water-exchange reactions on lanthanide ions in water/1-ethyl-3-methylimidazolium trifluoromethylsufate ([EMIm][OTf]). J Chem Phys 2018; 148:024503. [PMID: 29331119 DOI: 10.1063/1.4997008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report a kinetic study of the water exchange on lanthanide ions in water/[1-ethyl-3-methylimidazolium][trifluoromethylsufate] (water/[EMIm][OTf]). The results from 17O-NMR measurements show that the water-exchange rates in water/[EMIm][OTf] increase with decreasing size of the lanthanide ions. This trend for water-exchange is similar to the previously reported trend in water/1-ethyl-3-methylimidazolium ethyl sulfate (water/[EMIm][EtSO4]) but opposite to that in water. To gain atomic-level insight into these water-exchange reactions, molecular dynamics simulations for lanthanide ions in water/[EMIm][OTf] have been performed using the atomic-multipole-optimized-energetics-for-biomolecular-application polarizable force field. Our molecular dynamics simulations reproduce the experimental water-exchange rates in terms of the trend and provide possible explanations for the observed experimental behavior. The smaller lanthanide ions in water/[EMIm][OTf] undergo faster water exchange because the smaller lanthanide ions coordinate to the first shell [OTf]- anions more tightly, resulting in a stronger screening effect for the second-shell water. The screening effect weakens the interaction of the lanthanide ions with the second-shell water molecules, facilitating the dissociation of water from the second-shell and subsequent association of water molecules from the outer solvation shells.
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Affiliation(s)
- Yi-Jung Tu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Zhijin Lin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Matthew J Allen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
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46
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Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Duque-Redondo E, Kazuo Y, López-Arbeloa I, Manzano H. Cs-137 immobilization in C-S-H gel nanopores. Phys Chem Chem Phys 2018; 20:9289-9297. [PMID: 29564427 DOI: 10.1039/c8cp00654g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cementation is a widespread technique to immobilize nuclear waste due to the low leachability of cementitious materials. The capacity of calcium silicate hydrate (C-S-H), the main component of cement, to retain radionuclide Cs has been empirically studied at the macroscale, yet the specific molecular scale mechanisms that govern the retention have not been determined. In this work, we employed molecular dynamics simulations to investigate the adsorption and diffusivity of Cs into a C-S-H gel nanopore. From the simulations, it was possible to distinguish three types of Cs adsorption configurations on the C-S-H: an inner-sphere surface site where Cs is strongly bound, an outer-sphere surface site where Cs is loosely bound, and Cs free in the nanopore. For each configuration, we determined the sorption energy, and the diffusion coefficients, up to two orders of magnitude lower than in bulk water due to the effect of nanoconfinement in the worst case scenario. It has also proved that Cs cannot displace the intrinsic Ca from the C-S-H surface, and we calculated the binding strength and the residence time of the cations in the surface adsorption sites. Finally, we quantified the average number of adsorption sites per nm2 of the C-S-H surface. All these results are the first insights into Cs retention in cement at the molecular scale and will be useful to build macroscopic diffusion models and devise cement formulations to improve radionuclide Cs retention from spent nuclear fuel.
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Affiliation(s)
- Eduardo Duque-Redondo
- Molecular Spectroscopy Laboratory, Department of Physical Chemistry, University of the Basque Country UPV/EHU, Aptdo. 664, 48080, Bilbao, Spain.
| | - Yamada Kazuo
- Fukushima Branch, National Institute for Environmental Studies, Miharu, Tamura, Fukushima, 963-7700, Japan
| | - Iñigo López-Arbeloa
- Molecular Spectroscopy Laboratory, Department of Physical Chemistry, University of the Basque Country UPV/EHU, Aptdo. 664, 48080, Bilbao, Spain.
| | - Hegoi Manzano
- Department of Condensed Matter Physics, University of the Basque Country UPV/EHU, Aptdo. 664, Bilbao, Spain.
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48
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Migliorati V, Serva A, Sessa F, Lapi A, D’Angelo P. Influence of Counterions on the Hydration Structure of Lanthanide Ions in Dilute Aqueous Solutions. J Phys Chem B 2018; 122:2779-2791. [DOI: 10.1021/acs.jpcb.7b12571] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Valentina Migliorati
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Serva
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sessa
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Lapi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
- Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione c/o Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola D’Angelo
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
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49
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Sessa F, Migliorati V, Serva A, Lapi A, Aquilanti G, Mancini G, D'Angelo P. On the coordination of Zn2+ ion in Tf2N− based ionic liquids: structural and dynamic properties depending on the nature of the organic cation. Phys Chem Chem Phys 2018; 20:2662-2675. [DOI: 10.1039/c7cp07497b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Zn2+ coordination structure changes when the Zn(Tf2N)2 salt is dissolved in ionic liquids resulting in more favorable interactions among solvent cations and anions.
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Affiliation(s)
- Francesco Sessa
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | | | - Alessandra Serva
- 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
| | | | | | - Paola D'Angelo
- Dipartimento di Chimica
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
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50
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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