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Goswami A, Peña-Torres A, Jónsson EÖ, Egorov SA, Jónsson H. Evidence of Sharp Transitions between Octahedral and Capped Trigonal Prism States of the Solvation Shell of the Aqueous Fe 3+ Ion. J Phys Chem Lett 2024; 15:4523-4530. [PMID: 38634894 DOI: 10.1021/acs.jpclett.4c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The structure of the solvation shell of the aqueous Fe3+ ion has been a subject of controversy due to discrepancies between experiments and different levels of theory. We address this issue by performing simulations for a wide range of ion concentrations, using various potential energy functions, supplemented by density functional theory calculations of selected configurations. The solvation shell undergoes abrupt transitions between two states: a hexacoordinated octahedral (OH) state and a capped trigonal prism (CTP) state with 7-fold coordination. The lifetime of these states is dependent on concentration. In dilute FeCl3 solutions, the lifetimes of both are similar (≈1 ns). However, the lifetime of the OH state increases with ion concentration, while that of the CTP state decreases slightly. When a uniform negative background charge is used instead of explicit counterions, the lifetime of the OH state is greatly overestimated. These findings underscore the need for further experimental measurements and higher-level simulations.
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Affiliation(s)
- Amrita Goswami
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Alejandro Peña-Torres
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Elvar Ö Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Sergei A Egorov
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, United States
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
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Riefer A, Hackert-Oschätzchen M, Plänitz P, Meichsner G. Characterization of iron(III) in aqueous and alkaline environments with ab initio and ReaxFF potentials. J Chem Phys 2024; 160:082501. [PMID: 38411229 DOI: 10.1063/5.0182460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The iron(III) complexes [Fe(H2O)n(OH)m]3-m (n + m = 5, 6, m ≤ 3) and corresponding proton transfer reactions are studied with total energy calculations, the nudged elastic band (NEB) method, and molecular dynamics (MD) simulations using ab initio and a modification of reactive force field potentials, the ReaxFF-AQ potentials, based on the implementation according to Böhm et al. [J. Phys. Chem. C 120, 10849-10856 (2016)]. Applying ab initio potentials, the energies for the reactions [Fe(H2O)n(OH)m]3-m + H2O → [Fe(H2O)n-1(OH)m+1]2-m + H3O+ in a gaseous environment are in good agreement with comparable theoretical results. In an aqueous (aq) or alkaline environment, with the aid of NEB computations, respective minimum energy paths with energy barriers of up to 14.6 kcal/mol and a collective transfer of protons are modeled. Within MD simulations at room temperature, a permanent transfer of protons around the iron(III) ion is observed. The information gained concerning the geometrical and energetic properties of water and the [Fe(H2O)n(OH)m]3-m complexes from the ab initio computations has been used as reference data to optimize parameters for the O-H-Fe interaction within the ReaxFF-AQ approach. For the optimized ReaxFF-AQ parameter set, the statistical properties of the basic water model, such as the radial distribution functions and the proton hopping functions, are evaluated. For the [Fe(H2O)n(OH)m]3-m complexes, it was found that while geometrical and energetic properties are in good agreement with the ab initio data for gaseous environment, the statistical properties as obtained from the MD simulations are only partly in accordance with the ab initio results for the iron(III) complexes in aqueous or alkaline environments.
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Affiliation(s)
- Arthur Riefer
- Chair of Manufacturing Technology with Focus Machining, Institute of Manufacturing Technology and Quality Management (IFQ), Faculty of Mechanical Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Matthias Hackert-Oschätzchen
- Chair of Manufacturing Technology with Focus Machining, Institute of Manufacturing Technology and Quality Management (IFQ), Faculty of Mechanical Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Philipp Plänitz
- AQcomputare Gesellschaft für Materialberechnung mbH, 09125 Chemnitz, Germany
| | - Gunnar Meichsner
- Chair of Manufacturing Technology with Focus Machining, Institute of Manufacturing Technology and Quality Management (IFQ), Faculty of Mechanical Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
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3
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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: 0] [Impact Index Per Article: 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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Li P. Bridging the 12-6-4 Model and the Fluctuating Charge Model. Front Chem 2021; 9:721960. [PMID: 34368089 PMCID: PMC8339297 DOI: 10.3389/fchem.2021.721960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022] Open
Abstract
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r4 based on theory. Hence, we developed the 12-6-4 model and showed it could solve this deficiency in a physically meaningful way. However, our previous research also found that the 12-6-4 model overestimated the coordination numbers (CNs) for some highly charged metal ions. And we attributed this artifact to that the current 12-6-4 scheme lacks a correction for the interactions among the first solvation shell water molecules. In the present study, we considered the ion-included dipole interaction by using the 12-6 model with adjusting the atomic charges of the first solvation shell water molecules. This strategy not only considers the ion-induced dipole interaction between ion and the first solvation shell water molecules but also well accounts for the increased repulsion among these water molecules compared to the bulk water molecules. We showed this strategy could well reproduce the experimental HFE and IOD values for Mg2+, Zn2+, Al3+, Fe3+, and In3+ and solve the CN overestimation issue of the 12-6-4 model for Fe3+ and In3+. Moreover, our simulation results showed good agreement with previous ab initio MD simulations. In addition, we derived the physical relationship between the C4 parameter and induced dipole moment, which agreed well with our simulation results. Finally, we discussed the implications of the present work for simulating metalloproteins. Due to the fluctuating charge model uses a similar concept to the 12-6 model with adjusting atomic charges, we believe the present study builds a bridge between the 12-6-4 model and the fluctuating charge model.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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Lin L, Husek J, Biswas S, Baumler SM, Adel T, Ng KC, Baker LR, Allen HC. Iron(III) Speciation Observed at Aqueous and Glycerol Surfaces: Vibrational Sum Frequency and X-ray. J Am Chem Soc 2019; 141:13525-13535. [PMID: 31345028 DOI: 10.1021/jacs.9b05231] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lu Lin
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jakub Husek
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Somnath Biswas
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Stephen M. Baumler
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Tehseen Adel
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ka Chon Ng
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - L. Robert Baker
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heather C. Allen
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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6
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Structure of the nearest surrounding of ions in aqueous solutions of iron(III) chloride by x-ray diffraction method. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chen Y, Bylaska EJ, Weare JH. Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations. GEOCHEMICAL TRANSACTIONS 2017; 18:3. [PMID: 29086806 PMCID: PMC5374091 DOI: 10.1186/s12932-017-0040-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). RESULTS The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe3+. The water molecules capping surface Fe3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe3+, those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. CONCLUSIONS Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH2 distances in the DFT calculations it was proposed that the surface Fe3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination. Graphical abstract All first principle calculations, at all practically achievable levels, for the goethite 100 aqueous interface support a long bond and weak interaction between the exposed surface Fe3+ and water molecules capping the surface. This result is supported by bond valence theory calculations and is indicative that each surface Fe3+ is coordinated with only 5 neighbors.
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Affiliation(s)
- Ying Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 USA
| | - Eric J. Bylaska
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - John H. Weare
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 USA
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9
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Mahendran V, Philip J. Macromolecular conformation changes at oil-water interface in the presence of cations. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Zhang H, Waychunas GA, Banfield JF. Molecular Dynamics Simulation Study of the Early Stages of Nucleation of Iron Oxyhydroxide Nanoparticles in Aqueous Solutions. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b03801] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hengzhong Zhang
- Department
of Earth and Planetary Science, University of California, Berkeley, California 94720, United States
| | - Glenn A. Waychunas
- Earth
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jillian F. Banfield
- Department
of Earth and Planetary Science, University of California, Berkeley, California 94720, United States
- Earth
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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11
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Cheng Z, Li G, Liu M. A metal-enhanced fluorescence sensing platform based on new mercapto rhodamine derivatives for reversible Hg(2+) detection. JOURNAL OF HAZARDOUS MATERIALS 2015; 287:402-411. [PMID: 25679802 DOI: 10.1016/j.jhazmat.2015.01.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/21/2014] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
A new metal-enhanced fluorescence (MEF) chemosensor HMS-Ag-R-2SH for Hg(2+) has been prepared via a simple and effective method. The fluorescent chemosensor was based on a mercapto rhodamine derivatives linked with Ag nanoparticles, and the Ag nanoparticles were supported on hexagonal mesoporous silica material (HMS). Transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), absorption spectroscopy and fluorescence spectroscopy techniques were employed to characterize morphology, mesostructure and spectral features of the chemosensor. This chemosensor works in a nearly pure aqueous solution with a broad pH range. The output signals include color change and fluorescence. Moreover, HMS-Ag-R-2SH presents excellent anti-disturbance ability when exposed to a series of competitive cations such as Ag(+), K(+), Li(+), Na(+), Ba(2+), Ca(2+), Cd(2+), Co(2+), Cu(2+), Mg(2+), Mn(2+), Ni(2+), Pb(2+), Zn(2+), Al(3+), Cr(3+) and Fe(3+). The selectivity of this chemosensor was significantly improved due to the introduction of the sulphydryl. The chemosensor showed a lower detection limit of 2.1ppb for Hg(2+). Importantly, HMS-Ag-R-2SH could be regenerated with sodium sulfide solution for several cycles and maintain a high sensitivity.
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Affiliation(s)
- ZhuHong Cheng
- State Key Laboratory of Fine Chemicals, College of Chemical Engineering, Dalian University of Technology, Dalian 116024, PR China
| | - Gang Li
- State Key Laboratory of Fine Chemicals, College of Chemical Engineering, Dalian University of Technology, Dalian 116024, PR China.
| | - MeiMei Liu
- State Key Laboratory of Fine Chemicals, College of Chemical Engineering, Dalian University of Technology, Dalian 116024, PR China
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12
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Miliordos E, Xantheas SS. Ground and Excited States of the [Fe(H2O)6]2+ and [Fe(H2O)6]3+ Clusters: Insight into the Electronic Structure of the [Fe(H2O)6]2+–[Fe(H2O)6]3+ Complex. J Chem Theory Comput 2015; 11:1549-63. [DOI: 10.1021/ct501143c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Evangelos Miliordos
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box
999, MS K1-83, Richland, Washington 99352, United States
| | - Sotiris S. Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box
999, MS K1-83, Richland, Washington 99352, United States
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13
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Loerbroks C, van Rijn J, Ruby MP, Tong Q, Schüth F, Thiel W. Reactivity of Metal Catalysts in Glucose-Fructose Conversion. Chemistry 2014; 20:12298-309. [DOI: 10.1002/chem.201402437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Indexed: 11/06/2022]
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Bogatko S, Cauët E, Geerlings P, De Proft F. On the coupling of solvent characteristics to the electronic structure of solute molecules. Phys Chem Chem Phys 2014; 16:3807-14. [PMID: 24435016 DOI: 10.1039/c3cp54944e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.
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Affiliation(s)
- Stuart Bogatko
- Eenheid Algemene Chemie, Vrije Universiteit Brussel (VUB), Faculteit Wetenschappen, Pleinlaan 2, 1050 Brussels, Belgium.
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15
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Khoshtariya DE, Dolidze TD, Shushanyan M, van Eldik R. Long-range electron transfer with myoglobin immobilized at Au/mixed-SAM junctions: mechanistic impact of the strong protein confinement. J Phys Chem B 2014; 118:692-706. [PMID: 24369906 DOI: 10.1021/jp4101569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horse muscle myoglobin (Mb) was tightly immobilized at Au-deposited ~15-Å-thick mixed-type (1:1) alkanethiol SAMs, HS-(CH₂)₁₁-COOH/HS-(CH₂)₁₁-OH, and placed in contact with buffered H₂O or D₂O solutions. Fast-scan cyclic voltammetry (CV) and a Marcus-equation-based analysis were applied to determine unimolecular standard rate constants and reorganization free energies for electron transfer (ET), under variable-temperature (15-55 °C) and -pressure (0.01-150 MPa) conditions. The CV signal was surprisingly stable and reproducible even after multiple temperature and pressure cycles. The data analysis revealed the following values: standard rate constant, 33 s⁻¹ (25 °C, 0.01 MPa, H₂O); reorganization free energy, 0.5 ± 0.1 eV (throughout); activation enthalpy, 12 ± 3 kJ mol⁻¹; activation volume, -3.1 ± 0.2 cm³ mol⁻¹; and pH-dependent solvent kinetic isotope effect (k(H)⁰/k(D)⁰), 0.7-1.4. Furthermore, the values for the rate constant and reorganization free energy are very similar to those previously found for cytochrome c electrostatically immobilized at the monocomponent Au/HS-(CH₂)₁₁-COOH junction. In vivo, Mb apparently forms a natural electrostatic complex with cytochrome b₅ (cyt-b₅) through the "dynamic" (loose) docking pattern, allowing for a slow ET that is intrinsically coupled to the water's removal from the "defective" heme iron (altogether shaping the biological repair mechanism for Mb's "met" form). In contrary, our experiments rather mimic the case of a "simple" (tight) docking of the redesigned (mutant) Mb with cyt-b₅ (Nocek et al. J. Am. Chem. Soc. 2010, 132, 6165-6175). According to our analysis, in this configuration, Mb's distal pocket (linked to the "ligand channel") seems to be arrested within the restricted configuration, allowing the rate-determining reversible ET process to be coupled only to the inner-sphere reorganization (minimal elongation/shortening of an Fe-OH₂ bond) rather than the pronounced detachment (rebinding) of water and, hence, to be much faster.
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Affiliation(s)
- Dimitri E Khoshtariya
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg , 91058 Erlangen, Germany
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Bogatko S, Cauët E, Bylaska E, Schenter G, Fulton J, Weare J. The aqueous Ca2+ system, in comparison with Zn2+, Fe3+, and Al3+: an ab initio molecular dynamics study. Chemistry 2013; 19:3047-60. [PMID: 23315704 DOI: 10.1002/chem.201202821] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Indexed: 11/08/2022]
Abstract
Herein, we report on the structure and dynamics of the aqueous Ca(2+) system studied by using ab initio molecular dynamics (AIMD) simulations. Our detailed study revealed the formation of well-formed hydration shells with characteristics that were significantly different to those of bulk water. To facilitate a robust comparison with state-of-the-art X-ray absorption fine structure (XAFS) data, we employ a 1st principles MD-XAFS procedure and directly compare simulated and experimental XAFS spectra. A comparison of the data for the aqueous Ca(2+) system with those of the recently reported Zn(2+), Fe(3+), and Al(3+) species showed that many of their structural characteristics correlated well with charge density on the cation. Some very important exceptions were found, which indicated a strong sensitivity of the solvent structure towards the cation's valence electronic structure. Average dipole moments for the 2nd shell of all cations were suppressed relative to bulk water.
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Affiliation(s)
- Stuart Bogatko
- Chemistry and Biochemistry Department, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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Cauët E, Bogatko SA, Bylaska EJ, Weare JH. Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics. Inorg Chem 2012; 51:10856-69. [DOI: 10.1021/ic301346k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Emilie Cauët
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Stuart A. Bogatko
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric J. Bylaska
- Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington
99352, United States
| | - John H. Weare
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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Bogatko S, Geerlings P. Factors influencing Al3+-dimer speciation and stability from density functional theory calculations. Phys Chem Chem Phys 2012; 14:8058-66. [DOI: 10.1039/c2cp40885f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations. J Chem Phys 2010; 132:194502. [PMID: 20499974 DOI: 10.1063/1.3421542] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn(2+) ion (T approximately 300 K, rho approximately 1 gm/cm(3)) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules ( approximately 15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.). In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical (QM) region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure (EXAFS) spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is (maximally located at 2.13-2.15 A versus 2.072 A EXAFS experiment). The widths of the peak of the simulated EXAFS spectra agree well with the data (8.4 A(2) versus 8.9 A(2) in experiment). Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d(10) electronic structure of the valence shell of the Zn(2+) ion is retained. The simulations show substantial and complex charge relocation on both the Zn(2+) ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D (3.3 D AIMD/MM) versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell (2.8 D). No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations (256 waters) there is a significant reduction in the second shell to bulk exchanges.
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Affiliation(s)
- Emilie Cauët
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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Terrier C, Vitorge P, Gaigeot MP, Spezia R, Vuilleumier R. Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La3+. J Chem Phys 2010; 133:044509. [DOI: 10.1063/1.3460813] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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