1
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McDonogh DP, Gale JD, Raiteri P, Gebauer D. Redefined ion association constants have consequences for calcium phosphate nucleation and biomineralization. Nat Commun 2024; 15:3359. [PMID: 38637527 PMCID: PMC11026415 DOI: 10.1038/s41467-024-47721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Calcium orthophosphates (CaPs), as hydroxyapatite (HAP) in bones and teeth are the most important biomineral for humankind. While clusters in CaP nucleation have long been known, their speciation and mechanistic pathways to HAP remain debated. Evidently, mineral nucleation begins with two ions interacting in solution, fundamentally underlying solute clustering. Here, we explore CaP ion association using potentiometric methods and computer simulations. Our results agree with literature association constants for Ca2+ and H2PO4-, and Ca2+ and HPO42-, but not for Ca2+ and PO43- ions, which previously has been strongly overestimated by two orders of magnitude. Our data suggests that the discrepancy is due to a subtle, premature phase separation that can occur at low ion activity products, especially at higher pH. We provide an important revision of long used literature constants, where association of Ca2+ and PO43- actually becomes negligible below pH 9.0, in contrast to previous values. Instead, [CaHPO4]0 dominates the aqueous CaP speciation between pH ~6-10. Consequently, calcium hydrogen phosphate association is critical in cluster-based precipitation in the near-neutral pH regime, e.g., in biomineralization. The revised thermodynamics reveal significant and thus far unexplored multi-anion association in computer simulations, constituting a kinetic trap that further complicates aqueous calcium phosphate speciation.
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Affiliation(s)
- David P McDonogh
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstr. 9, 30167, Hannover, Germany
| | - Julian D Gale
- Curtin Institute for Computation and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA, 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA, 6845, Australia.
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstr. 9, 30167, Hannover, Germany.
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2
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Schuitemaker A, Koziara KB, Raiteri P, Gale JD, Demichelis R. New model for aspartic acid species in aqueous calcium carbonate growth environments: challenges and perspectives. Phys Chem Chem Phys 2024; 26:4909-4921. [PMID: 38261361 DOI: 10.1039/d3cp04674e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The lack of experimental data on the dynamics of aspartic acid species in water for its range of protonation states and the details of their atomic-level interaction with aqueous calcium carbonate species is a driver for accurate force field development. A classical model that is consistent with the few pieces of experimental data available and with first principles calculations has been developed. The complex dynamics of the aspartate anions relevant to biomineralization and calcium carbonate crystal growth has been explored in water, providing a quantitative description of solvation structure and free energies, including conformational free energy profiles and pairing free energies. The model has been used to probe the structure and dynamics of aqueous calcium aspartate homo- and hetero-chiral clusters, confirming their unlikelihood due to weak and water-mediated interactions. This supports the hypothesis that the formation of such clusters, observed while growing vaterite in the presence of acidic chiral amino acids, is favoured by the presence of the crystal surface.
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Affiliation(s)
- Alicia Schuitemaker
- Australian Research Council Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales, Australia
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Katarzyna B Koziara
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Paolo Raiteri
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julian D Gale
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Raffaella Demichelis
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
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3
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Vuković F, Garcia NA, Perera S, Turchi M, Andersson MP, Solvang M, Raiteri P, Walsh TR. Atomistic simulations of calcium aluminosilicate interfaced with liquid water. J Chem Phys 2023; 159:104704. [PMID: 37694746 DOI: 10.1063/5.0164817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
The dissolution behavior of calcium aluminosilicate based glass fibers, such as stone wool fibers, is an important consideration in mineral wool applications for both the longevity of the mineral wool products in humid environments and limiting the health impacts of released and inhaled fibers from the mineral wool product. Balancing these factors requires a molecular-level understanding of calcium aluminosilicate glass dissolution mechanisms, details that are challenging to resolve with experiment alone. Molecular dynamics simulations are a powerful tool capable of providing complementary atomistic insights regarding dissolution; however, they require force fields capable of describing not-only the calcium aluminosilicate surface structure but also the interactions relevant to dissolution phenomena. Here, a new force field capable of describing amorphous calcium aluminosilicate surfaces interfaced with liquid water is developed by fitting parameters to experimental and first principles simulation data of the relevant oxide-water interfaces, including ab initio molecular dynamics simulations performed for this work for the wüstite and periclase interfaces. Simulations of a calcium aluminosilicate surface interfaced with liquid water were used to test this new force field, suggesting moderate ingress of water into the porous glass interface. This design of the force field opens a new avenue for the further study of calcium and network-modifier dissolution phenomena in calcium aluminosilicate glasses and stone wool fibers at liquid water interfaces.
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Affiliation(s)
- F Vuković
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - N A Garcia
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - S Perera
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - M Turchi
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - M P Andersson
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - M Solvang
- Group Research and Development, ROCKWOOL A/S, 2640 Hedehusene, Denmark
| | - P Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, Perth, Western Australia 6845, Australia
| | - T R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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4
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Armstrong B, Silvestri A, Demichelis R, Raiteri P, Gale JD. Solubility-consistent force field simulations for aqueous metal carbonate systems using graphical processing units. Philos Trans A Math Phys Eng Sci 2023; 381:20220250. [PMID: 37211028 DOI: 10.1098/rsta.2022.0250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/15/2022] [Indexed: 05/23/2023]
Abstract
Crystallization of alkaline earth metal carbonates from water is important for biomineralization and environmental geochemistry. Here, large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of individual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to sample complex systems. Here, we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on graphical processing units thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallization, including ion-pairing and mineral-water interfacial structure and dynamics. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Blake Armstrong
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Alessandro Silvestri
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Raffaella Demichelis
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA 6845, Australia
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5
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Kraus P, Raiteri P, Gale JD. Computational workflows for perovskites: case study for lanthanide manganites. Phys Chem Chem Phys 2023; 25:14799-14811. [PMID: 37194375 DOI: 10.1039/d3cp00041a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Robust computational workflows are important for explorative computational studies, especially for cases where detailed knowledge of the system structure or other properties is not available. In this work, we propose a computational protocol for appropriate method selection for the study of lattice constants of perovskites using density functional theory, based strictly on open source software. The protocol does not require a starting crystal structure. We validate this protocol using a set of crystal structures of lanthanide manganites, surprisingly finding N12+U to be the best performing method for this class of materials out of the 15 density functional approximations studied. We also highlight that +U values derived from linear response theory are robust and their use leads to improved results. We investigate whether the performance of methods for predicting the bond length of related gas phase diatomics correlates with their performance for bulk structures, showing that care is required when interpreting benchmark results. Finally, using defective LaMnO3 as a case study, we investigate whether the four shortlisted methods (HCTH120, OLYP, N12+U, PBE+U) can computationally reproduce the experimentally determined fraction of MnIV+ at which the orthorhombic to rhombohedral phase transition occurs. The results are mixed, with HCTH120 providing good quantitative agreement with experiment, but failing to capture the spatial distribution of defects linked to the electronic structure of the system.
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Affiliation(s)
- Peter Kraus
- Institute for Material Science and Technology, Technische Universität Berlin, Hardenbergstr. 40, 10623 Berlin, Germany.
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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6
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Al-Qatatsheh A, Capricho JC, Raiteri P, Juodkazis S, Salim N, Hameed N. Crosslinking Rapidly Cured Epoxy Resin Thermosets: Experimental and Computational Modeling and Simulation Study. Polymers (Basel) 2023; 15:polym15051325. [PMID: 36904565 PMCID: PMC10007365 DOI: 10.3390/polym15051325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
The power of computational modeling and simulation for establishing clear links between materials' intrinsic properties and their atomic structure has more and more increased the demand for reliable and reproducible protocols. Despite this increased demand, no one approach can provide reliable and reproducible outcomes to predict the properties of novel materials, particularly rapidly cured epoxy-resins with additives. This study introduces the first computational modeling and simulation protocol for crosslinking rapidly cured epoxy resin thermosets based on solvate ionic liquid (SIL). The protocol combines several modeling approaches, including quantum mechanics (QMs) and molecular dynamics (MDs). Furthermore, it insightfully provides a wide range of thermo-mechanical, chemical, and mechano-chemical properties, which agree with experimental data.
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Affiliation(s)
- Ahmed Al-Qatatsheh
- School of Engineering, Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Jaworski C. Capricho
- School of Engineering, Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Paolo Raiteri
- School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, Perth, WA 6845, Australia
| | - Saulius Juodkazis
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Nisa Salim
- School of Engineering, Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Nishar Hameed
- School of Engineering, Swinburne University of Technology, Melbourne, VIC 3122, Australia
- Correspondence:
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7
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Armstrong BI, Willans M, Pearson EL, Becker T, Hackett MJ, Raiteri P. Revisiting the Conformational Isomerism of Dihaloethanes: A Hybrid Computational and Experimental Laboratory for the Undergraduate Curriculum. ACS Phys Chem Au 2023; 3:157-166. [PMID: 36968445 PMCID: PMC10037444 DOI: 10.1021/acsphyschemau.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
The conformational isomerism of disubstituted ethanes is a well-known concept that is part of every chemistry curriculum. Due to the species' simplicity, studying the (free) energy difference between the gauche and anti isomers has been the testing ground of experimental and computational techniques, such as Raman and IR spectroscopy, quantum chemistry, and atomistic simulations. While students normally receive formal training in spectroscopic techniques during their early undergraduate years, computational methods often receive less attention. In this work, we revisit the conformational isomerism of 1,2-dichloroethane and 1,2-dibromoethane and design a hybrid computational and experimental laboratory for our undergraduate chemistry curriculum with a focus on introducing computational techniques as a complementary research tool to experimentation. We show how commonly available Raman spectrometers and atomistic simulations performed on desktop computers can be combined to study the conformational isomerism of disubstituted ethanes while discussing the advantages and limitations of the different approaches.
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Affiliation(s)
- Blake I. Armstrong
- School of Molecular and Life Sciences and Curtin Institute for Computation, Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
| | - Meg Willans
- School of Molecular and Life Sciences and Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
| | - Emma L. Pearson
- School of Molecular and Life Sciences and Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
| | - Thomas Becker
- School of Molecular and Life Sciences and Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
| | - Mark J. Hackett
- School of Molecular and Life Sciences and Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
| | - Paolo Raiteri
- School of Molecular and Life Sciences and Curtin Institute for Computation, Curtin University, PO Box U1987, Perth, Western Australia6845, Australia
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8
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Silvestri A, Raiteri P, Gale JD. Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability. J Chem Theory Comput 2022; 18:5901-5919. [PMID: 36073829 DOI: 10.1021/acs.jctc.2c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative example. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for individual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na+ and Cl- are found to be surprisingly different and of opposite sign, despite the ions having very similar hydration free energies.
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Affiliation(s)
- Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
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9
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Kahil K, Raiteri P, Gale JD, Rez P. Calculations of the Evolution of the Ca L 23 Fine Structure in Amorphous Calcium Carbonate. J Phys Chem B 2022; 126:5103-5109. [PMID: 35763361 DOI: 10.1021/acs.jpcb.2c03440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amorphous calcium carbonate (ACC) has been found in many different organisms. Biogenic ACC is frequently a precursor in the formation of calcite and aragonite. The process of structural transformation is therefore of great interest in the study of crystallization pathways in biomineralization. Changes in the prepeak/main peak (L2'/L2) intensity ratio of the Ca L23-edge X-ray absorption spectroscopy (XAS) of Ca-rich particles in skeleton-building cells of sea urchin larva revealed that ACC precipitates through a continuum of states rather than through abrupt phase transitions involving two distinct phases as formerly believed. Using an atomic multiplet code, we show that only a tetragonal or "umbrella-like" distortion of the Ca coordination polyhedron can give rise to the observed continuum of states. We also show on the basis of the structures obtained from previous molecular dynamics simulations of hydrated nanoparticles that the Ca L23-edge is not sensitive to atomic arrangements in the early stages of the transformation process.
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Affiliation(s)
- Keren Kahil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Paolo Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Peter Rez
- Department of Physics, Arizona State University, Tempe, Arizona 85287-1504 United States
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10
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Schuitemaker A, Aufort J, Koziara KB, Demichelis R, Raiteri P, Gale JD. Simulating the binding of key organic functional groups to aqueous calcium carbonate species. Phys Chem Chem Phys 2021; 23:27253-27265. [PMID: 34870292 DOI: 10.1039/d1cp04226b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.
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Affiliation(s)
- Alicia Schuitemaker
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julie Aufort
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Katarzyna B Koziara
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Paolo Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julian D Gale
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
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11
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Gale JD, LeBlanc LM, Spackman PR, Silvestri A, Raiteri P. A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination. J Chem Theory Comput 2021; 17:7827-7849. [PMID: 34735764 DOI: 10.1021/acs.jctc.1c00832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range damping of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.
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Affiliation(s)
- Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Luc M LeBlanc
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Peter R Spackman
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Alessandro Silvestri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
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12
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Heberling F, Klačić T, Raiteri P, Gale JD, Eng PJ, Stubbs JE, Gil-Díaz T, Begović T, Lützenkirchen J. Structure and Surface Complexation at the Calcite(104)-Water Interface. Environ Sci Technol 2021; 55:12403-12413. [PMID: 34478280 DOI: 10.1021/acs.est.1c03578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Calcite is the most stable polymorph of calcium carbonate (CaCO3) under ambient conditions and is ubiquitous in natural systems. It plays a major role in controlling pH in environmental settings. Electrostatic phenomena at the calcite-water interface and the surface reactivity of calcite in general have important environmental implications. They may strongly impact nutrient and contaminant mobility in soils and other subsurface environments, they control oil recovery from limestone reservoirs, and they may impact the safety of nuclear waste disposal sites. Besides the environmental relevance, the topic is significant for industrial applications and cultural heritage preservation. In this study, the structure of the calcite(104)-water interface is investigated on the basis of a new extensive set of crystal truncation rod data. The results agree with recently reported structures and resolve previous ambiguities with respect to the coordination sphere of surface Ca ions. These structural features are introduced into an electrostatic three-plane surface complexation model, describing ion adsorption and charging at the calcite-water interface. Inner surface potential data for calcite, as measured with a calcite single-crystal electrode, are used as constraints for the model in addition to zeta potential data. Ion adsorption parameters are compared with molecular dynamics simulations. All model parameters, including protonation constants, ion-binding parameters, and Helmholtz capacitances, are within physically and chemically plausible ranges. A PhreeqC version of the model is presented, which we hope will foster application of the model in environmental studies.
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Affiliation(s)
- Frank Heberling
- Institute for Nuclear Waste Disposal, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Tin Klačić
- Division of Physical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Paolo Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987 Perth, WA 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987 Perth, WA 6845, Australia
| | - Peter J Eng
- Center for Advanced Radiation Sources, The University of Chicago, 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Joanne E Stubbs
- Center for Advanced Radiation Sources, The University of Chicago, 5734 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Teba Gil-Díaz
- Institute for Nuclear Waste Disposal, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
- Institute of Geosciences, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749 Jena, Germany
| | - Tajana Begović
- Division of Physical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Johannes Lützenkirchen
- Institute for Nuclear Waste Disposal, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
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13
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Huang Y, Rao A, Huang S, Chang C, Drechsler M, Knaus J, Chan JCC, Raiteri P, Gale JD, Gebauer D. Aufdeckung der Rolle von Hydrogencarbonat‐Ionen bei der Bildung von Calciumcarbonat im nahezu neutralen pH‐Bereich. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yu‐Chieh Huang
- Fachbereich Chemie, Physikalische Chemie Universität Konstanz Deutschland
| | - Ashit Rao
- Physics of Complex Fluids Group and MESA+ Institute Faculty of Science and Technology University of Twente Enschede Niederlande
| | - Shing‐Jong Huang
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Chun‐Yu Chang
- Department of Chemistry National Taiwan University Taipei Taiwan
| | | | - Jennifer Knaus
- Fachbereich Chemie, Physikalische Chemie Universität Konstanz Deutschland
- stimOS GmbH Konstanz Deutschland
| | | | - Paolo Raiteri
- Curtin Institute for Computation/, The Institute for Geoscience Research (TIGeR) School of Molecular and Life Sciences Curtin University Perth Australien
| | - Julian D. Gale
- Curtin Institute for Computation/, The Institute for Geoscience Research (TIGeR) School of Molecular and Life Sciences Curtin University Perth Australien
| | - Denis Gebauer
- Institut für Anorganische Chemie Leibniz Universität Hannover Callinstraße 9 30167 Hannover Deutschland
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14
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Huang YC, Rao A, Huang SJ, Chang CY, Drechsler M, Knaus J, Chan JCC, Raiteri P, Gale JD, Gebauer D. Uncovering the Role of Bicarbonate in Calcium Carbonate Formation at Near-Neutral pH. Angew Chem Int Ed Engl 2021; 60:16707-16713. [PMID: 33973691 PMCID: PMC8362096 DOI: 10.1002/anie.202104002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Indexed: 11/30/2022]
Abstract
Mechanistic pathways relevant to mineralization are not well‐understood fundamentally, let alone in the context of their biological and geological environments. Through quantitative analysis of ion association at near‐neutral pH, we identify the involvement of HCO3− ions in CaCO3 nucleation. Incorporation of HCO3− ions into the structure of amorphous intermediates is corroborated by solid‐state nuclear magnetic resonance spectroscopy, complemented by quantum mechanical calculations and molecular dynamics simulations. We identify the roles of HCO3− ions as being through (i) competition for ion association during the formation of ion pairs and ion clusters prior to nucleation and (ii) incorporation as a significant structural component of amorphous mineral particles. The roles of HCO3− ions as active soluble species and structural constituents in CaCO3 formation are of fundamental importance and provide a basis for a better understanding of physiological and geological mineralization.
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Affiliation(s)
- Yu-Chieh Huang
- Department of Chemistry, Physical Chemistry, University of Konstanz, Konstanz, Germany
| | - Ashit Rao
- Physics of Complex Fluids Group and MESA+ Institute, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Shing-Jong Huang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Yu Chang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | | | - Jennifer Knaus
- Department of Chemistry, Physical Chemistry, University of Konstanz, Konstanz, Germany.,stimOS GmbH, Konstanz, Germany
| | | | - Paolo Raiteri
- Curtin Institute for Computation/, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Julian D Gale
- Curtin Institute for Computation/, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstraße 9, 30167, Hannover, Germany
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15
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Schuitemaker A, Raiteri P, Demichelis R. The atomic structure and dynamics at the CaCO 3 vaterite-water interface: A classical molecular dynamics study. J Chem Phys 2021; 154:164504. [PMID: 33940811 DOI: 10.1063/5.0049483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Classical molecular and lattice dynamics were applied to explore the structure and dynamics of water on different surfaces of vaterite, the least abundant calcium carbonate polymorph. Surfaces were generated starting from the three possible structural models for vaterite (monoclinic, hexagonal/trigonal, and triclinic) and pre-screened using their surface energies in an implicit solvent. Surfaces with energies lower than 0.55 J/m2 were then run in explicit water. The majority of these surfaces dissolve in less than 100 ns, highlighting the low stability of this phase in abiotic environments. Three stable surfaces were identified; they exhibited only minor structural changes when in contact with explicit water and did not show any tendency to dissolve during 1 µs molecular dynamics simulations. The computed water density profiles show that all these surfaces have two distinct hydration layers. The water residence time at the various calcium sites was computed to be within 0.7 and 20.5 ns, which suggests that specific Ca ions will be more readily available to bind with organic molecules present in solution. This analysis is a step forward in understanding the structure of this complex mineral and its role in biomineralization, as it provides a solid theoretical background to explore its surface chemistry. In particular, this study provides realistic surface models and predicts the effect of water exchange at the surface active sites on the adsorption of other molecules.
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Affiliation(s)
- Alicia Schuitemaker
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia
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16
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Raiteri P, Kraus P, Gale JD. Molecular dynamics simulations of liquid-liquid interfaces in an electric field: The water-1,2-dichloroethane interface. J Chem Phys 2020; 153:164714. [PMID: 33138425 DOI: 10.1063/5.0027876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The polarized interface between two immiscible liquids plays a central role in many technological processes. In particular, for electroanalytical and ion extraction applications, an external electric field is typically used to selectively induce the transfer of ionic species across the interfaces. Given that it is experimentally challenging to obtain an atomistic insight into the ion transfer process and the structure of liquid-liquid interfaces, atomistic simulations have often been used to fill this knowledge gap. However, due to the long-range nature of the electrostatic interactions and the use of 3D periodic boundary conditions, the use of external electric fields in molecular dynamics simulations requires special care. Here, we show how the simulation setup affects the dielectric response of the materials and demonstrate how by a careful design of the system it is possible to obtain the correct electric field on both sides of a liquid-liquid interface when using standard 3D Ewald summation methods. In order to prove the robustness of our approach, we ran extensive molecular dynamics simulations with a rigid-ion and polarizable force field of the water/1,2-dichloroethane interface in the presence of weak external electric fields.
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Affiliation(s)
- Paolo Raiteri
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Peter Kraus
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
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17
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Stout MJ, Skelton BW, Sobolev AN, Raiteri P, Massi M, Simpson PV. Synthesis and Photochemical Properties of Re(I) Tricarbonyl Complexes Bound to Thione and Thiazol-2-ylidene Ligands. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew J. Stout
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley 6102, Perth, Western Australia, Australia
| | - Brian W. Skelton
- School of Molecular Sciences and CMCA, the University of Western Australia, 35 Stirling Highway, 6009 Perth, Western Australia, Australia
| | - Alexandre N. Sobolev
- School of Molecular Sciences and CMCA, the University of Western Australia, 35 Stirling Highway, 6009 Perth, Western Australia, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and School of Life and Molecular Sciences, Curtin University, Kent Street, Bentley 6102, Perth, Western Australia, Australia
| | - Massimiliano Massi
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley 6102, Perth, Western Australia, Australia
| | - Peter V. Simpson
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley 6102, Perth, Western Australia, Australia
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18
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Raiteri P, Schuitemaker A, Gale JD. Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics. J Phys Chem B 2020; 124:3568-3582. [PMID: 32259444 DOI: 10.1021/acs.jpcb.0c01582] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The speciation of calcium carbonate in water is important to the geochemistry of the world's oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here, it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs to form larger species is stable, though with an equilibrium constant that is lower than for ion pairing itself.
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Affiliation(s)
- Paolo Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Alicia Schuitemaker
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
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19
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Silvestri A, Ataman E, Budi A, Stipp SLS, Gale JD, Raiteri P. Wetting Properties of the CO 2-Water-Calcite System via Molecular Simulations: Shape and Size Effects. Langmuir 2019; 35:16669-16678. [PMID: 31714788 DOI: 10.1021/acs.langmuir.9b02881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO2 and the pore fluids. In this context, the interfacial tension (IFT) between CO2 and the aqueous fluid and the contact angle, θ, with the pore mineral surfaces are the two key parameters that control the capillary pressure in the pores of the candidate host rock. Knowledge of these two parameters and their dependence on the local conditions of pressure, temperature, and salinity is essential for the correct prediction of structural and residual trapping. We have performed classical molecular dynamics simulations to predict the CO2-water IFT and the CO2-water-calcite contact angle. The IFT results are consistent with previous simulations, where simple point charge water models have been shown to underestimate the water surface tension, thus affecting the simulated IFT values. When combined with the EPM2 CO2 model, the SPC/Fw water model indeed underestimates the IFT in the low-pressure region at all temperatures studied. On the other hand, at high pressure and low temperature, the IFT is overestimated by ∼5 mN/m. Literature data regarding the CO2/water/calcite contact angle on calcite are contradictory. Using our new set of force field parameters, we performed NVT simulations at 323 K and 20 MPa to calculate the contact angle of a water droplet on the calcite {10.4} surface in a CO2 atmosphere. We performed simulations for both spherical and cylindrical droplet configurations for different initial radii to study the size dependence of the water contact angle on calcite in the presence of CO2. Our results suggest that the contact angle of a cylindrical droplet, is independent of droplet size, for droplets with a radius of 50 Å or more. On the contrary, spherical droplets make a contact angle that is strongly influenced by their size. At the largest size explored in this study, both spherical and cylindrical droplets converge to the same contact angle, 38°, indicating that calcite is strongly wetted by water.
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Affiliation(s)
- A Silvestri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences , Curtin University , PO Box U1987, Perth , WA 6845 , Australia
| | - E Ataman
- Nano-Science Center, Department of Chemistry , University of Copenhagen , Universitetsparken 5 , København Ø DK-2100 , Denmark
| | - A Budi
- Institute for Frontier Materials , Deakin University , Geelong , VIC 3216 , Australia
| | - S L S Stipp
- Department of Physics , Technical University of Denmark , Fysikvej , DK-2800 Kongens Lyngby , Denmark
| | - J D Gale
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences , Curtin University , PO Box U1987, Perth , WA 6845 , Australia
| | - P Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences , Curtin University , PO Box U1987, Perth , WA 6845 , Australia
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20
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Garcia N, Malini RI, Freeman CL, Demichelis R, Raiteri P, Sommerdijk NAJM, Harding JH, Gale JD. Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing. Cryst Growth Des 2019; 19:6422-6430. [PMID: 32063806 PMCID: PMC7011744 DOI: 10.1021/acs.cgd.9b00889] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/01/2019] [Indexed: 05/12/2023]
Abstract
Classical molecular dynamics simulations and free energy methods have been used to obtain a better understanding of the molecular processes occurring prior to the first nucleation event for calcium phosphate biominerals. The association constants for the formation of negatively charged complexes containing calcium and phosphate ions in aqueous solution have been computed, and these results suggest that the previously proposed calcium phosphate building unit, [Ca(HPO4)3]4-, should only be present in small amounts under normal experimental conditions. However, the presence of an activation barrier for the removal of an HPO4 2- ion from this complex indicates that this species could be kinetically trapped. Aggregation pathways involving CaHPO4, [Ca(HPO4)2]2-, and [Ca(HPO4)3]4- complexes have been explored with the finding that dimerization is favorable up to a Ca/HPO4 ratio of 1:2.
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Affiliation(s)
- Natalya
A. Garcia
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR),
and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Riccardo Innocenti Malini
- Department
of Materials Science and Engineering, University
of Sheffield, Sheffield, S1 3JD, United Kingdom
- Laboratory
for Protection and Physiology, Empa, Swiss
Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Colin L. Freeman
- Department
of Materials Science and Engineering, University
of Sheffield, Sheffield, S1 3JD, United Kingdom
| | - Raffaella Demichelis
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR),
and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR),
and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Nico A. J. M. Sommerdijk
- Department
of Chemical Engineering and Chemistry, Technische
Universiteit Eindhoven, P.O. Box 513, Eindhoven, Netherlands
| | - John H. Harding
- Department
of Materials Science and Engineering, University
of Sheffield, Sheffield, S1 3JD, United Kingdom
| | - Julian D. Gale
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR),
and School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
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21
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Jiang W, Athanasiadou D, Zhang S, Demichelis R, Koziara KB, Raiteri P, Nelea V, Mi W, Ma JA, Gale JD, McKee MD. Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture. Nat Commun 2019; 10:2318. [PMID: 31127116 PMCID: PMC6534569 DOI: 10.1038/s41467-019-10383-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 05/09/2019] [Indexed: 11/08/2022] Open
Abstract
Since Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid L-Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when D-Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality amplification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.
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Affiliation(s)
- Wenge Jiang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin, P. R. China, 300072
- Faculty of Dentistry, McGill University, Montreal, QC, Canada, H3A 0C7
| | | | - Shaodong Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), and School of Molecular and Life Science, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Katarzyna B Koziara
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), and School of Molecular and Life Science, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), and School of Molecular and Life Science, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Valentin Nelea
- Faculty of Dentistry, McGill University, Montreal, QC, Canada, H3A 0C7
| | - Wenbo Mi
- Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparation Technology, School of Science, Tianjin University, Tianjin, P. R. China, 300354
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin, P. R. China, 300072
| | - Julian D Gale
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), and School of Molecular and Life Science, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Marc D McKee
- Faculty of Dentistry, McGill University, Montreal, QC, Canada, H3A 0C7.
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada, H3A 0C7.
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22
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Abstract
Equilibrium and nonequilibrium molecular dynamics (MD) are used to investigate the thermal conductivity of binary hard-sphere fluids. It is found that the thermal conductivity of a mixture can not only lie outside the series and parallel bounds set by their pure component values, but can lie beyond even the pure component fluid values. The MD simulations verify that revised Enskog theory can accurately predict nonequilibrium thermal conductivities at low densities and this theory is applied to explore the model parameter space. Only certain mass and size ratios are found to exhibit conductivity enhancements above the parallel bounds and dehancement below the series bounds. The anomalous dehancement is experimentally accessible in helium-hydrogen gas mixtures and a review of the literature confirms the existence of mixture thermal conductivity below the series bound and even below the pure fluid values, in accordance with the predictions of revised Enskog theory. The results reported here may reignite the debate in the nanofluid literature on the possible existence of anomalous thermal conductivities outside the series and parallel bounds as this Rapid Communication demonstrates they are a fundamental feature of even simple fluids.
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Affiliation(s)
- Craig Moir
- School of Engineering, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
- Curtin Institute for Computation, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Leo Lue
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Julian D Gale
- Curtin Institute for Computation, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Marcus N Bannerman
- School of Engineering, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
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23
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Tan NSL, Simpson PV, Nealon GL, Sobolev AN, Raiteri P, Massi M, Ogden MI, Lowe AB. Rhodium(I)‐α‐Phenylvinylfluorenyl Complexes: Synthesis, Characterization, and Evaluation as Initiators in the Stereospecific Polymerization of Phenylacetylene. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nicholas Sheng Loong Tan
- Curtin Institute for Functional Molecules and Interfaces (CIFMI) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
| | - Peter V. Simpson
- Curtin Institute for Functional Molecules and Interfaces (CIFMI) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
| | - Gareth L. Nealon
- Centre for Microscopy, Characterisation and Analysis (CMCA), M310 University of Western Australia 35 Stirling Highway 6009 Perth WA Australia
| | - Alexandre N. Sobolev
- Centre for Microscopy, Characterisation and Analysis (CMCA), M310 University of Western Australia 35 Stirling Highway 6009 Perth WA Australia
| | - Paolo Raiteri
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
- Curtin Institute for Computation (CIC) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- The Institute for Geoscience Research (TIGeR) Curtin University Kent Street, Bentley 6102 Perth WA Australia
| | - Massimiliano Massi
- Curtin Institute for Functional Molecules and Interfaces (CIFMI) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
| | - Mark I. Ogden
- Curtin Institute for Functional Molecules and Interfaces (CIFMI) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
| | - Andrew B. Lowe
- Curtin Institute for Functional Molecules and Interfaces (CIFMI) Curtin University Kent Street, Bentley 6102 Perth WA Australia
- School of Molecular and Life Sciences (MLS) Curtin University Kent Street, Bentley 6102 Perth, WA Australia
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24
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Söngen H, Reischl B, Miyata K, Bechstein R, Raiteri P, Rohl AL, Gale JD, Fukuma T, Kühnle A. Resolving Point Defects in the Hydration Structure of Calcite (10.4) with Three-Dimensional Atomic Force Microscopy. Phys Rev Lett 2018; 120:116101. [PMID: 29601750 DOI: 10.1103/physrevlett.120.116101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 05/26/2023]
Abstract
It seems natural to assume that defects at mineral surfaces critically influence interfacial processes such as the dissolution and growth of minerals in water. The experimental verification of this claim, however, is challenging and requires real-space methods with utmost spatial resolution, such as atomic force microscopy (AFM). While defects at mineral-water interfaces have been resolved in 2D AFM images before, the perturbation of the surrounding hydration structure has not yet been analyzed experimentally. In this Letter, we demonstrate that point defects on the most stable and naturally abundant calcite (10.4) surface can be resolved using high-resolution 3D AFM-even within the fifth hydration layer. Our analysis of the hydration structure surrounding the point defect shows a perturbation of the hydration with a lateral extent of approximately one unit cell. These experimental results are corroborated by molecular dynamics simulations.
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Affiliation(s)
- Hagen Söngen
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Bernhard Reischl
- Curtin Institute for Computation and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Kazuki Miyata
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ralf Bechstein
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Paolo Raiteri
- Curtin Institute for Computation and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
- The Institute for Geoscience Research (TIGeR), Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
- The Institute for Geoscience Research (TIGeR), Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Takeshi Fukuma
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Angelika Kühnle
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
- Physical Chemistry I, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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25
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Demichelis R, Garcia NA, Raiteri P, Innocenti Malini R, Freeman CL, Harding JH, Gale JD. Simulation of Calcium Phosphate Species in Aqueous Solution: Force Field Derivation. J Phys Chem B 2018; 122:1471-1483. [DOI: 10.1021/acs.jpcb.7b10697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raffaella Demichelis
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Natalya A. Garcia
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Paolo Raiteri
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Riccardo Innocenti Malini
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
- Laboratory
for Biomimetic Membranes and Textiles, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen 9014, Switzerland
| | - Colin L. Freeman
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - John H. Harding
- Department
of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Julian D. Gale
- Curtin
Institute for Computation, The Institute for Geoscience Research (TIGeR)
and Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
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26
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Caporale C, Bader CA, Sorvina A, MaGee KDM, Skelton BW, Gillam TA, Wright PJ, Raiteri P, Stagni S, Morrison JL, Plush SE, Brooks DA, Massi M. Cover Feature: Investigating Intracellular Localisation and Cytotoxicity Trends for Neutral and Cationic Iridium Tetrazolato Complexes in Live Cells (Chem. Eur. J. 62/2017). Chemistry 2017. [DOI: 10.1002/chem.201704087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chiara Caporale
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry; Curtin University; Kent Street Bentley 6102 WA Australia
| | - Christie A. Bader
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide Australia
| | - Alexandra Sorvina
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide Australia
| | - Karen D. M. MaGee
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry; Curtin University; Kent Street Bentley 6102 WA Australia
| | - Brian W. Skelton
- School of Molecular Sciences; University of Western Australia; 35 Stirling Highway, Crawley Perth, WA 6009 Australia
| | - Todd A. Gillam
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide Australia
| | - Phillip J. Wright
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry; Curtin University; Kent Street Bentley 6102 WA Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and Department of Chemistry; Curtin University; Kent Street Bentley 6102 WA Australia
| | - Stefano Stagni
- Department of Industrial Chemistry “Toso Montanari”-; University of Bologna; viale del Risorgimento 4 Bologna 40136 Italy
| | - Janna L. Morrison
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide, South Australia 5000 Australia
| | - Sally E. Plush
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide Australia
- Future Industries Institute; University of South Australia; Mawson Lakes, SA 5095 Australia
| | - Douglas A. Brooks
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research; University of South Australia; Adelaide Australia
| | - Massimiliano Massi
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry; Curtin University; Kent Street Bentley 6102 WA Australia
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27
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Caporale C, Bader CA, Sorvina A, MaGee KDM, Skelton BW, Gillam TA, Wright PJ, Raiteri P, Stagni S, Morrison JL, Plush SE, Brooks DA, Massi M. Investigating Intracellular Localisation and Cytotoxicity Trends for Neutral and Cationic Iridium Tetrazolato Complexes in Live Cells. Chemistry 2017; 23:15666-15679. [PMID: 28782852 DOI: 10.1002/chem.201701352] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 12/20/2022]
Abstract
A family of five neutral cyclometalated iridium(III) tetrazolato complexes and their methylated cationic analogues have been synthesised and characterised. The complexes are distinguished by variations of the substituents or degree of π conjugation on either the phenylpyridine or tetrazolato ligands. The photophysical properties of these species have been evaluated in organic and aqueous media, revealing predominantly a solvatochromic emission originating from mixed metal-to-ligand and ligand-to-ligand charge transfer excited states of triplet multiplicity. These emissions are characterised by typically long excited-state lifetimes (∼hundreds of ns), and quantum yields around 5-10 % in aqueous media. Methylation of the complexes caused a systematic red-shift of the emission profiles. The behaviour and the effects of the different complexes were then examined in cells. The neutral species localised mostly in the endoplasmic reticulum and lipid droplets, whereas the majority of the cationic complexes localised in the mitochondria. The amount of complexes found within cells does not depend on lipophilicity, which potentially suggests diverse uptake mechanisms. Methylated analogues were found to be more cytotoxic compared to the neutral species, a behaviour that might to be linked to a combination of uptake and intracellular localisation.
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Affiliation(s)
- Chiara Caporale
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry, Curtin University, Kent Street, Bentley, 6102 WA, Australia
| | - Christie A Bader
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, Australia
| | - Alexandra Sorvina
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, Australia
| | - Karen D M MaGee
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry, Curtin University, Kent Street, Bentley, 6102 WA, Australia
| | - Brian W Skelton
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Todd A Gillam
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, Australia
| | - Phillip J Wright
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry, Curtin University, Kent Street, Bentley, 6102 WA, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and Department of Chemistry, Curtin University, Kent Street, Bentley, 6102 WA, Australia
| | - Stefano Stagni
- Department of Industrial Chemistry "Toso Montanari"-, University of Bologna, viale del Risorgimento 4, Bologna, 40136, Italy
| | - Janna L Morrison
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Sally E Plush
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, Australia.,Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Douglas A Brooks
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, Adelaide, Australia
| | - Massimiliano Massi
- Curtin Institute of Functional Molecules and Interfaces and Department of Chemistry, Curtin University, Kent Street, Bentley, 6102 WA, Australia
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28
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Affiliation(s)
- Marco De La Pierre
- Department of Chemistry Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR) Curtin University PO Box U1987 Perth WA 6845 Australia
| | - Paolo Raiteri
- Department of Chemistry Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR) Curtin University PO Box U1987 Perth WA 6845 Australia
| | - Andrew G. Stack
- Chemical Sciences Division Oak Ridge National Laboratory PO Box 2008, MS-6110 Oak Ridge TN 37831 USA
| | - Julian D. Gale
- Department of Chemistry Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR) Curtin University PO Box U1987 Perth WA 6845 Australia
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29
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Abstract
Determining a complete atomic-level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO3 ) in water, computer simulations have been used to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca2+ only adsorbs after CO32- . In contrast to the conventional picture, ion pairs prefer to bind at the upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Migration of the first carbonate ion to a growth site is found to be rate-limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.
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Affiliation(s)
- Marco De La Pierre
- Department of Chemistry, Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Paolo Raiteri
- Department of Chemistry, Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Andrew G Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6110, Oak Ridge, TN, 37831, USA
| | - Julian D Gale
- Department of Chemistry, Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), Curtin University, PO Box U1987, Perth, WA, 6845, Australia
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30
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Carter DJ, Raiteri P, Barnard KR, Gielink R, Mocerino M, Skelton BW, Vaughan JG, Ogden MI, Rohl AL. Difference Hirshfeld fingerprint plots: a tool for studying polymorphs. CrystEngComm 2017. [DOI: 10.1039/c6ce02535h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Reischl B, Raiteri P, Gale JD, Rohl AL. Can Point Defects in Surfaces in Solution be Atomically Resolved by Atomic Force Microscopy? Phys Rev Lett 2016; 117:226101. [PMID: 27925727 DOI: 10.1103/physrevlett.117.226101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 06/06/2023]
Abstract
While the atomic force microscope (AFM) is able to image mineral surfaces in solution with atomic resolution, so far, it has been a matter of debate whether imaging point defects is also possible under these conditions. The difficulties stem from the limited knowledge of what types of defects may be stable in the presence of an AFM tip, as well as from the complicated imaging mechanism involving interactions between hydration layers over the surface and around the tip apex. Here, we present atomistic molecular dynamics and free energy calculations of the AFM imaging of vacancies and ionic substitutions in the calcite (101[over ¯]4) surface in water, using a new silica AFM tip model. Our results indicate that both calcium and carbonate vacancies, as well as a magnesium substitution, could be resolved in an AFM experiment, albeit with different imaging mechanisms.
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Affiliation(s)
- Bernhard Reischl
- Curtin Institute for Computation and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western Australia 6845, Australia
| | - Julian D Gale
- Curtin Institute for Computation and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western Australia 6845, Australia
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western Australia 6845, Australia
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32
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Affiliation(s)
- Ran Drori
- Department
of Chemistry and Molecular Design Institute, New York University, New York, New York 10003, United States
| | - Chao Li
- Department
of Chemistry and Molecular Design Institute, New York University, New York, New York 10003, United States
| | - Chunhua Hu
- Department
of Chemistry and Molecular Design Institute, New York University, New York, New York 10003, United States
| | - Paolo Raiteri
- Curtin
Institute for Computation and Department of Chemistry, Curtin University, Perth, Western Australia 6845, Australia
| | - Andrew L. Rohl
- Curtin
Institute for Computation and Department of Chemistry, Curtin University, Perth, Western Australia 6845, Australia
| | - Michael D. Ward
- Department
of Chemistry and Molecular Design Institute, New York University, New York, New York 10003, United States
| | - Bart Kahr
- Department
of Chemistry and Molecular Design Institute, New York University, New York, New York 10003, United States
- Department
of Advanced Science and Engineering (TWIns), Waseda University, Tokyo, Japan
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33
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Abstract
The understanding of the molecular mechanisms underlying the early stages of crystallisation is still incomplete. In the case of calcium carbonate, experimental and computational evidence suggests that phase separation relies on so-called pre-nucleation clusters (PNCs). A thorough thermodynamic analysis of the enthalpic and entropic contributions to the overall free energy of PNC formation derived from three independent methods demonstrates that solute clustering is driven by entropy. This can be quantitatively rationalised by the release of water molecules from ion hydration layers, explaining why ion association is not limited to simple ion pairing. The key role of water release in this process suggests that PNC formation should be a common phenomenon in aqueous solutions.
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Affiliation(s)
| | - Paolo Raiteri
- Department of Chemistry, Curtin Institute for Computation and Institute for Geoscience Research, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - John K Berg
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitätsstraße 10, D-78464, Konstanz, Germany
| | - Andreas Kempter
- Reactive Systems and Inorganic Nanomaterials Research, BASF SE, D-67056, Ludwigshafen, Germany
| | - Julian D Gale
- Department of Chemistry, Curtin Institute for Computation and Institute for Geoscience Research, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Denis Gebauer
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitätsstraße 10, D-78464, Konstanz, Germany
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34
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Olson IA, Shtukenberg AG, Hakobyan G, Rohl AL, Raiteri P, Ward MD, Kahr B. Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals. J Phys Chem Lett 2016; 7:3112-3117. [PMID: 27478906 DOI: 10.1021/acs.jpclett.6b01459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals.
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Affiliation(s)
- Isabel A Olson
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Alexander G Shtukenberg
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Gagik Hakobyan
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry, Curtin University , P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Paolo Raiteri
- Curtin Institute for Computation and Department of Chemistry, Curtin University , P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Michael D Ward
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
- Graduate School of Advanced Science and Engineering (TWIns), Waseda University , Tokyo, Japan
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35
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Zhu Q, Shtukenberg AG, Carter DJ, Yu TQ, Yang J, Chen M, Raiteri P, Oganov AR, Pokroy B, Polishchuk I, Bygrave PJ, Day GM, Rohl AL, Tuckerman ME, Kahr B. Resorcinol Crystallization from the Melt: A New Ambient Phase and New "Riddles". J Am Chem Soc 2016; 138:4881-9. [PMID: 26986837 DOI: 10.1021/jacs.6b01120] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structures of the α and β phases of resorcinol, a major commodity chemical in the pharmaceutical, agrichemical, and polymer industries, were the first polymorphic pair of molecular crystals solved by X-ray analysis. It was recently stated that "no additional phases can be found under atmospheric conditions" (Druzbicki, K. et al. J. Phys. Chem. B 2015, 119, 1681). Herein is described the growth and structure of a new ambient pressure phase, ε, through a combination of optical and X-ray crystallography and by computational crystal structure prediction algorithms. α-Resorcinol has long been a model for mechanistic crystal growth studies from both solution and vapor because prisms extended along the polar axis grow much faster in one direction than in the opposite direction. Research has focused on identifying the absolute sense of the fast direction-the so-called "resorcinol riddle"-with the aim of identifying how solvent controls crystal growth. Here, the growth velocity dissymmetry in the melt is analyzed for the β phase. The ε phase only grows from the melt, concomitant with the β phase, as polycrystalline, radially growing spherulites. If the radii are polar, then the sense of the polar axis is an essential feature of the form. Here, this determination is made for spherulites of β resorcinol (ε, point symmetry 222, does not have a polar axis) with additives that stereoselectively modify growth velocities. Both β and ε have the additional feature that individual radial lamellae may adopt helicoidal morphologies. We correlate the appearance of twisting in β and ε with the symmetry of twist-inducing additives.
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Affiliation(s)
- Qiang Zhu
- Department of Geosciences, Stony Brook University , Stony Brook, New York 11794, United States
| | - Alexander G Shtukenberg
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Damien J Carter
- Curtin Institute for Computation, Nanochemistry Research Institute and Department of Chemistry, Curtin University , P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Tang-Qing Yu
- Department of Chemistry and Courant Institute, New York University , New York City, New York 10003, United States
| | - Jingxiang Yang
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
| | - Ming Chen
- Department of Chemistry and Courant Institute, New York University , New York City, New York 10003, United States
| | - Paolo Raiteri
- Curtin Institute for Computation, Nanochemistry Research Institute and Department of Chemistry, Curtin University , P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Artem R Oganov
- Department of Geosciences, Stony Brook University , Stony Brook, New York 11794, United States
| | - Boaz Pokroy
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology , Haifa 32000, Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology , Haifa 32000, Israel
| | - Peter J Bygrave
- School of Chemistry, University of Southampton , Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Graeme M Day
- School of Chemistry, University of Southampton , Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Andrew L Rohl
- Curtin Institute for Computation, Nanochemistry Research Institute and Department of Chemistry, Curtin University , P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Mark E Tuckerman
- Department of Chemistry and Courant Institute, New York University , New York City, New York 10003, United States.,New York University-East China Normal University Center for Computational Chemistry at NYU Shanghai , 3663 Zhongshan Road North, Shanghai 200062, China
| | - Bart Kahr
- Department of Chemistry and Molecular Design Institute, New York University , New York City, New York 10003, United States
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36
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Fiorini V, Zacchini S, Raiteri P, Mazzoni R, Zanotti V, Massi M, Stagni S. Negatively charged Ir(iii) cyclometalated complexes containing a chelating bis-tetrazolato ligand: synthesis, photophysics and the study of reactivity with electrophiles. Dalton Trans 2016; 45:12884-96. [DOI: 10.1039/c6dt02524b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The synthesis, the reactivity toward electrophiles and use for Ir(iii) based soft salts of new anionic Ir(iii) complexes containing a bis-tetrazolato ligand are described herein.
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Affiliation(s)
- Valentina Fiorini
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Stefano Zacchini
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Paolo Raiteri
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
- Curtin Institute for Computation
| | - Rita Mazzoni
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Valerio Zanotti
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Massimiliano Massi
- Department of Chemistry and Nanochemistry Research Institute
- Curtin University
- Perth
- Australia
| | - Stefano Stagni
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
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37
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Simpson PV, Skelton BW, Raiteri P, Massi M. Photophysical and photochemical studies of tricarbonyl rhenium(i) N-heterocyclic carbene complexes containing azide and triazolate ligands. NEW J CHEM 2016. [DOI: 10.1039/c5nj03301b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rhenium NHC complexes bound to azide anions readily react with alkynes to form the corresponding triazolate complexes, a new class of photochemically active species.
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Affiliation(s)
- Peter V. Simpson
- Nanochemistry Research Institute – Department of Chemistry
- Curtin University
- Bentley 6102 WA
- Australia
| | - Brian W. Skelton
- Centre for Microscopy
- Characterisation and Analysis
- University of Western Australia
- Crawley 6009 WA
- Australia
| | - Paolo Raiteri
- Nanochemistry Research Institute – Department of Chemistry
- Curtin University
- Bentley 6102 WA
- Australia
| | - Massimiliano Massi
- Nanochemistry Research Institute – Department of Chemistry
- Curtin University
- Bentley 6102 WA
- Australia
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38
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Karamertzanis PG, Raiteri P, Galindo A. The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration. J Chem Theory Comput 2015; 6:1590-607. [PMID: 26615693 DOI: 10.1021/ct900693q] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We propose a novel, anisotropic rigid-body intermolecular potential model to predict the properties of water and the hydration free energies of neutral organic solutes. The electrostatic interactions of water and the solutes are modeled using atomic multipole moments up to hexadecapole; these are obtained from distributed multipole analysis of the quantum mechanically computed charge densities and include average polarization effects in solution. The repulsion-dispersion water-water interactions are modeled with a three-site, exp-6 model fitted to the experimental liquid water density and oxygen-oxygen radial distribution function at ambient conditions. The proposed water model reproduces well several water properties not used in its parametrization, including vapor-liquid coexistence densities, the maximum in liquid water density at atmospheric pressure, the structure of ordered ice polymorphs, and the liquid water heat capacity. The model is used to compute the hydration free energy of 10 neutral organic solutes using explicit-solvent free energy perturbation. The solute-solute repulsion-dispersion intermolecular potential is obtained from previous parametrizations on organic crystal structures. In order to calculate the free energies of hydration, water-solute repulsion-dispersion interactions are modeled using Lorenz-Berthelot combining rules. The root-mean-square error of the predicted hydration free energies is 1.5 kcal mol(-1), which is comparable to the error found using a continuum mean-field quantum mechanical approach parametrized using experimental free energy of hydration data. The results are also contrasted with explicit-solvent hydration free energies obtained with an atomic charge representation of the solute's charge density computed at the same level of theory used to compute the distributed multipoles. Replacing the multipole description of the solute's charge density with an atomic charge model changes the free energy of hydration by as much as 3 kcal mol(-1) and provides an estimate for the effect of the modeling quality of the intermolecular electrostatic forces in free energy of solvation calculations.
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Affiliation(s)
- Panagiotis G Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
| | - Paolo Raiteri
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
| | - Amparo Galindo
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
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39
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Werrett MV, Wright PJ, Simpson PV, Raiteri P, Skelton BW, Stagni S, Buckley AG, Rigby PJ, Massi M. Rhenium tetrazolato complexes coordinated to thioalkyl-functionalised phenanthroline ligands: synthesis, photophysical characterisation, and incubation in live HeLa cells. Dalton Trans 2015; 44:20636-47. [PMID: 26563409 DOI: 10.1039/c5dt03470a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three new complexes of formulation fac-[Re(CO)3(diim)L], where diim is either 1,10-phenanthroline or 1,10-phenanthroline functionalised at position 5 by a thioalkyl chain, and L is either a chloro or aryltetrazolato ancillary ligand, were synthesised and photophysically characterised. The complexes exhibit phosphorescent emission with maxima around 600 nm, originating from triplet metal-to-ligand charge transfer states with partially mixed ligand-to-ligand charge transfer character. The emission is relatively long-lived, within the 200-400 ns range, and with quantum yields of 2-4%. The complexes were trialed as cellular markers in live HeLa cells, along with two previously reported rhenium tetrazolato complexes bound to unsubstituted 1,10-phenanthroline. All five complexes exhibit good cellular uptake and non-specific perinuclear localisation. Upon excitation at 405 nm, the emission from the rhenium complexes could be clearly distinguished from autofluorescence, as demonstrated by spectral detection within the live cells. Four of the complexes did not appear to be toxic, however prolonged excitation could result in membrane blebbing. No major sign of photobleaching was detected upon multiple imaging on the same cell sample.
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Affiliation(s)
- Melissa V Werrett
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent St., 6102 Bentley, WA, Australia.
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40
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Vaughan JG, Reid BL, Wright PJ, Ramchandani S, Skelton BW, Raiteri P, Muzzioli S, Brown DH, Stagni S, Massi M. Photophysical and Photochemical Trends in Tricarbonyl Rhenium(I) N-Heterocyclic Carbene Complexes. Inorg Chem 2014; 53:3629-41. [DOI: 10.1021/ic403138a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jamila G. Vaughan
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Brodie L. Reid
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Phillip J. Wright
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Sushil Ramchandani
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Brian W. Skelton
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Crawley 6009 Western Australia, Australia
| | - Paolo Raiteri
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Sara Muzzioli
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, viale del Risorgimento 4, Bologna 40126, Italy
| | - David H. Brown
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
| | - Stefano Stagni
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, viale del Risorgimento 4, Bologna 40126, Italy
| | - Massimiliano Massi
- Nanochemistry Research Institute, Department of Chemistry, Curtin University, Kent Street, Bentley 6102 Western Australia, Australia
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41
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Werrett MV, Muzzioli S, Wright PJ, Palazzi A, Raiteri P, Zacchini S, Massi M, Stagni S. Proton-Induced Reversible Modulation of the Luminescent Output of Rhenium(I), Iridium(III), and Ruthenium(II) Tetrazolate Complexes. Inorg Chem 2013; 53:229-43. [DOI: 10.1021/ic402187e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Melissa V. Werrett
- Department
of Chemistry, Curtin University, GPO Box U 1987, Perth, Australia, 6845
| | - Sara Muzzioli
- Department of Industrial Chemistry “Toso
Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Phillip J. Wright
- Department
of Chemistry, Curtin University, GPO Box U 1987, Perth, Australia, 6845
| | - Antonio Palazzi
- Department of Industrial Chemistry “Toso
Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Paolo Raiteri
- Department
of Chemistry, Curtin University, GPO Box U 1987, Perth, Australia, 6845
| | - Stefano Zacchini
- Department of Industrial Chemistry “Toso
Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Massimiliano Massi
- Department
of Chemistry, Curtin University, GPO Box U 1987, Perth, Australia, 6845
| | - Stefano Stagni
- Department of Industrial Chemistry “Toso
Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
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42
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Wallace AF, Hedges LO, Fernandez-Martinez A, Raiteri P, Gale JD, Waychunas GA, Whitelam S, Banfield JF, De Yoreo JJ. Microscopic evidence for liquid-liquid separation in supersaturated CaCO3 solutions. Science 2013; 341:885-9. [PMID: 23970697 DOI: 10.1126/science.1230915] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent experimental observations of the onset of calcium carbonate (CaCO3) mineralization suggest the emergence of a population of clusters that are stable rather than unstable as predicted by classical nucleation theory. This study uses molecular dynamics simulations to probe the structure, dynamics, and energetics of hydrated CaCO3 clusters and lattice gas simulations to explore the behavior of cluster populations before nucleation. Our results predict formation of a dense liquid phase through liquid-liquid separation within the concentration range in which clusters are observed. Coalescence and solidification of nanoscale droplets results in formation of a solid phase, the structure of which is consistent with amorphous CaCO3. The presence of a liquid-liquid binodal enables a diverse set of experimental observations to be reconciled within the context of established phase-separation mechanisms.
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Affiliation(s)
- Adam F Wallace
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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43
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MaGee KDM, Wright PJ, Muzzioli S, Siedlovskas CM, Raiteri P, Baker MV, Brown DH, Stagni S, Massi M. Enhanced deep-blue emission from Pt(II) complexes bound to 2-pyridyltetrazolate and an ortho-xylene-linked bis(NHC)cyclophane. Dalton Trans 2013; 42:4233-6. [PMID: 23400310 DOI: 10.1039/c3dt50225b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The coordination of 2-pyridyltetrazolate and ortho-xylene-linked bis(NHC)cyclophane to Pt(II) yielded a novel complex characterised by enhanced pure deep-blue emission, whose intensity can be modulated via methylation of the tetrazole ring.
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Affiliation(s)
- Karen D M MaGee
- Department of Chemistry, Curtin University, Kent Street, 6102 Bentley WA, Australia
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44
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Wright PJ, Affleck MG, Muzzioli S, Skelton BW, Raiteri P, Silvester DS, Stagni S, Massi M. Ligand-Induced Structural, Photophysical, and Electrochemical Variations in Tricarbonyl Rhenium(I) Tetrazolato Complexes. Organometallics 2013. [DOI: 10.1021/om400356n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Phillip J. Wright
- Department of Chemistry, Curtin University, Kent Street, Bentley 6102 WA, Australia
| | - Mark G. Affleck
- Department of Chemistry, Curtin University, Kent Street, Bentley 6102 WA, Australia
| | - Sara Muzzioli
- Department of Industrial Chemistry
“Toso Montanari”, University of Bologna, Viale del Risorgimento 4, Bologna 40126, Italy
| | - Brian W. Skelton
- Centre for Microscopy, Characterisation
and Analysis, University of Western Australia, Crawley 6009 WA, Australia
| | - Paolo Raiteri
- Department of Chemistry, Curtin University, Kent Street, Bentley 6102 WA, Australia
| | - Debbie S. Silvester
- Department of Chemistry, Curtin University, Kent Street, Bentley 6102 WA, Australia
| | - Stefano Stagni
- Department of Industrial Chemistry
“Toso Montanari”, University of Bologna, Viale del Risorgimento 4, Bologna 40126, Italy
| | - Massimiliano Massi
- Department of Chemistry, Curtin University, Kent Street, Bentley 6102 WA, Australia
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45
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Wright PJ, Muzzioli S, Skelton BW, Raiteri P, Lee J, Koutsantonis G, Silvester DS, Stagni S, Massi M. One-step assembly of Re(i) tricarbonyl 2-pyridyltetrazolato metallacalix[3]arene with aqua emission and reversible three-electron oxidation. Dalton Trans 2013; 42:8188-91. [DOI: 10.1039/c3dt50988e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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46
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Vaughan JG, Reid BL, Ramchandani S, Wright PJ, Muzzioli S, Skelton BW, Raiteri P, Brown DH, Stagni S, Massi M. The photochemistry of rhenium(i) tricarbonyl N-heterocyclic carbene complexes. Dalton Trans 2013; 42:14100-14. [DOI: 10.1039/c3dt51614h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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Wright PJ, Muzzioli S, Werrett MV, Raiteri P, Skelton BW, Silvester DS, Stagni S, Massi M. Synthesis, Photophysical and Electrochemical Investigation of Dinuclear Tetrazolato-Bridged Rhenium Complexes. Organometallics 2012. [DOI: 10.1021/om300870a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Phillip J. Wright
- Department of Chemistry, Curtin University, Kent Street, Bentley WA 6102, Australia
| | - Sara Muzzioli
- Department of Physical and Inorganic
Chemistry, University of Bologna, Viale
del Risorgimento, I-40126 Bologna, Italy
| | - Melissa V. Werrett
- Department of Chemistry, Curtin University, Kent Street, Bentley WA 6102, Australia
| | - Paolo Raiteri
- Department of Chemistry, Curtin University, Kent Street, Bentley WA 6102, Australia
| | - Brian W. Skelton
- Center for Microscopy, Characterization
and Analysis, University of Western Australia, Crawley 6009 WA, Australia
| | - Debbie S. Silvester
- Department of Chemistry, Curtin University, Kent Street, Bentley WA 6102, Australia
| | - Stefano Stagni
- Department of Physical and Inorganic
Chemistry, University of Bologna, Viale
del Risorgimento, I-40126 Bologna, Italy
| | - Massimiliano Massi
- Department of Chemistry, Curtin University, Kent Street, Bentley WA 6102, Australia
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48
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Demichelis R, Raiteri P, Gale JD, Dovesi R. A new structural model for disorder in vaterite from first-principles calculations. CrystEngComm 2012. [DOI: 10.1039/c1ce05976a] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Raiteri P, Demichelis R, Gale JD, Kellermeier M, Gebauer D, Quigley D, Wright LB, Walsh TR. Exploring the influence of organic species on pre- and post-nucleation calcium carbonate. Faraday Discuss 2012. [DOI: 10.1039/c2fd20052j] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Melis C, Raiteri P, Colombo L, Mattoni A. Self-assembling of zinc phthalocyanines on ZnO (1010) surface through multiple time scales. ACS Nano 2011; 5:9639-9647. [PMID: 22047169 DOI: 10.1021/nn203105w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We adopt a hierarchic combination of theoretical methods to study the assembling of zinc phthalocyanines (ZnPcs) on a ZnO (1010) surface through multiple time scales. Atomistic simulations, such as model potential molecular dynamics and metadynamics, are used to study the energetics and short time evolution (up to ∼100 ns) of small ZnPc aggregates. The stability and the lifetime of large clusters is then studied by means of an atomistically informed coarse-grained model using classical molecular dynamics. Finally, the macroscopic time scale clustering phenomenon is studied by Metropolis Monte Carlo algorithms as a function of temperature and surface coverage. We provide evidence that at room temperature the aggregation is likely to occur at sufficiently high coverage, and we characterize the nature, morphology, and lifetime of ZnPc's clusters. We identify the molecular stripes oriented along [010] crystallographic directions as the most energetically stable aggregates.
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Affiliation(s)
- Claudio Melis
- Dipartimento di Fisica, Università di Cagliari, I-09042 Monserrato (Ca), Italy.
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