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Hendry D, Rohl AL, Rasmussen CL, Zabatiero J, Cliff DP, Smith SS, Mackenzie J, Pattinson CL, Straker L, Campbell A. Objective Measurement of Posture and Movement in Young Children Using Wearable Sensors and Customised Mathematical Approaches: A Systematic Review. Sensors (Basel) 2023; 23:9661. [PMID: 38139507 PMCID: PMC10747033 DOI: 10.3390/s23249661] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Given the importance of young children's postures and movements to health and development, robust objective measures are required to provide high-quality evidence. This study aimed to systematically review the available evidence for objective measurement of young (0-5 years) children's posture and movement using machine learning and other algorithm methods on accelerometer data. From 1663 papers, a total of 20 papers reporting on 18 studies met the inclusion criteria. Papers were quality-assessed and data extracted and synthesised on sample, postures and movements identified, sensors used, model development, and accuracy. A common limitation of studies was a poor description of their sample data, yet over half scored adequate/good on their overall study design quality assessment. There was great diversity in all aspects examined, with evidence of increasing sophistication in approaches used over time. Model accuracy varied greatly, but for a range of postures and movements, models developed on a reasonable-sized (n > 25) sample were able to achieve an accuracy of >80%. Issues related to model development are discussed and implications for future research outlined. The current evidence suggests the rapidly developing field of machine learning has clear potential to enable the collection of high-quality evidence on the postures and movements of young children.
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Affiliation(s)
- Danica Hendry
- School of Allied Health, Curtin University, Perth, WA 6102, Australia; (D.H.); (C.L.R.); (J.Z.); (L.S.)
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
| | - Andrew L. Rohl
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
- School of Electrical Engineering, Computing and Mathematical Sciences, Curtin University, Perth, WA 6845, Australia
| | - Charlotte Lund Rasmussen
- School of Allied Health, Curtin University, Perth, WA 6102, Australia; (D.H.); (C.L.R.); (J.Z.); (L.S.)
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
| | - Juliana Zabatiero
- School of Allied Health, Curtin University, Perth, WA 6102, Australia; (D.H.); (C.L.R.); (J.Z.); (L.S.)
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
| | - Dylan P. Cliff
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
- Early Start, School of Education, University of Wollongong, Keiraville, NSW 2522, Australia
| | - Simon S. Smith
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
- Institute for Social Science Research, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Janelle Mackenzie
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
- School of Computer Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Cassandra L. Pattinson
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
- Institute for Social Science Research, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Leon Straker
- School of Allied Health, Curtin University, Perth, WA 6102, Australia; (D.H.); (C.L.R.); (J.Z.); (L.S.)
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
| | - Amity Campbell
- School of Allied Health, Curtin University, Perth, WA 6102, Australia; (D.H.); (C.L.R.); (J.Z.); (L.S.)
- ARC Centre of Excellence for the Digital Child, Brisbane, ACT 2609, Australia; (A.L.R.); (D.P.C.); (S.S.S.); (J.M.); (C.L.P.)
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Miyazawa K, Tracey J, Reischl B, Spijker P, Foster AS, Rohl AL, Fukuma T. Tip dependence of three-dimensional scanning force microscopy images of calcite-water interfaces investigated by simulation and experiments. Nanoscale 2020; 12:12856-12868. [PMID: 32520063 DOI: 10.1039/d0nr02043e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.
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Affiliation(s)
- Keisuke Miyazawa
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan. and Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - John Tracey
- Department of Applied Physics, Aalto University, Helsinki FI-00076, Finland.
| | - Bernhard Reischl
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, PO Box 64, FI-00014, Finland and Curtin Institute for Computation, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Peter Spijker
- Department of Applied Physics, Aalto University, Helsinki FI-00076, Finland.
| | - Adam S Foster
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan and Department of Applied Physics, Aalto University, Helsinki FI-00076, Finland.
| | - Andrew L Rohl
- Curtin Institute for Computation and School of Electrical Engineering, Computing and Mathematical Sciences, Curtin University, P.O. Box U1987, Perth, Western Australia 6845, Australia
| | - Takeshi Fukuma
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan. and Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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Jones F, Rohl AL. Using Molecular Modelling to Understand and Predict the Impact of Organic Additives as Crystal Growth Modifiers. Aust J Chem 2020. [DOI: 10.1071/ch19388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Empirical molecular modelling was used to investigate the impact of organic additives on crystal morphology and inhibition. The replacement energy was found to correlate reasonably well with the degree of inhibition as determined from conductivity data. The replacement energy was also able to predict the barium sulfate face on which additive adsorption was most likely. While the ability of the organic functional groups to sit in the vacant sulfate lattice positions (the so-called ‘lattice matching’ criteria) appears intuitively sensible, it was found that this is not a sufficient criterion to predict real behaviour. A better criterion is the overall replacement energy as it takes into consideration the number of Ba–Oorganic interactions and whether the adsorption process overall is energetically favourable (by including the hydration energy of the ions). Thus, the replacement energy can successfully predict the effect of organic molecules on the crystal growth modification of barium sulfate.
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Abstract
Macrocyclic compounds such as DOTP and NOTP are found to inhibit precipitation of barium sulfate just as potently as their non-cyclic counterparts depending on the ionisation state of the molecule.
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Affiliation(s)
- Tomoko Radomirovic
- Chemistry, School of Molecular and Life Sciences
- Curtin University
- Perth WA
- 6845 Australia
| | - Mark I. Ogden
- Curtin Institute of Functional Molecules and Interfaces
- and School of Molecular and Life Sciences
- Curtin University
- Perth WA
- 6845 Australia
| | - Andrew L. Rohl
- Curtin Institute for Computation and School of Molecular and Life Sciences
- Curtin University
- Perth WA
- 6845 Australia
| | - Franca Jones
- Curtin Institute of Functional Molecules and Interfaces
- and School of Molecular and Life Sciences
- Curtin University
- Perth WA
- 6845 Australia
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Wiebrands M, Malajczuk CJ, Woods AJ, Rohl AL, Mancera RL. Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0010/jib-2018-0010.xml. [PMID: 29927749 PMCID: PMC6167041 DOI: 10.1515/jib-2018-0010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 01/23/2018] [Accepted: 05/09/2018] [Indexed: 11/15/2022] Open
Abstract
Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.
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Affiliation(s)
- Michael Wiebrands
- Curtin Hub for Immersive Visualization and eResearch (HIVE), Curtin University, Perth, WA, Australia
| | - Chris J Malajczuk
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Centre and Curtin Institute for Computation, Curtin University, Perth, WA, Australia
| | - Andrew J Woods
- Curtin Hub for Immersive Visualization and eResearch (HIVE), Curtin University, Perth, WA, Australia
| | - Andrew L Rohl
- School of Molecular and Life Sciences and Curtin Institute for Computation, Curtin University, Perth WA, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Centre and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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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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Shtukenberg AG, Zhu Q, Carter DJ, Vogt L, Hoja J, Schneider E, Song H, Pokroy B, Polishchuk I, Tkatchenko A, Oganov AR, Rohl AL, Tuckerman ME, Kahr B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs. Chem Sci 2017; 8:4926-4940. [PMID: 28959416 PMCID: PMC5607859 DOI: 10.1039/c7sc00168a] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/30/2017] [Indexed: 11/21/2022] Open
Abstract
Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.
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Affiliation(s)
- Alexander G Shtukenberg
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
| | - Qiang Zhu
- Department of Physics and Astronomy , High Pressure Science and Engineering Center , University of Nevada Las Vegas , Nevada 89154 , USA .
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Damien J Carter
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Leslie Vogt
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Elia Schneider
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Hongxing Song
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Boaz Pokroy
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology , Skolkovo Innovation Center , 3 Nobel St. , Moscow 143026 , Russia
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Mark E Tuckerman
- Department of Chemistry , New York University , New York City , NY 10003 , USA
- Courant Institute of Mathematical Sciences , New York University , New York City , NY 10003 , USA
- 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 , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
- Department of Advanced Science and Engineering (TWIns) , Waseda University , Wakamatsucho, 3-2 , Shinjuku , 162-0056 Tokyo , Japan
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Wang Y, Arandiyan H, Tahini HA, Scott J, Tan X, Dai H, Gale JD, Rohl AL, Smith SC, Amal R. The controlled disassembly of mesostructured perovskites as an avenue to fabricating high performance nanohybrid catalysts. Nat Commun 2017; 8:15553. [PMID: 28541308 PMCID: PMC5458515 DOI: 10.1038/ncomms15553] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/05/2017] [Indexed: 12/03/2022] Open
Abstract
Versatile superstructures composed of nanoparticles have recently been prepared using various disassembly methods. However, little information is known on how the structural disassembly influences the catalytic performance of the materials. Here we show how the disassembly of an ordered porous La0.6Sr0.4MnO3 perovskite array, to give hexapod mesostructured nanoparticles, exposes a new crystal facet which is more active for catalytic methane combustion. On fragmenting three-dimensionally ordered macroporous (3DOM) structures in a controlled manner, via a process that has been likened to retrosynthesis, hexapod-shaped building blocks can be harvested which possess a mesostructured architecture. The hexapod-shaped perovskite catalyst exhibits excellent low temperature methane oxidation activity (T90%=438 °C; reaction rate=4.84 × 10−7 mol m−2 s−1). First principle calculations suggest the fractures, which occur at weak joints within the 3DOM architecture, afford a large area of (001) surface that displays a reduced energy barrier for hydrogen abstraction, thereby facilitating methane oxidation. Disassembly of three-dimensionally ordered materials generates nanoparticles with new structural and physicochemical properties. Here the authors show a fragmentation strategy applied to a perovskite material leading to nanostructures with improved catalytic activity in the methane combustion.
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Affiliation(s)
- Yuan Wang
- Particles and Catalysis Research Group, School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Hamidreza Arandiyan
- Particles and Catalysis Research Group, School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Hassan A Tahini
- Integrated Materials Design Centre (IMDC), School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason Scott
- Particles and Catalysis Research Group, School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Xin Tan
- Integrated Materials Design Centre (IMDC), School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Hongxing Dai
- Beijing Key Laboratory for Green Catalysis and Separation, and Laboratory of Catalysis Chemistry and Nanoscience, Beijing University of Technology, Beijing 100124, China
| | - Julian D Gale
- Department of Chemistry, Curtin Institute for Computation, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Andrew L Rohl
- Department of Chemistry, Curtin Institute for Computation, Curtin University, PO Box U1987, Perth, Western Australia 6845, Australia
| | - Sean C Smith
- Integrated Materials Design Centre (IMDC), School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Rose Amal
- Particles and Catalysis Research Group, School of Chemical Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
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Cullen DR, Pengon J, Rattanajak R, Chaplin J, Kamchonwongpaisan S, Massera C, Mocerino M, Rohl AL. Synthesis, Stereochemistry and Antiparasitic Activity of Derivatives of (4R)-4,6-Dihydroxy-N-methyl-1,2,3,4-tetrahydroisoquinoline. ChemistrySelect 2017. [DOI: 10.1002/slct.201602036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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)
- Danica R. Cullen
- Department of Chemistry; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Jutharat Pengon
- BIOTEC Medical Molecular Biology Research Unit; National Science and Technology Development Agency; 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Roonglawan Rattanajak
- BIOTEC Medical Molecular Biology Research Unit; National Science and Technology Development Agency; 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Jason Chaplin
- Epichem Pty Ltd; Suite 5, 3 Brodie-Hall Drive Bentley WA 6102 Australia
| | - Sumalee Kamchonwongpaisan
- BIOTEC Medical Molecular Biology Research Unit; National Science and Technology Development Agency; 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale; Università degli Studi di Parma; Viale delle Scienze 17/A 43124 Parma Italy
| | - Mauro Mocerino
- Department of Chemistry; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Andrew L. Rohl
- Curtin Institute for Computation and Department of Chemistry; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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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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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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Tracey J, Miyazawa K, Spijker P, Miyata K, Reischl B, Canova FF, Rohl AL, Fukuma T, Foster AS. Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy. Nanotechnology 2016; 27:415709. [PMID: 27609045 DOI: 10.1088/0957-4484/27/41/415709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (10[Formula: see text]4) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.
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Affiliation(s)
- John Tracey
- COMP Centre of Excellence, Department of Applied Physics, Aalto University, Helsinki FI-00076, Finland
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13
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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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14
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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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15
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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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16
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Vaughan J, Carter DJ, Rohl AL, Ogden MI, Skelton BW, Simpson PV, Brown DH. Silver(I), gold(I) and palladium(II) complexes of a NHC-pincer ligand with an aminotriazine core: a comparison with pyridyl analogues. Dalton Trans 2016; 45:1484-95. [PMID: 26672744 DOI: 10.1039/c5dt04213e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dinuclear silver, di- and tetra-nuclear gold, and mononuclear palladium complexes with chelating C,N,C diethylaminotriazinyl-bridged bis(NHC) pincer ligands were prepared and characterised. The silver and gold complexes exist in a twisted, helical conformation in both the solution- and the solid state. In contrast, an analogous dinuclear gold complex with pyridyl-bridged NHCs exists in a linear conformation. Computational studies have been performed to rationalise the formation of twisted/helical vs. linear forms.
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Affiliation(s)
- Jamila Vaughan
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - Damien J Carter
- Science & Maths Education Centre, Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Andrew L Rohl
- Curtin Institute for Computation, Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Mark I Ogden
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - Brian W Skelton
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Peter V Simpson
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - David H Brown
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
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17
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Affiliation(s)
- Damien J. Carter
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
| | - Andrew L. Rohl
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
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Carter DJ, Rohl AL. Benchmarking Calculated Lattice Parameters and Energies of Molecular Crystals Using van der Waals Density Functionals. J Chem Theory Comput 2014; 10:3423-37. [DOI: 10.1021/ct500335b] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [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)
- Damien J. Carter
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Andrew L. Rohl
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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Abstract
Banded spherulites of aspirin have been crystallized from the melt in the presence of salicylic acid either generated from aspirin decomposition or added deliberately (2.6-35.9 mol %). Scanning electron microscopy, X-ray diffraction analysis, and optical polarimetry show that the spherulites are composed of helicoidal crystallites twisted along the <010> growth directions. Mueller matrix imaging reveals radial oscillations in not only linear birefringence, but also circular birefringence, whose origin is explained through slight (∼1.3°) but systematic splaying of individual lamellae in the film. Strain associated with the replacement of aspirin molecules by salicylic acid molecules in the crystal structure is computed to be large enough to work as the driving force for the twisting of crystallites.
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Affiliation(s)
- Xiaoyan Cui
- Department of Chemistry, New York University, 100 Washington Square East, Silver Center, Room 1001, New York, New York 10003, United States
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Marks NA, Carter DJ, Sassi M, Rohl AL, Sickafus KE, Uberuaga BP, Stanek CR. Chemical evolution via beta decay: a case study in strontium-90. J Phys : Condens Matter 2013; 25:065504. [PMID: 23315221 DOI: 10.1088/0953-8984/25/6/065504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Using (90)Sr as a representative isotope, we present a framework for understanding beta decay within the solid state. We quantify three key physical and chemical principles, namely momentum-induced recoil during the decay event, defect creation due to physical displacement, and chemical evolution over time. A fourth effect, that of electronic excitation, is also discussed, but this is difficult to quantify and is strongly material dependent. The analysis is presented for the specific cases of SrTiO(3) and SrH(2). By comparing the recoil energy with available threshold displacement data we show that in many beta-decay situations defects such as Frenkel pairs will not be created during decay as the energy transfer is too low. This observation leads to the concept of chemical evolution over time, which we quantify using density functional theory. Using a combination of Bader analysis, phonon calculations and cohesive energy calculations, we show that beta decay leads to counter-intuitive behavior that has implications for nuclear waste storage and novel materials design.
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Affiliation(s)
- N A Marks
- Nanochemistry Research Institute, Curtin University, Perth, WA 6845, Australia.
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Carter DJ, Rohl AL. Noncovalent Interactions in SIESTA Using the vdW-DF Functional: S22 Benchmark and Macrocyclic Structures. J Chem Theory Comput 2011; 8:281-9. [DOI: 10.1021/ct200679b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Damien J. Carter
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
| | - Andrew L. Rohl
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
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23
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Affiliation(s)
- Damien J. Carter
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, “The Hub of Advanced Computing in Western Australia”, Technology Park, Kensington, WA, Australia
| | - Andrew L. Rohl
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, “The Hub of Advanced Computing in Western Australia”, Technology Park, Kensington, WA, Australia
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Abstract
A comprehensive study of the effects of nine organic additives on the formation of calcium sulfate scale in a pipe system was conducted using a multiple pipe flow system. Several factors that influence the inhibitory capability of phosphonic and carboxylic additives such as their chemical structure, their concentration, and the run time were closely scrutinized. Results showed that the organic additives influence the deposition of calcium sulfate on the walls of a pipe flow system at various levels. The superiority of the phosphonic additives, especially N,N,N′,N′-ethylenediaminetetramethylenephosphonic acid (EDTP) and nitrilotrimethylenephosphonic acid (NTMP), to other organic compounds with respect to scale prevention is discussed thoroughly. For the first time, it was demonstrated that a solution with a given concentration of inhibitor that is continuously refreshed in a pipe reactor becomes less effective over time. The morphology of the scales formed in the presence of different additives is also studied, using scanning electron microscopy.
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Wood PA, Francis D, Marshall WG, Moggach SA, Parsons S, Pidcock E, Rohl AL. A study of the high-pressure polymorphs of L-serine using ab initio structures and PIXEL calculations. CrystEngComm 2008. [DOI: 10.1039/b801571f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Jones F, Jones P, Ogden MI, Richmond WR, Rohl AL, Saunders M. The interaction of EDTA with barium sulfate. J Colloid Interface Sci 2007; 316:553-61. [PMID: 17904573 DOI: 10.1016/j.jcis.2007.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 08/31/2007] [Accepted: 09/03/2007] [Indexed: 10/22/2022]
Abstract
Ethylenediaminetetraacetic acid (EDTA) is a known complexing agent that interacts with a host of cations. In this paper, various techniques are used to elucidate the mechanism of interaction between EDTA and barium sulfate surfaces. It is shown that complexation with metal ions is not sufficient to explain the inhibition of barite crystallization but that other processes such as chemisorption must also occur. EDTA is shown to always adsorb as the mono-protonated species - suggesting that the molecule is able to lose a proton when it adsorbs at lower pH. Molecular modelling shows that the interaction of the surface barium ions with the carboxylate group is an important one. Finally, in situ turbidity measurements provide information about the mechanism of nucleation/growth modification. It is found that the EDTA molecule inhibits barium sulfate nucleation and that this could be its primary means of inhibiting precipitation of barium sulfate.
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Affiliation(s)
- Franca Jones
- A.J. Parker CRC for Integrated Hydrometallurgical Solutions, Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth WA 6845, Australia.
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Abstract
The adsorption of phosphonate molecules onto mineral surfaces is of interest due to their use as scale inhibitors. Molecular modeling is an important tool that can aid the fundamental understanding of how these inhibitors operate. This paper presents an empirical molecular mechanics study of the adsorption of a series of straight chain phosphonate molecules onto barium sulfate. It has been found that inhibition can be predicted for this straight chain series of molecules, which differ by the number of phosphonate groups present as well as by the chain length. Even more importantly, the modeling results can predict which faces will be preferred, and this has been verified by scanning and transmission electron microscopy on the resultant barite particles. It has been found that, in general, lattice matching results in the lowest replacement energy for all of the organic molecules investigated. The agreement between the experiment and the model confirms that the dominant mechanism of interaction for the additives on barium sulfate is via the deprotonated phosphonate groups with the barium ions on the surface.
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Affiliation(s)
- Franca Jones
- AJ Parker Co-operative Research Centre for Hydrometallurgy, Nanochemistry Research Institute, Curtin University of Technology, GPO Box U1987, Perth WA 6845, Australia.
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Paglia G, Buckley CE, Rohl AL. Comment on “Examination of Spinel and Nonspinel Structural Models for γ-Al2O3by DFT and Rietveld Refinement Simulations”. J Phys Chem B 2006; 110:20721-3; author reply 20724-6. [PMID: 17034265 DOI: 10.1021/jp061648m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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)
- Gianluca Paglia
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-2320, USA
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Abstract
We have used density functional calculations to examine the (101) surfaces of KDP, under vacuum, nitrogen, and aqueous conditions, and these simulations are found to agree well with nanoscale experimental studies demonstrating that the density functional calculations are providing a good description of the surfaces of this complex inorganic salt.
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Affiliation(s)
- Damien J Carter
- Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, Western Australia 6845, Australia, School of Physics, The University of Sydney, Sydney, New South Wales, Australia, and iVEC, The hub of advanced computing in Western Australia, 26 Dick Perry Avenue, Technology Park, Kensington, Western Australia, Australia
| | - Andrew L Rohl
- Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, Western Australia 6845, Australia, School of Physics, The University of Sydney, Sydney, New South Wales, Australia, and iVEC, The hub of advanced computing in Western Australia, 26 Dick Perry Avenue, Technology Park, Kensington, Western Australia, Australia
| | - Julian D Gale
- Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, Western Australia 6845, Australia, School of Physics, The University of Sydney, Sydney, New South Wales, Australia, and iVEC, The hub of advanced computing in Western Australia, 26 Dick Perry Avenue, Technology Park, Kensington, Western Australia, Australia
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Benedict JB, Cohen DE, Lovell S, Rohl AL, Kahr B. What is Syncrystallization? States of the pH Indicator Methyl Red in Crystals of Phthalic Acid. J Am Chem Soc 2006; 128:5548-59. [PMID: 16620129 DOI: 10.1021/ja0601181] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [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
The concept of syncrystallization was reinvestigated by focusing on phthalic acid (PA) grown with methyl red (MR). Crystals are alternately red and yellow in adjacent growth sectors. X-ray structures of MR and its cocrystals, revealing MR in the neutral, zwitterionic, and protonated states, as well as measurements of linear birefringence and linear dichroism of mixed crystals, were used to investigate mechanisms of PA coloring. These experiments were complemented by force field calculations of the lowest energy stable surfaces of expressed facets and energies of MR on and in crystals, as well as molecular orbital calculations of MR. Two MR species were detected in PA having distinct energies, polarizations, and face selectivities. Assignments of structures to these MRs, previously thought to be neutral and protonated, required a nuanced analysis of hydrogen bonds. The essential difference between yellow and red species is whether the MR carboxylic acid proton is inter- or intramolecularly hydrogen bound. Inferences about mixed crystal structure drawn from an examination of cocrystals of PA and MR are inconsistent with polarization spectroscopy signaling caution when using stoichiometric compounds as models of dilute solid solutions. Upon heating mixed crystals, linear dichroism diminishes and oriented, elongated pools of MR separate and pass through the bulk in directions perpendicular to the direction of elongation. These bâtonnets subsequently crystallize leaving macroscopic oriented crystals of a MR-rich phase within PA. No evidence was found for the simultaneous crystallization of MR and PA; however, the MR reorientation on heating as well as the separation and recrystallization of a MR-rich phase are distinct processes that could be embraced by the literal meaning of syncrystallization.
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Affiliation(s)
- Jason B Benedict
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, USA
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Barbon A, Bellinazzi M, Benedict JB, Brustolon M, Fleming SD, Jang SH, Kahr B, Rohl AL. Luminescent Probes of Crystal Growth: Surface Charge and Polar Axis Sense in Dye-Doped Potassium Hydrogen Phthalate. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200453839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Barbon A, Bellinazzi M, Benedict JB, Brustolon M, Fleming SD, Jang SH, Kahr B, Rohl AL. Luminescent Probes of Crystal Growth: Surface Charge and Polar Axis Sense in Dye-Doped Potassium Hydrogen Phthalate. Angew Chem Int Ed Engl 2004; 43:5328-31. [PMID: 15382151 DOI: 10.1002/anie.200453839] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonio Barbon
- Dipartimento di Chimica Fisica, Università di Padova, Via Loredan 2, 35131 Padova, Italy
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Abstract
Epitaxial relationships between the surfaces of inorganic and bioorganic crystals can be an important factor in crystal nucleation and growth processes in a variety of biological environments. Crystalline cholesterol monohydrate (ChM), a constituent of both gallstone and atherosclerotic plaques, is often found in association with assorted mineral phases. Using in situ atomic force microscopy (AFM) and well-characterized model bile solutions, the nucleation and epitaxial growth of ChM on calcite (104) surfaces in real-time is demonstrated. The growth rates of individual cholesterol islands formed on calcite substrates were determined at physiological temperatures. Evidence of Ostwald's ripening was also observed under these experimental conditions. The energetics of various (104) calcite/(001) ChM interfaces were calculated to determine the most stable interfacial structure. These simulations suggest that the interface is fully hydrated and that cholesterol hydroxyl groups are preferentially positioned above carbonate ions in the calcite surface. This combination of experimental and theoretical work provides a clearer picture of how preexisting mineral seeds might provide a viable growth template that can reduce the energetic barrier to cholesterol nucleation under some physiological conditions.
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Affiliation(s)
- M Crina Frincu
- Department of Chemistry, Georgetown University, 37th and O Streets NW, Washington, DC 20057-1227, USA
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Carter DJ, Ogden MI, Rohl AL. Incorporation of Cyano Transition Metal Complexes in KCl Crystals—Experimental and Computational Studies. Aust J Chem 2003. [DOI: 10.1071/ch02260] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Experimental and computational studies of the incorporation of hexacyanoferrate(II), hexacyanocobaltate(III), and hexacyanoferrate(III) into potassium chloride crystals are described. The experimental results showed that the extent of incorporation follows the trend hexacyanoferrate(II) » hexacyanoferrate(III) > hexacyanocobaltate(III). Computational modelling produced replacement energies that match the experimental trend. The calculated geometry of the incorporated complexes was also found to match well with previous experimental results.
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Fogg AM, Freij AJ, Rohl AL, Ogden MI, Parkinson GM. Toward a Fundamental Understanding of Molecular Recognition: A Synthetic and Computational Study of Morphological Control of Ca3Al2(OH)12. J Phys Chem B 2002. [DOI: 10.1021/jp015528k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Fogg
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Australia
| | - Amal J. Freij
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Australia
| | - Andrew L. Rohl
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Australia
| | - Mark I. Ogden
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Australia
| | - Gordon M. Parkinson
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth 6845, Australia
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40
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Mingos PMD, Rohl AL. Size and shape characteristics of inorganic molecular ions and their relevance to crystallization problems. Inorg Chem 2002. [DOI: 10.1021/ic00019a039] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gale JD, Rohl AL, Milman V, Warren MC. An ab Initio Study of the Structure and Properties of Aluminum Hydroxide: Gibbsite and Bayerite. J Phys Chem B 2001. [DOI: 10.1021/jp011795e] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julian D. Gale
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, Molecular Simulations, Inc., The Quorum, Barnwell Road, Cambridge, CB5 8RE, U.K., and Department of Earth Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
| | - Andrew L. Rohl
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, Molecular Simulations, Inc., The Quorum, Barnwell Road, Cambridge, CB5 8RE, U.K., and Department of Earth Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
| | - Victor Milman
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, Molecular Simulations, Inc., The Quorum, Barnwell Road, Cambridge, CB5 8RE, U.K., and Department of Earth Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
| | - Michele C. Warren
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, Molecular Simulations, Inc., The Quorum, Barnwell Road, Cambridge, CB5 8RE, U.K., and Department of Earth Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
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Ogden MI, Rohl AL, Gale JD. An ab initio study of the influence of crystal packing on the host-guest interactions of calix[4]arene crystal structures. Chem Commun (Camb) 2001:1626-7. [PMID: 12240414 DOI: 10.1039/b104193m] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [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
We report the first quantum mechanical calculations of p-tert-butylcalix[4]arene inclusion complexes in the crystalline state with geometrical aspects demonstrating good agreement with experiment, while comparison of the configurations calculated for an isolated complex and in the crystal, illustrate that crystal packing forces contribute to the observed structure of the host-guest assembly.
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Affiliation(s)
- M I Ogden
- School of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, 6845, Australia.
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Affiliation(s)
- Sean D. Fleming
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA 6845, Australia, and Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Andrew L. Rohl
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA 6845, Australia, and Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Steve C. Parker
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA 6845, Australia, and Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Gordon M. Parkinson
- A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA 6845, Australia, and Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
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Gale JD, Rohl AL, Watling HR, Parkinson GM. Theoretical Investigation of the Nature of Aluminum-Containing Species Present in Alkaline Solution. J Phys Chem B 1998. [DOI: 10.1021/jp983044r] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [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)
- Julian D. Gale
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, and A. J. Parker Cooperative Research Centre for Hydrometallurgy, CSIRO Minerals, P.O. Box 90, Bentley, Western Australia 6982
| | - Andrew L. Rohl
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, and A. J. Parker Cooperative Research Centre for Hydrometallurgy, CSIRO Minerals, P.O. Box 90, Bentley, Western Australia 6982
| | - Helen R. Watling
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, and A. J. Parker Cooperative Research Centre for Hydrometallurgy, CSIRO Minerals, P.O. Box 90, Bentley, Western Australia 6982
| | - Gordon M. Parkinson
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, SW7 2AY, U.K., A. J. Parker Cooperative Research Centre for Hydrometallurgy, School of Applied Chemistry, Curtin University of Technology, P.O. Box U1987, Perth, Western Australia 6845, and A. J. Parker Cooperative Research Centre for Hydrometallurgy, CSIRO Minerals, P.O. Box 90, Bentley, Western Australia 6982
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Watling HR, Fleming SD, van Bronswijk W, Rohl AL. Ionic structure in caustic aluminate solutions and the precipitation of gibbsite. ACTA ACUST UNITED AC 1998. [DOI: 10.1039/a807420h] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [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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Nygren MA, Gay DH, Richard A. Catlow C, Wilson MP, Rohl AL. Incorporation of growth-inhibiting diphosphonates into steps on the calcite cleavage plane surface. ACTA ACUST UNITED AC 1998. [DOI: 10.1039/a806585c] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [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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Barlow S, Rohl AL, Shi S, Freeman CM, O'Hare D. Molecular Mechanics Study of Oligomeric Models for Poly(ferrocenylsilanes) Using the Extensible Systematic Forcefield (ESFF). J Am Chem Soc 1996. [DOI: 10.1021/ja953680s] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen Barlow
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK, and Molecular Simulations, Inc., 9685 Scranton Road, San Diego, California 92121
| | - Andrew L. Rohl
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK, and Molecular Simulations, Inc., 9685 Scranton Road, San Diego, California 92121
| | - Shengua Shi
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK, and Molecular Simulations, Inc., 9685 Scranton Road, San Diego, California 92121
| | - Clive M. Freeman
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK, and Molecular Simulations, Inc., 9685 Scranton Road, San Diego, California 92121
| | - Dermot O'Hare
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK, and Molecular Simulations, Inc., 9685 Scranton Road, San Diego, California 92121
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