ORCID Profile
0000-0003-0692-0505
Current Organisation
Curtin University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Theoretical and Computational Chemistry not elsewhere classified | Theoretical and Computational Chemistry | Mineralogy and Crystallography | Theoretical And Computational Chemistry Not Elsewhere Classified | Condensed Matter Physics | Statistical Mechanics | Inorganic Geochemistry | Surfaces and Structural Properties of Condensed Matter | Mineralogy And Crystallography | Condensed Matter Imaging |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Earth Sciences | Expanding Knowledge in the Physical Sciences | Treatments (e.g. chemicals, antibiotics) | Earth sciences | Physical sciences
Related Links
Publications
Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories
Publisher: American Chemical Society (ACS)
Date: 18-07-2011
DOI: 10.1021/JA204714K
Abstract: Mineral growth and dissolution are often treated as occurring via a single reversible process that governs the rate of reaction. We show that multiple distinct intermediate states can occur during both growth and dissolution. Specifically, we used metadynamics, a method for efficiently exploring the free-energy landscape of a system, coupled to umbrella s ling and reactive flux calculations to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped barite (BaSO(4)) surface. The activation energies calculated for the rate-limiting reactions, which are different for attachment and detachment, precisely match those measured experimentally during both growth and dissolution. These results can potentially explain anomalous non-steady-state mineral reaction rates observed experimentally and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.
Promoting transparency and reproducibility in enhanced molecular simulations
Publisher: Springer Science and Business Media LLC
Date: 30-07-2019
Uncovering the Atomistic Mechanism for Calcite Step Growth
Publisher: Wiley
Date: 13-04-2017
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 (CaCO
Photophysical and photochemical studies of tricarbonyl rhenium(i ) N-heterocyclic carbene complexes containing azide and triazolate ligands
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5NJ03301B
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.
Atomistic simulations of calcium aluminosilicate interfaced with liquid water
Publisher: AIP Publishing
Date: 11-09-2023
DOI: 10.1063/5.0164817
Reactive force field simulation of proton diffusion in BaZrO3using an empirical valence bond approach
Publisher: IOP Publishing
Date: 03-08-2011
DOI: 10.1088/0953-8984/23/33/334213
Abstract: A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO(3) has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO(3) have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.
Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities
Publisher: IOP Publishing
Date: 23-01-2017
Anhydrous Calcium Oxalate Polymorphism: A Combined Computational and Synchrotron X-ray Diffraction Study
Publisher: American Chemical Society (ACS)
Date: 15-09-2016
Derivation of an Accurate Force-Field for Simulating the Growth of Calcium Carbonate from Aqueous Solution: A New Model for the Calcite−Water Interface
Publisher: American Chemical Society (ACS)
Date: 18-02-2010
DOI: 10.1021/JP910977A
Revisiting the Conformational Isomerism of Dihaloethanes: A Hybrid Computational and Experimental Laboratory for the Undergraduate Curriculum
Publisher: American Chemical Society (ACS)
Date: 12-01-2023
Structure and Surface Complexation at the Calcite(104)–Water Interface
Publisher: American Chemical Society (ACS)
Date: 03-09-2021
Molecular dynamics simulations of liquid–liquid interfaces in an electric field: The water–1,2-dichloroethane interface
Publisher: AIP Publishing
Date: 28-10-2020
DOI: 10.1063/5.0027876
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.
Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics
Publisher: American Chemical Society (ACS)
Date: 28-10-2005
DOI: 10.1021/JP054359R
Abstract: Recently, we have introduced a new method, metadynamics, which is able to s le rarely occurring transitions and to reconstruct the free energy as a function of several variables with a controlled accuracy. This method has been successfully applied in many different fields, ranging from chemistry to biophysics and ligand docking and from material science to crystal structure prediction. We present an important development that speeds up metadynamics calculations by orders of magnitude and renders the algorithm much more robust. We use multiple interacting simulations, walkers, for exploring and reconstructing the same free energy surface. Each walker contributes to the history-dependent potential that, in metadynamics, is an estimate of the free energy. We show that the error on the reconstructed free energy does not depend on the number of walkers, leading to a fully linear scaling algorithm even on inexpensive loosely coupled clusters of PCs. In addition, we show that the accuracy and stability of the method are much improved by combining it with a weighted histogram analysis. We check the validity of our new method on a realistic application.
Rhodium(I)‐α‐Phenylvinylfluorenyl Complexes: Synthesis, Characterization, and Evaluation as Initiators in the Stereospecific Polymerization of Phenylacetylene
Publisher: Wiley
Date: 08-01-2019
Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability.
Publisher: American Chemical Society (ACS)
Date: 08-09-2022
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 ex le. 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 in idual 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
The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration
Publisher: American Chemical Society (ACS)
Date: 02-04-2010
DOI: 10.1021/CT900693Q
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.
Short-Range Structure of Amorphous Calcium Hydrogen Phosphate
Publisher: American Chemical Society (ACS)
Date: 02-04-2019
Wetting Properties of the CO2–Water–Calcite System via Molecular Simulations: Shape and Size Effects
Publisher: American Chemical Society (ACS)
Date: 13-09-2019
DOI: 10.26434/CHEMRXIV.9809834.V1
Abstract: Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO 2 and the pore fluids. In this context, the interfacial tension (IFT) between CO 2 and the aqueous fluid and the contact angle, theta, 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 CO 2 –water IFT and the CO 2 –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 CO 2 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 water 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 CO 2 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 CO 2 . Our results suggest that the contact angle of a cylindrical water droplet on calcite {10.4}, in the presence of CO 2 , 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 degrees, indicating that calcite is strongly wetted by water.
Exploring the role of ions and amino acids in directing the growth of minerals from solution
Publisher: Mineralogical Society
Date: 02-2008
DOI: 10.1180/MINMAG.2008.072.1.273
Abstract: The influence of both sulphate ions and aspartic acid on directing the growth of baryte has been explored using computer simulation. Both species are found to significantly reduce the activation free-energy to growth under appropriate conditions, with the influence of sulphate being surface specific. This offers the potential for a new approach to morphology control without inhibition that may have implications for biomineralization.
2D versus 3D competition at the early stages of growth for Ge on Si(001) by molecular dynamics
Publisher: Elsevier BV
Date: 02-2002
Structural Correspondence of Solution, Liquid Crystal, and Crystalline Phases of the Chromonic Mesogen Sunset Yellow
Publisher: American Chemical Society (ACS)
Date: 02-07-2014
DOI: 10.1021/CG500752X
Stress and strain distributions in Ge dots on Si(001) by molecular dynamics simulation.
Publisher: WORLD SCIENTIFIC
Date: 04-2001
The Structure of CaSO4 Nanorods: The Precursor of Gypsum
Publisher: American Chemical Society (ACS)
Date: 06-06-2019
Exploring the influence of organic species on pre- and post-nucleation calcium carbonate
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2FD20052J
Rhenium tetrazolato complexes coordinated to thioalkyl-functionalised phenanthroline ligands: synthesis, photophysical characterisation, and incubation in live HeLa cells
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5DT03470A
Abstract: Thioalkyl-functionalised Re(I) tetrazolato complexes highlight good accumulation and lack of photobleaching in live He-La cells.
Simulation of Calcium Phosphate Species in Aqueous Solution: Force Field Derivation
Publisher: American Chemical Society (ACS)
Date: 19-01-2018
Abstract: A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO
The atomic structure and dynamics at the CaCO3 vaterite-water interface: A classical molecular dynamics study
Publisher: AIP Publishing
Date: 23-04-2021
DOI: 10.1063/5.0049483
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.
Topological Defects and Bulk Melting of Hexagonal Ice
Publisher: American Chemical Society (ACS)
Date: 03-2005
DOI: 10.1021/JP050690Z
Abstract: We use classical molecular dynamics combined with the recently developed metadynamics method [Laio, A. Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 20] to study the process of bulk melting in hexagonal ice. Our simulations show that bulk melting is mediated by the formation of topological defects which preserve the coordination of the tetrahedral network. Such defects cluster to form a defective region involving about 50 molecules with a surprisingly long lifetime. The subsequent formation of coordination defects triggers the transition to the liquid state.
Synthesis and Photochemical Properties of Re(I) Tricarbonyl Complexes Bound to Thione and Thiazole-2-ylidene Ligands
Publisher: American Chemical Society (ACS)
Date: 19-05-2020
DOI: 10.26434/CHEMRXIV.12324875.V1
Abstract: Three Re(I) tricarbonyl complexes, with general formulation Re(N^L)(CO) 3 X (where N^L is a bidentate ligand containing a pyridine functionalized in the position 2 with a thione or a thiazol-2-ylidene group and X is either chloro or bromo) were synthesized and their reactivity explored in terms of solvent-dependent ligand substitution, both in the ground and excited states. When dissolved in acetonitrile, the complexes bound to the thione ligand underwent ligand exchange with the solvent resulting in the formation of Re(NCMe) 2 (CO) 3 X. The exchange was found to be reversible, and the starting complex was reformed upon removal of the solvent. On the other hand, the complexes appeared inert in dichloromethane or acetone. Conversely, the complex bound to the thiazole-2-ylidene ligand did not display any ligand exchange reaction in the dark, but underwent photoactivated ligand substitution when excited to its lowest metal-to-ligand charge transfer manifold. Photolysis of this complex in acetonitrile generated multiple products, including Re(I) tricarbonyl and dicarbonyl solvato-complexes as well as free thiazole-2-ylidene ligand.
A Quantum Mechanically Derived Force Field To Predict CO2 Adsorption on Calcite {10.4} in an Aqueous Environment
Publisher: American Chemical Society (ACS)
Date: 20-10-2017
The Multiple Structures of Vaterite
Publisher: American Chemical Society (ACS)
Date: 17-05-2013
DOI: 10.1021/CG4002972
Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture
Publisher: Springer Science and Business Media LLC
Date: 24-05-2019
DOI: 10.1038/S41467-019-10383-X
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 lification. 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.
Anisotropy of Earth's D″ layer and stacking faults in the MgSiO3 post-perovskite phase
Publisher: Springer Science and Business Media LLC
Date: 12-2005
DOI: 10.1038/NATURE04439
Abstract: The post-perovskite phase of (Mg,Fe)SiO3 is believed to be the main mineral phase of the Earth's lowermost mantle (the D'' layer). Its properties explain numerous geophysical observations associated with this layer-for ex le, the D'' discontinuity, its topography and seismic anisotropy within the layer. Here we use a novel simulation technique, first-principles metadynamics, to identify a family of low-energy polytypic stacking-fault structures intermediate between the perovskite and post-perovskite phases. Metadynamics trajectories identify plane sliding involving the formation of stacking faults as the most favourable pathway for the phase transition, and as a likely mechanism for plastic deformation of perovskite and post-perovskite. In particular, the predicted slip planes are {010} for perovskite (consistent with experiment) and {110} for post-perovskite (in contrast to the previously expected {010} slip planes). Dominant slip planes define the lattice preferred orientation and elastic anisotropy of the texture. The {110} slip planes in post-perovskite require a much smaller degree of lattice preferred orientation to explain geophysical observations of shear-wave anisotropy in the D'' layer.
Water Structure, Dynamics and Ion Adsorption at the Aqueous {010} Brushite Surface
Publisher: MDPI AG
Date: 03-08-2018
DOI: 10.3390/MIN8080334
Abstract: Understanding the growth processes of calcium phosphate minerals in aqueous environments has implications for both health and geology. Brushite, in particular, is a component of certain kidney stones and is used as a bone implant coating. Understanding the water–brushite interface at the molecular scale will help inform the control of its growth. Liquid-ordering and the rates of water exchange at the brushite–solution interface have been examined through the use of molecular dynamics simulation and the results compared to surface X-ray diffraction data. This comparison highlights discrepancies between the two sets of results, regardless of whether force field or first principles methods are used in the simulations, or the extent of water coverage. In order to probe other possible reasons for this difference, the free energies for the adsorption of several ions on brushite were computed. Given the exothermic nature found in some cases, it is possible that the discrepancy in the surface electron density may be caused by adsorption of excess ions.
Silicon diffusion in competitive TiSi2 phases by molecular dynamics simulations
Publisher: Elsevier BV
Date: 03-2001
Enhanced deep-blue emission from Pt(ii) complexes bound to 2-pyridyltetrazolate and an ortho-xylene-linked bis(NHC)cyclophane
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3DT50225B
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.
On classical and non-classical views on nucleation
Publisher: American Journal of Science (AJS)
Date: 11-2018
DOI: 10.2475/09.2018.05
Wetting Properties of the CO
Publisher: American Chemical Society (ACS)
Date: 12-11-2019
DOI: 10.1021/ACS.LANGMUIR.9B02881
Abstract: Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO
Superionic Conduction in Substoichiometric LiAl Alloy: AnAb InitioStudy
Publisher: American Physical Society (APS)
Date: 18-09-2009
Timoshenko Bending and Eshelby Twisting Predicted in Molecular Nanocrystals
Publisher: American Chemical Society (ACS)
Date: 03-10-2018
Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing
Publisher: American Chemical Society (ACS)
Date: 10-09-2019
Is the Calcite–Water Interface Understood? Direct Comparisons of Molecular Dynamics Simulations with Specular X-ray Reflectivity Data
Publisher: American Chemical Society (ACS)
Date: 27-02-2013
DOI: 10.1021/JP310943S
Thermodynamically Consistent Force Field for Molecular Dynamics Simulations of Alkaline-Earth Carbonates and Their Aqueous Speciation
Publisher: American Chemical Society (ACS)
Date: 21-10-2015
Ligand-Induced Structural, Photophysical, and Electrochemical Variations in Tricarbonyl Rhenium(I) Tetrazolato Complexes
Publisher: American Chemical Society (ACS)
Date: 17-06-2013
DOI: 10.1021/OM400356N
A Supramolecular Ice Growth Inhibitor
Publisher: American Chemical Society (ACS)
Date: 30-09-2016
DOI: 10.1021/JACS.6B08267
Entropy Drives Calcium Carbonate Ion Association
Publisher: Wiley
Date: 14-09-2016
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.
Simulation of Crystallization of Biominerals
Publisher: Annual Reviews
Date: 07-2018
DOI: 10.1146/ANNUREV-MATSCI-070317-124327
Abstract: Biominerals are crucial materials that play a vital role in many forms of life. Understanding the various steps through which ions in aqueous environment associate to form increasingly structured particles that eventually transform into the final crystalline or amorphous poly(a)morph in the presence of biologically active molecules is therefore of great significance. In this context, computer modeling is now able to provide an accurate atomistic picture of the dynamics and thermodynamics of possible association events in solution, as well as to make predictions as to particle stability and possible alternative nucleation pathways, as a complement to experiment. This review provides a general overview of the most significant computational methods and of their achievements in this field, with a focus on calcium carbonate as the most abundant biomineral.
The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 12-05-2020
DOI: 10.26434/CHEMRXIV.12279911
Abstract: Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2 / and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure, / meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamics / based on both DFT and two different force field models. Additionally, the simulated structures are / used to calculate the corresponding structure factors, which in turn are compared to those obtained / from experiment, thereby avoiding the need for fitting or subjective interpretation. In general, there / is a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of the / structure of water at the interface. Of the three simulation methods examined, the DFT results were / found to agree best with the experimental structure. /
Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface
Publisher: American Chemical Society (ACS)
Date: 09-2020
DOI: 10.26434/CHEMRXIV.12899831.V1
Abstract: Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.
Difference Hirshfeld fingerprint plots: a tool for studying polymorphs
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6CE02535H
N-Heterocyclic carbenes as π*-acceptors in luminescent Re(i) triscarbonyl complexes
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1DT11233C
Abstract: Two rhenium(I) carbonyl complexes of the type fac-[Re(CO)(3)(N^C)X] where N^C is an N-heterocyclic carbene [3-butyl-1-(2'-pyridyl)benzimidazolin-2-ylidene] and X is either Cl or Br have been synthesised via an in situ method from [Re(CO)(5)X] and a respective benzimidazolium salt. The complexes have been characterised by (1)H and (13)C NMR, infra-red spectroscopy and in the case of the bromo-complex by a single-crystal X-ray diffraction study. The photophysical properties of the complexes have been investigated, revealing similar phosphorescent emission which was attributed to radiative decay from a (3)MLCT state partially mixed with a (3)LLCT state. However, the analysis of excited state lifetime and quantum yield values revealed distinct photophysical behaviour for the two complexes, which was attributed to the more labile nature of the bromo ligand with respect to the chloro one. The explanation was supported by the time-dependent emission profile change in diluted acetonitrile solutions.
Examining the Accuracy of Density Functional Theory for Predicting the Thermodynamics of Water Incorporation into Minerals: The Hydrates of Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 14-08-2013
DOI: 10.1021/JP4048105
A Universal Force Field for Materials, Periodic GFN-FF: Implementation and Examination
Publisher: American Chemical Society (ACS)
Date: 04-11-2021
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 d ing 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.
Resolving Point Defects in the Hydration Structure of Calcite (10.4) with Three-Dimensional Atomic Force Microscopy
Publisher: American Physical Society (APS)
Date: 13-03-2018
Stable prenucleation mineral clusters are liquid-like ionic polymers
Publisher: Springer Science and Business Media LLC
Date: 20-12-2011
DOI: 10.1038/NCOMMS1604
Stress, strain and elastic energy at nanometric Ge dots on Si(0 0 1)
Publisher: Elsevier BV
Date: 03-2002
Self-Assembling of Zinc Phthalocyanines on ZnO (101̅0) Surface through Multiple Time Scales
Publisher: American Chemical Society (ACS)
Date: 10-11-2011
DOI: 10.1021/NN203105W
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.
Does the Structural Water within Gypsum Remain Crystalline at the Aqueous Interface?
Publisher: American Chemical Society (ACS)
Date: 27-09-2021
Simulating the binding of key organic functional groups to aqueous calcium carbonate species
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D1CP04226B
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.
Unravelling the Shuttling Mechanism in a Photoswitchable Multicomponent Bistable Rotaxane
Publisher: Wiley
Date: 21-04-2008
The photochemistry of rhenium(i) tricarbonyl N-heterocyclic carbene complexes
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3DT51614H
Abstract: The photophysical and photochemical properties of the new tricarbonyl rhenium(I) complexes bound to N-heterocyclic carbene ligands (NHC), fac-[Re(CO)3(N^C)X] (N^C = 1-phenyl-3-(2-pyridyl)imidazole or 1-quinolinyl-3-(2-pyridyl)imidazole X = Cl or Br), are reported. The photophysics of these complexes highlight phosphorescent emission from triplet metal-to-ligand ((3)MLCT) excited states, typical of tricarbonyl rhenium(I) complexes, with the pyridyl-bound species displaying a ten-fold shorter excited state lifetime. On the other hand, these pyridyl-bound species display solvent-dependent photochemical CO dissociation following what appear to be two different mechanisms, with a key step being the formation of cationic tricarbonyl solvato-complexes, being themselves photochemically active. The photochemical mechanisms are illustrated with a combination of NMR, IR, UV-Vis, emission and X-ray structural characterization techniques, clearly demonstrating that the presence of the NHC ligand is responsible for the previously unobserved photochemical behavior in other photoactive tricarbonyl rhenium(I) species. The complexes bound to the quinolinyl-NHC ligand (which possess a lower-energy (3)MLCT) are photostable, suggesting that the photoreactive excited state is not any longer thermally accessible. The photochemistry of the pyridyl complexes was investigated in acetonitrile solutions and also in the presence of triethylphosphite, showing a competing and bifurcated photoreactivity promoted by the trans effect of both the NHC and phosphite ligands.
Resorcinol Crystallization from the Melt: A New Ambient Phase and New “Riddles”
Publisher: American Chemical Society (ACS)
Date: 05-04-2016
DOI: 10.1021/JACS.6B01120
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 in idual radial lamellae may adopt helicoidal morphologies. We correlate the appearance of twisting in β and ε with the symmetry of twist-inducing additives.
Negatively charged Ir(iii ) cyclometalated complexes containing a chelating bis-tetrazolato ligand: synthesis, photophysics and the study of reactivity with electrophiles
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C6DT02524B
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.
The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 12-05-2020
DOI: 10.26434/CHEMRXIV.12279911.V1
Abstract: Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure,meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamicsbased on both DFT and two different force field models. Additionally, the simulated structures areused to calculate the corresponding structure factors, which in turn are compared to those obtainedfrom experiment, thereby avoiding the need for fitting or subjective interpretation. In general, thereis a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of thestructure of water at the interface. Of the three simulation methods examined, the DFT results werefound to agree best with the experimental structure.
Structure and Dynamics of Water at Step Edges on the Calcite {101̅4} Surface
Publisher: American Chemical Society (ACS)
Date: 25-08-2016
Synthesis and Photochemical Properties of Re(I) Tricarbonyl Complexes Bound to Thione and Thiazol-2-ylidene Ligands
Publisher: American Chemical Society (ACS)
Date: 24-08-2020
Influence of Temperature and Anisotropic Pressure on the Phase Transitions inα
Publisher: American Physical Society (APS)
Date: 23-04-2008
Can Point Defects in Surfaces in Solution be Atomically Resolved by Atomic Force Microscopy?
Publisher: American Physical Society (APS)
Date: 23-11-2016
Dehydroxylation of kaolinite to metakaolin-a molecular dynamics study
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C0JM01748E
Strain maps at the atomic scale below Ge pyramids and domes on a Si substrate
Publisher: AIP Publishing
Date: 13-05-2002
DOI: 10.1063/1.1475775
Abstract: In this letter, the strain field below uncapped Ge islands of a different shape on a Si(001) substrate is estimated by molecular dynamics simulations at a realistic scale. Comparison to the Fourier transform maps of transmission electron micrographs, recently reported in literature, shows a very good agreement. We point out that the complex deformation in silicon, just below the edges of the Ge islands, is far from being uniaxial. The stress distribution generated by such a strain determines the range of interdot repulsion.
Evolution of theGe ∕ Si (
Publisher:
American Physical Society (APS)
Date:
23-06-2004
Publisher: American Physical Society (APS)
Date: 23-06-2004
Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO 3 Solutions
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-08-2013
Abstract: The initial transition from a disordered solution to the formation of nuclei that grow into crystals continues to be a puzzle. Recent experiments suggested the formation of stable ordered clusters that appear prior to the formation of the first nuclei. Wallace et al. (p. 885 see the Perspective by Myerson and Trout ) used molecular dynamics to look at the potential structure and dynamics of these clusters and lattice gas simulations to explore the population dynamics of the cluster populations prior to nucleation. A liquid-liquid phase separation process was observed whereby one phase becomes more concentrated in ions and becomes the precursor for nuclei to form.
Determining the Complete Stability of Calcite Kink Sites: Real vs Ideal
Publisher: American Chemical Society (ACS)
Date: 05-07-2023
Synthesis, Photophysical and Electrochemical Investigation of Dinuclear Tetrazolato-Bridged Rhenium Complexes
Publisher: American Chemical Society (ACS)
Date: 29-10-2012
DOI: 10.1021/OM300870A
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 02-04-2020
DOI: 10.26434/CHEMRXIV.11879805.V2
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 have 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 is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 21-02-2020
DOI: 10.26434/CHEMRXIV.11879805.V1
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 have 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 is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Influence of isotropic and biaxial strain on proton conduction in Y-doped BaZrO3: a reactive molecular dynamics study
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3TA12800H
Water Is the Key to Nonclassical Nucleation of Amorphous Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 19-11-2010
DOI: 10.1021/JA108508K
Abstract: Calcium carbonate is a ubiquitous mineral that represents one of the most significant biominerals, a major contributor to carbon sequestration through geological deposits, and a technological hindrance as a result of scale formation. Amorphous calcium carbonate is intimately involved in the nucleation and growth of this material, yet much remains undiscovered regarding the atomic detail. Through dynamical simulation we demonstrate that nucleation of amorphous calcium carbonate follows a nonclassical pathway. This arises from the addition of ion pairs to clusters exhibiting a consistently exothermic free energy that persists with increasing particle size. Furthermore, the disruption of the surrounding water of solvation by the atomically rough surface reduces the barrier to growth to the order of ambient thermal energy, thereby allowing the amorphous phase to grow faster than crystalline polymorphs. Amorphous calcium carbonate nanoparticles are also found to exploit size-dependent water content to render itself more stable than the favored bulk phase, calcite, below a critical diameter of close to 4 nm.
Self-diffusion of silicon in TiSi2 competing phases by tight-binding molecular dynamics
Publisher: Elsevier BV
Date: 03-2001
Simulation of structural phase transitions by metadynamics
Publisher: Walter de Gruyter GmbH
Date: 05-2005
DOI: 10.1524/ZKRI.220.5.489.65078
Abstract: We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illus trated on various kinds of crystals and the advantages with respect to previous schemes are emphasized. The relevance of the new method for the problem of crystal structure prediction is also discussed.
Proton-Induced Reversible Modulation of the Luminescent Output of Rhenium(I), Iridium(III), and Ruthenium(II) Tetrazolate Complexes
Publisher: American Chemical Society (ACS)
Date: 20-12-2013
DOI: 10.1021/IC402187E
Abstract: One of the distinct features of metal-tetrazolate complexes is the possibility of performing electrophilic additions onto the imine-type nitrogens of the coordinated five-membered ring. These reactions, in particular, provide a useful tool for varying the main structural and electronic properties of the starting tetrazolate complexes. In this paper, we demonstrate how the use of a simple protonation-deprotonation protocol enables us to reversibly change, to a significant extent, the light-emission output and performance of a series of Re(I)-tetrazolate-based phosphors of the general formulation fac-[Re(N(∧)N)(CO)3L], where N(∧)N denotes diimine-type ligands such as 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen) and L represents a series of different 5-aryl tetrazolates. Indeed, upon addition of triflic acid to these neutral Re(I) complexes, a consistent blue shift (Δλmax ca. 50 nm) of the emission maximum is observed and the protonated species also display increased quantum yield values (4-13 times greater than the starting compounds) and longer decay lifetimes. This alteration can be reversed to the initial condition by further treating the protonated Re(I) complex with a base such as triethylamine. Interestingly, the reversible modulation of luminescent features by the same protonation-deprotonation mechanism appears as a quite general characteristic of photoactive metal tetrazolate complexes, even for compounds in which the 2-pyridyl tetrazolate ligands coordinate the metal center with a bidentate mode, such as the corresponding Ir(III) cyclometalates [Ir(C(∧)N)2L] and the Ru(II) polypyridyl derivatives [Ru(bpy)2L](+). In these cases, the protonation of the starting materials leads to red-shifted and more intense emissions for the Ir(III) complexes, while almost complete quenching is observed in the case of the Ru(II) analogues.
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 02-04-2020
DOI: 10.26434/CHEMRXIV.11879805
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 have 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 is stable, though with an equilibrium constant that is lower than for ion pairing itself.
Correlations among Hydrogen Bonds in Liquid Water
Publisher: American Physical Society (APS)
Date: 16-08-2004
Ion Pairing and Multiple Ion Binding in Calcium Carbonate Solutions Based on a Polarizable AMOEBA Force Field and Ab Initio Molecular Dynamics
Publisher: American Chemical Society (ACS)
Date: 07-04-2020
Energy distribution in Ge islands on Si(001): A spectral and site-resolved analysis versus size and morphology
Publisher: American Physical Society (APS)
Date: 16-12-2002
Synthesis, Structural, and Photophysical Investigation of Diimine Triscarbonyl Re(I) Tetrazolato Complexes.
Publisher: American Chemical Society (ACS)
Date: 26-01-2011
DOI: 10.1021/IC1015516
Abstract: The synthesis, structural, and photophysical properties of a novel family of neutral fac-[Re(N(∧)N)(CO)(3)(L)] complexes, where N(∧)N is either 2,2'-bipyridine or 1,10-phenanthroline and L is a para functionalized 5-aryltetrazolate [namely, 5-phenyltetrazolate (Tph(-)), 4-(tetrazolate-5-yl)benzaldehyde (Tbdz(-)), 5-(4-acetylphenyl)tetrazolate (Tacy(-)), and methyl 4-(tetrazolate-5-yl)benzoate (Tmeb(-))] are reported. The complexes were prepared by direct addition of the corresponding tetrazolate anion to the acetonitrile solvated fac-[Re(N(∧)N)(CO)(3)](+) precursor. NMR data demonstrate that the coordination of the metal fragment is regiospecific at the N2 atom of the tetrazolate ring. These conclusions are also supported by X-ray structural determinations. Photophysical data were obtained in diluted and deaerated dichloromethane solutions displaying broad and structureless profiles with emission maxima ranging from 566 to 578 nm. The absorption profiles indicate the presence of higher energy intraligand (IL) π-π* transitions and lower energies ligand-to-ligand charge transfer (LLCT) and metal-to-ligand charge transfer (MLCT). As the last two transitions are mixed, they are better described as a metal-ligand-to-ligand charge transfer (MLLCT), a result that is also supported by density functional theory (DFT) calculations. The complexes show excited state lifetime values ranging from 102 to 955 ns, with associated quantum yield between 0.012 and 0.099. Compared to the parent neutral chloro or bromo [Re(N(∧)N)(CO)(3)X], the complexes show a slightly improved performance because of the π accepting nature of the tetrazolato ligand. The metal-to-ligand backbonding is in fact depleting the Re center of electron density, thus widening the HOMO-LUMO gap and reducing the non-radiative decay mechanism in accordance with the energy gap law. Finally, the electron-withdrawing or donating nature of the substituent on the phenyltetrazolato ligand allows the fine-tuning of the photophysical properties.
Probing the Multiple Structures of Vaterite through Combined Computational and Experimental Raman Spectroscopy
Publisher: American Chemical Society (ACS)
Date: 17-11-2014
DOI: 10.1021/JP509958D
Blue emitting C-2-symmetrical dibenzothiazolyl substituted pyrrole, furan and thiophene
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3TC00760J
Critical Role of the Surface Reconstruction in the Thermodynamic Stability of{ 105 }
Publisher:
American Physical Society (APS)
Date:
06-06-2002
Publisher: American Physical Society (APS)
Date: 06-06-2002
Uncovering the Atomistic Mechanism for Calcite Step Growth
Publisher: Wiley
Date: 13-04-2017
A new structural model for disorder in vaterite from first-principles calculations
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C1CE05976A
The Thermal Stability of Lattice-Energy Minima of 5-Fluorouracil: Metadynamics as an Aid to Polymorph Prediction
Publisher: American Chemical Society (ACS)
Date: 15-03-2008
DOI: 10.1021/JP709764E
Abstract: This paper reports a novel methodology for the free-energy minimization of crystal structures exhibiting strong, anisotropic interactions due to hydrogen bonding. The geometry of the thermally expanded cell was calculated by exploiting the dependence of the free-energy derivatives with respect to cell lengths and angles on the average pressure tensor computed in short molecular dynamics simulations. All dynamic simulations were performed with an elaborate anisotropic potential based on a distributed multipole analysis of the isolated molecule charge density. Changes in structure were monitored via simulated X-ray diffraction patterns. The methodology was used to minimize the free energy at ambient conditions of a set of experimental and hypothetical 5-fluorouracil crystal structures, generated in a search for lattice-energy minima with the same model potential. Our results demonstrate that the majority ( approximately 75%) of lattice-energy minima are thermally stable at ambient conditions, and hence, the free-energy (like the lattice-energy) surface is complex and highly undulating. Metadynamics trajectories (Laio, A. Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562) started from the free-energy minima only produced transitions that preserved the hydrogen-bonding motif, and thus, further developments are needed for this method to efficiently explore such free-energy surfaces. The existence of so many free-energy minima, with large barriers for the alteration of the hydrogen-bonding motif, is consistent with the range of motifs observed in crystal structures of 5-fluorouracil and other 5-substituted uracils.
Point defects and stacking faults in TiSi2phases by tight binding molecular dynamics
Publisher: IOP Publishing
Date: 03-10-2002
One-step assembly of Re(i) tricarbonyl 2-pyridyltetrazolato metallacalix[3]arene with aqua emission and reversible three-electron oxidation
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3DT50988E
Abstract: The reaction of 2-pyridyltetrazolate with [Re(CO)5X] (X = Cl, Br) yielded the formation of an unexpected cyclic metallacalix[3]arene, as revealed by X-ray structural studies, characterised by aqua emission and reversible three-electron oxidation.
Atomistic Simulation of Atomic Force Microscopy Imaging of Hydration Layers on Calcite, Dolomite, and Magnesite Surfaces
Publisher: American Chemical Society (ACS)
Date: 27-05-2019
Investigating Intracellular Localisation and Cytotoxicity Trends for Neutral and Cationic Iridium Tetrazolato Complexes in Live Cells
Publisher: Wiley
Date: 07-08-2017
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 erse 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.
Aufdeckung der Rolle von Hydrogencarbonat‐Ionen bei der Bildung von Calciumcarbonat im nahezu neutralen pH‐Bereich
Publisher: Wiley
Date: 18-06-2021
Abstract: Die Grundlagen der Mineralisation und die entsprechenden Mechanismen sind noch nicht ausreichend verstanden. Dies ist insbesondere für biologische und geologische Systeme der Fall. In dieser Studie konnte die Beteiligung von HCO 3 − ‐Ionen an der Nukleation von CaCO 3 durch quantitative Untersuchungen der Ionenassoziationen im nahezu neutralen pH‐Bereich nachgewiesen werden. Der strukturelle Einbau von HCO 3 − ‐Ionen in amorphe Intermediate konnte mittels ssNMR belegt werden und wird des Weiteren durch quantenmechanische Berechnungen sowie Simulationen der Moleküldynamik gestützt. Der Einfluss von HCO 3 − ‐Ionen erstreckt sich dabei auf 1) eine konkurrierende Rolle in Gleichgewichten bezüglich der Bildung von Ionenpaaren und Ionenclustern vor der Nukleation sowie auf 2) den Einbau in amorphe Mineralpartikel als wichtige strukturelle Komponente. Der Einfluss dieser aktiv beteiligten löslichen Spezies auf die Bildung von Calciumcarbonat ist von fundamentaler Bedeutung, um die physiologische und geologische Mineralisation in ihren Grundsätzen besser zu verstehen.
Morphological and Compositional Evolution of theG e
Publisher: American Physical Society (APS)
Date: 27-05-2003
A reactive force field for aqueous-calcium carbonate systems
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1CP21034C
Abstract: A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water.
Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals
Publisher: American Chemical Society (ACS)
Date: 08-2016
DOI: 10.1021/ACS.JPCLETT.6B01459
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.
Investigating the Polymorphism in PR179: A Combined Crystal Structure Prediction and Metadynamics Study
Publisher: American Chemical Society (ACS)
Date: 30-09-2008
DOI: 10.1021/JP802977T
Abstract: The polymorphism of an industrial important pigment (PR179) was studied with a combination of standard crystal structure prediction and metadynamics. The former provided a starting set of candidate polymorphs whose structural and thermal stability were then probed by metadynamics. Moreover, metadynamics allowed for exploring the free energy surface to look for other possible polymorphs that were not included in the original set. Our calculations indicate that two structures have a high structural stability and are therefore good candidates to be found in experiments. The lower energy phase of the two indeed corresponds to the known polymorph, and we suggest that the other might be a metastable polymorph not yet experimentally discovered.
Why Are Some Crystals Straight?
Publisher: American Chemical Society (ACS)
Date: 23-06-2020
Calculations of the Evolution of the Ca L23 Fine Structure in Amorphous Calcium Carbonate
Publisher: American Chemical Society (ACS)
Date: 28-06-2022
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 (L
Crosslinking Rapidly Cured Epoxy Resin Thermosets: Experimental and Computational Modeling and Simulation Study
Publisher: MDPI AG
Date: 06-03-2023
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.
Photophysical and Photochemical Trends in Tricarbonyl Rhenium(I) N-Heterocyclic Carbene Complexes
Publisher: American Chemical Society (ACS)
Date: 25-03-2014
DOI: 10.1021/IC403138A
Abstract: A family of tricarbonyl Re(I) complexes of the formulation fac-[Re(CO)3(NHC)L] has been synthesized and characterized, both spectroscopically and structurally. The NHC ligand represents a bidentate N-heterocyclic carbene species where the central imidazole ring is substituted at the N3 atom by a butyl, a phenyl, or a mesityl group and substituted at the N1 atom by a pyridyl, a pyrimidyl, or a quinoxyl group. On the other hand, the ancillary L ligand alternates between chloro and bromo. For the majority of the complexes, the photophysical properties suggest emission from the lowest triplet metal-to-ligand charge transfer states, which are found partially mixed with triplet ligand-to-ligand charge transfer character. The nature and relative energy of the emitting states appear to be mainly influenced by the identity of the substituent on the N3 atom of the imidazole ring thus, the pyridyl complexes have blue-shifted emission in comparison to the more electron deficient pyrimidyl complexes. The quinoxyl complexes show an unexpected blue-shifted emission, possibly occurring from ligand-centered excited states. No significant variations were found upon changing the substituent on the imidazole N3 atom and/or the ancillary ligand. The photochemical properties of the complexes have also been investigated, with only the complexes bound to the pyridyl-substituted NHC ligands showing photoinduced CO dissociation upon excitation at 370 nm, as demonstrated by the change in the IR and NMR spectra as well as a red shift in the emission profile after photolysis. Temperature-dependent photochemical experiments show that CO dissociation occurs at temperatures as low as 233 K, suggesting that the Re-C bond cleaves from excited states of metal-to-ligand charge transfer nature rather than thermally activated ligand field excited states. A photochemical mechanism that takes into account the reactivity of the complexes bound to the pyridyl-NHC ligand as well as the stability of those bound to the pyrimidyl- and quinoxyl-NHC ligands is proposed.
Computational Insights into Mg2+ Dehydration in the Presence of Carbonate
Publisher: American Chemical Society (ACS)
Date: 16-02-0002
Virtual Probes of Mineral-Water Interfaces: The More Flops, the Better!
Publisher: Mineralogical Society of America
Date: 06-2013
Computational Insight into Calcium–Sulfate Ion Pair Formation
Publisher: American Chemical Society (ACS)
Date: 14-11-2017
A Computational Investigation into the Suitability of Purely Siliceous Zeolites as Reverse Osmosis Membranes
Publisher: American Chemical Society (ACS)
Date: 23-02-2011
DOI: 10.1021/JP109591F
Where Is the Most Hydrophobic Region? Benzopurpurine Self-Assembly at the Calcite–Water Interface
Publisher: American Chemical Society (ACS)
Date: 24-10-2017
Computational workflows for perovskites: case study for lanthanide manganites
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3CP00041A
Abstract: We propose and implement an open-source computational workflow, suitable for explorative studies of perovskites. We validate said workflow on a set of lanthanide manganites, and apply it to study the defect-induced phase transition in LaMnO 3 .
Exploring Polymorphism: The Case of Benzene
Publisher: Wiley
Date: 06-06-2005
Development of Accurate Force Fields for the Simulation of Biomineralization
Publisher: Elsevier
Date: 2013
Calcite (104) Surface–Electrolyte Structure: A 3D Comparison of Surface X-ray Diffraction and Simulations
Publisher: American Chemical Society (ACS)
Date: 28-07-2020
Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling
Publisher: MDPI AG
Date: 21-01-2022
DOI: 10.3390/APP12031139
Abstract: Molecular dynamics simulations of solids are often performed using anisotropic barostats that allow the shape and volume of the periodic cell to change during the simulation. Most existing schemes are based on a second-order differential equation that might lead to undesired oscillatory behaviors and should not be used in the equilibration phase. We recently introduced stochastic cell rescaling, a first-order stochastic barostat that can be used for both the equilibration and production phases. Only the isotropic and semi-isotropic variants have been formulated and implemented so far. In this paper, we develop and implement the equations of motion of the fully anisotropic variant and test them on Lennard-Jones solids, ice, gypsum, and gold. The algorithm has a single parameter that controls the relaxation time of the volume, results in the exponential decay of correlation functions, and can be effectively applied to a wide range of systems.
Determining the Adsorption Free Energies of Small Organic Molecules and Intrinsic Ions at the Terrace and Steps of Calcite
Publisher: American Chemical Society (ACS)
Date: 18-01-2022
Uncovering the Role of Bicarbonate in Calcium Carbonate Formation at Near‐Neutral pH
Publisher: Wiley
Date: 18-06-2021
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 HCO 3 − ions in CaCO 3 nucleation. Incorporation of HCO 3 − 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 HCO 3 − 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 HCO 3 − ions as active soluble species and structural constituents in CaCO 3 formation are of fundamental importance and provide a basis for a better understanding of physiological and geological mineralization.
Atomic-Scale Pathway of the Pyramid-to-Dome Transition during Ge Growth on Si(001)
Publisher: American Physical Society (APS)
Date: 17-11-2004
Separation of 18α(H)-, 18β(H)-oleanane and lupane by comprehensive two-dimensional gas chromatography
Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.CHROMA.2011.06.021
Abstract: 18α(H)-, 18β(H)-oleanane and lupane are angiosperm-derived biomarkers that are used as age indicators for the Late Cretaceous onwards when the first proliferation of angiosperms occurred. In addition, the 18α(H)-/18β(H)-oleanane ratio is employed as a thermal maturity parameter of crude oil. However, evidence has shown that accurate quantification of these compounds has been impeded by inadequate chromatographic separation by traditional one-dimensional gas chromatography. In this study, we present the separation of 18α(H)-, 18β(H)-oleanane and lupane with comprehensive two-dimensional gas chromatography (GC×GC). Furthermore, it was observed that 18β(H)-oleanane elutes earlier than 18α(H)-oleanane in second dimension (polarity) which we attribute to steric hindrance effects. Two GC conditions have been developed in order to achieve baseline separation of the triterpenoids of interest in complex mixtures such as sediment extracts and crude oils.
Of Machines and Men: Intelligent Diagnosis and the Shape of Things to Come
Publisher: Springer Science and Business Media LLC
Date: 2020
DOI: 10.1007/S11906-019-1010-3
Abstract: Artificial Intelligence (AI), although well established in many areas of everyday life, has only recently been trialed in the diagnosis and management of common clinical conditions. This editorial review highlights progress to date and suggests further improvements in and trials of AI in the management of conditions such as hypertension.
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Publisher: Elsevier BV
Date: 10-2009
Structure of hydrated calcium carbonates: A first-principles study
Publisher: Elsevier BV
Date: 09-2014
Anomalous heat transport in binary hard-sphere gases
Publisher: American Physical Society (APS)
Date: 29-03-2019
Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface
Publisher: American Chemical Society (ACS)
Date: 09-2020
DOI: 10.26434/CHEMRXIV.12899831
Abstract: Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields. The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed. / A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field. /
Stress induced surface melting during the growth of the Ge wetting layer on Si(001) and Si(111)
Publisher: Elsevier BV
Date: 07-2002
Formation of strain-induced Si-rich and Ge-rich nanowires at misfit dislocations in SiGe: A model supported by photoluminescence data
Publisher: AIP Publishing
Date: 07-04-2004
DOI: 10.1063/1.1705727
Abstract: Molecular dynamics simulations with the Tersoff potential of the strain distribution around 60° misfit dislocation in a heteroepitaxial SiGe film confirm that highly compressed and expanded, cylindrical nanometer-sized regions appear on opposite sides of the (111) glide plane. Such a configuration is suggested to generate opposite chemical potential gradients for Si and Ge diffusion and, as verified by a Monte Carlo simulation, in the formation of Si-rich and Ge-rich nanowires along the dislocation core. This model is supported by photoluminescence measurements as a function of annealing temperature and time.
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